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  • Wiley  (168,109)
  • American Physical Society  (121,195)
  • Annual Reviews
  • 2020-2024  (1,236)
  • 2005-2009  (206,061)
  • 1980-1984  (79,285)
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  • 101
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    The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone (2024)
    Wiley
    In:  EPIC3Environmental Microbiology, Wiley, 26, pp. e16568-e16568, ISSN: 1462-2912
    Details
    Publication Date: 2024-02-19
    Description: The long-term dynamics of microbial communities across geographic, hydrographic, and biogeochemical gradients in the Arctic Ocean are largely unknown. To address this, we annually sampled polar, mixed, and Atlantic water masses of the Fram Strait (2015–2019; 5–100 m depth) to assess microbiome composition, substrate concentrations, and oceanographic parameters. Longitude and water depth were the major determinants (~30%) of microbial community variability. Bacterial alpha diversity was highest in lower-photic polar waters. Community composition shifted from west to east, with the prevalence of, for example, Dadabacteriales and Thiotrichales in Arctic- and Atlantic-influenced waters, respectively. Concentrations of dissolved organic carbon peaked in the western, compared to carbohydrates in the chlorophyll-maximum of eastern Fram Strait. Interannual differences due to the time of sampling, which varied between early (June 2016/2018) and late (September 2019) phytoplankton bloom stages, illustrated that phytoplankton composition and resulting availability of labile substrates influence bacterial dynamics. We identified 10 species clusters with stable environmental correlations, representing signature populations of distinct ecosystem states. In context with published metagenomic evidence, our microbial-biogeochemical inventory of a key Arctic region establishes a benchmark to assess ecosystem dynamics and the imprint of climate change.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 102
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    Sedimentary ancient DNA of rotifers reveals responses to 200 years of climate change in two Kenyan crater lakes (2023)
    Wiley
    In:  EPIC3Freshwater Biology, Wiley, 68(11), pp. 1894-1916, ISSN: 0046-5070
    Details
    Publication Date: 2024-04-10
    Description: Sedimentary ancient DNA (sedaDNA) has proven to be a useful tool for palaeoenvironmental studies, but only a handful of studies exist so far for tropical regions. In this study we used sedaDNA to study the temporal succession of Brachionus spp. rotifer mitochondrial DNA haplotypes using two sediment cores from two climatically different alkaline-saline crater lakes from the Kenyan Rift Valley. Data were retrieved from a sediment core (dating back to AD 1800) from Lake Kageinya, located in the remote, hot and hyper-arid Suguta Valley. sedaDNA was used to study the temporal succession of mitochondrial DNA haplotypes of Brachionus spp. rotifers. The results were compared to previously published data from Lake Sonachi, a well-studied lake in the humid and colder mountainous region of Kenya near the town of Naivasha, now supported by a 210Pb age chronology. Both records extend back before the onset of substantial anthropogenic impact in these regions. The results revealed that climate—rather than anthropogenic impact—was most strongly correlated with haplotype changes in both lakes. During prolonged dry periods (such as from AD 1910 to the late AD 1960s), certain haplotypes persisted. Sudden changes and the emergence of alter native haplotypes were observed when climate became more humid or during episodes of highly variable climate (before AD 1910 and from AD 1960s onwards). Progressive changes in prevailing haplotypes during periods with variable climate could reflect local adaptation and/or be the result of immigration of new haplotypes after the eradication of previous populations during extreme environmental conditions (high temperatures, UV irradiation, pH and salinity). The results indicate that, despite adverse chemical conditions, sedaDNA in tropical lake sediments is preserved for at least a few hundred years. Therefore, its analysis provides a useful complementary palaeoenvironmental proxy for palaeolimnological reconstructions and novel insights on changes in rotifer populations through time.
    Repository Name: EPIC Alfred Wegener Institut
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  • 103
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    Destructive fishing: An expert‐driven definition and exploration of this quasi‐concept (2024)
    Wiley
    In:  EPIC3Conservation Letters, Wiley, ISSN: 1755-263X
    Details
    Publication Date: 2024-04-17
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Numerous policy and international frameworks consider that “destructive fishing” hampers efforts to reach sustainability goals. Though ubiquitous, “destructive fishing” is undefined and therefore currently immeasurable. Here we propose a definition developed through expert consultation: “Destructive fishing is any fishing practice that causes irrecoverable habitat degradation, or which causes significant adverse environmental impacts, results in long‐term declines in target or nontarget species beyond biologically safe limits and has negative livelihood impacts.” We show strong stakeholder support for a definition, consensus on many biological and ecological dimensions, and no clustering of respondents from different sectors. Our consensus definition is a significant step toward defining sustainable fisheries goals and will help interpret and implement global political commitments which utilize the term “destructive fishing.” Our definition and results will help reinforce the Food and Agricultural Organization's Code of Conduct and meaningfully support member countries to prohibit destructive fishing practices.〈/jats:p〉
    Repository Name: EPIC Alfred Wegener Institut
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  • 104
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    ‘Destructive fishing’—A ubiquitously used but vague term? Usage and impacts across academic research, media and policy (2022)
    Wiley
    In:  EPIC3Fish and Fisheries, Wiley, 23(5), pp. 1039-1054, ISSN: 1467-2960
    Details
    Publication Date: 2024-04-17
    Description: The term ‘destructive fishing’ appears in multiple international policy instruments intended to improve outcomes for marine biodiversity, coastal communities and sustainable fisheries. However, the meaning of ‘destructive fishing’ is often vague, limiting effectiveness in policy. Therefore, in this study, we systematically reviewed the use of ‘destructive fishing’ in three record types: academic literature, media articles and policy documents between 1976 and 2020. A more detailed analysis was performed on subsets of these records, considering the extent to which the term is characterised, geographic distribution of use, and specific impacts and practices associated with the term. We found that use of ‘destructive fishing’ relative to the generic term ‘fisheries’ has increased since the 1990s. Records focussed predominantly on fishing practices in South-eastern Asia, followed by Southern Asia and Europe. The term was characterised in detail in only 15% of records. Habitat damage and blast/poison fishing were the most associated ecological impacts and gear/practices, respectively. Bottom trawling and unspecified net fishing were regularly linked to destructive fishing. Importantly, the three record types use the term differently. Academic literature tends to specifically articulate the negative impacts, while media articles focus generally on associated gears/practices. Significant regional variation also exists in how the term is used and what phenomena it is applied to. This study provides evidence and recommendations to inform stakeholders in any future pursuit of a unified definition of ‘destructive fishing’ to support more meaningful implementation of global sustainability goals.
    Repository Name: EPIC Alfred Wegener Institut
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  • 105
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    Arctic nekton uncovered by eDNA metabarcoding: Diversity, potential range expansions, and pelagic‐benthic coupling (2023)
    Wiley
    In:  EPIC3Environmental DNA, Wiley, 5(3), pp. 503-518, ISSN: 2637-4943
    Details
    Publication Date: 2024-04-18
    Description: The Arctic Ocean is home to a unique fauna that is disproportionately affected by global warming but that remains under-studied. Due to their high mobility and responsiveness to global warming, cephalopods and fishes are good indicators of the reshuffling of Arctic communities. Here, we established a nekton biodiversity baseline for the Fram Strait, the only deep connection between the North Atlantic and Arctic Ocean. Using universal primers for fishes (12S) and cephalopods (18S), we amplified environmental DNA (eDNA) from seawater (50–2700 m) and deep-sea sediment samples collected at the LTER HAUSGARTEN observatory. We detected 12 cephalopod and 31 fish taxa in the seawater and seven cephalopod and 28 fish taxa in the sediment, including the elusive Greenland shark (Somniosus microcephalus). Our data suggest three fish (Mallotus villosus, Thunnus sp., and Micromesistius poutassou) and one squid (Histioteuthis sp.) range expansions. The detection of eDNA of pelagic origin in the sediment also suggests that M. villosus, Arctozenus risso, and M. poutassou as well as gonatid squids are potential contributors to the carbon flux. Continuous nekton monitoring is needed to understand the ecosystem impacts of rapid warming in the Arctic and eDNA proves to be a suitable tool for this endeavor.
    Repository Name: EPIC Alfred Wegener Institut
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  • 106
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    Permafrost Causes Unique Fine‐Scale Spatial Variability Across Tundra Soils (2021)
    Wiley
    In:  EPIC3Global Biogeochemical Cycles, Wiley, 35, pp. e2020GB006659-e2020GB006659, ISSN: 0886-6236
    Details
    Publication Date: 2024-04-22
    Description: Spatial analysis in earth sciences is often based on the concept of spatial autocorrelation, expressed by W. Tobler as the first law of geography: “everything is related to everything else, but near things are more related than distant things." Here, we show that subsurface soil properties in permafrost tundra terrain exhibit tremendous spatial variability. We describe the subsurface variability of soil organic carbon (SOC) and ground ice content from the centimeter to the landscape scale in three typical tundra terrain types common across the Arctic region. At the soil pedon scale, that is, from centimeters to 1–2 m, variability is caused by cryoturbation and affected by tussocks, hummocks and nonsorted circles. At the terrain scale, from meters to tens of meters, variability is caused by different generations of ice‐wedges. Variability at the landscape scale, that is, ranging hundreds of meters, is associated with geomorphic disturbances and catenary shifts. The co‐occurrence and overlap of different processes and landforms creates a spatial structure unique to permafrost environments. The coefficient of variation of SOC at the pedon scale (21%–73%) exceeds that found at terrain (17%–66%) and even landscape scale (24%–67%). Such high values for spatial variation are otherwise found at regional to continental scale. Clearly, permafrost soils do not conform to Tobler's law, but are among the most variable soils on Earth. This needs to be accounted for in mapping and predictions of the permafrost carbon feedbacks through various ecosystem processes. We conclude that scale deserves special attention in permafrost regions.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 107
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    THE CHANGING BIOGEOCHEMICAL CYCLES OF TUNDRA (2022)
    Wiley
    In:  EPIC3Multi‐Scale Biogeochemical Processes in Soil Ecosystems, Multi‐Scale Biogeochemical Processes in Soil Ecosystems, Hoboken, NJ, Wiley, pp. 157-181, ISBN: 9781119480471
    Details
    Publication Date: 2024-04-22
    Description: Tundra is experiencing more intense warming than any other ecosystem on earth. While warming is the most direct effect of climate change on tundra, warming leads to a cascade of environmental changes such as permafrost thaw, altered precipitation regimes, and increased wildfires. This chapter will first focus on how climate change is changing the environment of Arctic and subarctic tundra and then focus on how climate change is altering tundra's carbon, nitrogen, and phosphorus cycles with a focus on soils. Overall, tundra soils are shifting from being a carbon sink into a carbon source as rising temperatures increase microbial activity—a positive feedback to climate change. However, those rising temperatures are also increasing nutrient mineralization rates, which could increase ecosystem carbon storage via enhanced plant productivity as well as increase emissions of nitrous oxide, a powerful greenhouse gas. There is currently a disconnect between the large soil carbon losses measured in many in situ experiments and the strong plant carbon gains predicted by models. Ultimately, more research is needed on the interplay between tundra soils, nutrients, and plants to determine the magnitude of tundra's feedback to climate change.
    Repository Name: EPIC Alfred Wegener Institut
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  • 108
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    Spatially heterogeneous shifts in vegetation phenology induced by climate change threaten the integrity of the avian migration network (2024)
    Wiley
    In:  Global Change Biology vol. 30 no. e17148
    Details
    Publication Date: 2024-04-22
    Description: Phenological responses to climate change frequently vary among trophic levels, which can result in increasing asynchrony between the peak energy requirements of consumers and the availability of resources. Migratory birds use multiple habitats with seasonal food resources along migration flyways. Spatially heterogeneous climate change could cause the phenology of food availability along the migration flyway to become desynchronized. Such heterogeneous shifts in food phenology could pose a challenge to migratory birds by reducing their opportunity for food availability along the migration path and consequently influencing their survival and reproduction. We develop a novel graph-based approach to quantify this problem and deploy it to evaluate the condition of the heterogeneous shifts in vegetation phenology for 16 migratory herbivorous waterfowl species in Asia. We show that climate change-induced heterogeneous shifts in vegetation phenology could cause a 12% loss of migration network integrity on average across all study species. Species that winter at relatively lower latitudes are subjected to a higher loss of integrity in their migration network. These findings highlight the susceptibility of migratory species to climate change. Our proposed methodological framework could be applied to migratory species in general to yield an accurate assessment of the exposure under climate change and help to identify actions for biodiversity conservation in the face of climate-related risks.
    Keywords: bird migration ; climate change ; graph-based approach ; heterogeneous shifts ; network integrity ; phenological asynchrony ; vegetation phenology
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 109
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    Northeast Siberian Permafrost Ice-Wedge Stable Isotopes Depict Pronounced Last Glacial Maximum Winter Cooling (2021)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 48(7), pp. e2020GL092087-e2020GL092087, ISSN: 0094-8276
    Details
    Publication Date: 2024-04-20
    Description: Stable isotopes (δ18O, δD) of wedge ice hold potential to reconstruct past winter climate conditions. Here, we present records of the marine isotope stages (MIS) 3 and 2 including the last Glacial maximum (LGM) from Bol’shoy Lyakhovsky Island (NE Siberia). MIS 3 wedge ice dated from 52 to 40 Kyr b2k varies between −32 and −29‰ in δ18O. Colder LGM conditions are implied by δ18O of −37‰ around 25 Kyr b2k. Similar Deuterium excess values indicate comparable moisture sources during MIS 3 and MIS 2. Regional LGM climate reconstructions depend on the seasonal resolution of the proxies and model simulations. Our wedge-ice record reflects coldest winters during global minima in atmospheric CO2 and sea level. The extreme LGM winter cooling is not represented in model projections of global LGM climate where West Beringia shows noticeably little cooling or even warming in mean annual temperatures compared to the late Holocene.
