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Abstract: Genetic analyses of feline immunodeficiency viruses provide significant insights on the worldwide distribution and evolutionary history of this emerging pathogen. Large-scale screening of over 3000 samples from all species of Felidae indicates that at least some individuals from most species possess antibodies that cross react to FIV. Phylogenetic analyses of genetic variation in the pol-RT gene demonstrate that FIV lineages are species-specific and suggest that there has been a prolonged period of viral-host co-evolution. The clinical effects of FIV specific to species other than domestic cat are controversial. Comparative genomic analyses of all full-length FIV genomes confirmed that FIV is host specific. Recently sequenced lion subtype E is marginally more similar to Pallas cat FIV though env is more similar to that of domestic cat FIV, indicating a possible recombination between two divergent strains in the wild. Here we review global patterns of FIV seroprevalence and endemnicity, assess genetic differences within and between species-specific FIV strains, and interpret these with patterns of felid speciation to propose an ancestral origin of FIV in Africa followed by interspecies transmission and global dissemination to Eurasia and the Americas. Continued comparative genomic analyses of full-length FIV from all seropositive animals, along with whole genome sequence of host species, will greatly advance our understanding of the role of recombination, selection and adaptation in retroviral emergence. [Copyright &y& Elsevier]

The endangered Black-faced Spoonbill Platalea minor has experienced drastic reductions in population size, geographic distribution, and habitat availability throughout East Asia. In the present study, we examined population genetic structure and genetic diversity of Black-faced Spoonbills inhabiting five sites off the west coast of South Korea encompassing a few of its major breeding sites. Ten microsatellite loci and the mitochondrial sequence were used to assess patterns of genetic variation based on 63 individuals. Three ND2 haplotypes were found among 61 individuals; the remaining two were identified as Eurasian Spoonbills, revealing an unexpected hybridization between these two species having different ecological niches in South Korea—the Eurasian Spoonbill overwinters in inland areas, whereas the Black-faced Spoonbill inhabits coastal areas during the summer. Analyses of microsatellite variation revealed no discrete population structure among the five breeding sites but very weak genetic differentiation among geographically distant regions. Assignment tests identified several possible migrants among sites. Our findings suggested that Black-faced Spoonbills from the five breeding sites could be managed as a single population and highlighted the importance of conserving the populations from Maedo, Suhaam, and Namdong reservoir, which are geographically close and have retained high levels of genetic diversity and large populations. [ABSTRACT FROM AUTHOR]

Accurate taxonomic classification of wildlife species is crucial for guiding biological research and for developing effective management and conservation programs. The taxonomic status of Eurasian badgers from South Korea remains poorly resolved. Here we assessed the phylogenetic relationships and genetic variation of Eurasia badgers using partial mitochondrial fragments to elucidate the evolutionary history and taxonomic status of badgers from the Korean Peninsula. Forty-eight unique haplotypes from 125 individuals were observed. Phylogenetic reconstructions and reduced median networks indicate that Eurasian badgers consisted of four geographic clades (Japan, Eastern Eurasia, Western Eurasia, and Caucasus) with a relatively weak split observed within Eastern Eurasia. Estimated divergence time between the Japanese and Eastern Eurasian clades, including the Korean population, was 467,100 years (69,200–1,085,500 years). The results of this study support the hypothesis that the Japanese badger migrated from the Eurasian continent over the Korea-Japan land bridge and that the Korean Peninsula was an important refugia during the Pleistocene. Our study confirmed that the South Korean badger, Meles meles , belongs to the Eastern Eurasian clade. Based on these results and those of previous studies, we recommend that the scientific name of the Korean badger be changed from M. meles to Meles leucurus (Asian badger). [ABSTRACT FROM AUTHOR]

