Biology subjects

Wasser, S. K.

Publications and source records attributed to Wasser, S. K..

5 recordsLinked to original sources

bioRxiv2025

Elephants inhabiting two forested sites in western Uganda exhibit contrasting patterns of species identity, density, and history of hybridization

Elephant populations across much of Africa face severe rates of decline due to poaching and habitat loss. The recent decision by the International Union for the Conservation of Nature (IUCN) to separately list African forest (Loxodonta cyclotis) and savanna (L. africana) elephants on the IUCN Red List both highlights the different threats of extinction faced by these two species and emphasizes the need for genetic data to classify taxonomically undefined populations across the continent. This includes western Uganda - a region that harbors the largest known modern hybrid zone between the two species. We combined a new high-throughput amplicon sequencing (HTAS) approach with fecal DNA-based Capture Mark Recapture (CMR) analysis to infer the population sizes and species compositions of elephants living in two forests. We demonstrate that Kibale National Park hosts a relatively large elephant population (573 individuals, 95% CI: 410 to 916; 0.72 elephants/km2) composed primarily of hybrids (81.5%) and savanna elephants (17.7%), while Bwindi Impenetrable National Park hosts a smaller population (96 individuals, 95% CI: 64 to 145; 0.29 elephants/km2) composed of forest elephants (86.8%) and hybrids (13.2%). We then sequenced maternally inherited (mtDNA) and paternally inherited (AMELY) genetic markers and found that the two parks populations exhibit different patterns of sex-linked genetic variation. The contrasting patterns of species identity and genetic variation between these parks demonstrate different histories of hybridization and highlight the importance of site-specific monitoring where elephants are taxonomically undefined.

ecology↗

bioRxiv2023

Large-scale population genomics of Malayan pangolins reveals deep diversification and a new species

BackgroundArchipelagos and oceanic islands often present high percentage of endemism due to rapid speciation. The Malayan pangolin is a species distributing at both mainland (southern Yunnan, China) and oceanic islands via Malayan peninsula, which may result in deep differentiation among populations. In-depth investigation of population structure and genetic consequences for such species is of vital importance for their protection and conservation, practically for the critically endangered Malayan pangolin that is suffering from poaching, illegal trade, and habitat loss. ResultsHere we carried out a large-scale population genomic analysis for Malayan pangolins, and revealed three highly distinct genetic populations in this species, two of which are now being reported for the first time. Based on multiple lines of genomic and morphological evidence, we postulate the existence of a new pangolin species (Manis_1). Genetic diversity and recent inbreeding were both at a moderate level for both Malayan pangolins and Manis_1, but mainland Malayan pangolins presented relatively lower genetic diversity, higher inbreeding and fitness cost than island populations. ConclusionsWe found extremely deep and graded differentiation in Malayan pangolins, with two newly discovered genetic populations and a new pangolin species that is closely related to the Philippine pangolin than the typical Malayan pangolin, but a distant relative of the Indian pangolin. Anthropogenic factors did not significantly weaken the basis of genetic sustainability for Malayan pangolins, but mainland Malayan pangolins should be paid more attention for conservation due to higher genetic risks than island populations.

genomics↗

bioRxiv2020

Shift of maternal gut microbiome of Tibetan antelope (Pantholops hodgsonii) during the perinatal period

The maternal gut microbiome can influence and be affected by the substantial physiological changes taking place during the perinatal period. However, little information is known about the changes in the maternal gut microbiome during this period. Tibetan antelope (Pantholops hodgsonii) provide a unique system to address this issue because their summer migration cycle is synchronized with the perinatal period. We used 16S rRNA gene sequencing to generate gut microbiome profiles using fecal samples collected from female migratory Tibetan antelope. We then correlated microbiome diversity with fecal hormone metabolite concentrations of glucocorticoids (GCs) and triiodothyronine (T3) extracted from the same fecal samples. The maternal gut microbiome of Tibetan antelope was dominated by Firmicutes and Bacteroidetes. There was a clear separation in gut microbial composition by female reproductive states based on both hierarchical clustering and PCoA analyses. The shift in the maternal gut microbiome likely reflects the metabolic and immune system dynamics during the perinatal period. Overall, the microbiome diversity was higher in the late pregnancy compared to the postpartum period. The negative association between T3 and microbiome diversity may be moderated by the shift of reproductive states since the correlations disappeared when considering each reproductive state separately. Integrating the microbiome dimension, migration pattern and reproduction may have direct conservation implications as by establishing a baseline of the physiological changes during the migration/perinatal period, we can have a better understanding of the impacts of increasing human activities on the Tibetan Plateau on the reproductive health of Tibetan antelope.

