ALBERT

Description: Biological invasions of aquatic systems disrupt ecological communities, and cause major changes in diversity and ecosystem function. The Laurentian Great Lakes of North America have been dramatically altered by such invasions, especially zebra (Dreissena polymorpha) and quagga (D. rostriformis bugensis) mussels. Responses to mussel invasions have included increased water clarity, and decreased chlorophyll and phytoplankton abundance. Although not all systems have responded similarly, in general, mussels have changed nutrient dynamics and physical habitat conditions. Therefore examination of different impacts can help us further understand mechanisms that underlie ecosystem responses to biological invasions. To aid our understanding of ecosystem impacts, we sampled established locations along a well-studied trophic gradient in Green Bay, Lake Michigan, after the 1993 zebra mussel invasion. A strong trophic gradient remained during the period sampled after the mussel invasion (2000–2012). However, mean summer chlorophyll increased and other measures of phytoplankton biomass (microscope and electronic cell counting) did not change significantly. Multivariate analyses of phytoplankton community structure demonstrate a significant community shift after the invasion. Cyanobacteria increased in dominance, with Microcystis becoming the major summer taxon in lower Green Bay. Diatom diversity and abundance also increased and Chlorophyta became rare. Phytoplankton responses along the trophic gradient of Green Bay to zebra mussel invasion highlight the importance of mussel effects on nutrient dynamics and phytoplankton diversity and function.

Description: There have been few assessments of the performance of alternative resistance surfaces, and little is known about how connectivity modeling approaches differ in their ability to predict organism movements. In this paper, we evaluate the performance of four connectivity modeling approaches applied to two resistance surfaces in predicting the locations of highway crossings by American black bears in the northern Rocky Mountains, USA. We found that a resistance surface derived directly from movement data greatly outperformed a resistance surface produced from analysis of genetic differentiation, despite their heuristic similarities. Our analysis also suggested differences in the performance of different connectivity modeling approaches. Factorial least cost paths appeared to slightly outperform other methods on the movement-derived resistance surface, but had very poor performance on the resistance surface obtained from multi-model landscape genetic analysis. Cumulative resistant kernels appeared to offer the best combination of high predictive performance and sensitivity to differences in resistance surface parameterization. Our analysis highlights that even when two resistance surfaces include the same variables and have a high spatial correlation of resistance values, they may perform very differently in predicting animal movement and population connectivity.

Description: In this study, a collection of 24,840 expressed sequence tags (ESTs) generated from five mango (Mangifera indica L.) cDNA libraries was mined for EST-based simple sequence repeat (SSR) markers. Over 1,000 ESTs with SSR motifs were detected from more than 24,000 EST sequences with di- and tri-nucleotide repeat motifs the most abundant. Of these, 25 EST-SSRs in genes involved in plant development, stress response, and fruit color and flavor development pathways were selected, developed into PCR markers and characterized in a population of 32 mango selections including M. indica varieties, and related Mangifera species. Twenty-four of the 25 EST-SSR markers exhibited polymorphisms, identifying a total of 86 alleles with an average of 5.38 alleles per locus, and distinguished between all Mangifera selections. Private alleles were identified for Mangifera species. These newly developed EST-SSR markers enhance the current 11 SSR mango genetic identity panel utilized by the Australian Mango Breeding Program. The current panel has been used to identify progeny and parents for selection and the application of this extended panel will further improve and help to design mango hybridization strategies for increased breeding efficiency.

Description: Among the diversity of secondary metabolites which are produced by plants as means of defence against herbivores and microbes, pyrrolizidine alkaloids (PAs) are common in Boraginaceae, Asteraceae and some other plant families. Pyrrolizidine alkaloids are infamous as toxic compounds which can alkylate DNA und thus cause mutations and even cancer in herbivores and humans. Almost all genera of the family Boraginaceae synthesize and store this type of alkaloids. This review reports the available information on the present status (literature up to early 2014) of the pyrrolizidine alkaloids in the Boraginaceae and summarizes the topics structure, distribution, chemistry, chemotaxonomic significance, and biological properties.

Description: Extreme environments are characterised by the presence of physicochemical stressors and provide unique study systems to address problems in evolutionary ecology research. Sulphide springs provide an example of extreme freshwater environments; because hydrogen sulphide’s adverse physiological effects induce mortality in metazoans even at micromolar concentrations. Sulphide springs occur worldwide, but while microbial communities in sulphide springs have received broad attention, little is known about macroinvertebrates and fish inhabiting these toxic environments. We reviewed qualitative occurrence records of sulphide spring faunas on a global scale and present a quantitative case study comparing diversity patterns in sulphidic and adjacent non-sulphidic habitats across replicated river drainages in Southern Mexico. While detailed studies in most regions of the world remain scarce, available data suggests that sulphide spring faunas are characterised by low species richness. Dipterans (among macroinvertebrates) and cyprinodontiforms (among fishes) appear to dominate the communities in these habitats. At least in fish, there is evidence for the presence of highly endemic species and populations exclusively inhabiting sulphide springs. We provide a detailed discussion of traits that might predispose certain taxonomic groups to colonize sulphide springs, how colonizers subsequently adapt to cope with sulphide toxicity, and how adaptation may be linked to speciation processes.

Description: The Salix alba L. (white willow)—Salix fragilis L. (crack willow) complex includes closely related polyploid species, mainly tetraploid (2n = 4x = 76), which are dioecious and hence obligate allogamous. Because little is known about the genome constitution and chromosome behavior of these pure willow trees, genetic analysis of their naturally occurring interspecific polyploid hybrids is still very difficult. A two-way pseudo-testcross strategy was exploited using single-dose AFLP markers in order to assess the main inheritance patterns of tetraploid biotypes (disomy vs. tetrasomy) in segregating populations stemmed from S. alba × S. fragilis crosses and reciprocals. In addition, a genomic in situ hybridization (GISH) technology was implemented in willow to shed some light on the genome structure of S. alba and S. fragilis species, and their hybrids (allopolyploidy vs. autopolyploidy). The frequency of S. alba-specific molecular markers was almost double compared to that of S. fragilis-specific ones, suggesting the phylogenetic hypothesis of S. fragilis as derivative species from S. alba-like progenitors. Cytogenetic observations at pro-metaphase revealed about half of the chromosome complements being less contracted than the remaining ones, supporting an allopolyploid origin of both S. alba and S. fragilis. Both genetic segregation and genomic hybridization data are consistent with an allotetraploid nature of the Salix species. In particular, the vast majority of the AFLP markers were inherited according to disomic patterns in S. alba × S. fragilis populations and reciprocals. Moreover, in all S. alba against S. fragilis hybridizations and reciprocals, GISH signals were observed only on the contracted chromosomes whereas the non-contracted chromosomes were never hybridized. In conclusion, half of the chromosomes of the pure species S. alba and S. fragilis are closely related and they could share a common diploid ancestor, while the rest of chromosomes are morphologically differentiated in either S. alba or S. fragilis and they should derive from distinct diploid ancestors.

Description: Understanding the individual and interactive roles of consumer species is more than academic when the host plant is a subject of intense conservation interest. In a mesocosm experiment, we compared effects of common invertebrate grazers in San Francisco Bay seagrass (Zostera marina, eelgrass) beds, finding that some species (a native opisthobranch, Phyllaplysia taylori; a native isopod, Idotea resecata; and an introduced gastropod, Ilyanassa obsoleta) enhanced eelgrass growth through removal of epiphytic algae, as is often predicted for small invertebrate grazers on seagrasses, while one (an introduced caprellid amphipod, Caprella cf. drepanochir) had neutral effects. In contrast, the putatively-introduced gammaridean amphipod, Ampithoe valida, had strong negative effects on eelgrass (in addition to epiphytes) through consumption, as we had previously observed in the field during restoration programs. We tested whether other common grazer species could influence the effects of the eelgrass-grazing Ampithoe, and found that Idotea induced production of phenolic compounds and limited eelgrass damage by Ampithoe, without affecting Ampithoe abundance. These results have implications for restoration strategies, and contribute to a growing awareness of the importance of trait-mediated indirect grazer interactions through grazer-induced changes in plant traits, providing the first example in a seagrass system.

Description: Genotyping-by-sequencing (GBS) has recently emerged as a promising genomic approach for exploring plant genetic diversity on a genome-wide scale. However, many uncertainties and challenges remain in the application of GBS, particularly in non-model species. Here, we present a GBS protocol we developed and use for plant genetic diversity analysis. It uses two restriction enzymes to reduce genome complexity, applies Illumina multiplexing indexes for barcoding and has a custom bioinformatics pipeline for genotyping. This genetic diversity-focused GBS (gd-GBS) protocol can serve as an easy-to-follow lab guide to assist a researcher through every step of a GBS application with five main components: sample preparation, library assembly, sequencing, SNP calling and diversity analysis. Specifically, in this presentation, we provide a brief overview of the GBS approach, describe the gd-GBS procedures, illustrate it with an application to analyze genetic diversity in 20 flax (Linum usitatissimum L.) accessions and discuss related issues in GBS application. Following these lab bench procedures and using the custom bioinformatics pipeline, one could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species.

Description: Regional studies of biotic communities are important for characterising their normal spatial and temporal variation, but there are few such studies of tropical streams. This paper describes changes in invertebrate communities in Yuccabine Creek, a seasonal upland rainforest stream in tropical Australia, over three-year and decadal periods. Invertebrate abundance, richness and evenness were temporally stable, except after major drying or wet-season flows, from which they recovered quickly; however, three wet seasons contrasted in abundance patterns. Species’ responses to flood or drought varied depending on life-histories and habitat dynamics. Communities showed contrasts between wet, early-dry and late-dry seasons, with different characteristic species. Current velocity, leaf litter and substratum particle size were the main environmental correlates with species abundances and multivariate scores. Between-decade contrasts were due to antecedent rainfall and loss of canopy cover. Trophic composition varied seasonally, driven by abundances of predators and detritivores. Yuccabine Creek differs from comparable temperate streams in its high diversity of invertebrates, continual recruitment and spring-dominated continual leaf fall; and from some other tropical streams in its seasonal flow regime. Interpretation of invertebrate metrics in these streams needs to account for historical, antecedent and current conditions, but biannual samples would adequately characterise the fauna.

Description: Media constantly refer of unscrupulous producers that adulterate, alter or replace premium products in food chains with the goal to maximize illegally profits. Food traceability is a central issue for the identification of improper labeling of processed food and feed and there are rules aimed to protect consumers and producers against fraudulent substitution of quality products in food chain, but the tools available are not always appropriate. DNA-based markers proved very effective for fresh and processed food molecular authentication. In this review, we illustrate potential and limits of different DNA markers focusing on low, medium and high-throughput markers, in order to monitor the genetic identity of food components in meat, fish and plants net-chains.

Description: Manioc is an important root crop in the tropics and the most important staple food in the Amazon. Manioc is diverse but its diversity has not yet been clearly associated with environmental or social factors. Our study evaluates how variation in edaphic environments and in social factors influences manioc diversity among five ethnic groups of the Amazon region of Colombia. Inventories of landraces, genetic analysis of manioc diversity, visits to farmers’ swiddens and interviews with farmers were carried out during two years of field work. Morphotypic and genotypic diversity of manioc were large. The different ethnic groups of our study cultivate different sweet and bitter manioc landraces which they select and maintain in accordance with their ancestral rules and norms. Differences in available environments among indigenous communities (such as the presence of different soils) did not markedly affect manioc morphotypic or genotypic diversity, while social factors considerably influenced observed manioc diversity. Manioc diversity was explained by two parallel processes of manioc diversification: volunteer seedling selection and manioc seed exchange. We argue that, for a full understanding of manioc diversity, indigenous knowledge, as well as morphological and genetic variation should be taken into account.

Description: Tropical mangroves are considered one of the most productive ecosystems of the world, being characterized as nurseries and food sources for fish and other animals. Microorganisms play important roles in these environments, and the study of bacterial communities is of paramount importance for a better comprehension of mangrove dynamics. This study focused on the structure and composition of bacterial communities in mangrove sediments at different depths and points, located in Southeastern Brazil. Terminal Restriction Fragment Length Polymorphism (T-RFLP) was used to determine the community structure, and 16S rRNA gene pyrosequencing was used to characterize the community composition. Redundancy analysis of T-RFLP patterns revealed differences in bacterial community structure according to soil attributes and depth. The parameters K and depth presented significant correlation with general community structure. Most sequences were classified into the phylum Proteobacteria (88%), which presented differences according to the depth, where the classes Betaproteobacteria (21%) and Deltaproteobacteria (16%) were abundant at 10 cm and Epsilonproteobacteria (35%) was abundant at 40 cm depth. Clear differences were observed in community composition as shown by the differential distribution of the phyla Firmicutes (1.13% and 3.8%, for 10 cm and 40 cm respectively), Chloroflexi (2.8% and 0.75%), and Acidobacteria (2.75% and 0.57%) according to the depth. Bacterial diversity measurements indicated higher diversity in shallow samples. Taken together, our findings indicate that mangrove holds a diverse bacterial community, which is shaped by the variations found in the ecosystem, such as sediment properties and depth.

