ALBERT

Description: As ocean temperatures rise, species distributions are tracking towards historically cooler regions in line with their thermal affinity(1,2). However, different responses of species to warming and changed species interactions make predicting biodiversity redistribution and relative abundance a challenge(3,4). Here, we use three decades of fish and plankton survey data to assess how warming changes the relative dominance of warm-affinity and cold-affinity species(5,6). Regions with stable temperatures (for example, the Northeast Pacific and Gulf of Mexico) show little change in dominance structure, while areas with warming (for example, the North Atlantic) see strong shifts towards warm-water species dominance. Importantly, communities whose species pools had diverse thermal affinities and a narrower range of thermal tolerance showed greater sensitivity, as anticipated from simulations. The composition of fish communities changed less than expected in regions with strong temperature depth gradients. There, species track temperatures by moving deeper(2,7), rather than horizontally, analogous to elevation shifts in land plants(8). Temperature thus emerges as a fundamental driver for change in marine systems, with predictable restructuring of communities in the most rapidly warming areas using metrics based on species thermal affinities. The ready and predictable dominance shifts suggest a strong prognosis of resilience to climate change for these communities.

Description: Conservation and environmental management are principal countermeasures to the degradation of marine ecosystems and their services.However, in many cases, current practices are insufficient to reverse ecosystem declines. We suggest that restoration ecology, the science underlying the concepts and tools needed to restore ecosystems, must be recognized as an integral element for marine conservation and environmental management. Marine restoration ecology is a young scientific discipline, often with gaps between its application and the supporting science. Bridging these gaps is essential to using restoration as an effective management tool and reversing the decline of marine ecosystems and their services. Ecological restoration should address objectives that include improved ecosystem services, and it therefore should encompass social–ecological elements rather than focusing solely on ecological parameters. We recommend using existing management frameworks to identify clear restoration targets, to apply quantitative tools for assessment, and to make the re-establishment of ecosystem services a criterion for success.

Description: Coral reefs of the world face rapid degradation of biodiversity and ecosystem services, and marine protected areas (MPAs) are a commonly applied solution. Nevertheless, coral reefs continue to decline worldwide, raising questions about the adequacy of management and protection efforts. We argue that expanding the range of MPA targets to also include degraded reefs (i.e. 'DR-MPA'), could help reverse this trend. This approach requires new ecological criteria for MPA design, siting, and management. Rather than focusing solely on preserving healthy reefs, the proposed approach focuses on the potential for biodiversity recovery and renewal of ecosystem services. The new criteria highlight sites with the highest potential for recovery, the greatest resistance to future threats (e.g., temperature and acidification) and the largest contribution to connectivity of MPA networks. The DR-MPA approach is not a substitute for traditional MPA selection criteria; it is rather a complimentary framework when traditional approaches are inadequate. We believe that the DR-MPA approach can help to: 1. Enhance the natural, or restoration-assisted, recovery of degraded reefs and their ecosystem services, 2. Increase the total reef area available for protection, 3. Promote more resilient and better-connected MPA networks, and 4. More effectively contribute to improved conditions for human communities dependent on these ecosystem services. This article is protected by copyright. All rights reserved.

Description: © The Author(s), 2018]. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Global Ecology and Biogeography 27 (2018): 760-786, doi:10.1111/geb.12729.

Description: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community‐led open‐source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2). BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