zoology↗

bioRxiv2019

Prey partitioning between sympatric canid species revealed by DNA metabarcoding

The recovery of apex predators relies on restoring the full suite of trophic interactions within the ecosystem. Diet analysis with DNA metabarcoding technology can help deliver insights into these trophic interactions with fine-grained resolution. The recovery of wolves in Washington state offers an excellent case to study the trophic cascade impacts of the apex predators on the ecosystem and explore prey partitioning between sympatric canid species. We used DNA metabarcoding technology on scats to characterize the diet composition and its spatiotemporal variations of wolves and coyotes and quantified the diet niche overlap between these two canid species in northeastern Washington. In total, 19 different prey taxa were detected. Frequency of occurrence data showed that wolves primarily preyed upon deer (Odocoileus sp.) (47.47%) and moose (Alces alces) (42.42%). Coyotes also consumed moose (30.10%) and deer (21.36%), but snowshoe hares (Lepus americanus) were the most common prey (61.17%) in their diet. There were significant spatial variations in the wolf diet composition (p = 0.001) with wolves in the Dirty Shirt pack range consuming more moose (71.43%). Coyotes showed significant spatial and temporal dietary variations (season: p = 0.037; pack: p = 0.003; pack:season p = 0.043). Our data suggested that coyotes use ungulate carrion subsidies from wolves as food resources. DNA metabarcoding with fecal DNA provides an excellent noninvasive tool to characterize diet profile at the fine-grained level and can be applied to other carnivore species to help understand the impacts of recovery of apex predators on the local ecosystems.

ecology↗

bioRxiv2019

GENETIC RESILIENCE OF A ONCE ENDANGERED SPECIES, TIBETAN ANTELOPE (Pantholops hodgsonii)

Population reduction is generally assumed to reduce the populations genetic diversity and hence its ability to adapt to environmental change. However, if life history traits that promote gene flow buffer populations from such impacts, conservation efforts should aim to maintain those traits in vulnerable species. Tibetan antelope (Pantholops hodgsonii) has experienced population reduction by 95% due to poaching during the 20th century. We hypothesize that opportunities for gene flow provided by their sex-specific migration buffered their genetic diversity from the poaching impacts. We measured the mtDNA (control region, CR) and nuDNA (microsatellites or STRs) diversity, population differentiation, along with the change in effective population size (pre-poaching era vs. post-poaching era) and tested for a genetic bottleneck. Our results showed that Tibetan antelope maintained considerable genetic diversity in both mtDNA CR and STR markers (Hd = 0.9970 and Hobs = 0.8446, respectively), despite a marked reduction in post-poaching effective population size 368.9 (95% CI of 249.3 - 660.6) compared to the pre-poaching average (4.93x103 - 4.17x104). Post-poached populations also had low population structure and showed no evidence of a genetic bottleneck. Pairwise Fst values using CR haplotype frequencies were higher than those using STR allele frequencies, suggesting different degrees of gene flow mediated by females and males. This study suggests that the Tibetan antelopes sex-specific migration buffered their loss of genetic diversity in the face of severe demographic decline. These findings highlight the importance of recognizing the traits likely to maintain genetic diversity and promoting conservation efforts that allow them to be exercised. For Tibetan antelope, this requires assuring that their migration routes remain unobstructed by growing human disturbances while continuing to enforce anti-poaching law enforcement efforts.

genetics↗