Description: Chinese privet (Ligustrum sinense) was the most prevalent invasive shrub in the forestlands of Eastern Texas in 2006. We analyzed extensive field data collected by the Forest Inventory and Analysis Program of the U.S. Forest Service to quantify the range expansion of Chinese privet from 2006 to 2011. Our results indicated the presence of Chinese privet on sampled plots increased during this period. Chinese privet spread extensively in the north. Results of logistic regression, which classified 73% of the field plots correctly with regard to species presence and absence, indicated probability of invasion was correlated positively with elevation, adjacency (within 300 m) to water bodies, and site productivity, and was correlated negatively with stand age, site preparation (including clearing, slash burning, chopping, disking, bedding, and other practices clearly intended to prepare a site for regeneration), artificial regeneration (which refers to planting or direct seeding that results in at least 50% of the stand being comprised of stocked trees), and distance to the nearest road. Habitats most at risk to further invasion (likelihood of invasion > 40%) under current conditions occurred primarily in Northeast Texas. Practicing site preparation and artificial regeneration reduced the estimated probabilities of further invasion.

Description: We carried out an intensive sampling survey in ancient Lake Ohrid (Macedonia/Albania), covering all seasons, to determine total species number, relative species abundances and spatial distribution of Ostracoda. We identified 32 living species that belong to seven families (Candonidae, Ilyocyprididae, Cyprididae, Leptocytheridae, Limnocytheridae, Cytherideidae, and Darwinulidae) and 15 genera (Candona, Fabaeformiscandona, Candonopsis, Cypria, Cyclocypris, Ilyocypris, Eucypris, Prionocypris, Bradleystrandesia, Herpetocypris, Dolerocypris, Amnicythere, Paralimnocythere, Cytherissa, and Darwinula). Six additional species were identified from empty carapaces and valves. Dominant families in Lake Ohrid were Candonidae and Limnocytheridae, representing 53% and 16% of all species, respectively. Prevalence of species flocks in these two families confirms the “young” ancient status of the lake. Amnicythere displays a preference for oligo-haline to meso-haline waters, but some species are found in saline environments, which suggests Lake Ohrid has a marine history. Recent studies, however, indicate fluvial/glaciofluvial deposition at the onset of Lake Ohrid sedimentation. Candona is the most diverse genus in Lake Ohrid, represented by 12 living species. Paralimnocythere is represented by five living species and all other genera are represented by one or two species. Reports of Candona bimucronata, Ilyocypris bradyi, Eucypris virens, Eucypris sp., Prionocypris zenkeri, Bradleystrandesia reticulate, Herpetocypris sp. 2, and Dolerocypris sinensis are firsts for this lake. Living ostracodes were collected at the maximum water depth (280 m) in the lake (Candona hadzistei, C. marginatoides, C. media, C. ovalis, C. vidua, Fabaeformiscandona krstici, Cypria lacustris, C. obliqua and Amnicythere karamani). Cypria lacustris was overall the most abundant species and Cypria obliqua displayed the highest abundance at 280 m water depth. Principal environmental variables that influence ostracode distributions in Lake Ohrid are water depth and conductivity. In general, species richness, diversity and evenness were greater in waters 〈60 m deep, with highest values often found in the littoral zone, at depths 〈30 m. Candonids, however, displayed highest diversity in the sublittoral (30–50 m) and profundal (50–280 m) zones. The most frequent species encountered are taxa endemic to the lake (14 living species), which have a wide depth range (≤280 m), and display higher abundance with greater water depth. Non-endemic species were rare, limited to water depths 〈50 m, and were found mainly in the north part of the lake where anthropogenic pressure is high. Several cosmopolitan species were encountered for the first time, which suggests that these widespread species are new arrivals that may replace endemics as human impacts increase.

Description: The purpose of this study is to review theoretical and empirical findings in economics with respect to the challenging question of how to manage invasive species. The review revealed a relatively large body of literature on the assessment of damage costs of invasive species; single species and groups of species at different geographical scales. However, the estimated damage costs show large variation, from less than 1 million USD to costs corresponding to 12% of gross domestic product, depending on the methods employed, geographical scale, and scope with respect to inclusion of different species. Decisions regarding optimal management strategies, when to act in the invasion chain and which policy to choose, have received much less attention in earlier years, but have been subject to increasing research during the last decade. More difficult, but also more relevant policy issues have been raised, which concern the targeting in time and space of strategies under conditions of uncertainty. In particular, the weighting of costs and benefits from early detection and mitigation against the uncertain avoidance of damage with later control, when the precision in targeting species is typically greater is identified as a key challenge. The role of improved monitoring for detecting species and their spread and damage has been emphasized, but questions remain on how to achieve this in practice. This is in contrast to the relatively large body of literature on policies for mitigating dispersal by trade, which is regarded as one of the most important vectors for the spread of invasive species. On the other hand, the literature on how to mitigate established species, by control or adaptation, is much more scant. Studies evaluating causes for success or failure of policies against invasive in practice are in principal non-existing.

Description: The genus Silene (family Caryophyllaceae) comprises more than 700 species, which are widely distributed in temperate zones of the Northern Hemisphere, but are also present in Africa and have been introduced in other continents. Silene produces a high diversity of secondary metabolites and many of them show interesting biological and pharmacological activities. More than 450 compounds have been isolated; important classes include phytoecdysteroids (which mimic insect molting hormones), triterpene saponins (with detergent properties), volatiles, other terpenoids and phenolics. This review focusses on the phytochemical diversity, distribution of Silene secondary metabolites and their biological activities.

Description: The endorheic Lake Eyre Basin drains 1.2 million square kilometres of arid central Australia, yet provides habitat for only 30 species of freshwater fish due to the scarcity of water and extreme climate. The majority are hardy riverine species that are adapted to the unpredictable flow regimes, and capable of massive population booms following heavy rainfall and the restoration of connectivity between isolated waterholes. The remainder are endemic specialists from isolated springs with very restricted ranges, and many are listed under relevant state and national endangered species legislation and also by the International Union for Conservation of Nature (IUCN). For these spring communities, which are sustained by water from the Great Artesian Basin, survival is contingent on suitable habitat persisting alongside extractive mining, agriculture and the imposition of alien species. For the riverine species, which frequently undertake long migrations into ephemeral systems, preservation of the natural flow regime is paramount, as this reinstates riverine connectivity. In this study, fish were sampled from the Bulloo River in the east to the Mulligan River in the west, along a temporal timeframe and using a standard set of sampling gears. Fish presence was influenced by factors such as natural catchment divides, sampling time, ephemerality and the occurrence of connection flows and flooding. Despite the comparatively low diversity of species, the aquatic systems of this isolated region remain in good ecological condition, and as such they offer excellent opportunities to investigate the ecology of arid water systems. However, the presence of both endangered species (in the springs) and invasive and translocated species more widely indicates that active protection and management of this unique area is essential to maintain biodiversity and ecosystem integrity.

Description: Captive propagation of Pacific salmon is routine, but few captive breeding programs have been conducted to successfully re-establish extirpated wild populations. A captive breeding program for endangered Sakinaw Lake sockeye salmon was established from 84 adults between 2002 and 2005, just prior to extirpation of the wild population. After several years of absence, sockeye salmon released from captivity returned to spawn in Sakinaw Lake in 2010 and in all years thereafter. Freshwater survival rates of released hatchery fry and naturally produced progeny of reintroduced sockeye salmon have not limited abundance of the reintroduced population. In contrast, marine survival rates for Sakinaw sockeye salmon have been 〈1%, a level that precludes population restoration in the absence of supplementation. Genetic diversity commensurate with the number of parental founders has been maintained in captivity. The 517 adult second-generation captive fish that spawned in Sakinaw Lake in 2011 produced a smolt emigration of almost 28,000 juvenile fish with an effective population size of 132. Allelic richness and gene diversity levels in the smolts were similar to those observed in captivity. This indicates genetic contributions from all or most founding parents have been retained both in captivity and in the nascent reintroduced natural population.

Description: Information derived from high spatial resolution remotely sensed data is critical for the effective management of forested ecosystems. However, high spatial resolution data-sets are typically costly to acquire and process and usually provide limited geographic coverage. In contrast, moderate spatial resolution remotely sensed data, while not able to provide the spectral or spatial detail required for certain types of products and applications, offer inexpensive, comprehensive landscape-level coverage. This study assessed using an object-based approach to extrapolate detailed tree species heterogeneity beyond the extent of hyperspectral/LiDAR flightlines to the broader area covered by a Landsat scene. Using image segments, regression trees established ecologically decipherable relationships between tree species heterogeneity and the spectral properties of Landsat segments. The spectral properties of Landsat bands 4 (i.e., NIR: 0.76–0.90 µm), 5 (i.e., SWIR: 1.55–1.75 µm) and 7 (SWIR: 2.08–2.35 µm) were consistently selected as predictor variables, explaining approximately 50% of variance in richness and diversity. Results have important ramifications for ongoing management initiatives in the study area and are applicable to wide range of applications.

Description: Climate change is expected to alter temperature, precipitation, and seasonality with potentially acute impacts on Canada’s boreal. In this research we predicted future spatial distributions of biodiversity in Canada’s boreal for 2020, 2050, and 2080 using indirect indicators derived from remote sensing and based on vegetation productivity. Vegetation productivity indices, representing annual amounts and variability of greenness, have been shown to relate to tree and wildlife richness in Canada’s boreal. Relationships between historical satellite-derived productivity and climate data were applied to modelled scenarios of future climate to predict and map potential future vegetation productivity for 592 regions across Canada. Results indicated that the pattern of vegetation productivity will become more homogenous, particularly west of Hudson Bay. We expect climate change to impact biodiversity along north/south gradients and by 2080 vegetation distributions will be dominated by processes of seasonality in the north and a combination of cumulative greenness and minimum cover in the south. The Hudson Plains, which host the world’s largest and most contiguous wetland, are predicted to experience less seasonality and more greenness. The spatial distribution of predicted trends in vegetation productivity was emphasized over absolute values, in order to support regional biodiversity assessments and conservation planning.

Description: The editors of Diversity would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2013.

Description: Pollinators, especially bees, are essential to terrestrial ecosystems. They ensure the maintenance of certain ecological processes, like superior plants’ reproduction. In the past decades, agricultural intensification has caused extensive environmental changes, with major impacts on biodiversity, especially on the pollinators, which reflects the loss of fruits and seeds sets. Here, we review studies that elucidate the causes of decline of pollinators, consequences of landscape changes to agriculture and possibilities to bees’ conservation. Many studies have related the loss of pollinators to changes in the landscape, such as the conversion of native forests into cultivated areas, which causes loss of important elements for bees (e.g., sources of pollen, nectar and oil, as well as varied nesting sites). Studies involving landscape ecology allow us to assess the effects of different farming practices over the richness and abundance of pollinators. Among the landscape elements performing positive influence on bees, the presence of remaining forests nearby cultivated areas proved to be a very important factor. Nevertheless, studies that evaluate all ground cover with a more integrated approach are still required to assess the effects of landscape context on the diversity and on the abundance of bees related to productivity of crops. Researches like these could provide specific data that strengthen the need for the conservation of different plants and animals, and could offer subsidies to propose necessary information for the execution of public and private policies, aimed at the conservation of the biodiversity.

Description: Several studies have investigated the differentiation of mitochondrial DNA in Eurasian, African and American cattle as well as archaeological bovine material. A global survey of these studies shows that haplogroup distributions are more stable in time than in space. All major migrations of cattle have shifted the haplogroup distributions considerably with a reduction of the number of haplogroups and/or an expansion of haplotypes that are rare or absent in the ancestral populations. The most extreme case is the almost exclusive colonization of Africa by the T1 haplogroup, which is rare in Southwest Asian cattle. In contrast, ancient samples invariably show continuity with present-day cattle from the same location. These findings indicate strong maternal founder effects followed by limited maternal gene flow when new territories are colonized. However, effects of adaptation to new environments may also play a role.

Description: Molecular markers have proven to be invaluable tools for assessing plants’ genetic resources by improving our understanding with regards to the distribution and the extent of genetic variation within and among species. Recently developed marker technologies allow the uncovering of the extent of the genetic variation in an unprecedented way through increased coverage of the genome. Markers have diverse applications in plant sciences, but certain marker types, due to their inherent characteristics, have also shown their limitations. A combination of diverse marker types is usually recommended to provide an accurate assessment of the extent of intra- and inter-population genetic diversity of naturally distributed plant species on which proper conservation directives for species that are at risk of decline can be issued. Here, specifically, natural populations of forest trees are reviewed by summarizing published reports in terms of the status of genetic variation in the pure species. In general, for outbred forest tree species, the genetic diversity within populations is larger than among populations of the same species, indicative of a negligible local spatial structure. Additionally, as is the case for plants in general, the diversity at the phenotypic level is also much larger than at the marker level, as selectively neutral markers are commonly used to capture the extent of genetic variation. However, more and more, nucleotide diversity within candidate genes underlying adaptive traits are studied for signatures of selection at single sites. This adaptive genetic diversity constitutes important potential for future forest management and conservation purposes.

Description: Planarians are a group of free-living platyhelminths (triclads) best-known largely due to long-standing regeneration and pattern formation research. However, the group’s diversity and evolutionary history has been mostly overlooked. A few taxonomists have focused on certain groups, resulting in the description of many species and the establishment of higher-level groups within the Tricladida. However, the scarcity of morphological features precludes inference of phylogenetic relationships among these taxa. The incorporation of molecular markers to study their diversity and phylogenetic relationships has facilitated disentangling many conundrums related to planarians and even allowed their use as phylogeographic model organisms. Here, we present some case examples ranging from delimiting species in an integrative style, and barcoding them, to analysing their evolutionary history on a lower scale to infer processes affecting biodiversity origin, or on a higher scale to understand the genus level or even higher relationships. In many cases, these studies have allowed proposing better classifications and resulted in taxonomical changes. We also explain shortcomings resulting in a lack of resolution or power to apply the most up-to-date data analyses. Next-generation sequencing methodologies may help improve this situation and accelerate their use as model organisms.

