Diachronic monitoring of snow leopards at Sarychat-Ertash State Reserve (Kyrgyzstan) through scat genotyping: a pilot study

Snow leopards (Panthera uncia) are a keystone species of Central Asia’s high mountain ecosystem. The species is listed as vulnerable and is elusive, preventing accurate population assessments that could inform conservation actions. Non-invasive genetic monitoring conducted by citizen scientists offers avenues to provide key data on this species that would otherwise be inaccessible. From 2011 to 2015, OSI-Panthera citizen science expeditions tracked signs of presence of snow leopards along transects in the main valleys and crests of the Sarychat-Ertash State Reserve (Kyrgyzstan). Scat samples were genotyped at seven autosomal microsatellite loci and at a X/Y locus for sex identification, which allowed estimating a minimum of 11 individuals present in the reserve from 2011 to 2015. The genetic recapture of 7 of these individuals enabled diachronic monitoring, providing indications of individuals’ movements throughout the reserve. We found putative family relationships between several individuals. Our results demonstrate the potential of this citizen science program to get a precise description of a snow leopard population through time.

Spatial Genetic Structure of Long-tailed Ducks (Clangula hyemalis) among Alaskan, Canadian, and Russian Breeding Populations + Supplementary Appendix Tables S1 and S2 (See Article Tools)

<p class="Pa5" style="text-align: justify; text-justify: inter-ideograph;"><span style="font-size: 10.0pt; color: #221e1f;">Arctic ecosystems are changing at an unprecedented rate. How Arctic species are able to respond to such environmental change is partially dependent on the connections between local and broadly distributed populations. For species like the Long-tailed Duck (<em>Clangula hyemalis</em>), we have limited telemetry and band-recovery information from which to infer population structure and migratory connectivity; however, genetic analyses can offer additional insights. To examine population structure in the Long-tailed Duck, we characterized variation at mtDNA control region and microsatellite loci among four breeding areas in Alaska, Canada, and Russia. We observed significant differences in the variance of mtDNA haplotype frequencies between the Yukon-Kuskokwim Delta (YKD) and the three Arctic locations (Arctic Coastal Plain in Alaska, eastern Siberia, and central Canadian Arctic). However, like most sea duck genetic assessments, our study found no evidence of population structure based on autosomal microsatellite loci. Long-tailed Ducks use multiple wintering areas where pair formation occurs with some populations using both the Pacific and Atlantic Oceans. This situation provides a greater opportunity for admixture across breeding locales, which would likely homogenize the nuclear genome even in the presence of female philopatry. The observed mtDNA differentiation was largely due to the presence of two divergent clades: (A) a clade showing signs of admixture among all breeding locales and (B) a clade primarily composed of YKD samples. We hypothesize that the pattern of mtDNA differentiation reflects some degree of philopatry to the YKD and isolation of two refugial populations with subsequent expansion and admixture. We recommend additional genetic assessments throughout the circumpolar range of Long-tailed Ducks to further quantify aspects of genetic diversity and migratory connectivity in this species.</span></p>

Investigation of allelic polymorphism of 15 autosomal microsatellite loci, forming the multiplex individualized system for pcr-amplification "AmpFISTR®Identifiler" ("Applied Biosystems", USA), in mixed populations of inhabitants of some regions of Ukraine

We present data about an investigation of allelic polymorphism of 15 autosomal microsatellite, making up an individualizing panel that is widely used in forensic medical molecular-genetic researches in Ukraine.

The genetic structure of the Lithuanian wolf population

Lithuanian wolves form part of the larger Baltic population, the distribution of which is continuous across the region. In this paper, we evaluate the genetic diversity of the Lithuanian wolf population using mitochondrial DNA analysis and 29 autosomal microsatellite loci. Analysis of the mtDNA control region (647 bp) revealed 5 haplotypes distributed among 29 individuals and high haplotype diversity (0.658). Two haplotypes were distributed across the country, whilst the others were restricted to eastern Lithuania. Analysis of microsatellites revealed high heterozygosity (HE=0.709) and no evidence for a recent bottleneck. Using detection of first generation migrants, four individuals appeared to assign better with populations genetically differentiated from those resident in Lithuania. These immigrants were males carrying rare mitochondrial haplotypes and were encountered in the eastern part of the country, this indicates that Lithuania is subject to immigration from differentiated populations. Additionally, we did not detect any signs of recent hybridisation with dogs.

Rejection of a serial founder effects model of genetic and linguistic coevolution

Recent genetic studies attribute the negative correlation between population genetic diversity and distance from Africa to a serial founder effects (SFE) evolutionary process. A recent linguistic study concluded that a similar decay in phoneme inventories in human languages was also the product of the SFE process. However, the SFE process makes additional predictions for patterns of neutral genetic diversity, both within and between groups, that have not yet been tested on phonemic data. In this study, we describe these predictions and test them on linguistic and genetic samples. The linguistic sample consists of 725 widespread languages, which together contain 908 distinct phonemes. The genetic sample consists of 614 autosomal microsatellite loci in 100 widespread populations. All aspects of the genetic pattern are consistent with the predictions of SFE. In contrast, most of the predictions of SFE are violated for the phonemic data. We show that phoneme inventories provide information about recent contacts between languages. However, because phonemes change rapidly, they cannot provide information about more ancient evolutionary processes.

Sensitive males: inbreeding depression in an endangered bird

Attempts to conserve threatened species by establishing new populations via reintroduction are controversial. Theory predicts that genetic bottlenecks result in increased mating between relatives and inbreeding depression. However, few studies of wild sourced reintroductions have carefully examined these genetic consequences. Our study assesses inbreeding and inbreeding depression in a free-living reintroduced population of an endangered New Zealand bird, the hihi ( Notiomystis cincta ). Using molecular sexing and marker-based inbreeding coefficients estimated from 19 autosomal microsatellite loci, we show that (i) inbreeding depresses offspring survival, (ii) male embryos are more inbred on average than female embryos, (iii) the effect of inbreeding depression is male-biased and (iv) this population has a substantial genetic load. Male susceptibility to inbreeding during embryo and nestling development may be due to size dimorphism, resulting in faster growth rates and more stressful development for male embryos and nestlings compared with females. This work highlights the effects of inbreeding at early life-history stages and the repercussions for the long-term population viability of threatened species.

Multilocus genotypes from Charles Darwin's finches: biodiversity lost since the voyage of the Beagle

Genetic analysis of museum specimens offers a direct window into a past that can predate the loss of extinct forms. We genotyped 18 Galápagos finches collected by Charles Darwin and companions during the voyage of the Beagle in 1835, and 22 specimens collected in 1901. Our goals were to determine if significant genetic diversity has been lost since the Beagle voyage and to determine the genetic source of specimens for which the collection locale was not recorded. Using ‘ancient’ DNA techniques, we quantified variation at 14 autosomal microsatellite loci. Assignment tests showed several museum specimens genetically matched recently field-sampled birds from their island of origin. Some were misclassified or were difficult to classify. Darwin's exceptionally large ground finches ( Geospiza magnirostris ) from Floreana and San Cristóbal were genetically distinct from several other currently existing populations. Sharp-beaked ground finches ( Geospiza difficilis ) from Floreana and Isabela were also genetically distinct. These four populations are currently extinct, yet they were more genetically distinct from congeners than many other species of Darwin's finches are from each other. We conclude that a significant amount of the finch biodiversity observed and collected by Darwin has been lost since the voyage of the Beagle .