Complex Evolutionary History of Primate LentiviralvprGenes

AbstractVpx and Vpr are homologous proteins encoded by the human and simian immunodeficiency viruses. Vpr is encoded by each of the five primate lentiviral groups, whereas Vpx is restricted to members of the HIV-2 group. A recent report has proposed that thevpxgene was probably acquired from an ancestral member of the SIVagm group by nonhomologous recombination. Here, we suggest that this transfer event was more likely to have occurred via homologous recombination within the 3′ region of another gene,vif.Furthermore, phylogenetic analysis strongly suggests that there have been at least two other horizontal transfer events involving these genes: the first between ancestral members of the HIV-1 and HIV-2 groups, and the second between viruses isolated from the vervet and tantalus subspecies of African green monkey (Cercopithecus aethiopsssp)

MODISTools - downloading and processing MODIS remotely sensed data in R

Remotely sensed data – available at medium to high resolution across global spatial and temporal scales – are a valuable resource for ecologists. In particular, products from NASA's MODerate-resolution Imaging Spectroradiometer (MODIS), providing twice-daily global coverage, have been widely used for ecological applications. We present MODISTools, an R package designed to improve the accessing, downloading, and processing of remotely sensed MODIS data. MODISTools automates the process of data downloading and processing from any number of locations, time periods, and MODIS products. This automation reduces the risk of human error, and the researcher effort required compared to manual per-location downloads. The package will be particularly useful for ecological studies that include multiple sites, such as meta-analyses, observation networks, and globally distributed experiments. We give examples of the simple, reproducible workflow that MODISTools provides and of the checks that are carried out in the process. The end product is in a format that is amenable to statistical modeling. We analyzed the relationship between species richness across multiple higher taxa observed at 526 sites in temperate forests and vegetation indices, measures of aboveground net primary productivity. We downloaded MODIS derived vegetation index time series for each location where the species richness had been sampled, and summarized the data into three measures: maximum time-series value, temporal mean, and temporal variability. On average, species richness covaried positively with our vegetation index measures. Different higher taxa show different positive relationships with vegetation indices. Models had high R2 values, suggesting higher taxon identity and a gradient of vegetation index together explain most of the variation in species richness in our data. MODISTools can be used on Windows, Mac, and Linux platforms, and is available from CRAN and GitHub (https://github.com/seantuck12/MODISTools)

Insect occurrence in agricultural land‐uses depends on realized niche and geographic range properties

Geographic range size predicts species' responses to land-use change and intensification, but the reason why is not well established because many correlates of larger geographic ranges, such as realized niche breadth, may mediate species' responses to environmental change. Agricultural land uses (hereafter 'agroecosystems') have warm, dry and more variable microclimates than do cooler and wetter mature forests, so are predicted to filter for species that have warmer, drier and broader fundamental and realized niches. To test these predictions, we estimated species' realized niches, for temperature and precipitation, and geographic range sizes of 764 insect species by matching GBIF occurrence records to global climate layers, and modelled how species presence/absence in mature forest and nearby agroecosystems depend on species' realized niches or geographic ranges. The predicted species niche effects consistently matched the expected direction of microclimatic transition from mature forest to agroecosystems. We found a clear signal that species with preference for warmer and drier climates were more likely to be present in agroecosystems. In addition, the probability that species occurred in different land-use types was predicted better by species' realized niche than their geographic range size. However, niche effects are often context-dependent and varied amongst studies, taxonomic groups and regions used in this analysis: predicting which particular aspects of species' realized niche cause sensitivity to land-use change, and the underpinning mechanisms, remains a major challenge for future research and multiple components of species' realized niches may be important to consider. Using realized niches derived from open-source occurrence records can be a simple and widely applicable tool to help identify when biodiversity responds to the microclimate component of land-use change.CW and ADP were supported by the Natural Environmental Research Council (grants no. NE/L002531/1 and NE/M014533/1, respectively).info:eu-repo/semantics/publishedVersio

Atlas versus range maps: robustness of chorological relationships to distribution data types in European mammals

Aim Chorological relationships describe the patterns of distributional overlap among species. In addition to revealing biogeographical structure, the resulting clusters of species with similar geographical distributions can serve as natural units in conservation planning. Here, we assess the extent to which temporal, methodological and taxonomical differences in the source of species’ distribution data can affect the relationships that are found

A higher-level MRP supertree of placental mammals

BACKGROUND: The higher-level phylogeny of placental mammals has long been a phylogenetic Gordian knot, with disagreement about both the precise contents of, and relationships between, the extant orders. A recent MRP supertree that favoured 'outdated' hypotheses (notably, monophyly of both Artiodactyla and Lipotyphla) has been heavily criticised for including low-quality and redundant data. We apply a stringent data selection protocol designed to minimise these problems to a much-expanded data set of morphological, molecular and combined source trees, to produce a supertree that includes every family of extant placental mammals. RESULTS: The supertree is well-resolved and supports both polyphyly of Lipotyphla and paraphyly of Artiodactyla with respect to Cetacea. The existence of four 'superorders' – Afrotheria, Xenarthra, Laurasiatheria and Euarchontoglires – is also supported. The topology is highly congruent with recent (molecular) phylogenetic analyses of placental mammals, but is considerably more comprehensive, being the first phylogeny to include all 113 extant families without making a priori assumptions of suprafamilial monophyly. Subsidiary analyses reveal that the data selection protocol played a key role in the major changes relative to a previously published higher-level supertree of placentals. CONCLUSION: The supertree should provide a useful framework for hypothesis testing in phylogenetic comparative biology, and supports the idea that biogeography has played a crucial role in the evolution of placental mammals. Our results demonstrate the importance of minimising poor and redundant data when constructing supertrees