Description: Corsica Island is a sub-basin of the Northwestern Mediterranean Sea, with hydrological features typical of both oligotrophic systems and eutrophic coastal zones. Phytoplankton assemblages in two coastal ecosystems of Corsica (the deep Bay of Calvi and the shallow littoral of Bastia) show contrasting patterns over a one-year cycle. In order to determine what drives these variations, seasonal changes in littoral phytoplankton are considered together with environmental parameters. Our methodology combined a survey of the physico-chemical structure of the subsurface water with a characterization of the phytoplankton community structure. Sampling provided a detailed record of the seasonal changes and successions that occur in these two areas. Results showed that the two sampled stations presented different phytoplankton abundance and distribution patterns, notably during the winter–spring bloom period. Successions in pico-, nano-, and microphytoplankton communities appeared mainly driven by differences in the ability to acquire nutrients, and in community-specific growth rates. Phytoplankton structure and dynamics are discussed in relation to available data on the Northwestern Mediterranean Sea. These results confirm that integrated monitoring of coastal areas is a requisite for gaining a proper understanding of marine ecosystems.

Description: Cattle are our most important livestock species because of their production and role in human culture. Many breeds that differ in appearance, performance and environmental adaptation are kept on all inhabited continents, but the historic origin of the diverse phenotypes is not always clear. We give an account of the history of cattle by integrating archaeological record and pictorial or written sources, scarce until 300 years ago, with the recent contributions of DNA analysis. We describe the domestication of their wild ancestor, migrations to eventually all inhabited continents, the developments during prehistory, the antiquity and the Middle Ages, the relatively recent breed formation, the industrial cattle husbandry in the Old and New World and the current efforts to preserve the cattle genetic resources. Surveying the available information, we propose three main and overlapping phases during the development of the present genetic diversity: (i) domestication and subsequent wild introgression; (ii) natural adaptation to a diverse agricultural habitat; and (iii) breed development.

Description: Jatropha curcas L. (jatropha) is an undomesticated plant that has recently received great attention for its utilization in biofuel production, rehabilitation of wasteland, and rural development. Knowledge of genetic diversity and marker-trait associations is urgently needed for the design of breeding strategies. The main goal of this study was to assess the genetic structure and diversity in jatropha germplasm with co-dominant markers (Simple Sequence Repeats (SSR) and Single Nucleotide Polymorphism (SNP) in a diverse, worldwide, germplasm panel of 70 accessions. We found a high level of homozygosis in the germplasm that does not correspond to the purely outcrossing mating system assumed to be present in jatropha. We hypothesize that the prevalent mating system of jatropha comprise a high level of self-fertilization and that the outcrossing rate is low. Genetic diversity in accessions from Central America and Mexico was higher than in accession from Africa, Asia, and South America. We identified makers associated with the presence of phorbol esters. We think that the utilization of molecular markers in breeding of jatropha will significantly accelerate the development of improved cultivars.

Description: The Western Ghats is a global biodiversity hotspot and home to diverse and unique assemblages of amphibians. Several rivers originate from these mountains and hydropower is being tapped from them. The impacts of hydrological regulation of riparian ecosystems to wildlife and its habitat are poorly documented, and in particular the fate of frog populations is unknown. We examined the effects of dams on riparian frog communities in the Thamirabarani catchment in southern Western Ghats. We used nocturnal visual encounter surveys constrained for time, to document the species richness of frogs below and above the dam, and also at control sites in the same catchment. While we did not find differences in species richness below and above the dams, the frog community composition was significantly altered as a likely consequence of altered flow regime. The frog species compositions in control sites were similar to above-dam sites. Below-dam sites had a distinctly different species composition. Select endemic frog species appeared to be adversely impacted due to the dams. Below-dam sites had a greater proportion of generalist and widely distributed species. Dams in the Western Ghats appeared to adversely impact population of endemic species, particularly those belonging to the genus Nyctibatrachus that shows specialization for intact streams.

Description: Amazon dark earth (ADE) is known for its high organic matter content, biochar concentration and microbial diversity. The biochar amount suggests the existence of microorganisms capable of degrading aromatic hydrocarbons (AHs). In an effort to investigate the influence of bacteria on the resilience and fertility of these soils, we enriched five ADE soils with naphthalene and phenanthrene, and biodegradation assays with phenanthrene and diesel oil were carried out, as well. After DNA extraction, amplification and sequencing of the 16S rRNA bacterial gene, we identified 148 isolates as the Proteobacteria, Firmicutes and Actinobacteria phyla comprising genera closely related to AHs biodegradation. We obtained 128 isolates that degrade diesel oil and 115 isolates that degrade phenanthrene. Some isolates were successful in degrading both substrates within 2 h. In conclusion, the obtained isolates from ADE have degrading aromatic compound activity, and perhaps, the biochar content has a high influence on this.

Description: Detection of genetic diversity is important for characterisation of crop plant collections in order to detect the presence of valuable trait variation for use in breeding programs. A collection of faba bean (Vicia faba L.) genotypes was evaluated for intra- and inter-population diversity using a set of 768 genome-wide distributed single nucleotide polymorphism (SNP) markers, of which 657 obtained successful amplification and detected polymorphisms. Gene diversity and polymorphism information content (PIC) values varied between 0.022–0.500 and 0.023–1.00, with averages of 0.363 and 0.287, respectively. The genetic structure of the germplasm collection was analysed and a neighbour-joining (NJ) dendrogram was constructed. The faba bean accessions grouped into two major groups, with several additional smaller sub-groups, predominantly on the basis of geographical origin. These results were further supported by principal co-ordinate analysis (PCoA), deriving two major groupings which were differentiated on the basis of site of origin and pedigree relationships. In general, high levels of heterozygosity were observed, presumably due to the partially allogamous nature of the species. The results will facilitate targeted crossing strategies in future faba bean breeding programs in order to achieve genetic gain.

Description: This study examined seasonal differences in microbial community structure in the sediment of three streams in North Carolina’s Neuse River Basin. Microbes that reside in sediment are at the base of the food chain and have a profound influence on the health of freshwater stream environments. Terminal-Restriction Fragment Length Polymorphism (T-RFLP), molecular fingerprint analysis of 16S rRNA genes was used to examine the diversity of bacterial species in stream sediment. Sediment was sampled in both wet and dry seasons from an agricultural (Bear), mixed urban (Crabtree) and forested (Marks) Creek, and the microbiota examined. Gamma, Alpha and Beta proteobacteria were prevalent species of microbial taxa represented among all sites. Actinobacteria was the next most prevalent species observed, with greater occurrence in dry compared to the wet season. Discernable clustering was observed of Marks and Bear Creek samples collected during the wetter period (September–April), which corresponded with a period of higher precipitation and cooler surface water temperatures. Although not statistically significant, microbial community structure appeared different between season (ANOSIM, R = 0.60; p 〈 0.10). Principal components analysis confirmed this pattern and showed that the bacterial groups were separated by wet and dry seasonal periods. These results suggest seasonal differences among the microbial community structure in sediment of freshwater streams and that these communities may respond to changes in precipitation during wetter periods.

Description: Novel leafy seadragon (Phycodurus eques) microsatellite loci were developed via standard cloning techniques and tested for use in population genetics studies. Six out of a total of twelve microsatellites tested were usable for population analysis. Seadragon samples from Western Australia (N = 6), Southern Australia (N = 11), and a captive group (N = 11) were analyzed. Here, we present leafy seadragon microsatellite primer sequences for all 12 loci and population genetics statistics for the six loci that amplified consistently and displayed adequate variability to estimate population parameters, such as diversity, population differences, and relatedness. Observed heterozygosities ranged from 0.225 to 0.926 and expected heterozygosities ranged from 0.278 to 0.650. Pairwise differences among populations (FST estimates) from samples collected off the southern coast of Western and South Australia, and captive animals ranged from a low of 0.188 between Southern Australia and captive animals, to a high of 0.212 between Western Australia and captive animals. Statistical assignment analyses suggested between one and three populations. Percent first order relatives among individuals was high and ranged from 40 within Western Australia to 55 within captive animals. These loci were tested on other species including weedy seadragons (Phyllopteryx taeniolatus), as well as assorted seahorses (Hippocampus reidi, H. erectus) and pipefish (Doryrhamphus dactyliophorus, D. pessuliferus, Corythoichthys intestinalis, Syngnathus leptorhynchus) with no success.

Description: Extreme overall divergence and high extinction rates are typical of insular endemics. Thus, detecting and understanding nativeness is critical on islands. Resilience to extinction is explored through a mechanistic approach focusing on midwife toads (Anura: Alytidae: Alytinae), an ancient lineage that includes continental and insular species. All alytines need urgent conservation action, including control of emerging diseases and spatially explicit reserve design aimed at ensuring ecosystem health and connectivity. The only extant insular alytine is additionally affected by an introduced continental predator. This alien species acts as a driver of the prey’s near-extinction and has not elicited any evolutionary response. Both IUCN criteria and EDGE scores show that alytines are top conservation priorities. However, there is a need for also considering phenotypic and ecological uniqueness in the assessment of conservation status and urgency. The reason is that phenotypes render ecosystems functional and insular ones uniquely so. In contrast, phylogenetic relatedness is just a constraint upon, not a motor of, evolutionary novelty. Insular species are indeed particularly susceptible, but can be similarly endangered as continental ones. This paradox may be solved by recognizing the insularity syndrome in any isolated or nearly-insular ecosystem, as a function of evolutionary and dispersal potentials. This predictive model may be useful for island biogeography, invasion biology and conservation planning.

Description: Urmia Lake, with a surface area between 4000 to 6000 km2, is a hypersaline lake located in northwest Iran. It is the saltiest large lake in the world that supports life. Urmia Lake National Park is the home of an almost endemic crustacean species known as the brine shrimp, Artemia urmiana. Other forms of life include several species of algae, bacteria, microfungi, plants, birds, reptiles, amphibians and mammals. As a consequence of this unique biodiversity, this lake has been selected as one of the 59 biosphere reserves by UNESCO. This paper provides a comprehensive species checklist that needs to be updated by additional research in the future.

Description: In 2005, three fishermen, with artisan fishing vessels and drift gillnets, accidentally captured around 200 dolphins between Vigia and Salinópolis in the Amazon River estuary. The dolphins died and they then prepared their vaginas and penises in order to sell them in the Ver-ao-Peso market in the city of Belem within the Brazilian state of Pará. We randomly sampled a minimal quantity of tissue of these sexual organs from 78 of these 200 dolphins and we determined the following results after sequencing 689 base pairs (bp) from the mitochondrial control region gene: (1) 96.15% (75/78) of these dolphins belonged to the species Sotalia guianensis. The other species detected were Steno brenadensis, Stenella coeruleoalba and Tursiops truncatus; (2) The levels of gene diversity found in this sample of S. guianensis were high (33 haplotypes, haplotype diversity of 0.917 and nucleotide diversity of 0.0045) compared to gene diversities found in other Brazilian S. guianensis locations; (3) All the population genetics methods employed indicated a clear population expansion in this population. This population expansion could have begun 400,000 years ago; (4) The haplotype divergence within this population could have begun around 2.1 millions of years ago (MYA), with posterior splits around 2.0–1.8 MYA, 1.7–1.8 MYA, 1–1.5 MYA, 0.6–0.8 MYA, 0.4–0.2 MYA and 0.16–0.02 MYA, all during the Pleistocene.

Description: Understanding mechanisms underlying insects’ host choice and plant susceptibility is important to the study of plant-insect interactions in general, and in the context of plant invasions. This study investigates the oviposition and feeding choices of the specialist weevil Exapion ulicis on the invasive plant species Ulex europaeus, gorse. To do so, we studied the oviposition and feeding preferences of the weevil in choice experiments, using pods and flowers, respectively, from gorses grown in a common garden. The plants used came from regions with different infestation histories: Brittany and Scotland belong to the native range, where the weevil is present, while Reunion and New Zealand belong to the invasive range, where the weevil was not initially introduced with gorse. Results of these experiments suggest that the oviposition choice of E. ulicis females is driven by cues located at the surface of pods and inside them, including pod size and pod seed content. Feeding-choice experiments showed a different pattern of preference compared to oviposition. Taken together with previous studies, our results reveal that E. ulicis uses several traits to choose its host, including whole-plant traits, flower traits and pod traits.

Description: The Wallacean island of Timor is of particular biological interest due to its relatively large size and transitional location between the Indo-Malayan and Australasian biogeographic realms. However, the origins and levels of endemism of its invertebrate fauna are poorly known. A recent study of Timorese ants revealed a diverse fauna with predominantly Indo-Malayan affinities, but species-level taxonomy was considered to be too poorly understood for an analysis of levels of endemism. The highly diverse Old World tropical genus Polyrhachis represents a notable exception, and here we analyse levels of endemism in the Polyrhachis fauna of Timor and surrounding islands. We supplement the species listed in the previous study with additional collections to record a total of 35 species of Polyrhachis from Timor and surrounding islands. Only 14 (40%) of the 35 species could be named (P. constricta, P. costulata, P. gab, P. sokolova, P. hera, P. illaudata, P. rixosa, P. acantha chrysophanes, P. saevissima, P. bicolor, P. cryptoceroides, P. dives, P. longipes and P. olybria), and the large majority of the remaining species have not previously been collected. These are very likely to be endemic to Timor and surrounding islands, and point to remarkably high levels (>50%) of endemism in the regional ant fauna.

