Historical sampling reveals dramatic demographic changes in western gorilla populations

Background: Today many large mammals live in small, fragmented populations, but it is often unclear whether this subdivision is the result of long-term or recent events. Demographic modeling using genetic data can estimate changes in long-term population sizes while temporal sampling provides a way to compare genetic variation present today with that sampled in the past. In order to better understand the dynamics associated with the divergences of great ape populations, these analytical approaches were applied to western gorillas (Gorilla gorilla) and in particular to the isolated and Critically Endangered Cross River gorilla subspecies (G. g. diehli).Results: We used microsatellite genotypes from museum specimens and contemporary samples of Cross River gorillas to infer both the long-term and recent population history. We find that Cross River gorillas diverged from the ancestral western gorilla population ~17,800 years ago (95% HDI: 760, 63,245 years). However, gene flow ceased only ~420 years ago (95% HDI: 200, 16,256 years), followed by a bottleneck beginning ~320 years ago (95% HDI: 200, 2,825 years) that caused a 60-fold decrease in the effective population size of Cross River gorillas. Direct comparison of heterozygosity estimates from museum and contemporary samples suggests a loss of genetic variation over the last 100 years.Conclusions: The composite history of western gorillas could plausibly be explained by climatic oscillations inducing environmental changes in western equatorial Africa that would have allowed gorilla populations to expand over time but ultimately isolate the Cross River gorillas, which thereafter exhibited a dramatic population size reduction. The recent decrease in the Cross River population is accordingly most likely attributable to increasing anthropogenic pressure over the last several hundred years. Isolation of diverging populations with prolonged concomitant gene flow, but not secondary admixture, appears to be a typical characteristic of the population histories of African great apes, including gorillas, chimpanzees and bonobos

Assessing Host-Virus Codivergence for Close Relatives of Merkel Cell Polyomavirus Infecting African Great Apes

It has long been hypothesized that polyomaviruses (PyV; family Polyomaviridae) codiverged with their animal hosts. In contrast, recent analyses suggested that codivergence may only marginally influence the evolution of PyV. We reassess this question by focusing on a single lineage of PyV infecting hominine hosts, the Merkel cell polyomavirus (MCPyV) lineage. By characterizing the genetic diversity of these viruses in seven African great ape taxa, we show that they exhibit very strong host specificity. Reconciliation analyses identify more codivergence than noncodivergence events. In addition, we find that a number of host and PyV divergence events are synchronous. Collectively, our results support codivergence as the dominant process at play during the evolution of the MCPyV lineage. More generally, our results add to the growing body of evidence suggesting an ancient and stable association of PyV and their animal hosts

Predicting range shifts of African apes under global change scenarios

Aim: Modelling African great ape distribution has until now focused on current or past conditions, while future scenarios remain scarcely explored. Using an ensemble forecasting approach, we predicted changes in taxon-specific distribution under future scenarios of climate, land use and human populations for (1) areas outside protected areas (PAs) only (assuming complete management effectiveness of PAs), (2) the entire study region and (3) interspecies range overlap. Location: Tropical Africa. Methods: We compiled occurrence data (n = 5,203) on African apes from the IUCN A.P.E.S. database and extracted relevant climate-, habitat- and human-related predictors representing current and future (2050) conditions to predict taxon-specific range change under a best- and a worst-case scenario, using ensemble forecasting. Results The predictive performance of the models varied across taxa. Synergistic interactions between predictors are shaping African ape distribution, particularly human-related variables. On average across taxa, a range decline of 50% is expected outside PAs under the best scenario if no dispersal occurs (61% in worst scenario). Otherwise, an 85% range reduction is predicted to occur across study regions (94% worst). However, range gains are predicted outside PAs if dispersal occurs (52% best, 21% worst), with a slight increase in gains expected across study regions (66% best, 24% worst). Moreover, more than half of range losses and gains are predicted to occur outside PAs where interspecific ranges overlap. Main Conclusions: Massive range decline is expected by 2050, but range gain is uncertain as African apes will not be able to occupy these new areas immediately due to their limited dispersal capacity, migration lag and ecological constraints. Given that most future range changes are predicted outside PAs, Africa's current PA network is likely to be insufficient for preserving suitable habitats and maintaining connected ape populations. Thus, conservation planners urgently need to integrate land use planning and climate change mitigation measures at all decision-making levels both in range countries and abroad

Contrasting and congruent patterns of genetic structuring in two Microtus vole species using museum specimens

The common vole (Microtus arvalis) and the field vole (Microtus agrestis) are morphologically similar species but are ecological distinctive and differ in the details of their evolutionary history as revealed by mitochondrial DNA (mtDNA). The aim of this study is to describe patterns of genetic variability using microsatellite markers in populations of the common and field vole in Poland using museum specimens, to assess the degree of congruence with mtDNA variation and thereby determine the factors that influence current patterns of gene flow. We genotyped 190 individuals of the common vole at 11 loci and 190 individuals of the field vole at 13 loci. Overall differentiation based on F ST was higher for the common vole than in the field vole. We detected a significant isolation by distance pattern for both species. Bayesian analysis in STRUCTURE identified Eastern and Western geographic groups in Poland based on microsatellites for both species. The location of river barriers is likely to be the main factor in these partitions. The eastern-western subdivision with microsatellites does not coincide with the distribution of mtDNA lineages for either species. Unlike previous studies in the common and field vole elsewhere in Europe, we found no evidence of reproductive isolation between the mtDNA lineages of these species at their contact zones in Poland. This study highlights the different roles of evolutionary history and landscape in shaping contemporary genetic structure in voles in Poland