    Repository Name: EPIC Alfred Wegener Institut
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  • 110
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    Thermohydrological Impact of Forest Disturbances on Ecosystem‐Protected Permafrost (2022)
    Wiley
    In:  EPIC3Journal of Geophysical Research: Biogeosciences, Wiley, 127(5)
    Details
    Publication Date: 2024-04-23
    Description: Boreal forests cover over half of the global permafrost area and protect underlying permafrost. Boreal forest development, therefore, has an impact on permafrost evolution, especially under a warming climate. Forest disturbances and changing climate conditions cause vegetation shifts and potentially destabilize the carbon stored within the vegetation and permafrost. Disturbed permafrost-forest ecosystems can develop into a dry or swampy bush- or grasslands, shift toward broadleaf- or evergreen needleleaf-dominated forests, or recover to the pre-disturbance state. An increase in the number and intensity of fires, as well as intensified logging activities, could lead to a partial or complete ecosystem and permafrost degradation. We study the impact of forest disturbances (logging, surface, and canopy fires) on the thermal and hydrological permafrost conditions and ecosystem resilience. We use a dynamic multilayer canopy-permafrost model to simulate different scenarios at a study site in eastern Siberia. We implement expected mortality, defoliation, and ground surface changes and analyze the interplay between forest recovery and permafrost. We find that forest loss induces soil drying of up to 44%, leading to lower active layer thicknesses and abrupt or steady decline of a larch forest, depending on disturbance intensity. Only after surface fires, the most common disturbances, inducing low mortality rates, forests can recover and overpass pre-disturbance leaf area index values. We find that the trajectory of larch forests after surface fires is dependent on the precipitation conditions in the years after the disturbance. Dryer years can drastically change the direction of the larch forest development within the studied period.
    Repository Name: EPIC Alfred Wegener Institut
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  • 111
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    A temperature‐controlled, circular maintenance system for studying growth and development of pelagic tunicates (salps) (2024)
    Wiley
    In:  EPIC3Limnology and Oceanography Methods, Wiley, ISSN: 1541-5856
    Details
    Publication Date: 2024-02-29
    Description: Salps have attracted attention as zooplankton organisms that may be able to expand their habitat range and increase their ecological importance in the face of ongoing global warming. Due to their gelatinous nature, unique feeding strategy, and reproductive ecology such changes could have profound impacts on regional marine ecosystems. While their role in the regional carbon cycle is receiving attention, our knowledge of their physiology and life cycle is still limited. This knowledge gap is mainly due to their fragile gelatinous nature, which makes it difficult to capture and maintain intact specimen in the laboratory. We present here a modified kreisel tank system that has been tested onboard a research vessel with the Southern Ocean salp Salpa thompsoni and at a research station with Salpa fusiformis and Thalia democratica from the Mediterranean Sea. Successful maintenance over days to weeks allowed us to obtain relative growth and developmental rates comparable to in situ field samples of S. thompsoni and S. fusiformis, and provided insights into previously unknown features of their life cycle (e.g., testes development). Our results show that traditional methods of estimating growth, such as cohort analysis, may lead to a general overestimation of growth rates and neglect individual strategies (e.g., shrinkage), which can affect the results and conclusions drawn from population dynamic models. By providing a starting point for the successful maintenance of different species, comparable experiments on the physiology of salps is made possible. This will contribute to refining model parameters and improving the reliability of the predictions.
    Repository Name: EPIC Alfred Wegener Institut
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  • 112
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    Physiological response of an Antarctic cryptophyte to increasing temperature, CO2, and irradiance (2023)
    Wiley
    In:  EPIC3Limnology and Oceanography, Wiley, 68(8), pp. 1880-1894, ISSN: 0024-3590
    Details
    Publication Date: 2024-03-01
    Description: The Southern Ocean, a globally important CO2 sink, is one of the most susceptible regions in the world to climate change. Phytoplankton of the coastal shelf waters around the Western Antarctic Peninsula have been experiencing rapid warming over the past decades and current ongoing climatic changes will expose them to ocean acidification and high light intensities due to increasing stratification. We conducted a multiple-stressor experiment to evaluate the response of the still poorly studied key Antarctic cryptophyte species Geminigera cryophila to warming in combination with ocean acidification and high irradiance. Based on the thermal growth response of G. cryophila, we grew the cryptophyte at suboptimal (2°C) and optimal (4°C) temperatures in combination with two light intensities (medium light: 100 μmol photons m−2 s−1 and high light [HL]: 500 μmol photons m−2 s−1) under ambient (400 μatm pCO2) and high pCO2 (1000 μatm pCO2) conditions. Our results reveal that G. cryophila was not susceptible to high pCO2, but was strongly affected by HL at 2°C, as both growth and carbon fixation were significantly reduced. In comparison, warming up to 4°C stimulated the growth of the cryptophyte and even alleviated the previously observed negative effects of HL at 2°C. When grown, however, at temperatures above 4°C, the cryptophyte already reached its maximal thermal limit at 8°C, pointing out its vulnerability toward even higher temperatures. Hence, our results clearly indicate that warming and high light and not pCO2 control the growth of G. cryophila.
    Repository Name: EPIC Alfred Wegener Institut
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  • 113
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    The physiological response of an Antarctic key phytoplankton species to low iron and manganese concentrations (2023)
    Wiley
    In:  EPIC3Limnology and Oceanography, Wiley, 68(9), pp. 2153-2166, ISSN: 0024-3590
    Details
    Publication Date: 2024-03-01
    Description: Iron (Fe) and manganese (Mn) availability and the divergent requirements of phytoplankton species were recently shown to be potential important drivers of Southern Ocean community composition. Knowledge about Antarctic phytoplankton species requirements for Fe and Mn remains, however, scarce. By performing laboratory experiments and additional calculations of the photosynthetic electron transport, we investigated the response of the ecologically important species Phaeocystis antarctica under a combination of different Fe and Mn concentrations. Fe deprivation alone provoked typical physiological characteristics of Fe limitation in P. antarctica (e.g., lowered growth and photosynthetic efficiency). In comparison, under Mn deprivation alone, the growth and carbon production of P. antarctica were not impacted. Its tolerance to cope with low Mn concentrations resulted from an efficient photoacclimation strategy, including a higher number of active photosystems II through which fewer electrons were transported. This strategy allowed us to maintain similar high growth and carbon production rates as FeMn-enriched cells. Due to its low Mn requirement, P. antarctica performed physiologically as Fe-deprived cells under the combined depletion of Fe and Mn. Hence, our study reveals that different from other Southern Ocean phytoplankton species, P. antarctica possesses a high capacity to cope with natural low Mn concentrations, which can facilitate its dominance over others, potentially explaining its ecological success across the Southern Ocean.
    Repository Name: EPIC Alfred Wegener Institut
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  • 114
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    Phaeocystis: A Global Enigma (2024)
    Annual Reviews
    In:  EPIC3Annual Review of Marine Science, Annual Reviews, 16(1), pp. 417-441, ISSN: 1941-1405
    Details
    Publication Date: 2024-03-01
    Description: The genus Phaeocystis is globally distributed, with blooms commonly occurring on continental shelves. This unusual phytoplankter has two major morphologies: solitary cells and cells embedded in a gelatinous matrix. Only colonies form blooms. Their large size (commonly 2 mm but up to 3 cm) and mucilaginous envelope allow the colonies to escape predation, but data are inconsistent as to whether colonies are grazed. Cultured Phaeocystis can also inhibit the growth of co-occurring phytoplankton or the feeding of potential grazers. Colonies and solitary cells use nitrate as a nitrogen source, although solitary cells can also grow on ammonium. Phaeocystis colonies might be a major contributor to carbon flux to depth, but in most cases, colonies are rapidly remineralized in the upper 300 m. The occurrence of large Phaeocystis blooms is often associated with environments with low and highly variable light and high nitrate levels, with Phaeocystis antarctica blooms being linked additionally to high iron availability. Emerging results indicate that different clones of Phaeocystis have substantial genetic plasticity, which may explain its appearance in a variety of environments. Given the evidence of Phaeocystis appearing in new systems, this trend will likely continue in the near future.
    Repository Name: EPIC Alfred Wegener Institut
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  • 115
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    Coupled U–Pb and 40Ar/39Ar chronology of late‐stage intrusions at Elba Island (Italy) supports late Miocene long‐lived magma reservoirs in the Tyrrhenian upper crust (2024)
    Wiley
    Details
    Publication Date: 2024-03-12
    Description: The late Miocene Monte Capanne and Porto Azzurro plutons are investigated by means of coupled U-Pb zircon and 40Ar/39Ar white mica dating to test the occurrence of long-lived magmatic systems in the upper crust. Zircon crystallized for 〉 1 Myr in both plutonic systems, with supersolidus conditions overlapping for ~220 kyr indicating previously unrecognized co-existence of the two reservoirs. The development of the Porto Azzurro high T-aureole is post-dated by continuous igneous zircon crystallization until ~ 6.0 Ma. By linking crystallization to post-emplacement cooling of late-stage pulses in both western and eastern Elba we constrain long-lived sizeable reservoirs (possibly the same reservoir) in the Tyrrhenian upper crust between ~8 and 6 Ma.
    Description: In press
    Description: OST1 Alla ricerca dei Motori Geodinamici
    Description: JCR Journal
    Keywords: 40Ar/39Ar white mica dating ; Elba Island ; long-lived magma reservoirs ; U–Pb zircon dating ; MioceneTyrrhenian crust ; upper crustal granites ; 04. Solid Earth
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 116
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    Distinct bacterial succession and functional response to alginate in the South, Equatorial, and North Pacific Ocean (2024)
    Wiley
    In:  EPIC3Environmental Microbiology, Wiley, 26(3), pp. e16594-e16594, ISSN: 1462-2912
    Details
    Publication Date: 2024-03-11
    Description: The availability of alginate, an abundant macroalgal polysaccharide, induces compositional and functional responses among marine microbes, but these dynamics have not been characterized across the Pacific Ocean. We investigated alginate-induced compositional and functional shifts (e.g., heterotrophic production, glucose turnover, hydrolytic enzyme activities) of microbial communities in the South Subtropical, Equatorial, and Polar Frontal North Pacific in mesocosms. We observed that shifts in response to alginate were site-specific. In the South Subtropical Pacific, prokaryotic cell counts, glucose turnover, and peptidase activities changed the most with alginate addition, along with the enrichment of the widest range of particle-associated taxa (161 amplicon sequence variants; ASVs) belonging to Alteromonadaceae, Rhodobacteraceae, Phormidiaceae, and Pseudoalteromonadaceae. Some of these taxa were detected at other sites but only enriched in the South Pacific. In the Equatorial Pacific, glucose turnover and heterotrophic prokaryotic production increased most rapidly; a single Alteromonas taxon dominated (60% of the community) but remained low (〈2%) elsewhere. In the North Pacific, the particle-associated community response to alginate was gradual, with a more limited range of alginate-enriched taxa (82 ASVs). Thus, alginate-related ecological and biogeochemical shifts depend on a combination of factors that include the ability to utilize alginate, environmental conditions, and microbial interactions.
    Repository Name: EPIC Alfred Wegener Institut
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  • 117
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    Epizoic yellow sponge (Poecilosclerida, Demospongiae) expansion on living Scleractinian corals in Bintan, Riau Archipelago, Indonesia (2024)
    Wiley
    In:  Marine Ecology vol. 2024 no. e12796
    Details
    Publication Date: 2024-03-14
    Description: Coral reef ecosystems in Indonesia are under threat due to changes in the environment driven by global climate change, along with local disturbances such as sedimentation and eutrophication. Consequently, comprehensive coral reef monitoring \nactivities have been initiated at numerous locations across Indonesia. In this study, the \nfindings from coral reef health surveys across 14 reef sites (within 40 hectares) in the \nBintan area (Riau Archipelago, Indonesia; 100\xe2\x80\x89km southeast of Singapore) revealed a \npotentially novel epizoic yellow sponge species (Phorbas sp.) that overgrows coral colonies. This species, tentatively classified as a new Phorbas sp. (order Poecilosclerida: \nfamily Hymedesmiidae), was identified through a combined approach employing classical taxonomic methods along with DNA barcoding using the cytochrome c oxidase \nI (COI) gene. At every site, three permanent 20-m transects were established to annually monitor live coral coverage and species composition between 2014 and 2017. \nThe survey indicated a notable change in the overall coral cover during this period. \nThe abundance of coral diseases was investigated in 2014 and 2017. Additionally, the \nprogress of Phorbas sp., was closely monitored (i.e., every second day for one week) \nat Bintan Island (site 11) during the dry season in August 2017. This approach aimed \nto approximate the relative impact of each incident on the coral\'s condition. The results indicated that the most comprehensive change occurred due to the overgrowth \nof Phorbas sp., which affected 12 scleractinian coral species across eight genera in \nalmost all sites except one. The abundance of this epizoic sponge infestation was \nhighest at Pulau Beralas Pasir (site 10), constituting 22.9% of all recorded life forms, \nand lowest at Pulau Pangkil-Besar (site 13), with only 0.7%. The expansion of the thin \nyellow sponge tissue was estimated to increase by up to 0.51\xe2\x80\x89\xc2\xb1\xe2\x80\x890.48\xe2\x80\x89cm2 \n per day on \nPorites coral.
    Keywords: coral disease ; coral health ; expansion progress ; novel sponge ; yellow band disease
    Repository Name: National Museum of Natural History, Netherlands
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    Piecing the barcoding puzzle of Palearctic water frogs (Pelophylax) sheds light on amphibian biogeography and global invasions (2024)
    Wiley
    In:  Global Change Biology vol. 30 no. e17180
    Details
    Publication Date: 2024-03-21
    Description: Palearctic water frogs (genus Pelophylax) are an outstanding model in ecology and evolution, being widespread, speciose, either threatened or threatening to other species through biological invasions, and capable of siring hybrid offspring that escape the rules of sexual reproduction. Despite half a century of genetic research and hundreds of publications, the diversity, systematics and biogeography of Pelophylax still remain highly confusing, in no small part due to a lack of correspondence between studies. To provide a comprehensive overview, we gathered 〉13,000 sequences of barcoding genes from 〉1700 native and introduced localities and built multigene mitochondrial (~17 kb) and nuclear (~10 kb) phylogenies. We mapped all currently recognized taxa and their phylogeographic lineages (〉40) to get a grasp on taxonomic issues, cyto-nuclear discordances, the genetic makeup of hybridogenetic hybrids, and the origins of introduced populations. Competing hypotheses for the molecular calibration were evaluated through plausibility tests, implementing a new approach relying on predictions from the anuran speciation continuum. Based on our timetree, we propose a new biogeographic paradigm for the Palearctic since the Paleogene, notably by attributing a prominent role to the dynamics of the Paratethys, a vast paleo-sea that extended over most of Europe. Furthermore, our results show that distinct marsh frog lineages from Eastern Europe, the Balkans, the Near East, and Central Asia (P. ridibundus ssp.) are naturally capable of inducing hybridogenesis with pool frogs (P. lessonae). We identified 14 alien lineages (mostly of P. ridibundus) over ~20 areas of invasions, especially in Western Europe, with genetic signatures disproportionally pointing to the Balkans and Anatolia as the regions of origins, in line with exporting records of the frog leg industry and the stocks of pet sellers. Pelophylax thus emerges as one of the most invasive amphibians worldwide, and deserves much higher conservation concern than currently given by the authorities fighting biological invasions.