Description: European Research Council and EU, Grant/Award Number: AdG‐250189, PoC‐727440 and ERC‐SyG‐2013‐610028; Natural Environmental Research Council, Grant/Award Number: NE/L002531/1; National Science Foundation, Grant/Award Number: DEB‐1237733, DEB‐1456729, 9714103, 0632263, 0856516, 1432277, DEB‐9705814, BSR‐8811902, DEB 9411973, DEB 0080538, DEB 0218039, DEB 0620910, DEB 0963447, DEB‐1546686, DEB‐129764, OCE 95‐21184, OCE‐ 0099226, OCE 03‐52343, OCE‐0623874, OCE‐1031061, OCE‐1336206 and DEB‐1354563; National Science Foundation (LTER) , Grant/Award Number: DEB‐1235828, DEB‐1440297, DBI‐0620409, DEB‐9910514, DEB‐1237517, OCE‐0417412, OCE‐1026851, OCE‐1236905, OCE‐1637396, DEB 1440409, DEB‐0832652, DEB‐0936498, DEB‐0620652, DEB‐1234162 and DEB‐0823293; Fundação para a Ciência e Tecnologia, Grant/Award Number: POPH/FSE SFRH/BD/90469/2012, SFRH/BD/84030/2012, PTDC/BIA‐BIC/111184/2009; SFRH/BD/80488/2011 and PD/BD/52597/2014; Ciência sem Fronteiras/CAPES, Grant/Award Number: 1091/13‐1; Instituto Milenio de Oceanografía, Grant/Award Number: IC120019; ARC Centre of Excellence, Grant/Award Number: CE0561432; NSERC Canada; CONICYT/FONDECYT, Grant/Award Number: 1160026, ICM PO5‐002, CONICYT/FONDECYT, 11110351, 1151094, 1070808 and 1130511; RSF, Grant/Award Number: 14‐50‐00029; Gordon and Betty Moore Foundation, Grant/Award Number: GBMF4563; Catalan Government; Marie Curie Individual Fellowship, Grant/Award Number: QLK5‐CT2002‐51518 and MERG‐CT‐2004‐022065; CNPq, Grant/Award Number: 306170/2015‐9, 475434/2010‐2, 403809/2012‐6 and 561897/2010; FAPESP (São Paulo Research Foundation), Grant/Award Number: 2015/10714‐6, 2015/06743‐0, 2008/10049‐9, 2013/50714‐0 and 1999/09635‐0 e 2013/50718‐5; EU CLIMOOR, Grant/Award Number: ENV4‐CT97‐0694; VULCAN, Grant/Award Number: EVK2‐CT‐2000‐00094; Spanish, Grant/Award Number: REN2000‐0278/CCI, REN2001‐003/GLO and CGL2016‐79835‐P; Catalan, Grant/Award Number: AGAUR SGR‐2014‐453 and SGR‐2017‐1005; DFG, Grant/Award Number: 120/10‐2; Polar Continental Shelf Program; CENPES – PETROBRAS; FAPERJ, Grant/Award Number: E‐26/110.114/2013; German Academic Exchange Service; sDiv; iDiv; New Zealand Department of Conservation; Wellcome Trust, Grant/Award Number: 105621/Z/14/Z; Smithsonian Atherton Seidell Fund; Botanic Gardens and Parks Authority; Research Council of Norway; Conselleria de Innovació, Hisenda i Economia; Yukon Government Herschel Island‐Qikiqtaruk Territorial Park; UK Natural Environment Research Council ShrubTundra Grant, Grant/Award Number: NE/M016323/1; IPY; Memorial University; ArcticNet. DOI: 10.13039/50110000027. Netherlands Organization for Scientific Research in the Tropics NWO, grant W84‐194. Ciências sem Fronteiras and Coordenação de Pessoal de Nível Superior (CAPES, Brazil), Grant/Award Number: 1091/13‐1. National Science foundation (LTER), Award Number: OCE‐9982105, OCE‐0620276, OCE‐1232779. FCT ‐ SFRH / BPD / 82259 / 2011. U.S. Fish and Wildlife Service/State Wildlife federal grant number T‐15. Australian Research Council Centre of Excellence for Coral Reef Studies (CE140100020). Australian Research Council Future Fellowship FT110100609. M.B., A.J., K.P., J.S. received financial support from internal funds of University of Lódź. NSF DEB 1353139. Catalan Government fellowships (DURSI): 1998FI‐00596, 2001BEAI200208, MECD Post‐doctoral fellowship EX2002‐0022. National Science Foundation Award OPP‐1440435. FONDECYT 1141037 and FONDAP 15150003 (IDEAL). CNPq Grant 306595‐2014‐1

Description: The yolk sac is phylogenetically the oldest of the extraembryonic membranes. The human embryo retains a yolk sac, which goes through primary and secondary phases of development, but its importance is controversial. Although it is known to synthesize proteins, its transport functions are widely considered vestigial. Here, we report RNA-sequencing (RNA-seq) data for the human and murine yolk sacs and compare those data with data for the chicken. We also relate the human RNA-seq data to proteomic data for the coelomic fluid bathing the yolk sac. Conservation of transcriptomes across the species indicates that the human secondary yolk sac likely performs key functions early in development, particularly uptake and processing of macro- and micronutrients, many of which are found in coelomic fluid. More generally, our findings shed light on evolutionary mechanisms that give rise to complex structures such as the placenta. We identify genetic modules that are conserved across mammals and birds, suggesting these modules are part of the core amniote genetic repertoire and are the building blocks for both oviparous and viviparous reproductive modes. We propose that although a choriovitelline placenta is never established physically in the human, the placental villi, the exocoelomic cavity, and the secondary yolk sac function together as a physiological equivalent.

Description: Staphylococcus aureus is a notorious human bacterial pathogen with considerable capacity to develop antibiotic resistance. We have observed that human infections caused by highly drug-resistant S. aureus are more prolonged, complicated, and difficult to eradicate. Here we describe a metabolic adaptation strategy used by clinical S. aureus strains that leads to resistance to the last-line antibiotic, daptomycin, and simultaneously affects host innate immunity. This response was characterized by a change in anionic membrane phospholipid composition induced by point mutations in the phospholipid biosynthesis gene, cls2, encoding cardiolipin synthase. Single cls2 point mutations were sufficient for daptomycin resistance, antibiotic treatment failure, and persistent infection. These phenotypes were mediated by enhanced cardiolipin biosynthesis, leading to increased bacterial membrane cardiolipin and reduced phosphatidylglycerol. The changes in membrane phospholipid profile led to modifications in membrane structure that impaired daptomycin penetration and membrane disruption. The cls2 point mutations also allowed S. aureus to evade neutrophil chemotaxis, mediated by the reduction in bacterial membrane phosphatidylglycerol, a previously undescribed bacterial-driven chemoattractant. Together, these data illustrate a metabolic strategy used by S. aureus to circumvent antibiotic and immune attack and provide crucial insights into membrane-based therapeutic targeting of this troublesome pathogen.

