Demographic and environmental drivers of metagenomic viral diversity in vampire bats

Viruses infect all forms of life and play critical roles as agents of disease, drivers of biochemical cycles and sources of genetic diversity for their hosts. Our understanding of viral diversity derives primarily from comparisons among host species, precluding insight into how intraspecific variation in host ecology affects viral communities or how predictable viral communities are across populations. We test spatial, demographic and environmental hypotheses explaining viral richness and community composition across populations of common vampire bats, which occur in diverse habitats of North, Central and South America. We demonstrate marked variation in viral communities which was not consistently predicted by a null model of declining community similarity with increasing spatial or genetic distances separating populations. We also find no evidence that larger bat colonies host greater viral diversity. Instead, viral diversity follows an elevational gradient, is enriched by juvenile‐biased age structure, and declines with local anthropogenic food resources as measured by livestock density. Our results establish the value of linking the modern influx of metagenomic sequence data with comparative ecology, reveal that snapshot views of viral diversity are unlikely to be representative at the species level, and affirm existing ecological theories that link host ecology not only to single pathogen dynamics but also to viral communities

Is Poverty Decentralising? Quantifying Uncertainty in the Decentralisation of Urban Poverty

In this paper we argue that the recent focus on the suburbanisation of poverty is problematic because of the ambiguities and inconsistencies in defining suburbia. To improve transparency, replicability and comparability, we suggest that research on the geographical changes to the distribution of poverty should focus on three questions: (1) How centralised is urban poverty? (2) To what extent is it decentralising? (3) Is it becoming spatially dispersed? With respect to all three questions, the issue of quantifying uncertainty has been under-researched. The main contribution of the paper is to provide a practical and robust solution to the problem of inference based on a Bayesian multivariate conditional autoregressive (CAR) model, made accessible via the R-software package CARBayes. Our approach can be applied to spatio-temporally autocorrelated data, and can estimate both levels of and change in global RCIs (relative centralisation index), local RCIs and dissimilarity indices. We illustrate our method with an application to Scotland's four largest cities. Our results show that poverty was centralised in 2011 in Glasgow, Dundee and Aberdeen. Poverty in Edinburgh, however, was decentralised: non-poor households tend to live closer to the centre than poor ones, and increasingly so. We also find evidence of statistically significant reductions in centralisation of poverty in all four cities. To test whether this change is associated with poverty becoming more dispersed, we estimate changes to evenness and local decentralisation of poverty, revealing complex patterns of change

Oribatid mites show how climate and latitudinal gradients in organic matter can drive large-scale biodiversity patterns of soil communities

Aim: The factors determining spatial distributions and diversity of terrestrial invertebrates are typically investigated at small scales. Large‐scale studies are lacking for soil animals, which control microbial communities and represent one of the most diverse yet poorly known animal assemblages. Here, we analyzed a major group (Oribatida) to test whether belowground macroecological patterns can be predicted by climatic variables, vegetation and large‐scale variation in key soil properties. Location: We modelled the multivariate distribution of more than 100 species using biodiversity data collected across Great Britain in the framework of the Countryside Survey (http://www.countrysidesurvey.org.uk). Methods: We analyzed species‐level data from 582 samples collected across 162 hectads (10 × 10 km) covering the largest possible range of vegetation types, soil properties and climatic conditions within GB. We created the first large‐scale maps of soil animal diversity metrics at the GB scale, including novel estimates of metrics of phylogenetic diversity (PD). Using structural equation modelling, we quantified the direct and indirect effects of location (latitude, longitude), plant community structure and abiotic factors such as precipitation on species composition, richness and PD. Results: We found that variation in species composition follows a latitudinal gradient with diversity generally increasing northward. The latitudinal variation in species composition drives PD via changes in both species richness and phylogenetic distance between species. This gradient is mostly determined by latitudinal variation in precipitation and organic matter, which were very good predictors of species composition. Precipitation and organic matter were, however, relatively weak while statistically significant predictors of diversity metrics. Conclusions: Past studies have emphasized the unpredictability of species distributions and variation in species composition in hyper diverse soil animal communities. However, past studies were conducted at small scales, where stochastic factors may weaken the signal of deterministic factors. Oribatid mites in our study show for the first time that the large scale latitudinal gradients in climate and organic matter predict not only variation in species composition but also taxonomic and PD of soil animal communities

The ghosts of forests past and future : deforestation and botanical sampling in the Brazilian Amazon