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    A multiple baseline approach for marine heatwaves (2024)
    Wiley
    In:  EPIC3Limnology and Oceanography, Wiley, ISSN: 0024-3590
    Details
    Publication Date: 2024-02-09
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:p〉Marine heatwaves and other extreme temperature events can drive biological responses, including mass mortality. However, their effects depend on how they are experienced by biological systems (including human societies). We applied two different baselines (fixed and shifting) to a time series of North Sea water temperature to explore how slowly vs. quickly adapting systems would experience extreme temperatures. We tested if the properties of marine heatwaves and the association with atmospheric heatwaves were robust to a change in baseline. A fixed baseline produced an increase in the frequency and duration of marine heatwaves, which would be experienced as the new normal by slowly adapting systems; 7 of the 10 most severe heatwaves occurred between 1990 and 2018. The shifting baseline removed the trend in the frequency but not duration of heatwaves; the 1990s appeared as a period of change in the frequency of strong and severe heatwaves as compared to the 1980s. There were also common patterns among baselines: marine heatwaves were more frequent in late summer when temperatures peak; temperature variability was characterized by low frequency, large amplitude fluctuations (i.e., as red noise), known to drive extinction events. In addition, marine heatwaves occurred during or just after atmospheric heatwaves. Our work highlights the importance of identifying properties of marine heatwaves that are robust or contingent on a change in baseline.〈/jats:p〉
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    Ethical considerations for research on small‐scale fisheries and blue crimes (2021)
    Wiley
    In:  EPIC3Fish and Fisheries, Wiley, 22(6), pp. 1160-1166, ISSN: 1467-2960
    Details
    Publication Date: 2024-02-07
    Description: Crimes at sea—blue crimes—can have devastating impacts on small-scale fishing communities. Increasing calls to address “blue crimes” demand more research to address the drivers, patterns, actors and impacts of criminal activities in society and the oceans. This research and policy agenda, however, is not without risks as it might impact individual small-scale fishers and their communities, exacerbate existing inequalities and contribute to the criminalization of small-scale fishing practices. This paper discusses the risks and ethical challenges faced by a blue crimes research agenda to improve rather than worsen the plight of small-scale fishers. We identify eight inter-related ethical considerations: (i) pay attention to context and forms of involvement, (ii) cultivate reciprocal relationships and collaborations, (iii) evaluate and minimize risks, (iv) integrate storytelling and careful listening, (v) challenge reductionism, (vi) represent people, places, and practices carefully, (vii) follow communication ethics and (viii) consider the legal and policy implications. In light of a review of the literature on blue crimes and small-scale fisheries, we point to the need for ethically grounded research that is committed to reducing the associated burdens on small-scale fishers and their communities.
    Repository Name: EPIC Alfred Wegener Institut
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  • 121
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    Experiential learning, practices, and space for change: The institutional preconfiguration of community participation in flood risk reduction (2022)
    Wiley
    In:  EPIC3Journal of Flood Risk Management, Wiley, ISSN: 1753-318X
    Details
    Publication Date: 2024-02-07
    Description: Responding to societal challenges requires an understanding of how institutional change happens or does not happen. In the context of flood risk reduction, a central impediment of transformational change is a struggle over how public participation is understood and practiced. Risk institutions are often portrayed as resistant to change, which overlooks the individuals within institutions who struggle to implement innovative power-sharing approaches/arrangements. Using two rounds of qualitative interviews spread over 5 years, this research identifies factions within the risk sector—those who view participation as awareness raising and those who are struggling to make participation part of a wider commitment to power-sharing: a group that, for the purpose of this analysis, we call “mavericks.” Through focus on how mavericks struggle for change, this analysis uncovers tensions that arise as individuals attempt to alter prevailing knowledge-practices. The findings highlight the importance of experiential learning, active listening, and the alteration of space. By applying a relational conceptualisation, we explore how mavericks advocate for relationship building, which alters spaces of public participation and, in that way, lays the foundation for transformational social innovations. The conclusions offer flood risk researchers perspective on the institutional struggles that preconfigure how frontrunner projects are or are not able to facilitate the community participation needed to successfully implement societal transformations.
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    Dynamic species distribution models of Antarctic blue whales in the Weddell Sea using visual sighting and passive acoustic monitoring data (2024)
    Wiley
    In:  EPIC3Diversity and Distributions, Wiley, 30(1), pp. 87-105, ISSN: 1366-9516
    Details
    Publication Date: 2024-02-12
    Description: Aim: Species distribution models (SDMs) are essential tools in ecology and conservation. However, the scarcity of visual sightings of marine mammals in remote polar areas hinders the effective application of SDMs there. Passive acoustic monitoring (PAM) data provide year-round information and overcome foul weather limitations faced by visual surveys. However, the use of PAM data in SDMs has been sparse so far. Here, we use PAM-based SDMs to investigate the spatiotemporal distribution of the critically endangered Antarctic blue whale in the Weddell Sea. Location: The Weddell Sea. Methods: We used presence-only dynamic SDMs employing visual sightings and PAM detections in independent models. We compared the two independent models with a third combined model that integrated both visual and PAM data, aiming at leveraging the advantages of each data type: the extensive spatial extent of visual data and the broader temporal/environmental range of PAM data. Results: Visual and PAM data prove complementary, as indicated by a low spatial overlap between daily predictions and the low predictability of each model at detections of other data types. Combined data models reproduced suitable habitats as given by both independent models. Visual data models indicate areas close to the sea ice edge (SIE) and with low-to-moderate sea ice concentrations (SIC) as suitable, while PAM data models identified suitable habitats at a broader range of distances to SIE and relatively higher SIC. Main Conclusions: The results demonstrate the potential of PAM data to predict year-round marine mammal habitat suitability at large spatial scales. We provide reasons for discrepancies between SDMs based on either data type and give methodological recommendations on using PAM data in SDMs. Combining visual and PAM data in future SDMs is promising for studying vocalized animals, particularly when using recent advances in integrated distribution modelling methods.
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    Sustainability: We need to focus on overall system outcomes rather than simplistic targets (2024)
    Wiley
    In:  EPIC3People and Nature, Wiley, ISSN: 2575-8314
    Details
    Publication Date: 2024-02-12
    Description: Many of the global challenges that confront humanity are interlinked in a dynamic complex network, with multiple feedback loops, nonlinear interactions and interdependencies that make it difficult, if not impossible, to consider individual threats in isolation. These challenges are mainly dealt with, however, by considering individual threats in isolation (at least in political terms). The mitigation of dual climate and biodiversity threats, for example, is linked to a univariate 1.5°C global warming boundary and a global area conservation target of 30% by 2030. The situation has been somewhat improved by efforts to account for interactions through multidimensional target setting, adaptive and open management and market-based decision pathways. But the fundamental problem still remains—that complex systems such as those formed by the network of global threats have emergent properties that are more than the sum of their parts. We must learn how to deal with or live with these properties if we are to find effective ways to cope with the threats, individually and collectively. Here, we argue that recent progresses in complex systems research and related fields have enhanced our ability to analyse and model such entwined systems to the extent that it offers the promise of a new approach to sustainability. We discuss how this may be achieved, both in theory and in practice, and how human cultural factors play an important but neglected role that could prove vital to achieving success. Read the free Plain Language Summary for this article on the Journal blog.
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    Phylogenomic species delimitation of the twisted\xe2\x80\x90winged parasite genus Stylops (Strepsiptera) (2023)
    Wiley
    In:  Systematic Entomology
    Details
    Publication Date: 2024-02-22
    Description: The twisted-winged parasite genus Stylops has a history of different species concepts with varying host specificity resulting in diverse species diversity estimates in different regions of the Holarctic. The adoption of a supergeneralist species concept in Europe, proposing synonymization of all Western Palaearctic Stylops species, did not facilitate taxonomic clarity and obscured the available life-history data in the region for decades. Lack of molecular data has allowed divergent opinions on species hypotheses and little opportunity for evaluating them in this morphologically challenging genus. To solve these discrepancies and gain novel information about host associations, we applied whole-genome sequencing to 163 specimens, representing a significant portion of putative European species. We evaluate the existing and conflicting species hypotheses with molecular species delimitation using Species bOundry Delimitation using Astral (SODA)and use a maximum likelihood phylogeny to investigate host associations of the species. Furthermore, we evaluate the effect of a number of loci used in SODA for the number of inferred species. We find justification for synonymization of multiple species and indications of undescribed species, as well as new host\xe2\x80\x93parasite relationships. We show that the number of inferred species in SODA is exceedingly and positively correlated with the number of loci used, urging for cautious application. The results of our study bring clarity to the Western Palaearctic species diversity of Stylops. Furthermore, the comprehensive molecular dataset generated in this study will be a valuable resource for future studies on Stylops and the evolution of parasites in general.
    Keywords: [Released under the CC-BY NC 4.0 (\xe2\x80\x9cAttribution-NonCommercial 4.0 International\xe2\x80\x9d) ; License](https://creativecommons.org/licenses/by-nc/4.0/)
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    Tracing basal resource use across sea‐ice, pelagic, and benthic habitats in the early Arctic spring food web with essential amino acid carbon isotopes (2023)
    Wiley
    In:  EPIC3Limnology and Oceanography, Wiley, 68(4), pp. 862-877, ISSN: 0024-3590
    Details
    Publication Date: 2024-04-16
    Description: A rapidly warming Arctic Ocean and associated sea-ice decline is resulting in changing sea-ice protist communities, affecting productivity of under-ice, pelagic, and benthic fauna. Quantifying such effects is hampered by a lack of biomarkers suitable for tracing specific basal resources (primary producers and microorganisms) through food webs. We investigate the potential of δ13C values of essential amino acids (EAAs) (δ13CEAA values) to estimate the proportional use of diverse basal resources by organisms from the under-ice (Apherusa glacialis), pelagic (Calanus hyperboreus) and benthic habitats (sponges, sea cucumber), and the cryo-pelagic fish Boreogadus saida. Two approaches were used: baseline δ13CEAA values, that is, the basal resource specific δ13CEAA values, and δ13CEAA fingerprints, or mean-centred baseline δ13CEAA values. Substantial use of sub-ice algae Melosira arctica by all studied organisms suggests that its role within Arctic food webs is greater than previously recognized. In addition, δ13CEAA fingerprints from algae-associated bacteria were clearly traced to the sponges, with an individually variable kelp use by sea cucumbers. Although mean-centred δ13CEAA values in A. glacialis, C. hyperboreus, and B. saida tissues were aligned with microalgae resources, they were not fully represented by the filtered pelagic- and sea-ice particulate organic matter constituting the spring diatom-dominated algal community. Under-ice and pelagic microalgae use could only be differentiated with baseline δ13CEAA values as similar microalgae clades occur in both habitats. We suggest that δ13CEAA fingerprints combined with microalgae baseline δ13CEAA values are an insightful tool to assess the effect of ongoing changes in Arctic basal resources on their use by organisms.
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    A review of the tectonic, volcanological and hazard history of Vulcano (Aeolian Islands, Italy) (2024)
    Wiley
    Details
    Publication Date: 2024-04-08
    Description: Vulcano is one of the seven volcanic islands composing the Aeolian Islands archipelago (Southern Italy), which also includes three other active volcanoes. The island was orig-inally a stratovolcano like Stromboli; afterwards, its shape turned towards a complex structure composed of several volcanic landforms of different sizes. This is due to the great variability of the tectonic and volcanic phenomena, presently showing a volcano made by two calderas, a lava dome complex and two small active cones. The largest of them is the tuff cone of La Fossa, hosted in the middle of a 3- km-wide caldera struc-ture (La Fossa caldera), whose borders are visible on the southern and western sides of the island. Its last eruption occurred in 1888–1890. At present, Vulcano is charac-terized by weak shallow seismicity and intense fumarolic activity mainly concentrated within the crater of the La Fossa cone and along its rims during a recent unrest phase started in 2021, and measured with a multiparametric monitoring network.
    Description: Published
    Description: 471-487
    Description: OSV4: Preparazione alle crisi vulcaniche
    Description: JCR Journal
    Keywords: Aeolian Islands, Vulcano ; multihazard ; plumbing system ; unrest ; volcanic history ; stratigraphy ; tectonics ; 04.08. Volcanology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Dominant gingers – Discovery and inheritance of a new shell polymorphism in the great pond snail Lymnaea stagnalis (2023)
    Wiley
    In:  Ecology and Evolution vol. 13 no. 12
    Details
    Publication Date: 2024-04-16
    Description: Color polymorphism is a classic study system for evolutionary genetics. One of the most color-polymorphic animal taxa is mollusks, but the investigation of the genetic basis of color determination is often hindered by their life history and the limited avail-ability of genetic resources. Here, we report on the discovery of shell color polymor-phism in a much-used model species, the great pond snail Lymnaea stagnalis. While their shell is usually beige, some individuals from a Greek population show a distinct red shell color, which we nicknamed Ginger. Moreover, we found that the inheritance fits simple, single-locus Mendelian inheritance with dominance of the Ginger allele. We also compared crucial life-history traits between Ginger and wild-type individuals, and found no differences between morphs. We conclude that the relative simplicity of this polymorphism will provide new opportunities for a deeper understanding of the genetic basis of shell color polymorphism and its evolutionary origin.
    Keywords: evolution ; genetics ; life history ; Mendelian inheritance ; simultaneous hermaphrodites
    Repository Name: National Museum of Natural History, Netherlands
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    Developing model systems for dinoflagellates in the post‐genomic era (2023)
    Wiley
    In:  EPIC3Journal of Phycology, Wiley, 59(5), pp. 799-808, ISSN: 0022-3646
    Details
    Publication Date: 2024-04-08
    Description: Dinoflagellates are a diverse group of eukaryotic microbes that are ubiquitous in aquatic environments. Largely photosynthetic, they encompass symbiotic, parasitic, and free-living lineages with a broad spectrum of trophism. Many free-living taxa can produce bioactive secondary metabolites such as biotox- ins, some of which cause harmful algal blooms. In contrast, most symbiotic species are crucial for sustaining coral reef health. The year 2023 marked a decade since the first genome data of dinoflagellates became available. The growing genome-scale resources for these taxa are highlighting their remarkable evolutionary and genomic complexities. Here, we discuss the prospect of developing dinoflagellate models using the criteria of accessibil- ity, tractability, resources, research support, and promise. Moving forward in the post-genomic era, we argue for the development of fit-to-purpose models that tailor to specific biological contexts, and that a one-size-fits-all model is inadequate for encapsulating the complex biology, ecology, and evolutionary history of dinoflagellates.
