ORCID Profile
0000-0002-1819-3117
Current Organisation
Newcastle University
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Publisher: Springer Science and Business Media LLC
Date: 18-08-2021
Publisher: Wiley
Date: 22-03-2021
DOI: 10.1111/ELE.13732
Publisher: Oxford University Press (OUP)
Date: 06-04-2018
Abstract: Empirical population genetic studies generally rely on s ling subsets of the population(s) of interest and of the nuclear or organellar genome targeted, assuming each is representative of the whole. Violations of these assumptions may impact population-level parameter estimation and lead to spurious inferences. Here, we used targeted capture to sequence the full mitochondrial genome from 123 in iduals of the Galapagos giant tortoise endemic to Pinzón Island (Chelonoidis duncanensis) s led at 2 time points pre- and postbottleneck (circa 1906 and 2014) to explicitly assess differences in ersity estimates and demographic reconstructions based on subsets of the mitochondrial genome versus the full sequences and to evaluate potential biases associated with ersity estimates and demographic reconstructions from postbottlenecked s les alone. Haplotypic ersities were equal between the temporal s les based on the full mitochondrial genome, but single gene estimates suggested either decreases or increases in ersity depending upon the region. Demographic reconstructions based on the full sequence were more similar between the temporal s les than those based on the control region alone, or a subset of 3 regions, where the trends in population size changes shifted in magnitude and direction between the temporal s les. In all cases, the estimated coalescent point was more distant for the historical than contemporary s le. In summary, our results empirically demonstrate the influence of s ling bias when interpreting population genetic patterns and punctuate the need for careful consideration of potentially conflicting evolutionary signal across the mitochondrial genome.
Publisher: Elsevier BV
Date: 02-2016
Publisher: Wiley
Date: 13-08-2018
DOI: 10.1111/EVA.12682
Publisher: American Association for the Advancement of Science (AAAS)
Date: 28-10-2022
Abstract: The deepest marine ecosystem, the hadal zone, hosts endemic bio ersity resulting from geographic isolation and environmental selection pressures. However, the pan-ocean distribution of some fauna challenges the concept that the hadal zone is a series of isolated island-like habitats. Whether this remains true at the population genomic level is untested. We investigated phylogeographic patterns of the hipod, Bathycallisoma schellenbergi , from 12 hadal features across the Pacific, Atlantic, Indian, and Southern oceans and analyzed genome-wide single-nucleotide polymorphism markers and two mitochondrial regions. Despite a cosmopolitan distribution, populations were highly restricted to in idual features with only limited gene flow between topographically connected features. This lack of connectivity suggests that populations are on separate evolutionary trajectories, with evidence of potential cryptic speciation at the Atacama Trench. Together, this global study demonstrates that the shallower ocean floor separating hadal features poses strong barriers to dispersal, driving genetic isolation and creating pockets of ersity to conserve.
Publisher: Oxford University Press (OUP)
Date: 07-07-2018
Abstract: Genome-wide assessments allow for fuller characterization of genetic ersity, finer-scale population delineation, and better detection of demographically significant units to guide conservation compared with those based on "traditional" markers. Galapagos giant tortoises (Chelonoidis spp.) have long provided a case study for how evolutionary genetics may be applied to advance species conservation. Ongoing efforts to bolster tortoise populations, which have declined by 90%, have been informed by analyses of mitochondrial DNA sequence and microsatellite genotypic data, but could benefit from genome-wide markers. Taking this next step, we used double-digest restriction-site associated DNA sequencing to collect genotypic data at >26000 single nucleotide polymorphisms (SNPs) for 117 in iduals representing all recognized extant Galapagos giant tortoise species. We then quantified genetic ersity, population structure, and compared results to estimates from mitochondrial DNA and microsatellite loci. Our analyses detected 12 genetic lineages concordant with the 11 named species as well as previously described structure within one species, C. becki. Furthermore, the SNPs provided increased resolution, detecting admixture in 4 in iduals. SNP-based estimates of ersity and differentiation were significantly correlated with those derived from nuclear microsatellite loci and mitochondrial DNA sequences. The SNP toolkit presented here will serve as a resource for advancing efforts to understand tortoise evolution, species radiations, and aid conservation of the Galapagos tortoise species complex.
Publisher: Springer Science and Business Media LLC
Date: 25-02-2022
DOI: 10.1038/S41437-022-00510-8
Abstract: The Galapagos Archipelago is recognized as a natural laboratory for studying evolutionary processes. San Cristóbal was one of the first islands colonized by tortoises, which radiated from there across the archipelago to inhabit 10 islands. Here, we sequenced the mitochondrial control region from six historical giant tortoises from San Cristóbal (five long deceased in iduals found in a cave and one found alive during an expedition in 1906) and discovered that the five from the cave are from a clade that is distinct among known Galapagos giant tortoises but closely related to the species from Española and Pinta Islands. The haplotype of the in idual collected alive in 1906 is in the same clade as the haplotype in the contemporary population. To search for traces of a second lineage in the contemporary population on San Cristóbal, we closely examined the population by sequencing the mitochondrial control region for 129 in iduals and genotyping 70 of these for both 21 microsatellite loci and ,000 genome-wide single nucleotide polymorphisms [SNPs]. Only a single mitochondrial haplotype was found, with no evidence to suggest substructure based on the nuclear markers. Given the geographic and temporal proximity of the two deeply ergent mitochondrial lineages in the historical s les, they were likely sympatric, raising the possibility that the lineages coexisted. Without the museum s les, this important discovery of an additional lineage of Galapagos giant tortoise would not have been possible, underscoring the value of such collections and providing insights into the early evolution of this iconic radiation.
Publisher: Elsevier BV
Date: 02-2015
DOI: 10.1016/J.TREE.2014.11.009
Abstract: The global loss of bio ersity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.
Publisher: Wiley
Date: 25-09-2021
DOI: 10.1111/MEC.16176
Abstract: Whole genome sequencing provides deep insights into the evolutionary history of a species, including patterns of ersity, signals of selection, and historical demography. When applied to closely related taxa with a wealth of background knowledge, population genomics provides a comparative context for interpreting population genetic summary statistics and comparing empirical results with the expectations of population genetic theory. The Galapagos giant tortoises (Chelonoidis spp.), an iconic rapid and recent radiation, offer such an opportunity. Here, we sequenced whole genomes from three in iduals of the 12 extant lineages of Galapagos giant tortoise and estimate ersity measures and reconstruct changes in coalescent rate over time. We also compare the number of derived alleles in each lineage to infer how synonymous and nonsynonymous mutation accumulation rates correlate with population size and life history traits. Remarkably, we find that patterns of molecular evolution are similar within in iduals of the same lineage, but can differ significantly among lineages, reinforcing the evolutionary distinctiveness of the Galapagos giant tortoise species. Notably, differences in mutation accumulation among lineages do not align with simple population genetic predictions, suggesting that the drivers of purifying selection are more complex than is currently appreciated. By integrating results from earlier population genetic and phylogeographic studies with new findings from the analysis of whole genomes, we provide the most in-depth insights to date on the evolution of Galapagos giant tortoises, and identify discrepancies between expectation from population genetic theory and empirical data that warrant further scrutiny.
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Evelyn Jensen.