The remarkable biodiversity of the Brazilian Amazon is poorly documented and threatened by deforestation. When undocumented areas become deforested, in addition to losing the fauna and flora, we lose the opportunity to know which unique species had occupied a habitat. Here we quantify such knowledge loss by calculating how much of the Brazilian Amazon has been deforested and will likely be deforested until 2050 without having its tree flora sufficiently documented. To this end, we analysed 399 147 digital specimens of nearly 6000 tree species in relation to official deforestation statistics and future deforestation scenarios. We find that by 2017, 30% of all the localities where tree specimens had been collected were mostly deforested. Some 300 000 km(2)(12%; 485 25 x 25 km grid cells) of the Brazilian Amazon had been deforested by 2017, without having a single tree specimen recorded. An additional 250 000-900 000 km(2)of severely under-collected rainforest will likely become deforested by 2050. If future tree sampling is to cover this area, sampling effort has to increase two- to six-fold. Nearly 255 000 km(2)or 7% of rainforest in the Brazilian Amazon is easily accessible but does yet but remain under-collected. Our study highlights how progressing deforestation increases the risk of losing undocumented species of a hyper-diverse tree flora.Peer reviewe

Evolution of breeding plumages in birds: A multiple-step pathway to seasonal dichromatism in New World warblers (Aves: Parulidae)

Ecology and Evolution published by John Wiley & Sons Ltd Many species of birds show distinctive seasonal breeding and nonbreeding plumages. A number of hypotheses have been proposed for the evolution of this seasonal dichromatism, specifically related to the idea that birds may experience variable levels of sexual selection relative to natural selection throughout the year. However, these hypotheses have not addressed the selective forces that have shaped molt, the underlying mechanism of plumage change. Here, we examined relationships between life-history variation, the evolution of a seasonal molt, and seasonal plumage dichromatism in the New World warblers (Aves: Parulidae), a family with a remarkable diversity of plumage, molt, and life-history strategies. We used phylogenetic comparative methods and path analysis to understand how and why distinctive breeding and nonbreeding plumages evolve in this family. We found that color change alone poorly explains the evolution of patterns of biannual molt evolution in warblers. Instead, molt evolution is better explained by a combination of other life-history factors, especially migration distance and foraging stratum. We found that the evolution of biannual molt and seasonal dichromatism is decoupled, with a biannual molt appearing earlier on the tree, more dispersed across taxa and body regions, and correlating with separate life-history factors than seasonal dichromatism. This result helps explain the apparent paradox of birds that molt biannually but show breeding plumages that are identical to the nonbreeding plumage. We find support for a two-step process for the evolution of distinctive breeding and nonbreeding plumages: That prealternate molt evolves primarily under selection for feather renewal, with seasonal color change sometimes following later. These results reveal how life-history strategies and a birds\u27 environment act upon multiple and separate feather functions to drive the evolution of feather replacement patterns and bird coloration

Global trends of habitat destruction and consequences for parrot conservation

Human advance on natural habitats is a major cause of biodiversity loss. This transformation process represents a profound change in wooded environments, disrupting original communities of flora and fauna. Many species are highly dependent on forests, especially parrots (Psittaciformes) with almost a third of their species threatened by extinction. Most parrot species occur in tropical and subtropical forests, and given the forest dependence of most species, this is the main reason why habitat loss has been highlighted as the main threat for the group. Such habitat loss acts in synergy with other important threats (e.g., logging and poaching), which become especially problematic in certain developing countries along tropical latitudes. In this study, we used available information on parrot distributions, species traits, IUCN assessment, habitat loss and timber extraction for different periods, and distribution of protected areas, to determine conservation hotspots for the group, and analyze potential changes in the conservation status of these species. We detected four conservation hotspots for parrots: two in the Neotropics and two in Oceania, all of them facing different degrees of threat in regard of current habitat loss and agricultural trends. Our results suggest that the future of the group is subject to policymaking in specific regions, especially in the northeastern Andes and the Atlantic Forest. In addition, we predicted that agricultural expansion will have a further negative effect on the conservation status of parrots, pushing many parrot species to the edge of extinction in the near future. Our results have conservation implications by recommending protected areas in specific parrot conservation hotspots. Our recommendations to mitigate conservation risks to this group of umbrella species would also benefit many other coexisting species as well.Fil: Vergara Tabares, David Lautaro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Zoología Aplicada; ArgentinaFil: Cordier, Javier Maximiliano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Zoología Aplicada; ArgentinaFil: Landi, Marcos Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Zoología Aplicada; ArgentinaFil: Olah, George. Wildlife Messengers; Estados UnidosFil: Nori, Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Diversidad y Ecología Animal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto de Diversidad y Ecología Animal; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Zoología Aplicada; Argentin

Consequences of marine barriers for genetic diversity of the coral-specialist yellowbar angelfish from the Northwestern Indian Ocean

