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Temporal mitogenomics of the Galapagos giant tortoise from Pinzón reveals potential biases in population genetic inference

Lookup NU author(s): Dr Evelyn JensenORCiD

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Abstract

© The American Genetic Association 2018. All rights reserved.Empirical population genetic studies generally rely on sampling 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 individuals of the Galapagos giant tortoise endemic to Pinzón Island (Chelonoidis duncanensis) sampled at 2 time points pre- and postbottleneck (circa 1906 and 2014) to explicitly assess differences in diversity estimates and demographic reconstructions based on subsets of the mitochondrial genome versus the full sequences and to evaluate potential biases associated with diversity estimates and demographic reconstructions from postbottlenecked samples alone. Haplotypic diversities were equal between the temporal samples based on the full mitochondrial genome, but single gene estimates suggested either decreases or increases in diversity depending upon the region. Demographic reconstructions based on the full sequence were more similar between the temporal samples 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 samples. In all cases, the estimated coalescent point was more distant for the historical than contemporary sample. In summary, our results empirically demonstrate the influence of sampling bias when interpreting population genetic patterns and punctuate the need for careful consideration of potentially conflicting evolutionary signal across the mitochondrial genome.

Publication metadata

Author(s): Jensen EL, Miller JM, Edwards DL, Garrick RC, Tapia W, Caccone A, Russello MA

Publication type: Article

Publication status: Published

Journal: Journal of Heredity

Year: 2018

Volume: 109

Issue: 6

Pages: 631-640

Print publication date: 01/09/2018

Online publication date: 06/04/2018

Acceptance date: 03/04/2018

ISSN (print): 0022-1503

ISSN (electronic): 1465-7333

Publisher: Oxford University Press

URL: https://doi.org/10.1093/jhered/esy016

DOI: 10.1093/jhered/esy016

PubMed id: 29659893

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