Description: Defining units of conservation below the species level is a widely accepted conservation priority, but is especially challenging for widespread taxa that have experienced diverse geographic histories and exist across heterogenous environments. The lake chub (Pisces: Couesius plumbeus) is a widespread freshwater fish in North America and occurs from the southcentral USA to northwestern Alaska and Canada. We used mtDNA sequence analysis to test for divergent lineages predicted to occur as a result of survival of lake chub in distinct glacial refugia. Lake chub consisted of two major mtDNA lineages separated by 3.8% sequence divergence which are probably late to pre-Pleistocene in origin. We combined these data with those consistent with thermal adaptation in fish living in thermal springs versus those living in a lake with wide seasonal temperature variation, and with data on distribution of lake chub in major watershed units. We assessed these data against objective criteria developed to identify conservation units under Canadian endangered species legislation. Our analysis identified twelve major units of conservation within C. plumbeus that could be assessed under Canada’s Species-at-Risk Act. Our study illustrates how different character traits manifested at very different spatial scales can be used to define conservation units within widely-distributed taxa.

Description: Understanding the temporal and spatial scale at which habitat alteration impacts populations is important for conservation and management. Amphibians have declined more than other vertebrates, and pond-breeding species are particularly susceptible to habitat loss and fragmentation because they have terrestrial and aquatic life stages. One approach to management of pond-breeding species is protection of core upland habitat surrounding the breeding pond. We used genetic variation as an indicator of population status in a common amphibian species, spotted salamanders (Ambystoma maculatum), to determine how amount of suitable upland habitat relates to population status in the greater Charlotte, North Carolina, USA metropolitan area. We developed candidate models to evaluate the relative influence of historical and contemporary forested habitat availability on population genetic variation at two spatial scales of upland area (164 m and 2000 m) at four time intervals over the past seven decades (1938, 1978, 1993, 2005). We found that historical land cover best predicted contemporary allelic richness. Inbreeding coefficient and observed heterozygosity were not effectively predicted by forest cover at either spatial or temporal scales. Allelic richness was best predicted at the smaller spatial scale in the 1993 time interval. Predicting and understanding how future landscape configuration affects genetic variation of common and rare species is imperative for the conservation of amphibian and other wildlife populations.

Description: Identifying a soil core microbiome is crucial to appreciate the established microbial consortium, which is not usually subjected to change and, hence, possibly resistant/resilient to disturbances and a varying soil context. Fungi are a major part of soil biodiversity, yet the mechanisms driving their large-scale ecological ranges and distribution are poorly understood. The degree of fungal community overlap among 16 soil samples from distinct ecosystems and distant geographic localities (truffle grounds, a Mediterranean agro-silvo-pastoral system, serpentine substrates and a contaminated industrial area) was assessed by examining the distribution of fungal ITS1 and ITS2 sequences in a dataset of 454 libraries. ITS1 and ITS2 sequences were assigned to 1,660 and 1,393 Operational Taxonomic Units (OTUs; as defined by 97% sequence similarity), respectively. Fungal beta-diversity was found to be spatially autocorrelated. At the level of individual OTUs, eight ITS1 and seven ITS2 OTUs were found in all soil sample groups. These ubiquitous taxa comprised generalist fungi with oligotrophic and chitinolytic abilities, suggesting that a stable core of fungi across the complex soil fungal assemblages is either endowed with the capacity of sustained development in the nutrient-poor soil conditions or with the ability to exploit organic resources (such as chitin) universally distributed in soils.

Description: The predominant analytical approach to associate landscape patterns with gene flow processes is based on the association of cost distances with genetic distances between individuals. Mantel and partial Mantel tests have been the dominant statistical tools used to correlate cost distances and genetic distances in landscape genetics. However, the inherent high correlation among alternative resistance models results in a high risk of spurious correlations using simple Mantel tests. Several refinements, including causal modeling, have been developed to reduce the risk of affirming spurious correlations and to assist model selection. However, the evaluation of these approaches has been incomplete in several respects. To demonstrate the general reliability of the causal modeling approach with Mantel tests, it must be shown to be able to correctly identify a wide range of landscape resistance models as the correct drivers relative to alternative hypotheses. The objectives of this study were to (1) evaluate the effectiveness of the originally published causal modeling framework to support the correct model and reject alternative hypotheses of isolation by distance and isolation by barriers and to (2) evaluate the effectiveness of causal modeling involving direct competition of all hypotheses to support the correct model and reject all alternative landscape resistance models. We found that partial Mantel tests have very low Type II error rates, but elevated Type I error rates. This leads to frequent identification of support for spurious correlations between alternative resistance hypotheses and genetic distance, independent of the true resistance model. The frequency in which this occurs is directly related to the degree of correlation between true and alternative resistance models. We propose an improvement based on the relative support of the causal modeling diagnostic tests.

Description: Land-use degradation and climate change are well-known drivers of biodiversity loss, but little information is available about their potential interaction. Here, we focus on the effects of land-use and precipitation on ant diversity in cacao agroforestry. In Central Sulawesi, Indonesia, we selected 16 cacao agroforestry plots with a shaded vs. unshaded plot in each of eight villages differing in precipitation (1032–2051 mm annual rainfall). On each plot, 10 cacao trees with similar size and age (7–10 years) were selected for hand collection of ants on each cacao tree and the soil surface. In total, we found 80 ant species belonging to five subfamilies. Land-use intensification (removal of shade trees) and precipitation had no effect on species richness of ants per cacao tree (alpha diversity) and, in an additive partitioning approach, within-plot beta diversity. However, higher precipitation (but not shade) significantly increased ant species dissimilarity across cacao trees within a plot, with ant species showing contrasting responses to precipitation. Reduced precipitation causing drought stress appeared to contribute to convergence of ant community structure, presumably via reduced heterogeneity in cacao tree growth. In conclusion, reduced precipitation greatly influenced ant community dissimilarity and appeared to be more important for ant community structure than land-use intensification.

Description: In the terrestrial environment, endemic species and isolated populations of widespread species have the highest rates of extinction partly due to their low genetic diversity. To determine if this pattern holds in the marine environment, we examined genetic diversity in endemic coral reef angelfishes and isolated populations of widespread species. Specifically, this study tested the prediction that angelfish (genus: Centropyge) populations at Christmas and Cocos Islands have low genetic diversity. Analyses of a 436 base pair fragment of the mtDNA control region revealed that the endemic C. joculator exhibited high haplotype (h > 0.98 at both locations) and nucleotide (Christmas p% = 3.63, Cocos p% = 9.99) diversity. Similarly, isolated populations of widespread angelfishes (C. bispinosa and C. flavicauda) had high haplotype (h > 0.98) and nucleotide (p% = 2.81 and p% = 5.78%, respectively) diversity. Therefore, in contrast to terrestrial patterns, endemic and isolated populations of widespread angelfishes do not have low genetic diversity, rather their haplotype and nucleotide diversities were among the highest reported for marine fishes. High genetic diversity should reduce extinction risk in these species as it could provide the evolutionary potential to adapt to the rapidly changing environmental conditions forecast for coral reefs.

Description: Soft rot Enterobacteria in the genera Pectobacterium and Dickeya cause rotting of many crop plants. A new Dickeya isolate has been suggested to form a separate species, given the name Dickeya solani. This bacterium is spreading fast and replacing the closely related, but less virulent, potato pathogens. The genome of D. solani isolate D s0432-1 shows highest similarity at the nucleotide level and in synteny to D. dadantii strain 3937, but it also contains three large polyketide/fatty acid/non-ribosomal peptide synthetase clusters that are not present in D. dadantii 3937. These gene clusters may be involved in the production of toxic secondary metabolites, such as oocydin and zeamine. Furthermore, the D. solani genome harbors several specific genes that are not present in other Dickeya and Pectobacterium species and that may confer advantages for adaptation to new environments. In conclusion, the fast spreading of D. solani may be related to the acquisition of new properties that affect its interaction with plants and other microbes in the potato ecosystem.

Description: The genetic structure of the “Badda” common bean cultivated at Polizzi Generosa, a village of Sicily (Palermo, Italy), was investigated using biochemical and molecular markers. Seed storage protein analysis by using SDS-PAGE, confirmed the attribution to the Andean gene pool. Simple Sequence Repeats (SSR) (or microsatellite) molecular markers provided useful information on genetic variation and relationships between “Badda bianco” and “Badda nero” morphotypes. Based on SSR data, the nine accessions examined were grouped in three sub-clusters. The first sub-cluster included all the accessions belonging to the “Badda bianco”. Conversely, “Badda nero” was constituted by two well-distinguished sub-clusters, one of them forming a well-separated branch. This result suggests that two constitutive nuclei contributed to the genetic background of “Badda nero”. Moreover, technological and nutritional data evidenced a good seed protein content (mean value 240.7 g kg−1) and differences in seed hydration rate among accessions. Knowledge of genetic structure appear to be fundamental in planning safeguard strategies of an appreciate landrace such as the “Badda” bean.

Description: Domestic gardens may play a vital role in supporting urban insect biodiversity, despite their small size. This paper assesses the abundance, diversity and distribution of insects in urban domestic gardens in the tropics, through a study in the rapidly expanding Indian city of Bangalore. Fifty domestic gardens were studied using a combination of light traps and pitfall traps. We recorded a large number of insects, 2,185 insects from 10 orders, of which ants, bugs, beetles and flies were the most common. We found 25 species of trees (from 160 individuals) and 117 species of herbs and shrubs in the 50 sampled domestic gardens. The number of insect orders encountered was significantly related to the number of tree and herb/shrub species. Garden management practices also influenced the abundance and richness of insect orders. Thus, greater numbers of insects were observed in gardens with a greater proportion of bare soil relative to grass area and with less intensive weeding practices. More insect orders were encountered in gardens with a composting pit. Insect numbers were significantly reduced in gardens subjected to pesticide application. Most residents avoided application of pesticides and herbicides, citing health concerns.

Description: One of the biggest threats to coffee growers in East Africa are emerging vascular wilt diseases (tracheomycosis) caused by Fusarium spp. Many Trichoderma species are known to be natural antagonists of these pathogens and are widely used in biological control of fungal plant diseases. More recently, several Trichoderma spp., which exhibited high antifungal activity have been isolated as endophytes. Consequently, we have investigated the presence and the antagonistic activity of endophytic Trichoderma isolated from roots of healthy coffee plants (Coffea arabica) from the major coffee growing regions of Ethiopia. Our results showed that community of Trichoderma spp. in roots of C. arabica contains fungi from coffee rhizosphere, as well as putatively obligate endophytic fungi. The putatively “true” endophytic species, until now, isolated only from coffee plant ecosystems in Ethiopia and recently described as T. flagellatum and novel T. sp. C.P.K. 1812 were able to antagonize Fusarium spp., which cause coffee tracheomycosis. Moreover, we found that strains of these species are also highly antagonistic against other phytopathogenic fungi, such as Alternaria alternata, Botryotinia fuckeliana (anamorph: Botrytis cinerea), and Sclerotinia sclerotiorum.

Description: The “integrated evolutionary speed hypothesis” proposes that the rate of genetic evolution influences all major biogeographical patterns of diversity including those associated with temperature, water availability, productivity, spatial heterogeneity and area. Consistent with this theory, rates of genetic evolution correspond with patterns of diversity and diversification. Here we review the mechanisms that have been proposed to explain these biogeographic patterns in rates of genetic evolution. Tests of several proposed mechanisms have produced equivocal results, whereas others such as those invoking annual metabolic activity, or a “Red Queen” effect, remain unexplored. However, rates of genetic evolution have been associated with both productivity mediated rates of germ cell division and active metabolic rates and these explanations therefore justify further empirical investigation.

Description: We summarize research on diversity and trophic interactions under a trophic cascades model that is reframed and expanded from the traditional biomass- or abundance- based indirect effects and discuss the response of such “diversity cascades” to climate change and other global change parameters. The studies we summarize encompass dynamic processes in which species richness or evenness in one trophic level indirectly affects or is affected by changes in a non-adjacent level. The diversity cascade concept explicitly links trophic cascades models to the debates about biodiversity loss, exotic species gain, ecosystem services and biological control. First, we summarize the idea that the trophic cascades model includes different currencies and alternative processes. Second, we question the paradigm that trophic cascades weaken as the complexity of the community increases. Third, we illustrate the mechanisms by which diversity cascades may follow indirect bottom-up and top-down pathways. Fourth, we show how this diversity cascades model has been applied successfully to frame questions in conservation, agriculture and infectious disease. Finally, we examine the implications of diversity cascades for our understanding of how climate change affects biodiversity and call for an increase in the scope of experiments and focused hypotheses on indirect trophic effects and how these processes may lead to very large changes in biodiversity.