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    The second most abundant dinophyte in the ponds of a botanical garden is a species new to science (2024)
    Wiley
    In:  EPIC3Journal of Eukaryotic Microbiology, Wiley, 71(2), pp. e13015-e13015, ISSN: 1066-5234
    Details
    Publication Date: 2024-04-08
    Description: In the microscopy realm, a large body of dark biodiversity still awaits to be uncovered. Unarmoured dinophytes are particularly neglected here, as they only present inconspicuous traits. In a remote German locality, we collected cells, from which a monoclonal strain was established, to study morphology using light and electron microscopy and to gain DNA sequences from the rRNA operon. In parallel, we detected unicellular eukaryotes in ponds of the Botanical Garden Munich-Nymphenburg by DNA-metabarcoding (V4 region of the 18S rRNA gene), weekly sampled over the course of a year. Strain GeoK*077 turned out to be a new species of Borghiella with a distinct position in molecular phylogenetics and characteristic coccoid cells of ovoid shape as the most important diagnostic trait. Borghiella ovum, sp. nov., was also present in artificial ponds of the Botanical Garden and was the second most abundant dinophyte detected in the samples. More specifically, Borghiella ovum, sp. nov., shows a clear seasonality, with high frequency during winter months and complete absence during summer months. The study underlines the necessity to assess the biodiversity, particularly of the microscopy realm more ambitiously, if even common species such as formerly Borghiella ovum are yet unknown to science.
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    Testing the deep‐sea glacial disturbance hypothesis as a cause of low, present‐day Norwegian Sea diversity and resulting steep latitudinal diversity gradient, using fossil records (2024)
    Wiley
    In:  EPIC3Global Ecology and Biogeography, Wiley, ISSN: 1466-822X
    Details
    Publication Date: 2024-04-24
    Description: 〈jats:title〉Abstract〈/jats:title〉〈jats:sec〉〈jats:title〉Aim〈/jats:title〉〈jats:p〉Within the intensively‐studied, well‐documented latitudinal diversity gradient, the deep‐sea biodiversity of the present‐day Norwegian Sea stands out with its notably low diversity, constituting a steep latitudinal diversity gradient in the North Atlantic. The reason behind this has long been a topic of debate and speculation. Most prominently, it is explained by the deep‐sea glacial disturbance hypothesis, which states that harsh environmental glacial conditions negatively impacted Norwegian Sea diversities, which have not yet fully recovered. Our aim is to empirically test this hypothesis. Specific research questions are: (1) Has deep‐sea biodiversity been lower during glacials than during interglacials? 〈jats:italic〉(〈/jats:italic〉2) Was there any faunal shift at the Mid‐Brunhes Event (MBE) when the mode of glacial–interglacial climatic change was altered?〈/jats:p〉〈/jats:sec〉〈jats:sec〉〈jats:title〉Location〈/jats:title〉〈jats:p〉Norwegian Sea, deep sea (1819–2800 m), coring sites MD992277, PS1243, and M23352.〈/jats:p〉〈/jats:sec〉〈jats:sec〉〈jats:title〉Time period〈/jats:title〉〈jats:p〉620.7–1.4 ka (Middle Pleistocene–Late Holocene).〈/jats:p〉〈/jats:sec〉〈jats:sec〉〈jats:title〉Taxa studied〈/jats:title〉〈jats:p〉Ostracoda (Crustacea).〈/jats:p〉〈/jats:sec〉〈jats:sec〉〈jats:title〉Methods〈/jats:title〉〈jats:p〉We empirically test the deep‐sea glacial disturbance hypothesis by investigating whether diversity in glacial periods is consistently lower than diversity in interglacial periods. Additionally, we apply comparative analyses to determine a potential faunal shift at the MBE, a Pleistocene event describing a fundamental shift in global climate.〈/jats:p〉〈/jats:sec〉〈jats:sec〉〈jats:title〉Results〈/jats:title〉〈jats:p〉The deep Norwegian Sea diversity was not lower during glacial periods compared to interglacial periods. Holocene diversity was exceedingly lower than that of the last glacial period. Faunal composition changed substantially between pre‐ and post‐MBE.〈/jats:p〉〈/jats:sec〉〈jats:sec〉〈jats:title〉Main conclusions〈/jats:title〉〈jats:p〉These results reject the glacial disturbance hypothesis, since the low glacial diversity is the important precondition here. The present‐day‐style deep Norwegian Sea ecosystem was established by the MBE, more specifically by MBE‐induced changes in global climate, which has led to more dynamic post‐MBE conditions. In a broader context, this implies that the MBE has played an important role in the establishment of the modern polar deep‐sea ecosystem and biodiversity in general.〈/jats:p〉〈/jats:sec〉
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    Analysis of bacterial communities in a municipal duck pond during a phytoplankton bloom and isolation of Anatilimnocola aggregata gen. nov., sp. nov., Lacipirellula limnantheis sp. nov. and Urbifossiella limnaea gen. nov., sp. nov. belonging to the phylum Planctomycetes (2021)
    Wiley
    In:  EPIC3Environmental Microbiology, Wiley, 23(3), pp. 1379-1396, ISSN: 1462-2912
    Details
    Publication Date: 2024-05-03
    Description: Waterbodies such as lakes and ponds are fragile environments affected by human influences. Suitable conditions can result in massive growth of phototrophs, commonly referred to as phytoplankton blooms. Such events benefit heterotrophic bacteria able to use compounds secreted by phototrophs or their biomass as major nutrient source. One example of such bacteria are Planctomycetes, which are abundant on the surfaces of marine macroscopic phototrophs; however, less data are available on their ecological roles in limnic environments. In this study, we followed a cultivation-independent deep sequencing approach to study the bacterial community composition during a cyanobacterial bloom event in a municipal duck pond. In addition to cyanobacteria, which caused the bloom event, members of the phylum Planctomycetes were significantly enriched in the cyanobacteria-attached fraction compared to the free-living fraction. Separate datasets based on isolated DNA and RNA point towards considerable differences in the abundance and activity of planctomycetal families, indicating different activity peaks of these families during the cyanobacterial bloom. Motivated by the finding that the sampling location harbours untapped bacterial diversity, we included a complementary cultivation-dependent approach and isolated and characterized three novel limnic strains belonging to the phylum Planctomycetes.
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    Linking the Langevin equation to scaling properties of space plasma turbulence at sub-ion scales (2024)
    American Physical Society
    Details
    Publication Date: 2024-04-30
    Description: Current understanding of the kinetic-scale turbulence in weakly collisional plasmas still remains elusive. We employ a general framework in which the turbulent energy transfer is envisioned as a scale-to-scale Langevin process. Fluctuations in the sub-ion range show a global scale invariance, thus suggesting a homogeneous energy repartition. In this Letter, we interpret such a feature by linking the drift term of the Langevin equation to scaling properties of fluctuations. Theoretical expectations are verified on solar wind observations and numerical simulations, thus giving relevance to the proposed framework for understanding kinetic-scale turbulence in space plasmas.
    Description: Published
    Description: L042014
    Description: OSA3: Climatologia e meteorologia spaziale
    Description: JCR Journal
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    High Levels of CO 2 Exchange During Synoptic‐Scale Events Introduce Large Uncertainty Into the Arctic Carbon Budget (2021)
    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 48(9), ISSN: 0094-8276
    Details
    Publication Date: 2024-05-07
    Description: CO2 release from thawing permafrost is both a consequence of, and a driver for, global warming, making accurate information on the Arctic carbon cycle essential for climate predictions. Eddy covariance data obtained from Bayelva (Svalbard) in 2015, using well‐established processing and quality control techniques, indicate that most of the annual net CO2 uptake is due to high CO2 flux events in winter that are associated with strong winds and probably relate to technical limitations of the gas analyzer. Emission events may relate to either (unidentified) instrumental limitations or to physical processes such as CO2 advection. Excluding the high winter uptake events yields an annual CO2 budget close to zero; whether or not these events are included can, therefore, have a considerable effect on carbon budget calculations. Further investigation will be crucial to pinpoint the factors causing these high CO2 flux events and to derive scientifically substantiated flux processing standards.
    Repository Name: EPIC Alfred Wegener Institut
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    In contrast to diatoms, cryptophytes are susceptible to iron limitation, but not to ocean acidification (2022)
    Wiley
    In:  EPIC3Physiologia Plantarum, Wiley, 174(1), ISSN: 0031-9317
    Details
    Publication Date: 2024-05-07
    Description: Previous field studies in the Southern Ocean (SO) indicated an increased occurrence and dominance of cryptophytes over diatoms due to climate change. To gain a better mechanistic understanding of how the two ecologically important SO phytoplankton groups cope with ocean acidification (OA) and iron (Fe) availability, we chose two common representatives of Antarctic waters, the cryptophyte Geminigera cryophila and the diatom Pseudo-nitzschia subcurvata. Both species were grown at 2°C under different pCO2 (400 vs. 900 μatm) and Fe (0.6 vs. 1.2 nM) conditions. For P. subcurvata, an additional high pCO2 level was applied (1400 μatm). At ambient pCO2 under low Fe supply, growth of G. cryophila almost stopped while it remained unaffected in P. subcurvata. Under high Fe conditions, OA was not beneficial for P. subcurvata, but stimulated growth and carbon production of G. cryophila. Under low Fe supply, P. subcurvata coped much better with OA than the cryptophyte, but invested more energy into photoacclimation. Our study reveals that Fe limitation was detrimental for the growth of G. cryophila and suppressed the positive OA effect. The diatom was efficient in coping with low Fe, but was stressed by OA while both factors together strongly impacted its growth. The distinct physiological response of both species to OA and Fe limitation explains their occurrence in the field. Based on our results, Fe availability is an important modulator of OA effects on SO phytoplankton, with different implications on the occurrence of cryptophytes and diatoms in the future.
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  • 135
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    Coherent response of zoo‐ and phytoplankton assemblages to global warming since the Last Glacial Maximum (2024)
    Wiley
    In:  EPIC3Global Ecology and Biogeography, Wiley, ISSN: 0960-7447
    Details
    Publication Date: 2024-05-06
    Description: Aim: We are using the fossil record of different marine plankton groups to determine how their biodiversity has changed during past climate warming comparable to projected future warming. Location: North Atlantic Ocean and adjacent seas. Time series cover a latitudinal range from 75° N to 6° S. Time period: Past 24,000 years, from the Last Glacial Maximum (LGM) to the current warm period covering the last deglaciation. Major taxa studied: Planktonic foraminifera, dinoflagellates and coccolithophores. Methods: We analyse time series of fossil plankton communities using principal component analysis and generalized additive models to estimate the overall trend of temporal compositional change in each plankton group and to identify periods of significant change. We further analyse local biodiversity change by analysing species richness, species gains and losses, and the effective number of species in each sample, and compare alpha diversity to the LGM mean. Results: All plankton groups show remarkably similar trends in the rates and spatio-temporal dynamics of local biodiversity change and a pronounced non-linearity with climate change in the current warm period. Assemblages of planktonic foraminifera and dinoflagellates started to change significantly with the onset of global warming around 15,500 to 17,000 years ago and continued to change at the same rate during the current warm period until at least 5000 years ago, while coccolithophore assemblages changed at a constant rate throughout the past 24,000 years, seemingly irrespective of the prevailing temperature change. Main conclusions: Climate change during the transition from the LGM to the current warm period led to a long-lasting reshuffling of zoo- and phytoplankton assemblages, likely associated with the emergence of new ecological interactions and possibly a shift in the dominant drivers of plankton assemblage change from more abiotic-dominated causes during the last deglaciation to more biotic-dominated causes with the onset of the Holocene.
    Repository Name: EPIC Alfred Wegener Institut
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  • 136
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    Effects of bottom‐up factors on growth and toxin content of a harmful algae bloom dinoflagellate (2024)
    Wiley
    In:  EPIC3Limnology and Oceanography, Wiley, ISSN: 0024-3590
    Details
    Publication Date: 2024-05-30
    Description: The toxin-producing dinoflagellate Alexandrium pseudogonyaulax has become increasingly abundant in northern European waters, replacing other Alexandrium species. A. pseudogonyaulax produces goniodomins and lytic substances, which can be cytotoxic toward other organisms, including fish, but we still know little about the environmental conditions influencing its growth and toxicity. Here, we investigated the impacts of different nitrogen sources and light intensities, common bottom-up drivers of bloom formation, on the growth and toxin content of three A. pseudogonyaulax strains isolated from the Danish Limfjord. While the growth rates were significantly influenced by nitrogen source and light intensity, the intracellular toxin contents only showed strong differences between the exponential and stationary growth phases. Moreover, the photophysiological response of A. pseudogonyaulax showed little variation across varying light intensities, while light-harvesting pigments were significantly more abundant under low light conditions. This study additionally highlights considerable physiological variability between strains, emphasizing the importance of conducting laboratory experiments with several algal strains. A high physiological plasticity toward changing abiotic parameters points to a long-term establishment of A. pseudogonyaulax in northern European waters.
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  • 137
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    Effects of bottom‐up factors on growth and toxin content of a harmful algae bloom dinoflagellate (2024)
    Wiley
    In:  EPIC3Limnology and Oceanography, Wiley, ISSN: 0024-3590
    Details
    Publication Date: 2024-05-30
    Description: The toxin-producing dinoflagellate Alexandrium pseudogonyaulax has become increasingly abundant in northern European waters, replacing other Alexandrium species. A. pseudogonyaulax produces goniodomins and lytic substances, which can be cytotoxic toward other organisms, including fish, but we still know little about the environmental conditions influencing its growth and toxicity. Here, we investigated the impacts of different nitrogen sources and light intensities, common bottom-up drivers of bloom formation, on the growth and toxin content of three A. pseudogonyaulax strains isolated from the Danish Limfjord. While the growth rates were significantly influenced by nitrogen source and light intensity, the intracellular toxin contents only showed strong differences between the exponential and stationary growth phases. Moreover, the photophysiological response of A. pseudogonyaulax showed little variation across varying light intensities, while light-harvesting pigments were significantly more abundant under low light conditions. This study additionally highlights considerable physiological variability between strains, emphasizing the importance of conducting laboratory experiments with several algal strains. A high physiological plasticity toward changing abiotic parameters points to a long-term establishment of A. pseudogonyaulax in northern European waters.