Description: A long-standing hypothesis in adaptive radiation theory is that ecological opportunity constrains rates of phenotypic evolution, generating a burst of morphological disparity early in clade history. Empirical support for the early burst model is rare in comparative data, however. One possible reason for this lack of support is that most phylogenetic tests have focused on extant clades, neglecting information from fossil taxa. Here, I test for the expected signature of adaptive radiation using the outstanding 40-My fossil record of North American canids. Models implying time- and diversity-dependent rates of morphological evolution are strongly rejected for two ecologically important traits, body size and grinding area of the molar teeth. Instead, Ornstein–Uhlenbeck processes implying repeated, and sometimes rapid, attraction to distinct dietary adaptive peaks receive substantial support. Diversity-dependent rates of morphological evolution seem uncommon in clades, such as canids, that exhibit a pattern of replicated adaptive radiation. Instead, these clades might best be thought of as deterministic radiations in constrained Simpsonian subzones of a major adaptive zone. Support for adaptive peak models may be diagnostic of subzonal radiations. It remains to be seen whether early burst or ecological opportunity models can explain broader adaptive radiations, such as the evolution of higher taxa.

Description: Innate cellular immune responses are a critical first-line defense against invading bacterial pathogens. Leukocyte migration from the bloodstream to a site of infection is mediated by chemotactic factors that are often host-derived. More recently, there has been a greater appreciation of the importance of bacterial factors driving neutrophil movement during infection. Here, we describe the development of a zebrafish infection model to study Acinetobacter baumannii pathogenesis. By using isogenic A. baumannii mutants lacking expression of virulence effector proteins, we demonstrated that bacterial drivers of disease severity are conserved between zebrafish and mammals. By using transgenic zebrafish with fluorescent phagocytes, we showed that a mutation of an established A. baumannii global virulence regulator led to marked changes in neutrophil behavior involving rapid neutrophil influx to a localized site of infection, followed by prolonged neutrophil dwelling. This neutrophilic response augmented bacterial clearance and was secondary to an impaired A. baumannii phenylacetic acid catabolism pathway, which led to accumulation of phenylacetate. Purified phenylacetate was confirmed to be a neutrophil chemoattractant. These data identify a previously unknown mechanism of bacterial-guided neutrophil chemotaxis in vivo, providing insight into the role of bacterial metabolism in host innate immune evasion. Furthermore, the work provides a potentially new therapeutic paradigm of targeting a bacterial metabolic pathway to augment host innate immune responses and attenuate disease.

Description: Coral reefs provide ecosystem goods and services for millions of people in the tropics, but reef conditions are declining worldwide. Effective solutions to the crisis facing coral reefs depend in part on understanding the context under which different types of conservation benefits can be maximized. Our global analysis of nearly 1,800 tropical reefs reveals how the intensity of human impacts in the surrounding seascape, measured as a function of human population size and accessibility to reefs (“gravity”), diminishes the effectiveness of marine reserves at sustaining reef fish biomass and the presence of top predators, even where compliance with reserve rules is high. Critically, fish biomass in high-compliance marine reserves located where human impacts were intensive tended to be less than a quarter that of reserves where human impacts were low. Similarly, the probability of encountering top predators on reefs with high human impacts was close to zero, even in high-compliance marine reserves. However, we find that the relative difference between openly fished sites and reserves (what we refer to as conservation gains) are highest for fish biomass (excluding predators) where human impacts are moderate and for top predators where human impacts are low. Our results illustrate critical ecological trade-offs in meeting key conservation objectives: reserves placed where there are moderate-to-high human impacts can provide substantial conservation gains for fish biomass, yet they are unlikely to support key ecosystem functions like higher-order predation, which is more prevalent in reserve locations with low human impacts.

Description: Kelp forests (Order Laminariales) form key biogenic habitats in coastal regions of temperate and Arctic seas worldwide, providing ecosystem services valued in the range of billions of dollars annually. Although local evidence suggests that kelp forests are increasingly threatened by a variety of stressors, no comprehensive global analysis of change in kelp abundances currently exists. Here, we build and analyze a global database of kelp time series spanning the past half-century to assess regional and global trends in kelp abundances. We detected a high degree of geographic variation in trends, with regional variability in the direction and magnitude of change far exceeding a small global average decline (instantaneous rate of change = −0.018 y−1). Our analysis identified declines in 38% of ecoregions for which there are data (−0.015 to −0.18 y−1), increases in 27% of ecoregions (0.015 to 0.11 y−1), and no detectable change in 35% of ecoregions. These spatially variable trajectories reflected regional differences in the drivers of change, uncertainty in some regions owing to poor spatial and temporal data coverage, and the dynamic nature of kelp populations. We conclude that although global drivers could be affecting kelp forests at multiple scales, local stressors and regional variation in the effects of these drivers dominate kelp dynamics, in contrast to many other marine and terrestrial foundation species.