Predicting range shifts of African apes under global change scenarios

Aim: Modelling African great ape distribution has until now focused on current or past conditions, while future scenarios remain scarcely explored. Using an ensemble forecasting approach, we predicted changes in taxon-specific distribution under future scenarios of climate, land use and human populations for (1) areas outside protected areas (PAs) only (assuming complete management effectiveness of PAs), (2) the entire study region and (3) interspecies range overlap. Location: Tropical Africa. Methods: We compiled occurrence data (n = 5,203) on African apes from the IUCN A.P.E.S. database and extracted relevant climate-, habitat- and human-related predictors representing current and future (2050) conditions to predict taxon-specific range change under a best- and a worst-case scenario, using ensemble forecasting. Results: The predictive performance of the models varied across taxa. Synergistic interactions between predictors are shaping African ape distribution, particularly human-related variables. On average across taxa, a range decline of 50% is expected outside PAs under the best scenario if no dispersal occurs (61% in worst scenario). Otherwise, an 85% range reduction is predicted to occur across study regions (94% worst). However, range gains are predicted outside PAs if dispersal occurs (52% best, 21% worst), with a slight increase in gains expected across study regions (66% best, 24% worst). Moreover, more than half of range losses and gains are predicted to occur outside PAs where interspecific ranges overlap. Main Conclusions: Massive range decline is expected by 2050, but range gain is uncertain as African apes will not be able to occupy these new areas immediately due to their limited dispersal capacity, migration lag and ecological constraints. Given that most future range changes are predicted outside PAs, Africa's current PA network is likely to be insufficient for preserving suitable habitats and maintaining connected ape populations. Thus, conservation planners urgently need to integrate land use planning and climate change mitigation measures at all decision-making levels both in range countries and abroad

Upward Altitudinal Shifts in Habitat Suitability of Mountain Vipers since the Last Glacial Maximum

We determined the effects of past and future climate changes on the distribution of the Montivipera raddei species complex (MRC) that contains rare and endangered viper species limited to Iran, Turkey and Armenia. We also investigated the current distribution of MRC to locate unidentified isolated populations as well as to evaluate the effectiveness of the current network of protected areas for their conservation. Present distribution of MRC was modeled based on ecological variables and model performance was evaluated by field visits. Some individuals at the newly identified populations showed uncommon morphological characteristics. The distribution map of MRC derived through modeling was then compared with the distribution of protected areas in the region. We estimated the effectiveness of the current protected area network to be 10%, which would be sufficient for conserving this group of species, provided adequate management policies and practices are employed. We further modeled the distribution of MRC in the past (21,000 years ago) and under two scenarios in the future (to 2070). These models indicated that climatic changes probably have been responsible for an upward shift in suitable habitats of MRC since the Last Glacial Maximum, leading to isolation of allopatric populations. Distribution will probably become much more restricted in the future as a result of the current rate of global warming. We conclude that climate change most likely played a major role in determining the distribution pattern of MRC, restricting allopatric populations to mountaintops due to habitat alterations. This long-term isolation has facilitated unique local adaptations among MRC populations, which requires further investigation. The suitable habitat patches identified through modeling constitute optimized solutions for inclusion in the network of protected areas in the region

Comparative population genetic structure of the endangered southern brown bandicoot, Isoodon obesulus, in fragmented landscapes of Southern Australia

Genetic connectivity is a key factor for maintaining the persistence of populations in fragmented landscapes. In highly modified landscapes such us peri-urban areas, organisms' dispersal among fragmented habitat patches can be reduced due to the surrounding matrix, leading to subsequent decreased gene flow and increased potential extinction risk in isolated sub-populations. However, few studies have compared within species how dispersal/gene flow varies between regions and among different forms of matrix that might be encountered. In the current study, we investigated gene flow and dispersal in an endangered marsupial, the southern brown bandicoot (Isoodon obesulus) in a heavily modified peri-urban landscape in South Australia, Australia. We used 14 microsatellite markers to genotype 254 individuals which were sampled from 15 sites. Analyses revealed significant genetic structure. Our analyses also indicated that dispersal was mostly limited to neighbouring sites. Comparisons of these results with analyses of a different population of the same species revealed that gene flow/dispersal was more limited in this peri-urban landscape than in a pine plantation landscape approximately 400 km to the south-east. These findings increase our understanding of how the nature of fragmentation can lead to profound differences in levels of genetic connectivity among populations of the same species.You Li, Steven J.B. Cooper, Melanie L. Lancaster, Jasmin G. Packer, Susan M. Carthe