Description: An enhanced understanding of the temporal dynamics of intraspecific diversity is anticipated to improve the adequacy of conservation priorities, methods and metrics. We report on the comparative genetic composition of ex- and in-situ landrace cultivar populations from a potato diversity hotspot in the Andes. A total of 989 landrace cultivars belonging to contemporary custodian-farmer in situ collections from central Peru were compared with 173 accessions from a spatially analogous, but temporally differential ex situ composite genotype reference (CGR) set using 15 nuclear microsatellite markers. A total of 173 alleles were detected, with 129 alleles (74.6%) being shared between both populations. Both populations contain exclusive allelic diversity with 32 and 12 unique alleles belonging to the ex- and in-situ population, respectively. The mean unbiased expected heterozygosity values of the ex- and in-situ population are very similar, 0.749 versus 0.727, with a slightly wider range and standard deviation encountered for the in situ population. Analysis of Molecular Variance shows that 98.8% of the total variation is found within both populations, while the fixation index (Fst = 0.01236) corroborates that the populations are not well differentiated. Surprisingly, only 41.0% of the ex situ population encounters a similar landrace cultivar in 23.4% of the in situ population at a non-stringent threshold similarity coefficient of 0.80. While the ex- and in-situ population under comparison show similarities and unique features at the allelic level, their landrace cultivar composition is surprisingly distinct. Results affirm that crop evolution is an ongoing phenomenon and that change in fixed geographies is occurring.

Description: As marine environments change, the greatest ecological shifts—including resource usage and species interactions—are likely to take place in or near regions of biogeographic and phylogeographic transition. However, our understanding of where these transitional regions exist depends on the defining criteria. Here we evaluate phylogeographic transitions using a bootstrapping procedure that allows us to focus on either the strongest genetic transitions between a pair of contiguous populations, versus evaluation of transitions inclusive of the entire overlap between two intraspecific genetic lineages. We compiled data for the Atlantic coast of the United States, and evaluate taxa with short- and long-dispersing larval phases separately. Our results are largely concordant with previous biogeographic and phylogeographic analyses, indicating strong biotic change associated with the regions near Cape Cod, the Delmarva Peninsula, and eastern Florida. However, inclusive analysis of the entire range of sympatry for intraspecific lineages suggests that broad regions—the Mid-Atlantic Bight and eastern Florida–already harbor divergent intraspecific lineages, suggesting the potential for ecological evaluation of resource use between these lineages. This study establishes baseline information for tracking how such patterns change as predicted environmental changes take place.

Description: We describe and illustrate the biogeography of the cicadas inhabiting continental North America, north of Mexico. Species distributions were determined through our collecting efforts as well as label data from more than 110 institutional collections. The status of subspecies is discussed with respect to their distributions. As we have shown over limited geographic areas, the distribution of individual species is related to the habitat in which they are found. We discuss the biogeography of the genera with respect to their phylogenetic relationships. California is the state with the greatest alpha diversity (89 species, 46.6% of taxa) and unique species (35 species, 18.3% of taxa). Texas, Arizona, Colorado and Utah are the states with the next greatest alpha diversity with Texas, Arizona and Utah being next for unique species diversity. Maine, New Hampshire and Rhode Island are the states with the least amount of cicada diversity. Diversity is greatest in states and areas where there is a diversity of plant communities and habitats within these communities. Mountainous terrain also coincides with increases in diversity. Several regions of the focus area require additional collection efforts to fill in the distributions of several species.

Description: Here we investigate the interaction between ecology and climate concerning the distribution of rainforest species differentially distributed along altitudinal gradients of eastern Australia. The potential distributions of the two species closely associated with different rainforest types were modelled to infer the potential contribution of post-glacial warming on spatial distribution and altitudinal range shift. Nothofagus moorei is an integral element of cool temperate rainforest, including cloud forests at high elevation. This distinct climatic envelope is at increased risk with future global warming. Elaeocarpus grandis on the other hand is a lowland species and typical element of subtropical rainforest occupying a climatic envelope that may shift upwards into areas currently occupied by N. moorei. Climate envelope models were used to infer range shift differences between the two species in the past (21 thousand years ago), current and future (2050) scenarios, and to provide a framework to explain observed genetic diversity/structure of both species. The models suggest continuing contraction of the highland cool temperate climatic envelope and expansion of the lowland warm subtropical envelope, with both showing a core average increase in elevation in response to post-glacial warming. Spatial and altitudinal overlap between the species climatic envelopes was at a maximum during the last glacial maximum and is predicted to be a minimum at 2050.

Description: Land cover change has been one of the major drivers of change leading to an alteration of critical habitats for many of the threatened species worldwide. Species with a narrow range and specialized habitats such as wetland ecosystems are at higher risk. The present paper describes spatial and temporal land use and cover change over the period of last 34 years (1976–2010) in the Koshi Tappu Wildlife Reserve (KTWR), Nepal. High spatial resolution Indian Remote-Sensing Satellite (IRS) Linear Imaging and Self Scanning Sensor (LISS-4) from 2005 and medium spatial resolution Landsat Multispectral Scanner (MSS) from 1976; Thematic Mapper (TM) from 1989; Enhanced Thematic Mapper Plus (ETM+) from 1999 and TM from 2010 were used to generate a land use/land cover map and change analysis. Acquired IRS LISS-4 and Landsat image was orthorectified into Universal Transverse Mercator (UTM), Zone 45 based on generated digital terrain model (DTM) from a topographic map and Ground Control Point (GCP) from the field. After rectifying all the images, eCognition developer software was used for object-based image analysis (OBIA). The change in the land cover and land use types were compared with the potential habitat of twenty globally significant species present in the reserve. The habitat information was collected from the literature and a map was prepared based on ‘presence’ data, habits and habitats used to identify their distribution pattern. The analysis revealed that the KTWR has gone through significant changes in land cover and ecosystems over the last 34 years due to the change in river course and anthropogenic pressure leading to direct change in habitats of the species. Forests have been reduced by 94% from their original state whereas the grassland has increased by 79% from its original state. On the basis of total land cover, forests, river and stream, swamp and marshes decreased by 16%, 14% and 3% respectively over the last 34 years whereas the grassland has increased by 45%. These ecosystems are also an important habitat for the majority of the species, which is resulting in habitat loss. Notably, the wetland ecosystems (marshes/swamps and river/streams), being one of the most important habitat for many globally threatened species, have changed by more than 30% from their original state in 1976. Based on the analysis, recommendations for management interventions were made.

Description: While multifaceted, a chief aim when designating parks and protected areas is to support the preservation of biological diversity, in part, through representing and conserving the full range of landscape conditions observed throughout a representative area. Parks and protected areas are, however, typically developed using a static interpretation of current biodiversity and landscape conditions. The observed and potential climate change impacts to biodiversity have created a need to also contemplate how parks and protected areas will respond to climate change and how these areas will represent the future range of landscape conditions. To assess change in biodiversity, broad-scale ecosystem information can be sourced from indirect remotely sensed indicators. Quantifying biodiversity through indirect indicators allows characterization of inter-relationships between climate and biodiversity. Such characterizations support the assessment of possible implications of climatic change, as the indicators can be generated using modeled forecasts of future climatic conditions. In this paper we model and map impacts of climate change on British Columbia’s parks and protected areas by quantifying change in a number of remotely sensed indicators of biodiversity. These indicators are based on the measured amount of incoming solar energy used by vegetation and map the overall annual energy utilization, variability (seasonality), and latent or baseline energy. We compare current conditions represented by parks and protected areas, to those forecasted in the year 2065. Our results indicate that parks and protected areas are forecasted to become more productive and less seasonal, due to increased vegetation productivity in higher elevation environments. While increased vegetation productivity may be beneficial for biodiversity overall, these changes will be particularly problematic for sensitive and specialist species. Future gaps in vegetation conditions protected by parks and protected areas are observed in the eastern edge of the Rocky Mountains and the central interior region of British Columbia. Protected areas along the Coast Mountains, Vancouver Island highlands, and the Rocky Mountains show the greatest levels of change in the biodiversity indicators, including decreasing seasonality, with the Mountain Hemlock ecozone most at risk. Examples of large parks that are predicted to experience rapid change in vegetation characteristics include Strathcona, Garabaldi, and Kitlope. Our maps of future spatial distributions of indirect biodiversity indicators fill a gap in information products available for adaptive parks management and provide an opportunity for dialogue and further research on the use of future scenarios of landscape conditions in conservation planning.

Description: Although constituting more than 100,000 described species, protists are virtually ignored within the arena of biodiversity conservation. One reason is the widespread belief that the majority of protists have cosmopolitan distributions, in contrast to the highly hetereogenous biogeography of the “mega-Metazoa”. However, modern research reveals that about one third of the known protists have restricted distributions, which endorses their conservation, at least in special cases. Here, we report what probably ranks as the first successful conservation intervention focused directly on known protist diversity. It is justified by unique species, type localities, and landscape maintenance as evidence for legislation. The protected habitat comprises an ephemeral pond, which is now a “Natural Monument” for ciliated protozoa. This wetland occupies a natural depression on the Krauthügel (“cabbage hill”) south of the fortress of Salzburg City. When filled, the claviform pond has a size of ~30 × 15 m and a depth rarely surpassing 30 cm. Water is present only for some days or weeks, depending on heavy and/or prolonged rain. The pond occupied an agricultural field where root and leafy vegetables were cultivated for possibly more than 200 years. In the 1960s, this area became a grassland utilized as an autumn pasture, but was abandoned in the 1990s. Repeated sampling between 1982 and 2012 recovered a total of at least 150 ciliate taxa, of which 121 were identified to species level. Eight species were new to science, and an additional 10 poorly known species were reinvestigated and neotypified with populations from the Krauthügel pond. Both endemism and type localities justify the argument that the “integrative approach” in biodiversity and conservation issues should include protists and micro-metazoans. We argue that Krauthügel holds a unique reference node for biodiversity inventories to obtain the baseline knowledge—which is the prerequisite to monitor ecosystem integrity—and detect and evaluate impacts of natural and anthropogenic disturbances.

Description: Species distribution modeling is used in applied ecology; for example in predicting the consequences of global change. However, questions still remain about the robustness of model predictions. Here we estimate effects of landscape spatial configuration and organism flight ability—factors related to dispersal—on the accuracy of species distribution models. Distribution models were developed for 129 phytoplankton taxa, 164 littoral invertebrate taxa and 44 profundal invertebrate taxa sampled in 105 Swedish lakes, using six different modeling techniques (generalized linear models (GLM), multivariate adaptive regression splines (MARS), classification tree analysis (CTA), mixture discriminant analysis (MDA), generalized boosting models (GBM) and random forests (RF)). Model accuracy was not affected by dispersal ability (i.e., invertebrate flight ability), but the accuracy of phytoplankton assemblage predictions and, to a lesser extent, littoral invertebrate assemblages were related to ecosystem size and connectivity. Although no general pattern across species or spatial configuration was evident from our study, we recommend that dispersal and spatial configuration of ecosystems should be considered when developing species distribution models.

Description: Earth’s climate is warming, and there is evidence that increased temperature alters soil C cycling, which may result in a self-reinforcing (positive), microbial mediated feedback to the climate system. Though soil microbes are major drivers of soil C cycling, we lack an understanding of how temperature affects SOM decomposition. Numerous studies have explored, to differing degrees, the extent to which climate change may affect biodiversity. While there is ample evidence that community diversity begets ecosystem stability and resilience, we know of keystone species that perform functions whose effects far outweigh their relative abundance. In this paper, we first review the meaning of microbial diversity and how it relates to ecosystem function, then conduct a literature review of field-based climate warming studies that have made some measure of microbial diversity. Finally, we explore how measures of diversity may yield a larger, more complete picture of climate warming effects on microbial communities, and how this may translate to altered carbon cycling and greenhouse gas emissions. While warming effects seem to be ecosystem-specific, the lack of observable consistency between measures is due in some part to the diversity in measures of microbial diversity.

Description: Wetlands provide essential functions to the ecosphere that range from water filtration to flood control. Current methods of evaluating the quality of wetlands include assessing vegetation, soil type, and period of inundation. With recent advances in molecular and bioinformatic techniques, measurement of the structure and composition of soil bacterial communities have become an alternative to traditional methods of ecological assessment. The objective of the current study was to determine whether soil bacterial community composition and structure changed along a single transect in Macon County, AL. Proteobacteria were the most abundant phyla throughout the soils in the study (ranging from 42.1% to 49.9% of total sequences). Phyla Acidobacteria (37.4%) and Verrucomicrobia (7.0%) were highest in wetland soils, Actinobacteria (14.6%) was highest in the transition area, and Chloroflexi (1.6%) was highest in upland soils. Principle Components Analysis (relative abundance) and Principle Coordinates Analysis (PCoA) (Unifrac weighted metric) plots were generated, showing distinction amongst the ecosystem types through clustering by taxonomic abundance and Unifrac scores at 3% dissimilarity, respectively. Selected soil properties (soil organic carbon and phosphatase enzyme activity) also differed significantly in transition soil ecosystem types, while showing predominance in the wetland area. This study suggests that with further study the structure and composition of soil bacterial communities may eventually be an important indicator of ecological impact in wetland ecosystems.

Description: We used the mitochondria DNA COI (cytochrome c oxidase subunit I) sequence as a genetic marker to analyze the population genetic structure of two species of freshwater copepods, Neodiaptomus schmackeri (Poppe and Richard, 1892) and Mongolodiaptomus birulai (Rylov, 1922) from Taiwan. Four populations with 51 individuals of N. schmackeri and five populations with 65 individuals of M. birulai were included. We compared the nucleotide sequences of a 635-bp fragment of the COI gene of N. schmackeri and a 655-bp fragment of the COI gene of M. birulai, and eight and 14 unique haplotypes were recorded, respectively. Tseng-Wen reservoir and Wu-San-Tao reservoir are linked by a channel, and the gene flow between them was unrestricted (Fst = 0.058; Nm = 4.04; Fst, population differentiation parameter; Nm, the number of succesfull migrants per generation); the gene flow between all other populations of both species was restricted (Fst = 0.4–0.99; Nm = 0–0.37). Based on the COI gene diversification pattern, we suggest that most populations of N. schmackeri and M. birulai are isolated from each other. According to the neighbor-joining tree and the minimum spanning network (MSN), the species have similar metapopulation genetic structures. Genetic distance was not found to be correlated with geographical distance. The genetic diversification pattern was not shown to be comparable with geographical isolation owing to long-distance separation. The genetic structure of the present populations may result from serial extinction and redistribution of the populations formed in each reservoir relative to time. Human activity in the reservoirs with regards to water resource management and the fishery industry also exerts an effect on population redistribution.