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  • 138
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    Perspectives of species identification by MALDI‐TOF MS in monitoring—Stability of proteomic fingerprints in marine epipelagic copepods (2023)
    Wiley
    In:  EPIC3Molecular Ecology Resources, Wiley, 23(5), pp. 1077-1091, ISSN: 1755-098X
    Details
    Publication Date: 2024-05-08
    Description: We analysed the robustness of species identification based on proteomic composition to data processing and intraspecific variability, specificity and sensitivity of species-markers as well as discriminatory power of proteomic fingerprinting and its sensitivity to phylogenetic distance. Our analysis is based on MALDI-TOF MS (matrix-assisted laser desorption ionization time of flight mass spectrometry) data from 32 marine copepod species coming from 13 regions (North and Central Atlantic and adjacent seas). A random forest (RF) model correctly classified all specimens to the species level with only small sensitivity to data processing, demonstrating the strong robustness of the method. Compounds with high specificity showed low sensitivity, that is identification was based on complex pattern-differences rather than on presence of single markers. Proteomic distance was not consistently related to phylogenetic distance. A species-gap in proteome composition appeared at 0.7 Euclidean distance when using only specimens from the same sample. When other regions or seasons were included, intraspecific variability increased, resulting in overlaps of intra and inter-specific distance. Highest intraspecific distances (〉0.7) were observed between specimens from brackish and marine habitats (i.e., salinity probably affects proteomic patterns). When testing library sensitivity of the RF model to regionality, strong misidentification was only detected between two congener pairs. Still, the choice of reference library may have an impact on identification of closely related species and should be tested before routine application. We envisage high relevance of this time- and cost-efficient method for future zooplankton monitoring as it provides not only in-depth taxonomic resolution for counted specimens but also add-on information, such as on developmental stage or environmental conditions.
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  • 139
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    Essential omega‐3 fatty acids are depleted in sea ice and pelagic algae of the Central Arctic Ocean (2024)
    Wiley
    In:  EPIC3Global Change Biology, Wiley, 30(1), pp. e17090-e17090, ISSN: 1354-1013
    Details
    Publication Date: 2024-05-08
    Description: Microalgae are the main source of the omega-3 fatty acids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), essential for the healthy development of most marine and terrestrial fauna including humans. Inverse correlations of algal EPA and DHA proportions (% of total fatty acids) with temperature have led to suggestions of a warming-induced decline in the global production of these biomolecules and an enhanced importance of high latitude organisms for their provision. The cold Arctic Ocean is a potential hotspot of EPA and DHA production, but consequences of global warming are unknown. Here, we combine a full-seasonal EPA and DHA dataset from the Central Arctic Ocean (CAO), with results from 13 previous field studies and 32 cultured algal strains to examine five potential climate change effects; ice algae loss, community shifts, increase in light, nutrients, and temperature. The algal EPA and DHA proportions were lower in the ice-covered CAO than in warmer peripheral shelf seas, which indicates that the paradigm of an inverse correlation of EPA and DHA proportions with temperature may not hold in the Arctic. We found no systematic differences in the summed EPA and DHA proportions of sea ice versus pelagic algae, and in diatoms versus non-diatoms. Overall, the algal EPA and DHA proportions varied up to four-fold seasonally and 10-fold regionally, pointing to strong light and nutrient limitations in the CAO. Where these limitations ease in a warming Arctic, EPA and DHA proportions are likely to increase alongside increasing primary production, with nutritional benefits for a non-ice-associated food web.
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  • 140
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    Positioning possibilities for human geographies of the sea: Automatic Identification Systems and its role in spatialising understandings of shipping (2024)
    Wiley
    In:  EPIC3Geography Compass, Wiley, 18(4), ISSN: 1749-8198
    Details
    Publication Date: 2024-05-13
    Description: This paper positions possibilities for human geographies of the sea. The growing volume of work under this banner has been largely qualitative in its approach, reflecting, in turn, the questions posed by oceanic scholars. These questions necessitate corresponding methods. Whilst this is not necessarily a problem, and the current corpus of work has offered many significant contributions, in making sense of the human dimensions of maritime worlds, other questions—and methods—may generate knowledge that is useful within this remit of work. This paper considers the place of quantitative approaches in posing lines of enquiry about shipping, one of the prominent areas of concern under the banner of ‘human geographies of the seas’. There is longstanding work in transport geographies concerned with shipping, logistics, freight movement and global connections, which embraces quantitative methods which could be bridged to ask fresh questions about oceanic spatial phenomena past and present. This paper reviews the state of the art of human geographies of the sea and transport geographies and navigates how the former field may be stimulated by some of the interests of the latter and a broader range of questions about society-sea-space relations. The paper focuses on Automatic Identification Systems (or AIS) as a potentially useful tool for connecting debates, and deepening spatial understandings of the seas and shipping beyond current scholarship. To advance the argument the example of shipping layups is used to illustrate or rather, position, the point.
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  • 141
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    Rhythms and Clocks in Marine Organisms (2023)
    Annual Reviews
    In:  EPIC3Annual Review of Marine Science, Annual Reviews, 15(1), pp. 509-538, ISSN: 1941-1405
    Details
    Publication Date: 2024-05-10
    Description: The regular movements of waves and tides are obvious representations of the oceans’ rhythmicity. But the rhythms of marine life span across ecological niches and timescales, including short (in the range of hours) and long (in the range of days and months) periods. These rhythms regulate the physiology and behavior of individuals, as well as their interactions with each other and with the environment. This review highlights examples of rhythmicity in marine animals and algae that represent important groups of marine life across different habitats. The examples cover ecologically highly relevant species and a growing number of laboratory model systems that are used to disentangle key mechanistic principles. The review introduces fundamental concepts of chronobiology, such as the distinction between rhythmic and endogenous oscillator–driven processes. It also addresses the relevance of studying diverse rhythms and oscillators, as well as their interconnection, for making better predictions of how species will respond to environmental perturbations, including climate change. As the review aims to address scientists from the diverse fields of marine biology, ecology, and molecular chronobiology, all of which have their own scientific terms, we provide definitions of key terms throughout the article.
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  • 142
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    A research agenda for nonvascular photoautotrophs under climate change (2023)
    Wiley
    In:  EPIC3New Phytologist, Wiley, 237(5), pp. 1495-1504, ISSN: 0028-646X
    Details
    Publication Date: 2024-06-21
    Description: Nonvascular photoautotrophs (NVP), including bryophytes, lichens, terrestrial algae, and cyanobacteria, are increasingly recognized as being essential to ecosystem functioning in many regions of the world. Current research suggests that climate change may pose a substantial threat to NVP, but the extent to which this will affect the associated ecosystem functions and services is highly uncertain. Here, we propose a research agenda to address this urgent question, focusing on physiological and ecological processes that link NVP to ecosystem functions while also taking into account the substantial taxonomic diversity across multiple ecosystem types. Accordingly, we developed a new categorization scheme, based on microclimatic gradients, which simplifies the high physiological and morphological diversity of NVP and world-wide distribution with respect to several broad habitat types. We found that habitat-specific ecosystem functions of NVP will likely be substantially affected by climate change, and more quantitative process understanding is required on: (1) potential for acclimation; (2) response to elevated CO2; (3) role of the microbiome; and (4) feedback to (micro)climate. We suggest an integrative approach of innovative, multimethod laboratory and field experiments and ecophysiological modelling, for which sustained scientific collaboration on NVP research will be essential.
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  • 143
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    Testing the consistency of Holocene and Last Glacial Maximum spatial correlations in temperature proxy records (2021)
    Wiley
    In:  EPIC3Journal of Quaternary Science, Wiley, 36(1), pp. 20-28, ISSN: 0267-8179
    Details
    Publication Date: 2024-06-21
    Description: Holocene temperature proxy records are commonly used in quantitative synthesis and model-data comparisons. However, comparing correlations between time series from records collected in proximity to one another with the expected correlations based on climate model simulations indicates either regional or noisy climate signals in Holocene temperature proxy records. In this study, we evaluate the consistency of spatial correlations present in Holocene proxy records with those found in data from the Last Glacial Maximum (LGM). Specifically, we predict correlations expected in LGM proxy records if the only difference to Holocene correlations would be due to more time uncertainty and more climate variability in the LGM. We compare this simple prediction to the actual correlation structure in the LGM proxy records. We found that time series data of ice-core stable isotope records and planktonic foraminifera Mg/Ca ratios were consistent between the Holocene and LGM periods, while time series of Uk'37 proxy records were not as we found no correlation between nearby LGM records. Our results support the finding of highly regional or noisy marine proxy records in the compilation analysed here and suggest the need for further studies on the role of climate proxies and the processes of climate signal recording and preservation.
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  • 144
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    Biome‐ and timescale‐dependence of Holocene vegetation variability in the Northern Hemisphere (2023)
    Wiley
    In:  EPIC3Ecology and Evolution, Wiley, 13(10), pp. e10585-e10585, ISSN: 2045-7758
    Details
    Publication Date: 2024-06-21
    Description: Global climatic changes expected in the next centuries are likely to cause unparalleled vegetation disturbances, which in turn impact ecosystem services. To assess the significance of disturbances, it is necessary to characterize and understand typical natural vegetation variability on multi-decadal timescales and longer. We investigate this in the Holocene vegetation by examining a taxonomically harmonized and temporally standardized global fossil pollen dataset. Using principal component analysis, we characterize the variability in pollen assemblages, which are a proxy for vegetation composition, and derive timescale-dependent estimates of variability using the first-order Haar structure function. We find, on average, increasing fluctuations in vegetation composition from centennial to millennial timescales, as well as spatially coherent patterns of variability. We further relate these variations to pairwise comparisons between biome classes based on vegetation composition. As such, higher variability is identified for open-land vegetation compared to forests. This is consistent with the more active fire regimes of open-land biomes fostering variability. Needleleaf forests are more variable than broadleaf forests on shorter (centennial) timescales, but the inverse is true on longer (millennial) timescales. This inversion could also be explained by the fire characteristics of the biomes as fire disturbances would increase vegetation variability on shorter timescales, but stabilize vegetation composition on longer timecales by preventing the migration of less fire-adapted species.
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  • 145
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    COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies (2022)
    Wiley
    In:  Ecology and Evolution vol. 12 no. e9549 | H2020 European Institute of Innovation and Technology, Grant/Award Number: 813360; Nederlandse Organisatie voor Wetenschappelijk Onderzoek, Grant/ Award Number: 16.161.301
    Details
    Publication Date: 2024-06-13
    Description: Monitoring community composition of Foraminifera (single-celled marine protists) pro-vides valuable insights into environmental conditions in marine ecosystems. Despitethe efficiency of environmental DNA (eDNA) and bulk-sample DNA (bulk-DNA) me-tabarcoding to assess the presence of multiple taxa, this has not been straightforwardfor Foraminifera partially due to the high genetic variability in widely used ribosomalmarkers. Here, we test the correctness in retrieving foraminiferal communities by me-tabarcoding of mock communities, bulk-DNA from coral reef sediment samples, andeDNA from their associated ethanol preservative using the recently sequenced cy-tochrome c oxidase subunit 1 (COI) marker. To assess the detection success, we com-pared our results with large benthic foraminiferal communities previously reportedfrom the same sampling sites. Results from our mock communities demonstrate thatall species were detected in two mock communities and all but one in the remainingfour. Technical replicates were highly similar in number of reads for each assigned ASVin both the mock communities and bulk-DNA samples. Bulk-DNA showed a signifi-cantly higher species richness than their associated eDNA samples, and also detectedadditional species to what was already reported at the specific sites. Our study con-firms that metabarcoding using the foraminiferal COI marker adequately retrieves thediversity and community composition of both the mock communities and the bulk-DNA samples. With its decreased variability compared with the commonly used nu-clear 18 S rRNA, the COI marker renders bulk-DNA metabarcoding a powerful tool toassess foraminiferal community composition under the condition that the referencedatabase is adequate to the target taxa.
    Keywords: bulk-sample ; DNA ; community composition ; coral reef ; environmental DNA ; foraminifera ; metabarcoding
    Repository Name: National Museum of Natural History, Netherlands
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  • 146
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    Dispersal‐related plant traits are associated with range size in the Atlantic Forest (2024)
    Wiley
    In:  Diversity and Distributions vol. 2024 no. e13856
    Details
    Publication Date: 2024-06-06
    Description: Aim: The efficiency of animal-mediated seed dispersal is threatened by the decline of animal populations, especially in tropical forests. We hypothesise that large-seeded plants with animal-mediated dispersal tend to have limited geographic ranges and face an increased risk of extinction due to the potential decline in seed dispersal by large-bodied fruit-eating and seed-dispersing animals (frugivores). Location: Atlantic Forest, Brazil, South America. Taxon: Angiosperms. Methods: First, we collected dispersal-related traits (dispersal syndrome, fruit size, and seed size), growth form (tree, climber, and other) and preferred vegetation type (open and closed) data for 1052 Atlantic Forest plant species. Next, we integrated these with occurrence records, extinction risk assessments, and phylogenetic trees. Finally, we performed phylogenetic generalised least squares regressions to test the direct and interactive effects of dispersal-related traits and vegetation type on geographical range size. Results: Large-seeded species had smaller range sizes than small-seeded species, but only for species with animal-mediated dispersal, not for those dispersed by abiotic mechanisms. However, plants with abiotic dispersal had overall smaller range sizes than plants with animal-mediated dispersal. Furthermore, we found that species restricted to forests had smaller ranges than those occurring in open or mixed vegetation. Finally, at least 29% of the Atlantic Forest flora is threatened by extinction, but this was not related to plant dispersal syndromes. Main Conclusions: Large-seeded plants with animal-mediated dispersal may be suffering from dispersal limitation, potentially due to past and ongoing defaunation of large-bodied frugivores, leading to small range sizes. Other factors, such as deforestation and fragmentation, will probably modulate the effects of dispersal on range size, and ultimately extinction. Our study sheds light on the relationship between plant traits, mutualistic interactions, and distribution that are key to the functioning of tropical forests.
