Biology subjects

Gaughran, S. J.

Publications and source records attributed to Gaughran, S. J..

4 recordsLinked to original sources

bioRxiv2023

Whole-genome sequencing confirms multiple species of Galapagos giant tortoises

Galapagos giant tortoises are endemic to the Galapagos Archipelago, where they are found in isolated populations. While these populations are widely considered distinguishable in morphology, behavior, and genetics, the recent divergence of these taxa has made their status as species controversial. Here, we apply multispecies coalescent methods for species delimitation to whole genome resequencing data from 38 tortoises across all 13 extant taxa to assess support for delimiting these taxa as species. In contrast to previous studies based solely on divergence time, we find strong evidence to reject the hypothesis that all Galapagos giant tortoises belong to a single species. Instead, a conservative interpretation of model-based and divergence-based results indicates that these taxa form a species complex consisting of a minimum of 9 species, with some analyses supporting as many as 13 species. There is mixed support for the species status of taxa living on the same island, with some methods delimiting them as separate species and others suggesting multiple populations of a single species per island. These results make clear that Galapagos giant tortoise taxa represent different stages in the process of speciation, with some taxa further along in that evolutionary process than others. A better understanding of the more complex parts of that process is urgently needed, given the threatened status of Galapagos giant tortoises. Lay SummarySpecies delimitation is a challenging problem in evolutionary biology, but one that is central to the field. Distinguishing species can affect conservation management practices, from conservation status assessments to strategies for breeding programs. More fundamentally, understanding species boundaries affects our ability to assess biodiversity and to study evolutionary processes. The Galapagos Archipelago presents several radiations of closely related taxa that inspired Charles Darwin to develop his theory of evolution by natural selection and later led to foundational case studies in speciation. The Galapagos giant tortoises were one such inspiration. Nearly two centuries later, there is still an ongoing debate about the taxonomic status of these tortoises, with opinions on their status ranging from barely differentiated populations to separate species. Here, we present the first genomic species delimitation of Galapagos giant tortoises and provide convincing evidence that this group is a complex consisting of between 9 and 13 species. These results provide valuable guidance to conservation stakeholders in the Galapagos, while also adding an important case study to the delimitation of island species.

evolutionary biology↗

bioRxiv2022

Coyotes in New York city carry variable dog genomic ancestry and influence their interactions with humans

Coyotes are ubiquitous on the North American landscape as a result of their recent expansion across the continent. They have been documented in the heart of some of the most urbanized cities, such as Chicago, Los Angeles, and New York City. Here, we explored the genomic composition of coyotes in the New York metropolitan area to investigate if genomic demography and admixture differs from expected for urban-dwelling canids. We identified moderate-to-high estimates of relatedness among coyotes living in Queens and adjacent neighborhoods, suggestive of a relatively small population. Although we found low background levels of domestic dog ancestry across most coyotes in our sample, we identified a male suspected to be a first-generation coyote-dog hybrid, as well as his two putative backcrossed offspring that carried approximately 25% dog ancestry. The male coyote-dog hybrid and one backcrossed offspring each carried two mutations that are known to increase human-directed hypersociability in dogs and gray wolves. An additional, unrelated coyote with little dog ancestry also carries two of these mutations. These genetic patterns suggest that gene flow from domestic dogs may become an increasingly important consideration as coyotes continue to inhabit metropolitan regions.

evolutionary biology↗

bioRxiv2022

A chromosome-length assembly of the Hawaiian Monk seal (Neomonarchus schauinslandi) confirms genomic stability in the Pinnipeds and a prolonged history of "genetic purging"

The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here we report a chromosomal reference assembly for a male animal produced using a variety of methods including linked-read sequencing, Hi-C contiguity mapping, optical genome mapping, and nanopore long read sequencing. The final assembly consisted of 16 autosomes, an X and portions of the Y chromosomes. We compared variants in the reference animals to nine other HMS and to the human reference NA12878 confirming a low level of variation within the species and one-eighth that of the human reference. A lack of variation in several MHC genes was documented suggesting that this species may be at risk for infectious disease. Lastly, the HMS chromosomal assembly confirmed significant synteny with other pinnipeds. This reference should be a useful tool for long-term management of HMS and evolutionary studies of other carnivorans.

genomics↗

bioRxiv2017

Theory, practice, and conservation in the age of genomics: the Galapagos giant tortoise as a case study

High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in non-model species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that represent three species of Galapagos giant tortoises (Chelonoidis spp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNPs, thereby questioning decades of studies in non-model organisms. Using >20,000 genome-wide SNPs from 30 individuals from three Galapagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2-5 individuals, or hundreds of SNPs and 10 individuals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP-based study was likely due to unnatural grouping of individuals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few samples per population, and underscores the importance of sampling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions.\n\n\"Modern molecular techniques provide unprecedented power to understand genetic variation in natural populations. Nevertheless, application of this information requires sound understanding of population genetics theory.\"\n\n- Fred Allendorf (2017, p. 420)

evolutionary biology↗