Description: One goal of the LIFE project “Del.Ta.” (NAT/IT/000163) was the preparation of an Action Plan to protect the bottlenose dolphin community in the Pelagie Archipelago (Sicily, Italy). It stressed the importance of regular monitoring of the spatial and temporal distribution of dolphins in order to evaluate the impact of local activities. This study assesses whether land-based surveys could be an effective alternative to vessel-based surveys. During the summer of 2006, both surveys’ methodologies were used at Lampedusa, with 35 sightings recorded from land and 31 from a boat. Comparison was based on the assessment of the type of information they provided in relation to the presence of the animals and their behavior. Both methodologies were applicable, but there were differences in their requirements, potential information generated, costs, and sensitivity to weather conditions. Vessel-based surveys require well trained observers and enable photo-identification and observation of social interaction and morphology. Animal movements, interactions with anthropogenic elements and group dynamics are better collected from land but spatial data can be documented up to 1 nautical mile from the coast. Weather conditions have a significant platform specific effect on sighting frequencies. The high sighting frequency during land surveys provides support for the development of zero-impact land-based dolphins watching activity.

Description: Natural habitats are continuing to deteriorate in Europe with an increasing number of wild species which are also seriously threatened. Consequently, a coherent European ecological network (Natura 2000) for conservation of natural habitats and the wild fauna and flora (Council Directive 92/43/EEC) was created. Even so, there is currently no standardized methodology for surveillance and assessment of habitats, a lack that it is particularly problematic for those habitats occupying large areas (heathlands, forests, dunes, wetlands) and which require a great deal of effort to be monitored. In this paper we evaluate the changes affecting the European dry heaths (Nat-2000 4030) from the SCI Os Ancares–O Courel (Galicia, NW Spain) during the past decade. High-resolution aerial imagery analyses and Geographic Information Systems (GIS) were used. Losses of more than 7,000 ha (20.3%) of European dry heaths were computed during the 2003–2011 period in the SCI Os Ancares–O Courel, and also an increase of the degree of fragmentation was demonstrated for this habitat. Paradoxically, major impacts (afforestations, pasturelands) were financed by agri-environmental funds from the EU. Rather than promote biodiversity, these activities have provoked serious damages in this habitat of community interest, which is in complete opposition to the objectives of protection involved in the declaration of the SCI Os Ancares–O Courel.

Description: Soil microbial communities play an important role in plant health and soil quality. Researchers have developed a wide range of methods for studying the structure, diversity, and activity of microbes to better understand soil biology and plant-microbe interactions. Functional microbiological analyses of the rhizosphere have given new insights into the role of microbial communities in plant nutrition and plant protection against diseases. In this review, we present the most commonly used traditional as well as new culture-independent molecular methods to assess the diversity and function of soil microbial communities. Furthermore, we discuss advantages and disadvantages of these techniques and provide a perspective on emerging technologies for soil microbial community profiling.

Description: Here we characterize the genetic structure of Black Salamanders (Aneides flavipunctatus) in the Klamath Mountains of northwestern California and southwestern Oregon using mitochondrial and nuclear DNA sequences. We hypothesized that the Sacramento, Smith, Klamath, and Rogue River watersheds would represent distinct genetic populations based on prior ecological results, which suggest that Black Salamanders avoid high elevations such as the ridges that separate watersheds. Our mitochondrial results revealed two major lineages, one in the Sacramento River watershed, and another containing the Klamath, Smith, and Rogue River watersheds. Clustering analyses of our thirteen nuclear loci show the Sacramento watershed population to be genetically distinctive. Populations in the Klamath, Smith, and Rogue watersheds are also distinctive but not as differentiated and their boundaries do not correspond to watersheds. Our historical demographic analyses suggest that the Sacramento population has been isolated from the Klamath populations since the mid-Pleistocene, with negligible subsequent gene flow (2 Nm ≤ 0.1). The Smith and Rogue River watershed populations show genetic signals of recent population expansion. These results suggest that the Sacramento River and Klamath River watersheds served as Pleistocene refugia, and that the Rogue and Smith River watersheds were colonized more recently by northward range expansion from the Klamath.

Description: Although changes in habitat area, driven by changes in sea level, have long been considered as a possible cause of marine diversity change in the Phanerozoic, the lack of Pleistocene extinction in the Californian Province has raised doubts, given the large and rapid sea-level changes during the Pleistocene. Neutral models of metacommunities presented here suggest that diversity responds rapidly to changes in habitat area, with relaxation times of a few hundred to a few thousand years. Relaxation time is controlled partly by metacommunity size, implying that different provinces or trophic levels might have measurably different responses to changes in habitable area. Geologically short relaxation times imply that metacommunities should be able to stay nearly in equilibrium with all but the most rapid changes in area. A simulation of the Californian Province during the Pleistocene confirms this, with the longest lags in diversity approaching 20 kyr. The apparent lack of Pleistocene extinction in the Californian Province likely results from the difficulty of sampling rare species, coupled with repopulation from adjacent deep-water or warm-water regions.

Description: Climate change has created potential major threats to global biodiversity. The multiple components of climate change are projected to affect all pillars of biodiversity, from genes over species to biome level. Of particular concerns are “tipping points” where the exceedance of ecosystem thresholds will possibly lead to irreversible shifts of ecosystems and their functioning. As biodiversity underlies all goods and services provided by ecosystems that are crucial for human survival and wellbeing, this paper presents potential effects of climate change on biodiversity, its plausible impacts on human society as well as the setting in addressing a global crisis. Species affected by climate change may respond in three ways: change, move or die. Local species extinctions or a rapidly affected ecosystem as a whole respectively might move toward its particular “tipping point”, thereby probably depriving its services to human society and ending up in a global crisis. Urgent and appropriate actions within various scenarios of climate change impacts on biodiversity, especially in tropical regions, are needed to be considered. Foremost a multisectoral approach on biodiversity issues with broader policies, stringent strategies and programs at international, national and local levels is essential to meet the challenges of climate change impacts on biodiversity.

Description: This paper describes the utility of CMEIAS (Center for Microbial Ecology Image Analysis System) computer-assisted microscopy to extract data from accurately segmented images that provide 63 different insights into the ecophysiology of microbial populations and communities within biofilms and other habitats. Topics include quantitative assessments of: (i) morphological diversity as an indicator of impacts that substratum physicochemistries have on biofilm community structure and dominance-rarity relationships among populations; (ii) morphotype-specific distributions of biovolume body size that relate microbial allometric scaling, metabolic activity and growth physiology; (iii) fractal geometry of optimal cellular positioning for efficient utilization of allocated nutrient resources; (iv) morphotype-specific stress responses to starvation, environmental disturbance and bacteriovory predation; (v) patterns of spatial distribution indicating positive and negative cell–cell interactions affecting their colonization behavior; and (vi) significant methodological improvements to increase the accuracy of color-discriminated ecophysiology, e.g., differentiation of cell viability based on cell membrane integrity, cellular respiratory activity, phylogenetically differentiated substrate utilization, and N-acyl homoserine lactone-mediated cell–cell communication by bacteria while colonizing plant roots. The intensity of these ecophysiological attributes commonly varies at the individual cell level, emphasizing the importance of analyzing them at single-cell resolution and the proper spatial scale at which they occur in situ.

Description: Since the first descriptions of Antarctic subglacial lakes, there has been a growing interest and awareness of the possibility that life will exist and potentially thrive in these unique and little known environments. The unusual combination of selection pressures, and isolation from the rest of the biosphere, might have led to novel adaptations and physiology not seen before, or indeed to the potential discovery of relic populations that may have become extinct elsewhere. Here we report the first microbiological analysis of a sample taken from a former subglacial lake sediment in Antarctica (Lake Hodgson, on the Antarctic Peninsula). This is one of a number of subglacial lakes just emerging at the margins of the Antarctic ice sheet due to the renewed onset of deglaciation. Microbial diversity was divided into 23.8% Actinobacteria, 21.6% Proteobacteria, 20.2% Planctomycetes and 11.6% Chloroflexi, characteristic of a range of habitat types ( Overall, common sequences were neither distinctly polar, low temperature, freshwater nor marine). Twenty three percent of this diversity could only be identified to “unidentified bacterium”. Clearly these are diverse ecosystems with enormous potential.

Description: Using six years of remote sensing data, we estimated land and forest degradation inside 1788 protected areas across 19 countries in Latin America. From 2004–2009, the rate of land and forest degradation increased by 250% inside the protected areas, and the land and forest degradation totaled 1,097,618 hectares. Of the protected areas in our dataset, 45% had land and forest degradation. There were relatively large variations by major habitat type, with flooded grasslands/savannas and moist broadleaf forest protected areas having the highest rates of degradation. We found no association between a country’s rate of land and forest degradation inside protected areas and Gross Domestic Product (GDP) per capita, GDP growth, or rural population density. We found significant, but weak, associations between the rate of land and forest degradation inside protected areas and a country’s protected area system funding, the size of the protected area, and one International Union for the Conservation of Nature (IUCN) management category. Our results suggest a high degree of heterogeneity in the variables impacting land and forest degradation inside protected areas in Latin America, but that the targeting of protected area investments on a continental scale is plausible.

Description: The current measures of diversity for vegetation, namely alpha, beta, and gamma diversity are not logically consistent, which reduces their effectiveness as a framework for comparative vegetation analysis. The current terms mix concepts: specifically, while alpha diversity measures floristic diversity at a site, and gamma diversity measures floristic diversity regionally, beta diversity is a measure of diversity between two sites and measures a different phenomenon. We seek to rationalise measures of diversity providing a scalar set of measures. Our approach recognises vegetation diversity extends beyond species diversity and should include the various ways plants express themselves phenotypically. We propose four types of diversity, with a new set of prefixes: Type 1 diversity = the largest scale−the regional species pool; Type 2 diversity = the large habitat scale−where species in a habitat have been selected from the regional species pool; Type 3 diversity = intra-habitat expression of floristics, structure, and physiognomy; and Type 4 diversity = the finest scale of expression of vegetation diversity reflecting site selection of floristics, physiography, and phenotypic expression and reproductive strategy. This proposed framework adds significant new power to measures of diversity by extending the existing components to cover floristics, structure, physiognomy, and other forms of phenotypic expression.

Description: The Lachnospiraceae and Ruminococcaceae are two of the most abundant families from the order Clostridiales found in the mammalian gut environment, and have been associated with the maintenance of gut health. While they are both diverse groups, they share a common role as active plant degraders. By comparing the genomes of the Lachnospiraceae and Ruminococcaceae with the Clostridiaceae, a more commonly free-living group, we identify key carbohydrate-active enzymes, sugar transport mechanisms, and metabolic pathways that distinguish these two commensal groups as specialists for the degradation of complex plant material.

Description: Fish play a critical role in nutrient cycling and organic matter flow in aquatic environments. However, little is known about the microbial diversity within the gastrointestinal tracts that may be essential in these degradation activities. Panaque nigrolineatus is a loricariid catfish found in the Neotropics that have a rare dietary strategy of consuming large amounts of woody material in its natural environment. As a consequence, the gastrointestinal (GI) tract of P. nigrolineatus is continually exposed to high levels of cellulose and other recalcitrant wood compounds and is, therefore, an attractive, uncharacterized system to study microbial community diversity. Our previous 16S rRNA gene surveys demonstrated that the GI tract microbial community includes phylotypes having the capacity to degrade cellulose and fix molecular nitrogen. In the present study we verify the presence of a resident microbial community by fluorescence microscopy and focus on the cellulose-degrading members by culture-based and 13C-labeled cellulose DNA stable-isotope probing (SIP) approaches. Analysis of GI tract communities generated from anaerobic microcrystalline cellulose enrichment cultures by 16S rRNA gene analysis revealed phylotypes sharing high sequence similarity to known cellulolytic bacteria including Clostridium, Cellulomonas, Bacteroides, Eubacterium and Aeromonas spp. Related bacteria were identified in the SIP community, which also included nitrogen-fixing Azospirillum spp. Our ability to enrich for specialized cellulose-degrading communities suggests that the P. nigrolineatus GI tract provides a favorable environment for this activity and these communities may be involved in providing assimilable carbon under challenging dietary conditions.