    Keywords: defaunation ; extinction risk ; frugivory ; phylogeny ; range size ; seed dispersal ; tropical forest
    Repository Name: National Museum of Natural History, Netherlands
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  • 147
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    Timing and direction of faunal exchange between the Nearctic and the Palaearctic in Odonata (2024)
    Wiley
    In:  Journal of Biogeography vol. 2024 no. 14963
    Details
    Publication Date: 2024-06-06
    Description: Aim Species have different distribution patterns across the globe and among biogeographical regions. The Nearctic and Palaearctic regions share lineages because of their parallel biogeographic histories and ecological conditions. As the number of phylogenetic studies increases, there are more insights into past exchange events between these two regions and their effects on the current distribution of diversity. However, several groups have not been tested and an overall generalization is still missing. Here, we analyse the biogeographic history across multiple genera of odonates to elucidate a general process of species exchange, vicariance and species divergence between these two regions. Location The Holarctic, including the entire Nearctic and the East and West Palaearctic. Taxon 14 genera of Odonata (Insecta). Methods We reconstructed a time-calibrated phylogenetic tree for each genus to determine species relationships and divergence time using 3614 COI sequences of 259 species. Biogeographic ancestral range estimation was inferred for each phylogeny using BioGeoBEARS. Preferred habitat (lotic versus lentic) was established for each species. Results Exchange events were not restricted in time, direction or either lentic habitat or lotic habitat. Most genera crossed between both regions only once, and it was mainly across the Beringia, while three diverse anisopteran genera revealed multiple exchanges. Recent exchanges during the Pleistocene were associated with cold-dwelling and lentic species. Main Conclusions Our finding reveals the absence of a generalizable pattern of species exchange and divergence between the Nearctic and Palaearctic regions; instead, we found lineage-specific biogeographic patterns. This finding highlights the complexity of drivers and functional traits that shaped current diversity patterns. Moreover, it emphasizes that general conclusions cannot be formulated based on one single clade.
    Keywords: biogeography ; climate change ; damselflies ; dragonflies ; Holarctic
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  • 148
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    Pleistocene glacial and interglacial ecosystems inferred from ancient DNA analyses of permafrost sediments from Batagay megaslump, East Siberia (2022)
    Wiley
    In:  EPIC3Environmental DNA, Wiley, 4(6), pp. 1265-1283, ISSN: 2637-4943
    Details
    Publication Date: 2024-06-18
    Description: Pronounced glacial and interglacial climate cycles characterized northern ecosystems during the Pleistocene. Our understanding of the resultant community transformations and past ecological interactions strongly depends on the taxa found in fossil assemblages. Here, we present a shotgun metagenomic analysis of sedimentary ancient DNA (sedaDNA) to infer past ecosystem-wide biotic composition (from viruses to megaherbivores) from the Middle and Late Pleistocene at the Batagay megaslump, East Siberia. The shotgun DNA records of past vegetation composition largely agree with pollen and plant metabarcoding data from the same samples. Interglacial ecosystems at Batagay attributed to Marine Isotope Stage (MIS) 17 and MIS 7 were characterized by forested vegetation (Pinus, Betula, Alnus) and open grassland. The microbial and fungal communities indicate strong activity related to soil decomposition, especially during MIS17. The local landscape likely featured more open, herb-dominated areas, and the vegetation mosaic supported birds and small omnivorous mammals. Parts of the area were intermittently/partially flooded as suggested by the presence of water-dependent taxa. During MIS 3, the sampled ecosystems are identified as cold-temperate, periodically flooded grassland. Diverse megafauna (Mammuthus, Equus, Coelodonta) coexisted with small mammals (rodents). The MIS 2 ecosystems existed under harsher conditions, as suggested by the presence of cold-adapted herbaceous taxa. Typical Pleistocene megafauna still inhabited the area. The new approach, in which shotgun sequencing is supported by metabarcoding and pollen data, enables the investigation of community composition changes across a broad range of taxonomic groups and inferences about trophic interactions and aspects of soil microbial ecology.
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    Paleometagenomics reveals environmental microbiome response to vegetation changes in northern Siberia over the millennia (2023)
    Wiley
    In:  EPIC3Environmental DNA, Wiley, 5(6), pp. 1252-1264, ISSN: 2637-4943
    Details
    Publication Date: 2024-06-18
    Description: The study of environmental ancient DNA provides us with the unique opportunity to link environmental with ecosystem change over a millennial timescale. Paleorecords such as lake sediments contain genetic pools of past living organisms that are a valuable source of information to reconstruct how ecosystems were and how they changed in response to climate in the past. Here, we report on paleometagenomics of a sedimentary record in northern Siberia covering the past 6700 years. We integrated taxonomic with functional gene analysis, which enabled to shed light not only on community compositions but also on eco-physiological adaptations and ecosystem functioning. We reconstructed the presence of an open boreal forest 6700 years ago that over time was gradually replaced by tundra. This vegetation change had major consequences on the environmental microbiome, primarily enriching bacterial and archaeal ammonia oxidizers (e.g., Nitrospira, Nitrosopumilus, and Ca. Nitrosocosmicus) in the tundra ecosystem. We identified a core microbiome conserved through time and largely consisting of heterotrophic bacteria of the Bacteroidetes phylum (e.g., Mucilaginibacter) harboring numerous functional genes for degradation of plant-biomass and abiotic and biotic stress resistance. Archaea were also a key functional guild, involved in nitrogen and carbon cycling, not only methanogenesis but possibly also degradation of plant material via enzymes such as cellulases and amylases. Overall, the paleo-perspective offered by our study can have a profound impact on modern climate change biology, by helping to explain and predict the ecological interplay among multiple ecosystem levels based on past experiences.
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    Positioning possibilities for human geographies of the sea: Automatic Identification Systems and its role in spatialising understandings of shipping (2024)
    Wiley
    In:  EPIC3Geography Compass, Wiley, 18, ISSN: 1749-8198
    Details
    Publication Date: 2024-05-23
    Description: This paper positions possibilities for human geographies of the sea. The growing volume of work under this banner has been largely qualitative in its approach, reflecting, in turn, the questions posed by oceanic scholars. These questions necessitate corresponding methods. Whilst this is not necessarily a problem, and the current corpus of work has offered many significant contributions, in making sense of the human dimensions of maritime worlds, other questions—and methods—may generate knowledge that is useful within this remit of work. This paper considers the place of quantitative approaches in posing lines of enquiry about shipping, one of the prominent areas of concern under the banner of ‘human geographies of the seas’. There is longstanding work in transport geographies concerned with shipping, logistics, freight movement and global connections, which embraces quantitative methods which could be bridged to ask fresh questions about oceanic spatial phenomena past and present. This paper reviews the state of the art of human geographies of the sea and transport geographies and navigates how the former field may be stimulated by some of the interests of the latter and a broader range of questions about society-sea-space relations. The paper focuses on Automatic Identification Systems (or AIS) as a potentially useful tool for connecting debates, and deepening spatial understandings of the seas and shipping beyond current scholarship. To advance the argument the example of shipping layups is used to illustrate or rather, position, the point.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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    Positioning possibilities for human geographies of the sea: Automatic Identification Systems and its role in spatialising understandings of shipping (2024)
    Wiley
    In:  EPIC3Geography Compass, Wiley, 18, ISSN: 1749-8198
    Details
    Publication Date: 2024-05-23
    Description: This paper positions possibilities for human geographies of the sea. The growing volume of work under this banner has been largely qualitative in its approach, reflecting, in turn, the questions posed by oceanic scholars. These questions necessitate corresponding methods. Whilst this is not necessarily a problem, and the current corpus of work has offered many significant contributions, in making sense of the human dimensions of maritime worlds, other questions—and methods—may generate knowledge that is useful within this remit of work. This paper considers the place of quantitative approaches in posing lines of enquiry about shipping, one of the prominent areas of concern under the banner of ‘human geographies of the seas’. There is longstanding work in transport geographies concerned with shipping, logistics, freight movement and global connections, which embraces quantitative methods which could be bridged to ask fresh questions about oceanic spatial phenomena past and present. This paper reviews the state of the art of human geographies of the sea and transport geographies and navigates how the former field may be stimulated by some of the interests of the latter and a broader range of questions about society-sea-space relations. The paper focuses on Automatic Identification Systems (or AIS) as a potentially useful tool for connecting debates, and deepening spatial understandings of the seas and shipping beyond current scholarship. To advance the argument the example of shipping layups is used to illustrate or rather, position, the point.
    Repository Name: EPIC Alfred Wegener Institut
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    Climate, glacial and vegetation history of the polar Ural Mountains since c. 27 cal ka bp, inferred from a 54 m long sediment core from Lake Bolshoye Shchuchye (2022)
    Wiley
    In:  EPIC3Journal of Quaternary Science, Wiley, 37(5), pp. 818-835, ISSN: 0267-8179
    Details
    Publication Date: 2024-06-20
    Description: Because continuous and high-resolution records are scarce in the polar Urals, a multiproxy study was carried out on a 54 m long sediment succession (Co1321) from Lake Bolshoye Shchuchye. The sedimentological, geochemical, pollen and chironomid data suggest that glaciers occupied the lake's catchment during the cold and dry MIS 2 and document a change in ice extent around 23.5–18 cal ka bp. Subsequently, meltwater input, sediment supply and erosional activity decreased as local glaciers progressively melted. The vegetation around the lake comprised open, herb and grass-dominated tundra-steppe until the Bølling-Allerød, but shows a distinct change to probably moister conditions around 17–16 cal ka bp. Local glaciers completely disappeared during the Bølling-Allerød, when summer air temperatures were similar to today and low shrub tundra became established. The Younger Dryas is confined by distinct shifts in the pollen and chironomid records pointing to drier conditions. The Holocene is characterised by a denser vegetation cover, stabilised soil conditions and decreased minerogenic input, especially during the local thermal maximum between c. 10 and 5 cal ka bp. Subsequently, present-day vegetation developed and summer air temperatures decreased to modern, except for two intervals, which may represent the Little Ice Age and Medieval Warm Period.
    Repository Name: EPIC Alfred Wegener Institut
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    Risk assessment of war wrecks – a comprehensive approach investigating four wrecks containing munitions in the German Bight/North Sea (2024)
    Wiley
    In:  EPIC3Propellants Explosives Pyrotechnics, Wiley, 49(4), ISSN: 0721-3115
    Details
    Publication Date: 2024-07-05
    Description: Shipwrecks and dumped munition continue to be a major hazard, both in the North Sea but also on a global scale. Research within the EU Interreg project North Sea Wrecks (NSW), in cooperation with the German Aerospace Centre, Institute for the Protection of Maritime Infrastructures (DLR), is generating new insights into the status of wrecks, the potential leakage of pollutants from remaining munitions loads and the effects of contamination on exposed marine organisms in the North Sea environment. Further, historical documents are generated from archives to describe ship’s history and sinking scenario. These historical findings were compared to models and images of the visual inspections of the wrecks. Further, samples of water, sediment and organisms are being analysed for traces of explosives. Combining the results of these different fields of research allows for a better understanding of the environmental risks deriving from these wrecks. This process is shown below by focusing on the wreck of the German light cruiser SMS MAINZ, which sank in 1914. Data were compared to three additional wrecks situated also within the southern German Bight. Available data about the wrecks were preliminary assessed using a wreck risk model. Finally, wrecks were ranked according to their potential environmental risk.
    Repository Name: EPIC Alfred Wegener Institut
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    A Third of Organic Carbon Is Mineral Bound in Permafrost Sediments Exposed by the World's Largest Thaw Slump, Batagay, Siberia (2024)
    Wiley
    In:  EPIC3Permafrost and Periglacial Processes, Wiley, ISSN: 1045-6740
    Details
    Publication Date: 2024-06-24
    Description: Organic carbon (OC) in permafrost interacts with the mineral fraction of soil and sediments, representing 〈 1% to ~80% of the total OC pool. Quantifying the nature and controls of mineral-OC interactions is therefore crucial for realistic assessments of permafrost-carbon-climate feedbacks, especially in ice-rich regions facing rapid thaw and the development of thermo-erosion landforms. Here, we analyzed sediment samples from the Batagay megaslump in East Siberia, and we present total element concentrations , mineralogy, and mineral-OC interactions in its different stratigraphic units. Our findings indicate that up to 34 ± 8% of the OC pool interacts with mineral surfaces or elements. Interglacial deposits exhibit enhanced OC-mineral interactions, where OC has undergone greater microbial transformation and has likely low degradability. We provide a first-order estimate of ~12,000 tons of OC mobilized annually downslope of the headwall (i.e., the approximate mass of 30 large aircrafts), with a maximum of 38% interacting with OC via complexation with metals or associations to poorly crystalline iron oxides. These data imply that over one-third of the OC exposed by the slump is not readily available for mineralization, potentially leading to prolonged OC residence time in soil and sediments under stable physicochemical conditions.
    Repository Name: EPIC Alfred Wegener Institut
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    Crustal uplift rates implied by synchronously investigating Late Quaternary marine terraces in the Milazzo Peninsula, Northeast Sicily, Italy (2024)
    Wiley
    Details
    Publication Date: 2024-07-09
    Description: Late Quaternary crustal uplift is well recognized in northeast Sicily, southern Italy, a region also prone to damaging earthquakes such as the 1908 “Messina” earthquake (Mw 7.1), the deadliest seismic event reported within the Italian Earthquake Catalogue. Yet it is still understudied if, within the Milazzo Peninsula, crustal uplift rates are varying spatially and temporally and whether they may be either influenced by (i) local upper-plate faulting activity or (ii) deep geodynamic processes. To investigate the long-term crustal vertical movements in northeast Sicily, we have mapped a flight of Middle-Late Pleistocene marine terraces within the Milazzo Peninsula and in its southern area and refined their chronology, using a synchronous correlation approach driven by published age controls. This has allowed a new calculation of the associated crustal uplift rates, along a north–south oriented coastal-parallel transect within the investigated area. Our results show a decreasing uplift rate from south to north across the Milazzo Peninsula and beyond, and that the associated rates of uplift have been constant through the Late Quaternary. This spatially varying yet temporally constant vertical deformation helps to constrain the amount of uplift, allowing us to explore which is the driving mechanism(s), proposing a few related scenarios. We discuss our results in terms of tectonic implications and emphasize the importance of using appropriate approaches, as such applying a synchronous correlation method, to refine chronologies of undated palaeoshorelines when used for tectonic investigations.