As a well-studied felid with limited genetic diversity, the cheetah ( Acinonyx jubatus ) has shaped much of the scientific debate surrounding inbreeding depression. The species survived a population bottleneck ~ 12,000 years ago and was extirpated from > 75% of its historical range in the last century. Modern cheetahs produce poor-quality semen, a presumed manifestation of inbreeding depression. Within Felidae, a positive association between genetic diversity and semen quality is well supported by pedigree data and inter-species comparisons. However, this relationship has never been examined among individual cheetahs. Furthermore, whether ongoing population declines are exacerbating inbreeding depression in wild or captive cheetah populations is unknown. Using 12 microsatellite markers, we evaluated the relationship between heterozygosity and reproductive traits among wild ( n = 54) and captive ( n = 43) male cheetahs born from 1976–2007. We tested the hypotheses that genetic diversity has declined over the last ~ 30 years and is positively correlated with semen quality/breeding success in the cheetah. Findings revealed that genetic diversity has decreased in the wild, but not captive, population. Unexpectedly, heterozygosity was lower in proven versus unproven breeders and did not correlate with semen quality. A small proportion of all males (< 10%) produced relatively high quality ejaculates, with sperm traits similar to those of non-inbred felid species. These data suggest a more complex relationship between inbreeding and male cheetah reproductive traits than previously appreciated. Intensive management of captive cheetahs appears to be minimizing inbreeding, whereas the continued erosion of genetic diversity in wild males is of conservation concern. [ABSTRACT FROM AUTHOR]

Abstract: Estimates of survival for the young of a species are critical for population models. These models can often be improved by determining the effects of management actions and population abundance on this demographic parameter. We used multiple sources of data collected during 1982–2008 and a live-recapture dead-recovery modeling framework to estimate and model survival of Florida panther (Puma concolor coryi) kittens (age 0–1year). Overall, annual survival of Florida panther kittens was 0.323±0.071 (SE), which was lower than estimates used in previous population models. In 1995, female pumas from Texas (P. c. stanleyana) were released into occupied panther range as part of an intentional introgression program to restore genetic variability. We found that kitten survival generally increased with degree of admixture: F1 admixed and backcrossed to Texas kittens survived better than canonical Florida panther and backcrossed to canonical kittens. Average heterozygosity positively influenced kitten and older panther survival, whereas index of panther abundance negatively influenced kitten survival. Our results provide strong evidence for the positive population-level impact of genetic introgression on Florida panthers. Our approach to integrate data from multiple sources was effective at improving robustness as well as precision of estimates of Florida panther kitten survival, and can be useful in estimating vital rates for other elusive species with sparse data. [ABSTRACT FROM AUTHOR]

Abstract: Since 1994 wild vicuñas have been captured and shorn for their wool, yet, there remains a noticeable lack of data regarding the possible influence of capture and shearing upon vicuña biology. Therefore, we assessed post-capture group composition, genetic relatedness, and paternity among animals that were captured for live shearing and release. We captured twenty-six groups (134 animals) on the Chilean Altiplano. Seventy-three percent of Male Groups (designated prior to chase) contained exclusively adult males upon capture, whereas remaining “Male Groups” contained crias and/or adult females and crias. Forty-seven percent of Family Groups (designated prior to chase) contained 1 adult male, adult females, and the number of crias≤the number of adult females. Remaining Family Groups contained no or multiple adult males, and more crias than adult females. Average relatedness among all vicuñas was −0.007. Paternity analysis revealed that 35% of crias were captured with their biological mother and that only 1 cria was captured with both biological parents. Based on previous observations of group composition in the wild, animals from different groups may separate and/or mix during the chasing stage. Improvement of the chasing technique and instituting a post-capture monitoring program may aid in the detection of medium- and long-term impacts regarding group stability, cria survival, and ultimately wool production. [Copyright &y& Elsevier]

Abstract: Translocation of cymtDNA into the nuclear genome, also referred to as numt, has been reported in many species, including several closely related to the domestic cat (Felis catus). We describe the recent transposition of 12,536 bp of the 17 kb mitochondrial genome into the nucleus of the common ancestor of the five Panthera genus species: tiger, P. tigris; snow leopard, P. uncia; jaguar, P. onca; leopard, P. pardus; and lion, P. leo. This nuclear integration, representing 74% of the mitochondrial genome, is one of the largest to be reported in eukaryotes. The Panthera genus numt differs from the numt previously described in the Felis genus in: (1) chromosomal location (F2—telomeric region vs. D2—centromeric region), (2) gene make up (from the ND5 to the ATP8 vs. from the CR to the COII), (3) size (12.5 vs. 7.9 kb), and (4) structure (single monomer vs. tandemly repeated in Felis). These distinctions indicate that the origin of this large numt fragment in the nuclear genome of the Panthera species is an independent insertion from that of the domestic cat lineage, which has been further supported by phylogenetic analyses. The tiger cymtDNA shared around 90% sequence identity with the homologous numt sequence, suggesting an origin for the Panthera numt at around 3.5 million years ago, prior to the radiation of the five extant Panthera species. [Copyright &y& Elsevier]