Description: Genetic diversity within species provides the raw material for adaptation and evolution. Just as regions of high species diversity are conservation targets, identifying regions containing high genetic diversity and divergence within and among populations may be important to protect future evolutionary potential. When multiple co-distributed species show spatial overlap in high genetic diversity and divergence, these regions can be considered evolutionary hotspots. We mapped spatial population genetic structure for 17 animal species across the Mojave Desert, USA. We analyzed these in concurrence and located 10 regions of high genetic diversity, divergence or both among species. These were mainly concentrated along the western and southern boundaries where ecotones between mountain, grassland and desert habitat are prevalent, and along the Colorado River. We evaluated the extent to which these hotspots overlapped protected lands and utility-scale renewable energy development projects of the Bureau of Land Management. While 30–40% of the total hotspot area was categorized as protected, between 3–7% overlapped with proposed renewable energy project footprints, and up to 17% overlapped with project footprints combined with transmission corridors. Overlap of evolutionary hotspots with renewable energy development mainly occurred in 6 of the 10 identified hotspots. Resulting GIS-based maps can be incorporated into ongoing landscape planning efforts and highlight specific regions where further investigation of impacts to population persistence and genetic connectivity may be warranted.

Description: The northern Ethiopian landscape is dotted with small patches of church forests that are religious centers for the Ethiopian Orthodox Tewahido Church (EOTC). These sacred groves are what remain of the once vast tropical Afromontane dry forest. Herein we review the landscape pattern of sacred groves in the Amhara region of Ethiopia, and their local scale nutrient status at two sites, Zahara and Debresena. A total of 1,488 sacred groves were inventoried within the study area, yielding an overall density of one sacred grove for every twenty square kilometers. Sacred groves averaged a little over five hectares and were separated from one another by more than two kilometers. At the local scale we found that soil carbon and nitrogen stocks have decreased significantly between the forest interior and the clearing indicating decreased soil fertility. Together our data indicate that these sacred groves are vulnerable to loss because of their small average size, isolation from seed sources, and decreasing soil status.

Description: The fundamental biodiversity number, θ, as proposed by Hubbell, should be positively correlated with province area. Because θ can be calculated from preserved relative abundance distributions, this correlation can be tested in the fossil record for regions with known provinces. Late Ordovician (443–458 Ma) strata of Laurentia are divided into four geochemically and biologically distinct regions that reflect provinces in the epicontinental sea. We use existing and newly obtained bed-level census data to test whether Hubbell’s θ is positively correlated with the area of these four regions, corresponding roughly to the Appalachian Basin, Cincinnati Arch, Upper Mississippi Valley, and western United States and Canada. Results indicate a positive relationship between province area and θ that suggests the influence of provincial area, among other factors, on diversity. This correlation highlights the inherent link between diversity and abundance structure at local and regional scales, such that changes at one scale will necessarily affect the other. Since diversity at these smaller spatial scales is an important component of global biodiversity, determining the nature of this relationship in the fossil record has implications for understanding how diversity is assembled globally throughout the Phanerozoic.

Description: Preventing the loss of biodiversity is a major challenge in mega-diverse ecosystems such as coral reefs where there is a critical shortage of baseline demographic data. Threatened species assessments play a valuable role in guiding conservation action to manage and mitigate biodiversity loss, but they must be undertaken with precise information at an appropriate spatial scale to provide accurate classifications. Here we explore the regional conservation status of scleractinian corals on isolated Pacific Ocean atolls in the Republic of the Marshall Islands. We compile an integrated regional species list based upon new and historical records, and compare how well the regional threat classifications reflect species level priorities at a global scale. A similar proportion of the 240 species of hard coral recorded in the current survey are classified as Vulnerable at the regional scale as the global scale using the International Union for the Conservation of Nature (IUCN) Red List criteria (23% and 20% respectively), however there are distinct differences in the composition of species. When local abundance data is taken into account, a far greater proportion of the regional diversity (up to 80%) may face an elevated risk of local extinction. These results suggest coral communities on isolated Pacific coral reefs, which are often predicted to be at low risk, are still vulnerable due to the small and fragmented nature of their populations. This reinforces that to adequately protect biodiversity, ongoing threatened species monitoring and the documentation of species-level changes in abundance and distribution is imperative.

Description: Human activities such as land management and global warming have great impact on the environment. Among changes associated with the global warming, rising methane emission is a serious concern. Therefore, we assessed methane oxidation activity and diversity of aerobic methanotrophic bacteria in eight soil types (both unmanaged and agricultural) distributed across the European part of Russia. Using a culture-independent approach targeting pmoA gene, we provide the first baseline data on the diversity of methanotrophs inhabiting most typical soil types. The analysis of pmoA clone libraries showed that methanotrophic populations in unmanaged soils are less diverse than in agricultural areas. These clone sequences were placed in three groups of, so far, uncultured methanotrophs: USC-gamma, cluster I, and pmoA/amoA cluster, which are believed to be responsible for atmospheric methane oxidation in upland soils. Agricultural soils harbored methanotrophs related to genera Methylosinus, Methylocystis, Methylomicrobium, Methylobacter, and Methylocaldum. Despite higher numbers of detected molecular operational taxonomic units (MOTUs), managed soils showed decreased methane oxidation rates as observed in both in situ and laboratory experiments. Our results also suggest that soil restoration may have a positive effect on methane consumption by terrestrial ecosystems.

Description: The accuracy of ten methods of scaling (Smalian, Huber, Newton, Neloïd, paraboloid, cone, paracone, cylinder, truncated cone and truncated Neloïd) was evaluated on logs of 0.5, 1, 2 and 3 m cut to different heights of 27 teak trees. For this purpose, the volumes estimated by the ten formulas were compared with real volumes obtained by the technique of xylometer. The results obtained showed that the method of Huber was more efficient to calculate the volume of logs throughout the stem when the length was 0.5 m. For the other length logs, it was also the best formula when the logs came from the base of the stem. The formulas of Newton and Smalian gave in the center and top of the stem, in the case of 1 m and 2 m logs, relatively similar results and were better than other methods of scaling. As might be expected, the dendrometric method (cylinder, paraboloid, Neloïd, cone) gave worse results regardless of the length of logs considered. With logs of 0.5, 1, 2 and 3 m long, truncated forms of cone and Neloïd could also be used without significant errors in estimating the volume of teak logs. The model scaling obtained for the entire tree expresses the logarithm of the volume against the logarithm of the diameter and the logarithm of height.

Description: Measures of alpha diversity are more frequently used to detect environmental changes and subsequent impacts on biodiversity, while measures based on variability (beta diversity) are said to be more appropriate for detecting those impacts. Theory predicts that beta diversity should increase with disturbance frequency in patchy communities. Our objective in this study was to experimentally determine the effect of high and low disturbance regimes, frequency and intensity combined, on marine benthic alpha and beta diversity. The experiment was conducted in a rock pool system of the St. Lawrence estuary, Canada. Rock pools were disturbed by (1) nutrient enrichment and (2) draining according to three disturbance regimes (none, low, high). Disturbance regimes had little or no effect on alpha diversity of benthic algae and sessile animals. However, the low regime of nutrient enrichment induced greater within-group beta diversity than the reference rock pools, while the high disturbance regime induced equal or even smaller within-group beta diversity compared to the reference. Draining had an opposite effect on benthic beta diversity, with a greater variability of the community structure under the high regime of disturbance. Taking into account the effect of disturbance regimes on beta diversity could provide a useful diagnostic for disturbed benthic communities.

Description: Micro-relief heterogeneity can lead to substantial variability in microclimate and hence niche opportunities on a small scale. We explored the relationship between plant species richness and small-scale heterogeneity of micro-relief on the subtropical island of La Palma, Canary Islands. Overall, we sampled 40 plots in laurel and pine forests at four altitudinal bands. Species richness was recorded separately for various growth forms (i.e., mosses, herbaceous and woody plants). Site conditions such as altitude, slope, aspect, and tree density were measured. Micro-relief heterogeneity was characterized by surface structure and a subsequently derived surface heterogeneity index. The effect of micro-relief heterogeneity on species richness was analysed by means of linear mixed effect models and variance partitioning. Effects of micro-relief heterogeneity on species richness varied considerably between growth forms. While moss richness was affected significantly by micro-relief heterogeneity, herbaceous and woody plants richness responded mainly to larger-scale site conditions such as aspect and tree density. Our results stress the importance of small-scale relief heterogeneity for the explanation of spatial patterns of species richness. This poses new challenges as small-scale heterogeneity is largely underrepresented, e.g. with regard to its application in species distribution models.

Description: Unicellular saprobic fungi (yeasts) inhabit soils worldwide. Although yeast species typically occupy defined areas on the biome scale, their distribution patterns within a single type of vegetation, such as forests, are more complex. In order to understand factors that shape soil yeast communities, soils collected underneath decaying wood logs and under forest litter were analyzed. We isolated and identified molecularly a total of 25 yeast species, including three new species. Occurrence and distribution of yeasts isolated from these soils provide new insights into ecology and niche specialization of several soil-borne species. Although abundance of typical soil yeast species varied among experimental plots, the analysis of species abundance and community composition revealed a strong influence of wood log deposition and leakage of organic carbon. Unlike soils underneath logs, yeast communities in adjacent areas harbored a considerable number of transient (phylloplane-related) yeasts reaching 30% of the total yeast quantity. We showed that distinguishing autochthonous community members and species transient in soils is essential to estimate appropriate effects of environmental factors on soil fungi. Furthermore, a better understanding of species niches is crucial for analyses of culture-independent data, and may hint to the discovery of unifying patterns of microbial species distribution.

Description: The practice of adding organic amendments to crop soils is undergoing resurgence as an efficient way to restore soil organic matter content and to improve soil quality. The quantity and quality of the organic matter inputs affect soil physicochemical properties and soil microbiota, influencing different parameters such as microbial biomass and diversity, community structure and microbial activities or functions. The influence of organic amendments on soil quality has also effects on crop production and plant health. The enhancement of soil suppressiveness using organic amendments has been widely described, especially for soil-borne diseases. However, there is great variability in the effectiveness of suppression depending on the nature of the amendment, the crop, the pathogen, and the environmental conditions. Although the effects of organic amendments on soil properties have been widely studied, relationships between these properties and soil suppressiveness are not still well understood. Changes in soil physicochemical parameters may modulate the efficacy of suppression. However, the parameters more frequently associated to disease suppression appear to be related to soil microbiota, such as microbial biomass and activity, the abundance of specific microbial groups and some hydrolytic activities. This review focuses on the effect of organic amendments on soil microbial populations, diversity and activities; their ability to enhance plant health through disease suppression; and which of the parameters affected by the organic amendments are potentially involved in soil suppressiveness.

Description: The distribution and species assembly of Japanese Protura collected from forest soils were examined using published databases and statistical analysis. We used records from 3110 sites where 71 taxa were found. The species richness of Protura ranged from one to 16 species, and TWINSPAN analysis of regional populations indicated that the northern and southern regions could be separated into distinct groups. Three major species assemblages were identified by cluster analysis from points containing more than six species. Three groups reflected historical migration from northern and western linkages to the Asian continent. The northern assemblage showed a negative correlation to winter minimum temperature and the other two assemblages exhibited relationships to precipitation and temperature. Vegetation was not responsible for proturan distribution. These results suggest that the history of Protura invasion explains the biogeography of these soil-based, small arthropods and also that climate change will induce a shift in the distribution of species irrespective of changes in vegetation type.

Description: Wild barley [Hordeum vulgare ssp. spontaneum (C. Koch) Thell.] is a part of the primary gene pool with valuable sources of beneficial genes for barley improvement. This study attempted to develop a core subset of 269 accessions representing 16 countries from the Plant Gene Resources of Canada (PGRC) collection of 3,782 accessions, and to characterize them using barley simple sequence repeat (SSR) markers. Twenty-five informative primer pairs were applied to screen all samples and 359 alleles were detected over seven barley chromosomes. Analyses of the SSR data showed the effectiveness of the stratified sampling applied in capturing country-wise SSR variation. The frequencies of polymorphic alleles ranged from 0.004 to 0.708 and averaged 0.072. More than 24% or 7% SSR variation resided among accessions of 16 countries or two regions, respectively. Accessions from Israel and Jordan were genetically most diverse, while accessions from Lebanon and Greece were most differentiated. Four and five optimal clusters of accessions were obtained using STRUCTURE and BAPS programs and partitioned 16.3% and 20.3% SSR variations, respectively. The five optimal clusters varied in size from 15 to 104 and two clusters had only country-specific accessions. A genetic separation was detected between the accessions east and west of the Zagros Mountains only at the country, not the individual, level. These SSR patterns enhance our understanding of the wild barley gene pool, and are significant for conserving wild barley germplasm and exploring new sources of useful genes for barley improvement.

Description: Assessing biodiversity and the spatial structures of forest ecosystems are important for forestry and nature conservation. However, tropical forests of Bangladesh are only sparsely investigated. Here we determined biodiversity (alpha, beta and gamma), spatial species turnover and stand characteristics of one of the few remnant tropical forests in Bangladesh. Two differently protected areas of Satchari forest were compared. We recorded tree species composition, in a systematic plot design, measured diameter at breast height for each individual tree (to assess basal area), and calculated decay in similarity of tree species composition with geographical distance. The distance-decay was assessed separately for the whole study area and for two subsamples from Satchari National Park and Satchari Reserve Forest. Satchari National Park (strictly protected) had, despite its smaller area, a higher Alpha and Gamma diversity, but a lower Beta diversity than Satchari Reserve Forest. Variation in species composition was not significant between the two differently protected areas. Basal area increased significantly with protection status although tree individuals were of equal size in both areas. Plots in the Reserve Forest were associated with higher species turnover than in the National Park. We suggest anthropogenic disturbance, which occurs in the less strictly protected Reserve Forest, is the main driver for the detected spatial heterogeneity in species composition.