    Description: In press
    Description: OST2 Deformazione e Hazard sismico e da maremoto
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 156
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    TOROIDAL DNA CONDENSATES: Unraveling the Fine Structure and the Role of Nucleation in Determining Size (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 295-318 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Toroidal DNA condensates have attracted the attention of biophysicists, biochemists, and polymer physicists for more than thirty years. In the biological community, the quest to understand DNA toroid formation has been motivated by its relevance to gene packing in certain viruses and by the potential use of DNA toroids in artificial gene delivery (e.g., gene therapy). In the physical sciences, DNA toroids are appreciated as a superb model system for studying particle formation by the collapse of a semiflexible, polyelectrolyte polymer. This review focuses on experimental studies from the past few years that have significantly increased our understanding of DNA toroid structure and the mechanism of their formation. Highlights include structural studies that show the DNA strands within toroids to be packed in an ideal hexagonal lattice, and also in regions with a nonhexagonal lattice that are required by the topological constraints associated with winding DNA into a toroid. Recent studies of DNA toroid formation have also revealed that toroid size limits result from a complex interplay between kinetic and thermodynamic factors that govern both toroid nucleation and growth. The work discussed in this review indicates that it will ultimately be possible to obtain substantial control over DNA toroid dimensions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144500
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    STRUCTURAL AND SEQUENCE MOTIFS OF PROTEIN (HISTONE) METHYLATION ENZYMES (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 267-294 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: With genome sequencing nearing completion for the model organisms used in biomedical research, there is a rapidly growing appreciation that proteomics, the study of covalent modification to proteins, and transcriptional regulation will likely dominate the research headlines in the next decade. Protein methylation plays a central role in both of these fields, as several different residues (Arg, Lys, Gln) are methylated in cells and methylation plays a central role in the "histone code" that regulates chromatin structure and impacts transcription. In some cases, a single lysine can be mono-, di-, or trimethylated, with different functional consequences for each of the three forms. This review describes structural aspects of methylation of histone lysine residues by two enzyme families with entirely different structural scaffolding (the SET proteins and Dot1p) and methylation of protein arginine residues by PRMTs.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144452
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    ION CONDUCTION AND SELECTIVITY IN K+ CHANNELS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 153-171 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Potassium (K+) channels are tetrameric membrane-spanning proteins that provide a selective pore for the conductance of K+ across the cell membranes. These channels are most remarkable in their ability to discriminate K+ from Na+ by more than a thousandfold and conduct at a throughput rate near diffusion limit. The recent progress in the structural characterization of K+ channel provides us with a unique opportunity to understand their function at the atomic level. With their ability to go beyond static structures, molecular dynamics simulations based on atomic models can play an important role in shaping our view of how ion channels carry out their function. The purpose of this review is to summarize the most important findings from experiments and computations and to highlight a number of fundamental mechanistic questions about ion conduction and selectivity that will require further work.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144655
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    CHEMICAL SYNTHESIS OF PROTEINS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 91-118 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Proteins have become accessible targets for chemical synthesis. The basic strategy is to use native chemical ligation, Staudinger ligation, or other orthogonal chemical reactions to couple synthetic peptides. The ligation reactions are compatible with a variety of solvents and proceed in solution or on a solid support. Chemical synthesis enables a level of control on protein composition that greatly exceeds that attainable with ribosome-mediated biosynthesis. Accordingly, the chemical synthesis of proteins is providing previously unattainable insight into the structure and function of proteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144700
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    THE STRUCTURE-FUNCTION DILEMMA OF THE HAMMERHEAD RIBOZYME (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 415-440 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: A powerful approach to understanding protein enzyme catalysis is to examine the structural context of essential amino acid side chains whose deletion or modification negatively impacts catalysis. In principle, this approach can be even more powerful for RNA enzymes, given the wide variety and subtlety of functionally modified nucleotides now available. Numerous recent success stories confirm the utility of this approach to understanding ribozyme function. An anomaly, however, is the hammerhead ribozyme, for which the structural and functional data do not agree well, preventing a unifying view of its catalytic mechanism from emerging. To delineate the hammerhead structure-function comparison, we have evaluated and distilled the large body of biochemical data into a consensus set of functional groups unambiguously required for hammerhead catalysis. By examining the context of these functional groups within available structures, we have established a concise set of disagreements between the structural and functional data. The number and relative distribution of these inconsistencies throughout the hammerhead reaffirms that an extensive conformational rearrangement from the fold observed in the crystal structure must be necessary for cleavage to occur. The nature and energetic driving force of this conformational isomerization are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.122004.184428
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    SINGLE-MOLECULE RNA SCIENCE (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 399-414 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: The development of single-molecule detection and manipulation has allowed us to monitor the behavior of individual biological molecules and molecular complexes in real time. This approach significantly expands our capability to characterize complex dynamics of biological processes, allowing transient intermediate states and parallel kinetic pathways to be directly observed. Exploring this capability to elucidate complex dynamics, recent single-molecule experiments on RNA folding and catalysis have improved our understanding of the folding energy landscape of RNA and allowed us to better dissect complex RNA catalytic reactions, including translation by the ribosome.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144641
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    MODELING WATER, THE HYDROPHOBIC EFFECT, AND ION SOLVATION (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 173-199 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Water plays a central role in the structures and properties of biomoleculesĐ??proteins, nucleic acids, and membranesĐ??and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global propertiesĐ??water's thermodynamics, phase diagram, and solvation properties, for exampleĐ??and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of waterĐ??as a pure liquid and as a solventĐ??derive from the geometric and hydrogen bonding properties of water.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144517
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    PROTEIN-DNA RECOGNITION PATTERNS AND PREDICTIONS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 34 (2005), S. 379-398 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Structural data on protein-DNA complexes provide clues for understanding the mechanism of protein-DNA recognition. Although the structures of a large number of protein-DNA complexes are known, the mechanisms underlying their specific binding are still only poorly understood. Analysis of these structures has shown that there is no simple one-to-one correspondence between bases and amino acids within protein-DNA complexes; nevertheless, the observed patterns of interaction carry important information on the mechanisms of protein-DNA recognition. In this review, we show how the patterns of interaction, either observed in known structures or derived from computer simulations, confer recognition specificity, and how they can be used to examine the relationship between structure and specificity and to predict target DNA sequences used by regulatory proteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.34.040204.144537
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    THE LYMPHATIC VASCULATURE: Recent Progress and Paradigms (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Cell and Developmental Biology 21 (2005), S. 457-483 
    Details
    ISSN: 1081-0706
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Medicine
    Notes: The field of lymphatic research has been recently invigorated by the identification of genes and mechanisms that control various aspects of lymphatic development. We are beginning to understand how, starting from a subgroup of embryonic venous endothelial cells, the whole lymphatic system forms in a stepwise manner. The generation of genetically engineered mice with defects in different steps of the lymphangiogenic program has provided models that are increasing our understanding of the lymphatic system in health and disease. This knowledge, in turn, should lead to the development of better diagnostic methods and treatments of lymphatic disorders and tumor metastasis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.cellbio.21.012704.132338
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    THE PREPARATION OF SKELETAL CATALYSTS * (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 127-142 
    Details
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The preparation of skeletal catalysts is considered, with particular reference to the preparation of skeletal nickel and skeletal copper. Skeletal catalysts have physical properties that are highly desired for some industrial processes, and the means of controlling these properties to optimize performance is reviewed. The preparation can be affected by the initial alloy composition, the quenching process, the leaching procedure, aging and by the addition of promoters. These processes may affect either or both the chemical and physical characteristics of the catalysts. Preparation procedures need to be adjusted for individual reactions if optimal performance is required. The effect of the preparation conditions on the structure and catalytic performance of these systems is reviewed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.102303.140758
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    THE OXIDATION OF NIAL: What Can We Learn from Ab Initio Calculations? (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 167-207 
    Details
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: We review here the theory of the early stages of oxidation of the (110) surface of Ni1x Alx, based on ab initio calculations using a plane-wave pseudopotential method. The clean surface and several oxidized surfaces have been investigated, with oxygen coverages up to 2ML of oxygen (1ML = 3 O atoms per 2 surface Al atoms). The theory to date is a description in terms of equilibrium thermodynamics, with a comparison of the free energies of several surfaces of different composition, implemented at the atomic scale. Three environmental parameters are singled out as control variables in this treatment, namely the alloy composition x (assumed to be near 0.5), the temperature T and the partial pressure of oxygen pO2. With certain reasonable approximations an analytic formula for the surface energy ?? is derived in terms of these variables and some constants that are calculated ab initio together with others that are derived from experimental thermodynamic tables. At oxygen pressures just above the threshold for bulk oxidation of NiAl, the calculations explain the observed formation of a thin film of alumina in place of NiAl surface layers, with the consequent dissolution of Ni into the bulk. Ab initio calculations illustrate how the energetics of supplying Al to the surface depends on bulk stoichiometry, which alters the relative stability of different surface oxidation states so as to favour oxidation more if the alloy is Al-rich than if it is Ni-rich.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.101503.091652
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    DESIGNING CATALYSTS FOR CLEAN TECHNOLOGY, GREEN CHEMISTRY, AND SUSTAINABLE DEVELOPMENT (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 315-350 
    Details
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: There is a pressing need for cleaner fuels (free or aromatics and of minimal sulfur content) or ones that convert chemical energy directly to electricity, silently and without production of noxious oxides and particulates; chemical, petrochemical and pharmaceutical processes that may be conducted in a one-step, solvent-free manner and that use air as the preferred oxidant; and industrial processes that minimize consumption of energy, production of waste, or the use of corrosive, explosive, volatile, and nonbiodegradable materials. All these needs and other desiderata, such as the in situ production and containment of aggressive and hazardous reagents, and the avoidance of use of ecologically harmful elements, may be achieved by designing the appropriate heterogeneous inorganic catalyst, which ideally should be cheap, readily preparable and fully characterizable, preferably under in situ reaction conditions. A range of nanoporous and nanoparticle catalysts that meet most of the stringent demands of sustainable development and responsible (clean) technology is described. Specific examples that are highlighted include the production of adipic acid (precursor of polyamides and urethanes) without the use of concentrated nitric acid nor the production of greenhouse gases such as nitrous oxide; the production of caprolactam (precursor of nylon) without the use of oleum and hydroxylamine sulfate; and the terminal oxyfunctionalization of linear alkanes in air. The topic of biocatalysis and sustainable development is also briefly discussed for the epoxidation of terpenes and fatty acid methyl esters; for the generation of polymers, polylactides, and polyesters; and for the production of 1,3-propanediol from corn.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.102003.140852
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    POROUS ALUMINOPHOSPHATES :From Molecular Sieves to Designed Acid Catalysts (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 351-395 
    Details
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This review covers the synthesis, characterization, and physico-chemical properties of microporous and mesoporous aluminophosphates and silicoaluminophosphates molecular sieves. Particular emphasis is given to the materials that have found applications as acid catalysts. We consider the evolution of the synthesis procedures from the first discoveries to the current methodologies and give perspectives for new possible synthesis strategies. Emphasis is given to the use of specially prepared precursors/reactants designed for the use as molecular sieves. Experimental (especially MAS-NMR and FTIR spectroscopy) and theoretical approaches to the description of the Si insertion into the ALPO framework and to the acidic properties of SAPOs and MeAPSOs materials are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.103103.120732
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    THE DIFFUSION-MULTIPLE APPROACH TO DESIGNING ALLOYS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 51-73 
    Details
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The diffusion-multiple approachĐ??the creation of composition gradients and intermetallic phases by long-term annealing of junctions of three or more phases/alloysĐ??enables the generation of a large number of phases and compositions for efficient mapping of phase diagrams, phase properties, and kinetics. With an efficiency much higher than that of a conventional approach, many critical materials data, which otherwise would be too time-consuming and expensive to acquire, can be obtained and employed to accelerate alloy design. The critical data for structural materials design include phase diagrams, diffusion coefficients, precipitation kinetics, solution-strengthening effects, and precipitation-strengthening effects. All these data can be obtained from diffusion multiples. The combination of the diffusion-multiple approach with the CALPHAD approach can impact computational design of structural materials. The diffusion-multiple approach can also be applied to combinatorial screening of functional materials having unique physical, chemical, or other properties when micro-scale measurement techniques are available for these properties. Examples are shown to illustrate the progress made to date on applying the diffusion-multiple approach to accelerated design/discovery of materials.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.100303.111314
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    COMPOSITE MATERIALS FOR WIND POWER TURBINE BLADES (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 505-538 
    Details
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Renewable energy resources, of which wind energy is prominent, are part of the solution to the global energy problem. Wind turbine and the rotorblade concepts are reviewed, and loadings by wind and gravity as important factors for the fatigue performance of the materials are considered. Wood and composites are discussed as candidates for rotorblades. The fibers and matrices for composites are described, and their high stiffness, low density, and good fatigue performance are emphasized. Manufacturing technologies for composites are presented and evaluated with respect to advantages, problems, and industrial potential. The important technologies of today are prepreg (pre-impregnated) technology and resin infusion technology. The mechanical properties of fiber composite materials are discussed, with a focus on fatigue performance. Damage and materials degradation during fatigue are described. Testing procedures for documentation of properties are reviewed, and fatigue loading histories are discussed, together with methods for data handling and statistical analysis of (large) amounts of test data. Future challenges for materials in the field of wind turbines are presented, with a focus on thermoplastic composites, new structural materials concepts, new structural design aspects, structural health monitoring, and the coming trends and markets for wind energy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.100303.110641
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    CHEMICAL DESIGN AND IN SITU CHARACTERIZATION OF ACTIVE SURFACES FOR SELECTIVE CATALYSIS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 397-426 
    Details
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This review illustrates how catalytically active molecular structures are created on oxide surfaces by attachment of metal complexes with subsequent structural transformation and molecular imprinting on the surfaces. Also discussed is how the designed surfaces are characterized in situ by physical techniques including conventional and time-resolved X-ray absorption fine structure. The structural transformation and molecular imprinting for attached metal complexes can provide a new class of catalytic materials with a high complexity for selective catalysis including shape-selective and asymmetric catalysis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.102003.142526
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    APPLICATION OF EXAFS TO MOLTEN SALTS AND IONIC LIQUID TECHNOLOGY (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 29-49 
    Details
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This paper describes the use of extended X-ray absorption fine structure spectroscopy (EXAFS) to examine the structure of molten salts and ionic liquids and species dissolved in them. The EXAFS theory is briefly described as are the methods by which EXAFS of these systems can be studied. A range of applications have used EXAFS to investigate the structure of metallic species in ionic liquids from extraction studies to catalysts. The area of structural investigations of ionic liquids is still being developed, although growing rapidly, whereas the structure of molten salts has been studied using EXAFS in more detail.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.100303.121832
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    MATERIALS CHARACTERIZATION IN THE ABERRATION-CORRECTED SCANNING TRANSMISSION ELECTRON MICROSCOPE (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Materials Research 35 (2005), S. 539-569 
    Details
    ISSN: 1531-7331
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: In the nanoscience era, the properties of many exciting new materials and devices will depend on the details of their composition down to the level of single atoms. Thus the characterization of the structure and electronic properties of matter at the atomic scale is becoming ever more vital for economic and technological as well as for scientific reasons. The combination of atomic-resolution Z-contrast scanning transmission electron microscopy (STEM) and electron energy loss spectroscopy (EELS) represents a powerful method to link the atomic and electronic structure to macroscopic properties, allowing materials, nanoscale systems, and interfaces to be probed in unprecedented detail. Z-contrast STEM uses electrons that have been scattered to large angles for imaging. The relative intensity of each atomic column is roughly proportional to Z2, where Z is the atomic number. Recent developments in correcting the aberrations of the lenses in the electron microscope have pushed the achievable spatial resolution and the sensitivity for imaging and spectroscopy in the STEM into the sub-A??ngstrom (sub-A??) regime, providing a new level of insight into the structure/property relations of complex materials. Images acquired with an aberration-corrected instrument show greatly improved contrast. The signal-to-noise ratio is sufficiently high to allow sensitivity even to single atoms in both imaging and spectroscopy. This is a key achievement because the detection and measurement of the response of individual atoms has become a challenging issue to provide new insight into many fields, such as catalysis, ceramic materials, complex oxide interfaces, or grain boundaries. In this article, the state-of-the-art for the characterization of all of these different types of materials by means of aberration-corrected STEM and EELS are reviewed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.matsci.35.102103.090513
