Inferring Bottlenecks from Genome-Wide Samples of Short Sequence Blocks

The advent of the genomic era has necessitated the development of methods capable of analyzing large volumes of genomic data efficiently. Being able to reliably identify bottlenecks—extreme population size changes of short duration—not only is interesting in the context of speciation and extinction but also matters (as a null model) when inferring selection. Bottlenecks can be detected in polymorphism data via their distorting effect on the shape of the underlying genealogy. Here, we use the generating function of genealogies to derive the probability of mutational configurations in short sequence blocks under a simple bottleneck model. Given a large number of nonrecombining blocks, we can compute maximum-likelihood estimates of the time and strength of the bottleneck. Our method relies on a simple summary of the joint distribution of polymorphic sites. We extend the site frequency spectrum by counting mutations in frequency classes in short sequence blocks. Using linkage information over short distances in this way gives greater power to detect bottlenecks than the site frequency spectrum and potentially opens up a wide range of demographic histories to blockwise inference. Finally, we apply our method to genomic data from a species of pig (Sus cebifrons) endemic to islands in the center and west of the Philippines to estimate whether a bottleneck occurred upon island colonization and compare our scheme to Li and Durbin’s pairwise sequentially Markovian coalescent (PSMC) both for the pig data and using simulations. © 2015 by the Genetics Society of America

Extinction debt on reservoir land-bridge islands

Large dams cause extensive inundation of habitats, with remaining terrestrial habitat confined to highly fragmented archipelagos of land-bridge islands comprised of former hilltops. Isolation of biological communities on reservoir islands induces local extinctions and degradation of remnant communities. “Good practice” dam development guidelines propose using reservoir islands for species conservation, mitigating some of the detrimental impacts associated with flooding terrestrial habitats. The degree of species retention on islands in the long-term, and hence, whether they are effective for conservation is currently unknown. Here, we quantitatively review species' responses to isolation on reservoir islands. We specifically investigate island species richness in comparison with neighbouring continuous habitat, and relationships between island species richness and island area, isolation time, and distance to mainland and to other islands. Species' responses to isolation on reservoir islands have been investigated in only 15 of the > 58,000 large-dam reservoirs (dam height > 15m) operating globally. Research predominantly originates from wet tropical forest habitats and focuses on mammals, with species richness being the most widely-reported ecological metric. Terrestrial taxa are, overall, negatively impacted by isolation on reservoir islands. Reservoir island species richness declines with isolation time, and although the rate of loss is slower on larger islands, all islands exhibit depauperate species richness < 100 years after isolation, compared to continuous mainland habitats. Such a pattern of sustained and delayed species loss following large-scale habitat disturbance is indicative of an extinction debt existing for reservoir island species: this pattern is evident across all taxonomic groups and dams studied. Thus, reservoir islands cannot reliably be used for species conservation as part of impact mitigation measures, and should instead be included in area calculations for land impacted by dam creation. Environmental licensing assessments as a precondition for future dam development should explicitly consider the long-term fate of island communities when assessing biodiversity loss vs energy output

Decision Trees for Data Publishing May Exacerbate Conservation Conflict

First paragraph: Tulloch et al. have rightly highlighted the need to increase the accessibility of species occurrence data to better support conservation efforts. They present a tree to aid decisions regarding making data publicly available. Their tree is essentially a visual aid to existing protocols. However, we feel that, owing to its failure to explicitly account for likely disagreements among stakeholders throughout the process, the proposed method may inadvertently fuel conservation conflicts.Output Type: Lette

Integrating conflict, lobbying, and compliance to predict the sustainability of natural resource use

Acknowledgments: This study received funding from the European Research Council under the European Union’s H2020/ERC grant agreement no.679651 (ConFooBio) to N.B. A.B.D. is supported by a Leverhulme Trust Early Career Fellowship. We are grateful to Tim Coulson and E.J. Milner-Gulland for comments on previous versions of this manuscript. All authors conceived the study, developed the underlying theory and software, discussed the results, and wrote the manuscript. J.J.C. carried out the simulations and analyzed thedata.Peer reviewedPublisher PD

GMSE: an R package for generalised management strategy evaluation

1. Management strategy evaluation (MSE) is a powerful tool for simulating all key aspects of natural resource management under conditions of uncertainty. 2. We present the R package GMSE, which applies genetic algorithms to provide a generalised tool for simulating adaptive decision‐making management scenarios between stakeholders with competing objectives under complex social‐ecological interactions and uncertainty. 3. GMSE models can be agent‐based and spatially explicit, incorporating a high degree of realism through mechanistic modelling of links and feedbacks among stakeholders and with the ecosystem; additionally, user‐defined sub‐models can also be incorporated as functions into the broader GMSE framework. 4. We show how GMSE simulates a social‐ecological system using the example of an adaptively managed waterfowl population on an agricultural landscape; simulated waterfowl exploit agricultural land, causing conflict between conservation interests and the interest of food producers maximising their crop yield. 5. The R package GMSE is open source under GNU Public License; source code and documents are freely available on GitHub

Do Global Diversity Patterns of Vertebrates Reflect Those of Monocots?

