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Runs of homozygosity have utility in mammalian conservation and evolutionary studies

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A Correction to this article was published on 10 September 2018

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Abstract

Runs of homozygosity (ROHs) arise due the transmission from parents to offspring of segments that are either identical by decent (IBD) or identical by state (IBS). The former is due to consanguineous matings whereas the latter is due to demographic processes. ROHs reduce individual nucleotide diversity (θ) as a function of homozygosity, and thus ROH distributions and θ are expected to vary among species because inbreeding levels, recombination rates, and demographic histories vary widely. To help interpret genetic diversity within and among species, we utilized genome sequence data from 78 mammalian species to compare θ and ROH burden (i.e., number and length of ROHs in the genome) among groups of mammals to assess genomic signatures of inbreeding. We compared θ and ROHs: (i) among threatened and non-threatened mammals to determine the significance of contemporary conservation status; (ii) among carnivorous and non-carnivorous mammals to determine the relevance of trophic effects; (iii) relative to body size because mutation rates generally vary with body mass; and (iv) across mammals from different latitudes to test for gradients in genomic diversity (e.g., due to effects of historic climatic regimes). Our results illustrate the considerable variance in genomic diversity across mammals, and that trophic level, body mass, and latitude have significant effects on θ and ROH burden. However, conservation status was not a reliable indicator of genomic diversity. We argue that genetic or genomic diversity should be an explicit component of conservation status, as such diversity is critical to the long-term sustainability of populations, and anticipate that ROHs will become more commonly used to estimate inbreeding in wild animals.

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Change history

  • 10 September 2018

    The fourth author’s name was incorrect in the original publication and correct author name is given in this Correction.

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Acknowledgements

We thank Anders Albrechtsen for helpful comments and suggestions to the SNV calling pipeline, and members of the DeWoody lab group for constructive criticism on an earlier version of the manuscript. This work was conducted as a part of the “Next generation genetic monitoring” Working Group at the National Institute for Mathematical and Biological Synthesis, sponsored by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville.

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Authors and Affiliations

  1. Department of Forestry & Natural Resources, Purdue University, West Lafayette, IN, 47905, USA

    Anna Brüniche-Olsen, Kenneth F. Kellner & J. Andrew DeWoody

  2. Department of Biological Sciences, Purdue University, West Lafayette, IN, 47905, USA

    Chase J. Anderson & J. Andrew DeWoody

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  1. Anna Brüniche-Olsen
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  2. Kenneth F. Kellner
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  3. Chase J. Anderson
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  4. J. Andrew DeWoody
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Correspondence to Anna Brüniche-Olsen.

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Brüniche-Olsen, A., Kellner, K.F., Anderson, C.J. et al. Runs of homozygosity have utility in mammalian conservation and evolutionary studies. Conserv Genet 19, 1295–1307 (2018). https://doi.org/10.1007/s10592-018-1099-y

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