Temporal validation plots: quantifying how well correlative species distribution models predict species' range changes over time

1. The use of data documenting how species’ distributions have changed over time is crucial for testing how well correlative species distribution models (SDMs) predict species’ range changes. So far, however, little attention has been given to developing a reliable methodological framework for using such data. 2. We develop a new tool – the temporal validation (TV) plot – specifically aimed at making use of species’ distribution records at two times for a comprehensive assessment of the prediction accuracy of SDMs over time. 3. We extend existing presence–absence calibration plots to make use of distribution records from two time periods. TV plots visualize the agreement between change in modelled probabilities of presence and the probability of observing sites gained or lost between time periods. We then present three measures of prediction accuracy that can be easily calculated from TV plots. 4. We present our methodological framework using a virtual species in a simplified landscape and then provide a real-world case study using distribution records for two species of breeding birds from two time periods of intensive recording effort across Great Britain. 5. Together with existing approaches, TV plots and their associated measures offer a simple tool for testing how well SDMs model species’ observed range changes – perhaps the best way available to assess their ability to predict likely future changes

Capturing complexity: field-testing the use of ‘structure from motion’ derived virtual models to replicate standard measures of reef physical structure

Reef structural complexity provides important refuge habitat for a range of marine organisms, and is a useful indicator of the health and resilience of reefs as a whole. Marine scientists have recently begun to use ‘Structure from Motion’ (SfM) photogrammetry in order to accurately and repeatably capture the 3D structure of physical objects underwater, including reefs. There has however been limited research on the comparability of this new method with existing analogue methods already used widely for measuring and monitoring 3D structure, such as ‘tape and chain rugosity index (RI)’ and graded visual assessments. Our findings show that analogue and SfM RI can be reliably converted over a standard 10-m reef section (SfM RI = 1.348 × chain RI—0.359, r2 = 0.82; and Chain RI = 0.606 × SfM RI + 0.465) for RI values up to 2.0; however, SfM RI values above this number become increasingly divergent from traditional tape and chain measurements. Additionally, we found SfM RI correlates well with visual assessment grades of coral reefs over a 10 × 10 m area (SfM RI = 0.1461 × visual grade + 1.117; r2 = 0.83). The SfM method is shown to be affordable and non-destructive whilst also allowing the data collected to be archival, less biased by the observer, and broader in its scope of applications than standard methods. This work allows researchers to easily transition from analogue to digital structural assessment techniques, facilitating continued long-term monitoring, whilst also improving the quality and additional research value of the data collected

Human Population Density and Extinction Risk in the World's Carnivores

Understanding why some species are at high risk of extinction, while others remain relatively safe, is central to the development of a predictive conservation science. Recent studies have shown that a species' extinction risk may be determined by two types of factors: intrinsic biological traits and exposure to external anthropogenic threats. However, little is known about the relative and interacting effects of intrinsic and external variables on extinction risk. Using phylogenetic comparative methods, we show that extinction risk in the mammal order Carnivora is predicted more strongly by biology than exposure to high-density human populations. However, biology interacts with human population density to determine extinction risk: biological traits explain 80% of variation in risk for carnivore species with high levels of exposure to human populations, compared to 45% for carnivores generally. The results suggest that biology will become a more critical determinant of risk as human populations expand. We demonstrate how a model predicting extinction risk from biology can be combined with projected human population density to identify species likely to move most rapidly towards extinction by the year 2030. African viverrid species are particularly likely to become threatened, even though most are currently considered relatively safe. We suggest that a preemptive approach to species conservation is needed to identify and protect species that may not be threatened at present but may become so in the near future

Annual changes in the Biodiversity Intactness Index in tropical and subtropical forest biomes, 2001–2012

Few biodiversity indicators are available that reflect the state of broad-sense biodiversity—rather than of particular taxa—at fine spatial and temporal resolution. One such indicator, the Biodiversity Intactness Index (BII), estimates how the average abundance of the native terrestrial species in a region compares with their abundances in the absence of pronounced human impacts. We produced annual maps of modelled BII at 30-arc-second resolution (roughly 1 km at the equator) across tropical and subtropical forested biomes, by combining annual data on land use, human population density and road networks, and statistical models of how these variables affect overall abundance and compositional similarity of plants, fungi, invertebrates and vertebrates. Across tropical and subtropical biomes, BII fell by an average of 1.9 percentage points between 2001 and 2012, with 81 countries seeing an average reduction and 43 an average increase; the extent of primary forest fell by 3.9% over the same period. We did not find strong relationships between changes in BII and countries’ rates of economic growth over the same period; however, limitations in mapping BII in plantation forests may hinder our ability to identify these relationships. This is the first time temporal change in BII has been estimated across such a large region

Integrating ecology into macroevolutionary research

On 9 March, over 150 biologists gathered in London for the Centre for Ecology and Evolution spring symposium, ‘Integrating Ecology into Macroevolutionary Research’. The event brought together researchers from London-based institutions alongside others from across the UK, Europe and North America for a day of talks. The meeting highlighted methodological advances and recent analyses of exemplar datasets focusing on the exploration of the role of ecological processes in shaping macroevolutionary patterns