Population structure, inbreeding and stripe pattern abnormalities in plains zebras

doi:10.1111/mec.15728

. 2021 Jan;30(2):379-390.

doi: 10.1111/mec.15728. Epub 2020 Dec 2.

Population structure, inbreeding and stripe pattern abnormalities in plains zebras

Brenda Larison^{1

2}, Christopher B Kaelin^{3

4}, Ryan Harrigan^{1

2}, Corneliu Henegar³, Daniel I Rubenstein⁵, Pauline Kamath⁶, Ortwin Aschenborn⁷, Thomas B Smith^{1

2}, Gregory S Barsh^{3

4}

Affiliations

¹ Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA.
² Center for Tropical Research, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA.
³ HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
⁴ Department of Genetics, Stanford University, Stanford, CA, USA.
⁵ Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
⁶ School of Food and Agriculture, University of Maine, Orono, ME, USA.
⁷ School of Veterinary Medicine, University of Namibia, Neudamm Windhoek, Namibia.

PMID: 33174253
DOI: 10.1111/mec.15728

Population structure, inbreeding and stripe pattern abnormalities in plains zebras

Brenda Larison et al. Mol Ecol. 2021 Jan.

. 2021 Jan;30(2):379-390.

doi: 10.1111/mec.15728. Epub 2020 Dec 2.

Authors

Affiliations

¹ Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA.
² Center for Tropical Research, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA.
³ HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
⁴ Department of Genetics, Stanford University, Stanford, CA, USA.
⁵ Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
⁶ School of Food and Agriculture, University of Maine, Orono, ME, USA.
⁷ School of Veterinary Medicine, University of Namibia, Neudamm Windhoek, Namibia.

PMID: 33174253
DOI: 10.1111/mec.15728

Abstract

One of the most iconic wild equids, the plains zebra occupies a broad region of sub-Saharan Africa and exhibits a wide range of phenotypic diversity in stripe patterns that have been used to classify multiple subspecies. After decades of relative stability, albeit with a loss of at least one recognized subspecies, the total population of plains zebras has undergone an approximate 25% decline since 2002. Individuals with abnormal stripe patterns have been recognized in recent years but the extent to which their appearance is related to demography and/or genetics is unclear. Investigating population genetic health and genetic structure are essential for developing effective strategies for plains zebra conservation. We collected DNA from 140 plains zebra, including seven with abnormal stripe patterns, from nine locations across the range of plains zebra, and analyzed data from restriction site-associated and whole genome sequencing (RAD-seq, WGS) libraries to better understand the relationships between population structure, genetic diversity, inbreeding, and abnormal phenotypes. We found that genetic structure did not coincide with described subspecific variation, but did distinguish geographic regions in which anthropogenic habitat fragmentation is associated with reduced gene flow and increased evidence of inbreeding, especially in certain parts of East Africa. Further, zebras with abnormal striping exhibited increased levels of inbreeding relative to normally striped individuals from the same populations. Our results point to a genetic cause of stripe pattern abnormalities, and dramatic evidence of the consequences of habitat fragmentation.

Keywords: Equus quagga; inbreeding; population genomics; stripe pattern; zebra.

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References

REFERENCES

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1. Anderson, E. C., & Dunham, K. K. (2008). The influence of family groups on inferences made with the program Structure. Molecular Ecology Resources, 8(6), 1219-1229. https://doi.org/10.1111/j.1755-0998.2008.02355.x
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1. Bartlam-Brooks, H. L. A., Bonyongo, M. C., & Harris, S. (2011). Will reconnecting ecosystems allow long-distance mammal migrations to resume? A case study of a zebra Equus burchelli migration in Botswana. Oryx, 45(02), 210-216. https://doi.org/10.1017/s0030605310000414
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[1] Alexander, D. H., Novembre, J., & Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19(9), 1655-1664. https://doi.org/10.1101/gr.094052.109

[2] Alexander, D. H., Novembre, J., & Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19(9), 1655-1664. https://doi.org/10.1101/gr.094052.109

[3] Anderson, E. C., & Dunham, K. K. (2008). The influence of family groups on inferences made with the program Structure. Molecular Ecology Resources, 8(6), 1219-1229. https://doi.org/10.1111/j.1755-0998.2008.02355.x

[4] Anderson, E. C., & Dunham, K. K. (2008). The influence of family groups on inferences made with the program Structure. Molecular Ecology Resources, 8(6), 1219-1229. https://doi.org/10.1111/j.1755-0998.2008.02355.x

[5] Avise, J. (1989). A role for molecular genetics in the recognitiion and conservation of endangered species. Trends in Ecology & Evolution, 4, 279-281.

[6] Avise, J. (1989). A role for molecular genetics in the recognitiion and conservation of endangered species. Trends in Ecology & Evolution, 4, 279-281.

[7] Bartlam-Brooks, H. L. A., Bonyongo, M. C., & Harris, S. (2011). Will reconnecting ecosystems allow long-distance mammal migrations to resume? A case study of a zebra Equus burchelli migration in Botswana. Oryx, 45(02), 210-216. https://doi.org/10.1017/s0030605310000414

[8] Bartlam-Brooks, H. L. A., Bonyongo, M. C., & Harris, S. (2011). Will reconnecting ecosystems allow long-distance mammal migrations to resume? A case study of a zebra Equus burchelli migration in Botswana. Oryx, 45(02), 210-216. https://doi.org/10.1017/s0030605310000414

[9] Brown, D. M., Brenneman, R. A., Koepfli, K.-P., Pollinger, J. P., Milá, B., Georgiadis, N. J., Louis, E. E., Grether, G. F., Jacobs, D. K., & Wayne, R. K. (2007). Extensive population genetic structure in the giraffe. BMC Biology, 5, 57. https://doi.org/10.1186/1741-7007-5-57

[10] Brown, D. M., Brenneman, R. A., Koepfli, K.-P., Pollinger, J. P., Milá, B., Georgiadis, N. J., Louis, E. E., Grether, G. F., Jacobs, D. K., & Wayne, R. K. (2007). Extensive population genetic structure in the giraffe. BMC Biology, 5, 57. https://doi.org/10.1186/1741-7007-5-57

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Population structure, inbreeding and stripe pattern abnormalities in plains zebras

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Population structure, inbreeding and stripe pattern abnormalities in plains zebras

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