Biology subjects

White, K. S.

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

5 recordsLinked to original sources

bioRxiv2024

High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution

We report the development and performance of a novel genomics platform, TempO-LINC, for conducting high-throughput transcriptomic analysis on single cells and nuclei. TempO-LINC works by adding cell-identifying molecular barcodes onto highly selective and high-sensitivity gene expression probes within fixed cells, without having to first generate cDNA. Using an instrument-free combinatorial-indexing approach, all probes within the same fixed cell receive an identical barcode, enabling the reconstruction of single-cell gene expression profiles across as few as several hundred cells and up to 100,000+ cells per run. The TempO-LINC approach is easily scalable based on the number of barcodes and rounds of barcoding performed; however, for the experiments reported in this study, the assay utilized over 5.3 million unique barcodes. TempO-LINC has a robust protocol for fixing and banking cells and displays high-sensitivity gene detection from multiple diverse sample types. We show that TempO-LINC has an observed multiplet rate of less than 1.1% and a cell capture rate of [~]50%. Although the assay can accurately profile the whole transcriptome (19,683 human or 21,400 mouse genes), it can be targeted to measure only actionable/informative genes and molecular pathways of interest - thereby reducing sequencing requirements. In this study, we applied TempO-LINC to profile the transcriptomes of 89,722 cells across multiple sample types, including nuclei from mouse lung, kidney and brain tissues. The data demonstrated the ability to identify and annotate at least 50 unique cell populations and positively correlate expression of cell type-specific molecular markers within them. TempO-LINC is a robust new single-cell technology that is ideal for large-scale applications/studies across thousands of samples with high data quality.

genomics↗

bioRxiv2023

Unravelling the complex biogeographic and anthropogenic history of Alaska's mountain goats

AimWe used genetic tools to examine the population structure of mountain goats in Alaska, USA and assessed the demographic history of this species in relation to the natural and anthropogenic forces. LocationAlaska, USA TaxonNorth American mountain goat (Oreamnos americanus) MethodsSamples were collected between 2006 - 2020 from harvested animals and live captures. We genotyped 816 mountain goats at 18 microsatellite loci and identified the number of genetically distinct subpopulations across the state and assessed their genetic diversity. We used Bayesian computation software to investigate the demographic history relative to the known biogeographic history of the state. We also simulated island translocation events and compared simulations to empirical data to address the hypothesis that Baranof Island was a cryptic refugia. ResultsWe showed that Alaska has four genetically distinct subpopulations of mountain goats with some additional genetic structure within those subpopulations. The main split of mountain goats between Southcentral and Southeast Alaska occurred [~]14,000 years ago. Simulations of translocation events largely aligned with the current populations observed today except for Baranof Island which showed greater diversity than the translocation simulation. Main ConclusionsThe distribution and genetic structure of mountain goats in Alaska reflects a combination of natural and anthropogenic forces. A rapid northerly expansion through an ice-free corridor in combination with the isolated nature of the landscape led to low diversity and isolation 14,000 years ago in Southcentral Alaska and higher diversity in Southeast Alaska. Two of the three islands where mountain goat translocations have occurred match genetically with their source population, while Baranof Island appears to have a divergent population, consistent with the hypothesis of an endemic or cryptic population prior to the translocation event. This study highlights the value of considering both the natural and anthropogenic forces when assessing the biogeographic history of a species.

evolutionary biology↗

bioRxiv2022

Quantifying the effects of recent glacial history and future climate change on a unique population of mountain goats

Human disturbance and climate change can impact populations by disrupting movement corridors and reducing important habitat. Characterizing how animals respond to such environmental changes is valuable for conservation as many species, especially habitat specialists, can experience reduced genetic diversity when deleterious habitat change occurs, leading to an increased likelihood of extirpation. Mountain goats (Oreamnos americanus) exemplify this conservation challenge; their geographically isolated habitat can inhibit gene flow, making them susceptible to population declines in the face of anthropogenic-induced landscape change. To facilitate biologically informed population management of mountain goats in Glacier Bay National Park, Alaska, we characterized the fine-scale genetic population structure and examined how future climate change could impact the population density of these mountain goats. We used DNA samples to estimate diversity and depict the genealogical history. Climate response models allowed us to simulate changes to suitable habitat and predict how this might influence future population structure. Our results indicated that three genetically distinct subpopulations exist in Glacier Bay and that the population structure is reflective of the historic landscape patterns. Climate modeling predicted that demographic productivity was likely to be reduced for all subpopulations; additionally, we found that climate change likely degrades the suitability of movement corridors that facilitate gene flow between subpopulations, ultimately increasing the cost of travel. Understanding such fine-scale patterns are key to managing subpopulations, particularly with impending changes to the landscape.

evolutionary biology↗

bioRxiv2018

Extensive field-sampling reveals the uniqueness of a trophy mountain goat population

Collaborations between academic researchers and agencies is crucial for genetic data to have a tangible impact on conservation and wildlife management. Such partnerships are particularly important elusive species where the difficult terrain requires that a significant amount of resources and a combination of methods be used to estimate population parameters needed for conservation. We report and multi-year academic-agency collaboration on the North American mountain goat that used an extensive field sampling of genetic and phenotypic data to determine whether, and to what degree, genetic and phenotypic differences separate an isolated population of mountain goats on the Cleveland Peninsula form those in southeast Alaska. We observed significantly larger horns on the peninsula and the population appears demographically isolated. Isolation-by-distance accompanied by limited migration and low effective population size on the Cleveland Peninsula suggest this population will continue to lose genetic diversity. While the large horns of mountain goats have generated interest in re-opening mountain goat harvest on Cleveland Peninsula, our genetic data suggest this population is vulnerable to demographic and environmental perturbations and is unlikely to support a sustained harvest.

genetics↗

bioRxiv2018

Space, time, and captivity: quantifying factors influencing the microbiome of an alpine ungulate

The community of microorganisms in the gut is affected by host species, diet, and environment and is linked to normal functioning of the host organism. Although the microbiome fluctuates in response to host demands and environmental changes, there are core groups of microorganisms that remain relatively constant throughout the hosts lifetime. Ruminants are mammals that rely on highly specialized digestive and metabolic modifications, including microbiome adaptations, to persist in extreme environments. Here, we assayed the fecal microbiome of four mountain goat (Oreamnos americanus) populations in western North America. We quantified fecal microbiome diversity and composition among groups in the wild and captivity, across populations, and in a single group over time. There were no differences in community evenness or diversity across groups, although we observed a decreasing diversity trend across summer months. Pairwise sample estimates grouped the captive population distinctly from the wild populations, and moderately grouped the southern wild group distinctly from the two northern wild populations. We identified 33 genera modified by captivity, with major differences in key groups associated with cellulose degradation that likely reflect differences in diet. Our findings are consistent with other ruminant studies and provide baseline microbiome data in this enigmatic species, offering valuable insights into the health of wild alpine ungulates.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC=\"FIGDIR/small/475459v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (8K):\norg.highwire.dtl.DTLVardef@1d5256eorg.highwire.dtl.DTLVardef@8c973forg.highwire.dtl.DTLVardef@1db5b0org.highwire.dtl.DTLVardef@835191_HPS_FORMAT_FIGEXP M_FIG C_FIG SummaryThis study characterizes the microbiome of mountain goat (Oreamnos americanus) populations across populations and over summer months; we also quantified the effects of captivity to offer more insights into the health of alpine wildlife.

microbiology↗