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    THE EVOLUTIONARY ENIGMA OF MIXED MATING SYSTEMS IN PLANTS: Occurrence, Theoretical Explanations, and Empirical Evidence (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 47-79 
    Details
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Mixed mating, in which hermaphrodite plant species reproduce by both self- and cross-fertilization, presents a challenging problem for evolutionary biologists. Theory suggests that inbreeding depression, the main selective factor opposing the evolution of selfing, can be purged with self-fertilization, a process that is expected to yield pure strategies of either outcrossing or selfing. Here we present updated evidence suggesting that mixed mating systems are frequent in seed plants. We outline the floral and pollination mechanisms that can lead to intermediate outcrossing, review the theoretical models that address the stability of intermediate outcrossing, and examine relevant empirical evidence. A comparative analysis of estimated inbreeding coefficients and outcrossing rates suggests that mixed mating often evolves despite strong inbreeding depression. The adaptive significance of mixed mating has yet to be fully explained for any species. Recent theoretical and empirical work suggests that future progress will come from a better integration of studies of floral mechanisms, genetics, and ecology, and recognition of how selective pressures vary in space and time.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.091704.175539
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    BIODIVERSITY AND LITTER DECOMPOSITION IN TERRESTRIAL ECOSYSTEMS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 191-218 
    Details
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: We explore empirical and theoretical evidence for the functional significance of plant-litter diversity and the extraordinary high diversity of decomposer organisms in the process of litter decomposition and the consequences for biogeochemical cycles. Potential mechanisms for the frequently observed litter-diversity effects on mass loss and nitrogen dynamics include fungi-driven nutrient transfer among litter species, inhibition or stimulation of microorganisms by specific litter compounds, and positive feedback of soil fauna due to greater habitat and food diversity. Theory predicts positive effects of microbial diversity that result from functional niche complementarity, but the few existing experiments provide conflicting results. Microbial succession with shifting enzymatic capabilities enhances decomposition, whereas antagonistic interactions among fungi that compete for similar resources slow litter decay. Soil-fauna diversity manipulations indicate that the number of trophic levels, species identity, and the presence of keystone species have a strong impact on decomposition, whereas the importance of diversity within functional groups is not clear at present. In conclusion, litter species and decomposer diversity can significantly influence carbon and nutrient turnover rates; however, no general or predictable pattern has emerged. Proposed mechanisms for diversity effects need confirmation and a link to functional traits for a comprehensive understanding of how biodiversity interacts with decomposition processes and the consequences of ongoing biodiversity loss for ecosystem functioning.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.112904.151932
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    MODEL SELECTION IN PHYLOGENETICS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 445-466 
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    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Investigation into model selection has a long history in the statistical literature. As model-based approaches begin dominating systematic biology, increased attention has focused on how models should be selected for distance-based, likelihood, and Bayesian phylogenetics. Here, we review issues that render model-based approaches necessary, briefly review nucleotide-based models that attempt to capture relevant features of evolutionary processes, and review methods that have been applied to model selection in phylogenetics: likelihood-ratio tests, AIC, BIC, and performance-based approaches.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152633
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    CONSEQUENCES OF THE CRETACEOUS/PALEOGENE MASS EXTINCTION FOR MARINE ECOSYSTEMS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 295-317 
    Details
    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: One of the greatest mass extinctions in Earth's history occurred at the end of the Cretaceous era, sixty-five million years (Myr) ago. Considerable evidence indicates that the impact of a large asteroid or comet was the ultimate cause of this extraordinary event. At the time of mass extinction, the organic flux to the deep sea collapsed, and production of calcium carbonate by marine plankton radically declined. These biogeochemical processes did not fully recover for a few million years. The drastic decline and long lag in final recovery of these processes are most simply explained as consequences of open-ocean ecosystem alteration by the mass extinction. If this explanation is correct, the extent and timing of marine biogeochemical recovery from the end-Cretaceous event was ultimately contingent on the extent and timing of open-ocean ecosystem recovery. The biogeochemical recovery may in turn have created new evolutionary opportunities for a diverse array of marine organisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.35.021103.105715
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    THE GENETICS AND EVOLUTION OF FLUCTUATING ASYMMETRY (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 1-21 
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    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Variation in the subtle differences between right and left sides of bilateral characters, or fluctuating asymmetry (FA), has long been considered to be primarily environmental in origin, and this has promoted its use as a measure of developmental instability (DI) in populations. There is little evidence for specific genes that govern FA per se. Numerous studies show that FA levels in various characters are influenced by dominance and especially epistatic interactions among genes. An epistatic genetic basis for FA may complicate its primary use in comparisons of DI levels in outbred or wild populations subjected or not subjected to various environmental stressors. Although the heritability of FA typically is very low or zero, epistasis can generate additive genetic variation for FA that may allow it to evolve especially in populations subjected to bottlenecks, hybridizations, or periods of rapid environmental changes caused by various stresses.
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    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152640
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    MEASUREMENT OF INTERACTION STRENGTH IN NATURE (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 419-444 
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    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Understanding and predicting the dynamics of multispecies systems generally require estimates of interaction strength among species. Measuring interaction strength is difficult because of the large number of interactions in any natural system, long-term feedback, multiple pathways of effects between species pairs, and possible nonlinearities in interaction-strength functions. Presently, the few studies that extensively estimate interaction strength suggest that distributions of interaction strength tend to be skewed toward few strong and many weak interactions. Modeling studies indicate that such skewed patterns tend to promote system stability and arise during assembly of persistent communities. Methods for estimating interaction strength efficiently from traits of organisms, such as allometric relationships, show some promise. Methods for estimating community response to environmental perturbations without an estimate of interaction strength may also be of use. Spatial and temporal scale may affect patterns of interaction strength, but these effects require further investigation and new multispecies modeling frameworks. Future progress will be aided by development of long-term multispecies time series of natural communities, by experimental tests of different methods for estimating interaction strength, and by increased understanding of nonlinear functional forms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.091704.175535
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    INTRODUCTION OF NON-NATIVE OYSTERS: Ecosystem Effects and Restoration Implications (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 643-689 
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    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Oysters have been introduced worldwide to 73 countries, but the ecological consequences of the introductions are not fully understood. Economically, introduced oysters compose a majority of oyster harvests in many areas. Oysters are ecosystem engineers that influence many ecological processes, such as maintenance of biodiversity, population and food web dynamics, and nutrient cycling. Consequently, both their loss, through interaction of overharvest, habitat degradation, disease, poor water quality, and detrimental species interactions, and their gain, through introductions, can cause complex changes in coastal ecosystems. Introductions can greatly enhance oyster population abundance and production, as well as populations of associated native species. However, introduced oysters are also vectors for non-native species, including disease-causing organisms. Thus, substantial population, community, and habitat changes have accompanied new oysters. In contrast, ecosystem-level consequences of oyster introductions, such as impacts on flow patterns, sediment and nutrient dynamics, and native bioengineering species, are not well understood. Ecological risk assessments for future introductions must emphasize probabilities of establishment, spread, and impacts on vulnerable species, communities, and ecosystem properties. Many characteristics of oysters lead to predictions that they would be successful, high-impact members of recipient ecosystems. This conclusion leaves open the discussion of whether such impacts are desirable in terms of restoration of coastal ecosystems, especially where restoration of native oysters is possible.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152638
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    THE FUNCTIONAL SIGNIFICANCE OF RIBOSOMAL (r)DNA VARIATION: Impacts on the Evolutionary Ecology of Organisms (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 219-242 
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    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The multi-gene family that encodes ribosomal RNA (the rDNA) has been the subject of numerous review articles examining its structure and function, as well as its use as a molecular systematic marker. The purpose of this review is to integrate information about structural and functional aspects of rDNA that impact the ecology and evolution of organisms. We examine current understanding of the impact of length heterogeneity and copy number in the rDNA on fitness and the evolutionary ecology of organisms. We also examine the role that elemental ratios (biological stoichiometry) play in mediating the impact of rDNA variation in natural populations and ecosystems. The body of work examined suggests that there are strong reciprocal feedbacks between rDNA and the ecology of all organisms, from microbes to metazoans, mediated through increased phosphorus demand in organisms with high rRNA content.
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    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152620
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    LIFE-HISTORY EVOLUTION IN REPTILES (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 23-46 
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    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: Two consequences of terrestrial ectothermy (low energy needs and behavioral control of body temperatures) have had major consequences for the evolution of reptile life-history traits. For example, reproducing females can manipulate incubation temperatures and thus phenotypic traits of their offspring by retaining developing eggs in utero. This ability has resulted in multiple evolutionary transitions from oviparity to viviparity in cool-climate reptile populations. The spatial and temporal heterogeneity of operative temperatures in terrestrial habitats also has favored careful nest-site selection and a matching of embryonic reaction norms to thermal regimes during incubation (e.g., via temperature-dependent sex determination). Many of the life-history features in which reptiles differ from endothermic vertebratesĐ??such as their small offspring sizes, large litter sizes, and infrequent reproductionĐ??are direct consequences of ectothermy, reflecting freedom from heat-conserving constraints on body size and energy storage. Ectothermy confers immense flexibility, enabling a dynamic matching of life-history traits to local circumstances. This flexibility has generated massive spatial and temporal variation in life-history traits via phenotypic plasticity as well as adaptation. The diversity of life histories in reptiles can best be interpreted within a conceptual framework that views reptiles as low-energy, variable-temperature systems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152631
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    PHYLOGENOMICS (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 541-562 
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    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The continuous flow of genomic data is creating unprecedented opportunities for the reconstruction of molecular phylogenies. Access to whole-genome data means that phylogenetic analysis can now be performed at different genomic levels, such as primary sequences and gene order, allowing for reciprocal corroboration of the results. We critically review the different kinds of phylogenomic methods currently available, paying particular attention to method reliability. Our emphasis is on methods for the analysis of primary sequences because these are the most advanced. We discuss the important issue of statistical inconsistency and show how failing to fully capture the process of sequence evolution in the underlying models leads to tree reconstruction artifacts. We suggest strategies for detecting and potentially overcoming these problems. These strategies involve the development of better models, the use of an improved taxon sampling, and the exclusion of phylogenetically misleading data.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.35.112202.130205
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    BIODIVERSITY-ECOSYSTEM FUNCTION RESEARCH: Is It Relevant to Conservation? (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 267-294 
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    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: It has often been argued that conserving biodiversity is necessary for maintaining ecosystem functioning. We critically evaluate the current evidence for this argument. Although there is substantial evidence that diversity is able to affect function, particularly for plant communities, it is unclear if these patterns will hold for realistic scenarios of extinctions, multitrophic communities, or larger spatial scales. Experiments are conducted at small spatial scales, the very scales at which diversity tends to increase owing to exotics. Stressors may affect function by many pathways, and diversity-mediated effects on function may be a minor pathway, except in the case of multiple-stressor insurance effects. In general, the conservation case is stronger for stability measures of function than stock and flux measures, in part because it is easier to attribute value unambiguously to stability and in part because stock and flux measures of functions are anticipated to be more affected by multitrophic dynamics. Nor is biodiversity-ecosystem function theory likely to help conservation managers in practical decisions, except in the particular case of restoration. We give recommendations for increasing the relevance of this area of research for conservation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.102003.152636
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    INSECTS ON PLANTS: Diversity of Herbivore Assemblages Revisited (2005)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Ecology, Evolution, and Systematics 36 (2005), S. 597-620 
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    ISSN: 1543-592X
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology
    Notes: The diversity and composition of herbivore assemblages was a favored theme for community ecology in the 1970s and culminated in 1984 with Insects on Plants by Strong, Lawton and Southwood. We scrutinize findings since then, considering analyses of country-wide insect-host catalogs, field studies of local herbivore communities, and comparative studies at different spatial scales. Studies in tropical forests have advanced significantly and offer new insights into stratification and host specialization of herbivores. Comparative and long-term data sets are still scarce, which limits assessment of general patterns in herbivore richness and assemblage structure. Methods of community phylogenetic analysis, complex networks, spatial and among-host diversity partitioning, and metacommunity models represent promising approaches for future work.
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    URL: http://dx.doi.org/10.1146/annurev.ecolsys.36.091704.175520
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    Infrared Spectroscopic Observations of the Outer Planets, their Satellites, and the Asteroids (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 43-75 
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    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.18.090180.000355
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    Formation of the Terrestrial Planets (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 77-113 
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    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.18.090180.000453
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    Stellar Masses (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 115-164 
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    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.18.090180.000555
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    Stellar Chromospheres (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 439-488 
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    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.18.090180.002255
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    The Structure of Extended Extragalactic Radio Sources (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 165-218 
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    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.18.090180.001121
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    Microwave Background Radiation as a Probe of the Contemporary Structure and History of the Universe (1980)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 18 (1980), S. 537-560 
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    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.18.090180.002541
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    Abundances in Stellar Populations and the Interstellar Medium in Galaxies (1981)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 19 (1981), S. 77-113 
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    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.19.090181.000453
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    The Chemical Composition, Structure, and Dynamics of Globular Clusters (1981)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 19 (1981), S. 319-356 
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    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.19.090181.001535
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    The Evolution of Galaxies in Clusters (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 185-222 
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    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.22.090184.001153
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    Sagittarius a and its Environment (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 223-265 
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    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.22.090184.001255
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    Coronal Mass Ejections (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 267-289 
    Details
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.22.090184.001411
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    Astronomical Fourier Transform Spectroscopy Revisited (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 291-317 
    Details
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.22.090184.001451
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    Extragalactic Radio Jets (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 319-358 
    Details
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.22.090184.001535
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    High-Energy Neutral Radiations from the Sun (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 359-387 
    Details
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.22.090184.002043
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    Origin and History of the Outer Planets: Theoretical Models and Observational Constraints (1984)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Astronomy and Astrophysics 22 (1984), S. 389-424 
    Details
    ISSN: 0066-4146
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.aa.22.090184.002133
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