Few studies of global diversity gradients in plants exist, largely because the data are not available for all species involved. Instead, most global studies have focussed on vertebrates, as these taxa have historically been associated with the most complete data. Here, we address this shortfall by first investigating global diversity gradients in monocots, a morphologically and functionally diverse clade representing a quarter of flowering plant diversity, and then assessing congruence between monocot and vertebrate diversity patterns. To do this, we create a new dataset that merges biome-level associations for all monocot genera with country-level associations for almost all &sim;70,000 species. We then assess the evidence for direct versus indirect effects of this plant diversity on vertebrate diversity using a combination of linear regression and structural equation modelling (SEM). Finally, we also calculate overlap of diversity hotspots for monocots and each vertebrate taxon. Monocots follow a latitudinal gradient although with pockets of extra-tropical diversity, mirroring patterns in vertebrates. Monocot diversity is positively associated with vertebrate diversity, but the strength of correlation varies depending on the clades being compared. Monocot diversity explains marginal amounts of variance (&lt;10%) after environmental factors have been accounted for. However, correlations remain among model residuals, and SEMs apparently reveal some direct effects of monocot richness. Our results suggest that collinear responses to environmental gradients are behind much of the congruence observed, but that there is some evidence for direct effects of producer diversity on consumer diversity. Much remains to be done before broad-scale diversity gradients among taxa are fully explained. Our dataset of monocot distributions will aid in this endeavour

Above- and belowground carbon stocks are decoupled in secondary tropical forests and are positively related to forest age and soil nutrients respectively

Reducing atmospheric CO2 is an international priority. One way to assist stabilising and reducing CO2 is to promote secondary tropical forest regrowth on abandoned agricultural land. However, relationships between above- and belowground carbon stocks with secondary forest age and specific soil nutrients remain unclear. Current global estimates for CO2 uptake and sequestration in secondary tropical forests focus on aboveground biomass and are parameterised using relatively coarse metrics of soil fertility. Here, we estimate total carbon stocks across a chronosequence of regenerating secondary forest stands (40–120 years old) in Panama, and assess the relationships between both above- and belowground carbon stocks with stand age and specific soil nutrients. We estimated carbon stocks in aboveground biomass, necromass, root biomass, and soil. We found that the two largest carbon pools - aboveground biomass and soil – have distinct relationships with stand age and soil fertility. Aboveground biomass contained ~61-97 Mg C ha-1 (24-39 % total carbon stocks) and significantly increased with stand age, but showed no relationship with soil nutrients. Soil carbon stocks contained ~128-206 Mg C ha-1 (52-70 % total stocks) and were unrelated to stand age, but were positively related to soil nitrogen. Root biomass carbon stocks tracked patterns exhibited by aboveground biomass. Necromass carbon stocks did not increase with stand age, but stocks were held in larger pieces of deadwood in older stands. Comparing our estimates to published data from younger and older secondary forests in the surrounding landscape, we show that soil carbon recovers within 40 years of forest regeneration, but aboveground biomass carbon stocks continue to increase past 100 years. Above- and belowground carbon stocks appear to be decoupled in secondary tropical forests. Paired measures of above- and belowground carbon stocks are necessary to reduce uncertainty in large-scale models of atmospheric CO2 uptake and storage by secondary forests

Biodiversity, drug discovery, and the future of global health:Introducing the biodiversity to biomedicine consortium, a call to action

First paragraph: Looking to nature for medicine is nothing new – we have been doing it for tens of thousands of years and although modern pharmaceutical science has come a long way from those ancient roots, nature is and will always be an important source of useful compounds and inspiration. Dismissing nature in this regard is a huge mistake as evolution is the greatest problem solver and the myriad compounds produced by the immense variety of species we share the planet with have been honed by three billion years of trial and error. However, with every bit of habitat that disappears under the plough or concrete we impoverish nature and deprive ourselves of potential medicines.Additional co-authors: Uttam Babu Shrestha, Milica Pešić, Alexander Kagansk

A multispecies assessment of wildlife impacts on local community livelihoods

Conflicts between the interests of agriculture and wildlife conservation are a major threat to biodiversity and human wellbeing globally. Addressing such conflicts requires a thorough understanding of the impacts associated with living alongside protected wildlife. Despite this, most studies reporting on human‐wildlife impacts and the strategies used to mitigate them focus on a single species, thus over‐simplifying often complex systems of human‐wildlife interactions. In this study, we characterize the spatiotemporal patterns of impacts by multiple co‐occurring species on agricultural livelihoods in the eastern Okavango Delta Panhandle in northern Botswana. Using a database of 3,264 wildlife incidents recorded between 2009 and 2015 by the Department of Wildlife and National Parks, we show that a total of eight species – i.e. African elephant, hippopotamus, cheetah, crocodile, leopard, lion, spotted hyena and African wild dog – appear on incident reports, of which 56.5% are attributed to elephants. Most species were associated with only one type of damage (i.e. either damage to crops or livestock loss). Carnivores were primarily implicated in incident reports related to livestock loss, particularly towards the end of the dry season (May‐October). In contrast, herbivores were associated with crop loss incidents during the wet season (November‐April). Our study illustrates how local communities can face distinct livelihood challenges from different species at different times of the year. Such a multi‐species assessment has important implications for the design of conservation interventions aimed at addressing the costs of living with wildlife, and thereby mitigating the underlying conservation conflict. Our spatiotemporal, multi‐species approach is widely applicable to other regions where sustainable and long‐term solutions to conservation conflicts are needed for local communities and biodiversity

Biodiversity, drug discovery, and the future of global health: Introducing the biodiversity to biomedicine consortium, a call to action

Looking to nature for medicine is nothing new – we have been doing it for tens of thousands of years and although modern pharmaceutical science has come a long way from those ancient roots, nature is and will always be an important source of useful compounds and inspiration. Dismissing nature in this regard is a huge mistake as evolution is the greatest problem solver and the myriad compounds produced by the immense variety of species we share the planet with have been honed by three billion years of trial and error. However, with every bit of habitat that disappears under the plough or concrete we impoverish nature and deprive ourselves of potential medicines