© 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. Ocean circulation, geological history, geographic distance, and seascape heterogeneity play an important role in phylogeography of coral-dependent fishes. Here, we investigate potential genetic population structure within the yellowbar angelfish (Pomacanthus maculosus) across the Northwestern Indian Ocean (NIO). We then discuss our results with respect to the above abiotic features in order to understand the contemporary distribution of genetic diversity of the species. To do so, restriction site-associated DNA sequencing (RAD-seq) was utilized to carry out population genetic analyses on P. maculosus sampled throughout the species’ distributional range. First, genetic data were correlated to geographic and environmental distances, and tested for isolation-by-distance and isolation-by-environment, respectively, by applying the Mantel test. Secondly, we used distance-based and model-based methods for clustering genetic data. Our results suggest the presence of two putative barriers to dispersal; one off the southern coast of the Arabian Peninsula and the other off northern Somalia, which together create three genetic subdivisions of P. maculosus within the NIO. Around the Arabian Peninsula, one genetic cluster was associated with the Red Sea and the adjacent Gulf of Aden in the west, and another cluster was associated with the Arabian Gulf and the Sea of Oman in the east. Individuals sampled in Kenya represented a third genetic cluster. The geographic locations of genetic discontinuities observed between genetic subdivisions coincide with the presence of substantial upwelling systems, as well as habitat discontinuity. Our findings shed light on the origin and maintenance of genetic patterns in a common coral reef fish inhabiting the NIO, and reinforce the hypothesis that the evolution of marine fish species in this region has likely been shaped by multiple vicariance events

Legacy of logging roads in the Congo Basin: how persistent are the scars in forest cover?

Logging roads in the Congo Basin are often associated with forest degradation through fragmentation and access for other land uses. However, in concessions managed for timber production, secondary roads are usually closed after exploitation and are expected to disappear subsequently. Little is known about the effectiveness of this prescription and the factors affecting vegetation recovery rate on abandoned logging roads. In a novel approach we assessed logging roads as temporary elements in the forest landscape that vary in persistence depending on environmental conditions. We analyzed road persistence during the period 1986–2013 in adjacent parts of Cameroon, Central African Republic and Republic of Congo. Three successive phases of road recovery were identified on LANDSAT images: open roads with bare soil, roads in the process of revegetation after abandonment and disappeared roads no longer distinguishable from the surrounding forest. Field based inventories confirmed significant differences between all three categories in density and richness of woody species and cover of dominant herbs. We used dead-end road segments, built for timber exploitation, as sampling units. Only 6% of them were identified as being re-opened. Survival analyses showed median persistence of four years for open roads before changing to the revegetating state and 20 years for revegetating roads before disappearance. Persistence of revegetating roads was 25% longer on geologically poor substrates which might result from slower forest recovery in areas with lower levels of soil nutrient content. We highlight the contrast amongst forests growing on different types of substrate in their potential for ecosystem recovery over time after roads have been abandoned. Forest management plans need to take these constraints into account. Logging activities should be concentrated on the existing road network and sites of low soil resource levels should be spared from business-as-usual exploitation. (Résumé d'auteur

Local spatial regression models : a comparative analysis on soil contamination

Spatial data analysis focuses on both attribute and locational information. Local analyses deal with differences across space whereas global analyses deal with similarities across space. This paper addresses an experimental comparative study to analyse the spatial data by some weighted local regression models. Five local regression models have been developed and their estimation capacities have been evaluated. The experimental studies showed that integration of objective function based fuzzy clustering to geostatistics provides some accurate and general models structures. In particular, the estimation performance of the model established by combining the extended fuzzy clustering algorithm and standard regional dependence function is higher than that of the other regression models. Finally, it could be suggested that the hybrid regression models developed by combining soft computing and geostatistics could be used in spatial data analysis

Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts.

Disentangling the contribution of long-term evolutionary processes and recent anthropogenic impacts to current genetic patterns of wildlife species is key for assessing genetic risks and designing conservation strategies. Here, we used 80 whole nuclear genomes and 96 mitogenomes from populations of the Eurasian lynx covering a range of conservation statuses, climatic zones and subspecies across Eurasia to infer the demographic history, reconstruct genetic patterns and discuss the influence of long-term isolation and/or more recent human-driven changes. Our results show that Eurasian lynx populations shared a common history until 100 kya, when Asian and European populations started to diverge and both entered a period of continuous and widespread decline, with western populations, except Kirov, maintaining lower effective sizes than eastern populations. Population declines and increased isolation in more recent times likely drove the genetic differentiation between geographically and ecologically close westernmost European populations. By contrast, and despite the wide range of habitats covered, populations are quite homogeneous genetically across the Asian range, showing a pattern of isolation by distance and providing little genetic support for the several proposed subspecies. Mitogenomic and nuclear divergences and population declines starting during the Late Pleistocene can be mostly attributed to climatic fluctuations and early human influence, but the widespread and sustained decline since the Holocene is more probably the consequence of anthropogenic impacts which intensified during the last centuries, especially in western Europe. Genetic erosion in isolated European populations and lack of evidence for long-term isolation argue for the restoration of lost population connectivity