Description: Coral reef ecosystems are increasingly subject to severe, large-scale disturbances caused by climate change (e.g., coral bleaching) and other more direct anthropogenic impacts. Many of these disturbances cause coral loss and corresponding changes in habitat structure, which has further important effects on abundance and diversity of coral reef fishes. Declines in the abundance and diversity of coral reef fishes are of considerable concern, given the potential loss of ecosystem function. This study explored the effects of coral loss, recorded in studies conducted throughout the world, on the diversity of fishes and also on individual responses of fishes within different functional groups. Extensive (〉60%) coral loss almost invariably led to declines in fish diversity. Moreover, most fishes declined in abundance following acute disturbances that caused 〉10% declines in local coral cover. Response diversity, which is considered critical in maintaining ecosystem function and promoting resilience, was very low for corallivores, but was much higher for herbivores, omnivores and carnivores. Sustained and ongoing climate change thus poses a significant threat to coral reef ecosystems and diversity hotspots are no less susceptible to projected changes in diversity and function.

Description: Adaptation of reef corals to climate change is an issue of much debate, and often viewed as too slow a process to be of relevance over decadal time scales. This notion is based on the long sexual generation times typical for some coral species. However, the importance of somatic mutations during asexual reproduction and growth on evolution and adaptation (i.e., cell lineage selection) is rarely considered. Here we review the existing literature on cell lineage selection and show that the scope for somatic mutations to arise in the coral animal and associated Symbiodinium is large. For example, we estimate that ~100 million somatic mutations can arise within a branching Acropora coral colony of average size. Similarly, the large population sizes and rapid turn-over times of in hospite Symbiodinium likely result in considerable numbers of somatic mutations. While the fate of new mutations depends on many factors, including ploidy level and force and direction of selection, we argue that they likely play a key role in the evolution of reef corals.

Description: The co-occurrence of cryptic species of Hyalella amphipods is a challenge to our traditional views of how species assemble. Since these species have similar morphologies, it is not evident that they have developed phenotypic differences that would allow them to occupy different ecological niches. We examined the structure of a community of Hyalella amphipods in the littoral zone of a boreal lake to verify if temporal variation was present in relative abundances. Morphological and molecular analyses using the mitochondrial cytochrome c oxidase I (COI) gene enabled us to detect three cryptic species at the study site. No temporal variation was observed in the community, as one cryptic species was always more abundant than the two others. The relative abundances of each species in the community appeared constant at least for the open-water season, both for adult and juvenile amphipods. Niche differences are still to be found among these species, but it is suggested that migration from nearby sites may be an important factor explaining the species co-occurrence.

Description: Symbioses between microbes and higher organisms underpin high diversity in many ecosystems, including coral reefs, however mechanisms underlying the early establishment of symbioses remain unclear. Here we examine the roles of Symbiodinium type and cell surface recognition in the establishment of algal endosymbiosis in the reef-building coral, Acropora tenuis. We found 20–70% higher infection success (proportion of larvae infected) and five-fold higher Symbiodinium abundance in larvae exposed to ITS-1 type C1 compared to ITS-1 type D in the first 96 h following exposure. The highest abundance of Symbiodinium within larvae occurred when C1-type cells were treated with enzymes that modified the 40–100 kD glycome, including glycoproteins and long chain starch residues. Our finding of declining densities of Symbiodinium C1 through time in the presence of intact cell surface molecules supports a role for cell surface recognition molecules in controlling post-phagocytosis processes, leading to rejection of some Symbiodinium types in early ontogeny. Reductions in the densities of unmodified C1 symbionts after 96 h, in contrast to increases in D symbionts may suggest the early initiation of a winnowing process contributing to the establishment of Symbiodinium D as the dominant type in one-month old juveniles of A. tenuis.

Description: Hairy prairie-clover [Dalea villosa (Nutt.) Spreng. var. villosa] is a threatened Canadian wildflower. To facilitate the efforts of conserving this threatened plant, amplified fragment length polymorphism (AFLP) technique was applied to assess genetic diversity in a remnant hairy prairie-clover population in the Canadian Prairie. Three AFLP primer pairs were employed to genotype 610 individual plants from the population and 15 plants from a North Dakota composite population, and 100 polymorphic AFLP bands were analyzed. The assayed plants displayed 23% AFLP variation present between the remnant population and the North Dakota composite population, but maintained a high level (91%) of AFLP variation within patches of the remnant population. The individual genetic distinctiveness measured by average AFLP dissimilarity was positively associated with latitude and negatively with elevation. The among-patch AFLP variation was significantly related to inter-patch distance, indicating local genetic differentiation within the remnant population. However, the proportions of within-patch AFLP variation were not associated with any patch characteristics assessed (i.e., patch size, perimeter, nearest neighbor distance, mean inter-patch distance). No fine-scale genetic structure was found within three large patches, suggesting little genetic correlations present for plants five meters apart. Some genetically distinctive and diverse patches were also identified. These findings indicate that the genetic risk of the remnant hairy prairie-clover population in the Canadian Prairie is low.

Description: Landscape scale conservation planning efforts have been in place for the past several decades to maintain biodiversity. Objectives of past efforts have been to identify areas to create reserves based on species diversity, land ownership, and landscape context. Risk analysis has not often been included in these spatial analyses. Datasets such as the Southwest Regional Gap Analysis (SWReGAP) are now available as are processes that allow risk analysis to be viewed in a spatial context in relations to factors that affect habitats over broad scales. We describe a method to include four spatial datasets to provide coarse scale delineation on areas to focus conservation including species numbers, key habitats, land management and factors that influence habitats. We used the SWReGAP management status dataset to identify management categories for long-term intent of management for biodiversity. The New Mexico Department of Game and Fish identified a set of 290 Species of Greatest Conservation Need (SGCN). Species occurrences for these species were associated with hydrologic unit codes from the National Hydrography Dataset (NHD). Key habitats were identified by using the SWReGAP land cover dataset and NHD derivatives. Factors that influence habitats were identified and scored for 89 land cover types and 23 aquatic habitats identified by the NMDGF. Our final model prioritizes landscapes that are within key habitats, have high numbers of terrestrial and aquatic Species of Greatest Conservation Need taxa, may be potentially altered by multiple effects that influence habitats, and lack long-term legally-binding management plans protecting them from anthropogenic degradation. Similar to other efforts, riparian and aquatic habitats were identified as the most important for conservation. This information may be displayed spatially, allowing land managers and decision makers to understand the ecological context where multiple effects of potential factors may influence some habitats greater than others, and repeat process with CWCS revisions.

Description: This article summarises the sometimes controversial contributions made by the different sciences to predict the path of ocean acidification impacts on the diversity of coral reefs during the present century. Although the seawater carbonate system has been known for a long time, the understanding of acidification impacts on marine biota is in its infancy. Most publications about ocean acidification are less than a decade old and over half are about coral reefs. Contributions from physiological studies, particularly of coral calcification, have covered such a wide spectrum of variables that no cohesive picture of the mechanisms involved has yet emerged. To date, these studies show that coral calcification varies with carbonate ion availability which, in turn controls aragonite saturation. They also reveal synergies between acidification and the better understood role of elevated temperature. Ecological studies are unlikely to reveal much detail except for the observations of the effects of carbon dioxide springs in reefs. Although ocean acidification events are not well constrained in the geological record, recent studies show that they are clearly linked to extinction events including four of the five greatest crises in the history of coral reefs. However, as ocean acidification is now occurring faster than at any know time in the past, future predictions based on past events are in unchartered waters. Pooled evidence to date indicates that ocean acidification will be severely affecting reefs by mid century and will have reduced them to ecologically collapsed carbonate platforms by the century’s end. This review concludes that most impacts will be synergistic and that the primary outcome will be a progressive reduction of species diversity correlated with habitat loss and widespread extinctions in most metazoan phyla.

Description: The paper describes rich, a new R package to perform species richness estimation and comparison. Species richness is the simplest surrogate for the more complex concept of species biodiversity. It is relatively easy to assess although estimations strongly depend on sampling intensity with the consequence that richness estimations should be standardized to perform valid comparisons. The R package rich allows such corrections as well as the computation of various statistics and implements different randomization tests to compare cumulative and average species richness of two communities. These tests are useful for ranking sites or communities which is a classical goal in restoration ecology and conservation biology.

Description: Written for anyone interested in green development—including policy makers, architects, developers, builders, and homeowners—this practical guide focuses on the central question of how to conserve biodiversity in neighborhoods and to minimize development impacts on surrounding habitats. The Green Leap specifically helps move green development beyond the design stage by thoroughly addressing construction and post-construction issues. [...]

Description: In forest ecosystems, fungal mats are functionally important in nutrient and water uptake in litter and wood decomposition processes, in carbon resource allocation, soil weathering and in cycling of soil resources. Fungal mats can occur abundantly in forests and are widely distributed globally. We sampled ponderosa pine/white fir and mountain hemlock/noble fir communities at Crater Lake National Park for mat-forming soil fungi. Fungus collections were identified by DNA sequencing. Thirty-eight mat-forming genotypes were identified; members of the five most common genera (Gautieria, Lepiota, Piloderma, Ramaria, and Rhizopogon) comprised 67% of all collections. The mycorrhizal genera Alpova and Lactarius are newly identified as ectomycorrhizal mat-forming taxa, as are the saprotrophic genera Flavoscypha, Gastropila, Lepiota and Xenasmatella. Twelve typical mat forms are illustrated, representing both ectomycorrhizal and saprotrophic fungi that were found. Abundance of fungal mats was correlated with higher soil carbon to nitrogen ratios, fine woody debris and needle litter mass in both forest ecotypes. Definitions of fungal mats are discussed, along with some of the challenges in defining what comprises a fungal “mat”.

Description: Analysis was made of 3,923 records of 162 wild Passiflora specimens to assess the distribution of their diversity in Colombia, identify collection gaps, and explore their potential as indicator species. Despite variable collecting density among and within biogeographic regions, the Andean region clearly presents a higher species richness, particularly in the central coffee growing zone and the departments of Antioquia, Cundinamarca and Valle del Cauca. The elevational distribution of diversity shows a small peak below 500 m, and two higher ones between 1,000–2,000 and 2,500–3,000 m. This pattern corresponds to divergent adaptive trends among infrageneric divisions. The analysis on 19 climatic variables showed that the two principal variance components, explaining 77 percent of the total, are respectively associated with temperature and precipitation, without influence of seasonality. Distribution parameters allow recognizing more than 36 narrow endemics. Prediction of species distribution showed nine areas with very high richness (predicted sympatry of 41 to 54 species) in the Andean region, three of which correspond to collection gaps. Endemics were not particularly frequent there, so a prioritization of protected areas based on species richness would not favor their conservation. The sites with high Passiflora diversity are poorly represented in the current system of protected areas. Instead, their striking correspondence with ecotopes of the coffee growing zone imposes a conservation strategy integrating agricultural and environmental management at the landscape level. Reciprocally, several traits of Passiflora species make them particularly suited as indicators for any effort of conservation or restoration in this region of importance for the country.

Description: Public participation is a key element in nature conservation in Europe and a necessity for collecting broad scale data on biodiversity and its dynamics. However, vast societal differences exist between eastern and western European countries, resulting in problems for public participation in post-communist states as compared to western countries. Here, we compare diversity in monitoring practices and public participation in countries with different political histories. Drawing on in-depth ethnographic studies conducted in Lithuania and Poland, as well as a rapid assessment in Denmark, we have focused on the historical, cultural and social determinants of the volunteers’ participation in biodiversity monitoring. Our results indicate the reasons why volunteer involvement—as an expression of a participatory approach—has a lower incidence in the post-communist countries, compared to voluntarism common in occidental democracies. We discuss our results in the context of the main social factors considered to be a legacy of the Soviet regime.

Description: Humans harbor distinct commensal microbiota at various anatomic sites. There has been renewed interest in the contributions of microbiota activities to human health and disease. The microbiota of the gut is the most complex of all anatomic sites in terms of total numbers of bacteria that interact closely with the mucosal immune system and contribute various functions to host physiology. Especially in the proximal large intestine a diverse microbiota ferments complex substrates such as dietary fiber and host mucins, but also metabolizes bile acids and phytoestrogens that reach the large intestine. It is now well established that microbiota composition differs between but over time also within individuals. However, a thorough understanding of the sources of variations in microbiota composition, which is an important requirement for large population based microbiota studies is lacking. Microbiota composition varies depending on what kind of sample is collected, most commonly stool samples, stool swabs or superficial rectal or intestinal biopsies, and the time of collection. Microbiota dynamics are affected by life style factors including diet and exercise that determine what nutrients reach the proximal colon and how fast these nutrients pass through (transit time). Here we review sample collection issues in gut microbiota studies and recent findings about dynamics in microbiota composition. We recommend standardizing human microbiota analysis methods to facilitate comparison and pooling between studies. Finally, we outline a need for prospective microbiota studies in large human cohorts.

Description: Intense conversion of bottomland hardwood forests to rice and soybeans in the Mississippi River Valley of Arkansas has restricted the remaining forest to isolated fragments. Habitat fragmentation has proven to be detrimental to population sustainability of several species, and is the subject of intense study with often species and latitude specific responses. We compared both coarse land area classes and landscape fragmentation metrics from six 30 km × 30 km subsets centered on publicly owned management areas to bat captures obtained from a 2005 population study. Patch density was the strongest predictor of total captures (R2 = 0.801, p = 0.016) and of Myotis austroriparius captures (R2 = 0.856, p = 0.008). Our findings indicate that patch density and area are important predictors of bottomland bat captures.