Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)

Research output: Contribution to journalJournal articlepeer-review

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Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum). / Sánchez-Barreiro, Fatima; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; Westbury, Michael V.; de Manuel, Marc; Margaryan, Ashot; Ciucani, Marta M.; Vieira, Filipe G.; Patramanis, Yannis; Kalthoff, Daniela C.; Timmons, Zena; Sicheritz-Pontén, Thomas; Dalén, Love; Ryder, Oliver A.; Zhang, Guojie; Marques-Bonet, Tomas; Moodley, Yoshan; Gilbert, M. Thomas P.

In: Molecular Ecology, Vol. 30, No. 23, 2021, p. 6355-6369.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Sánchez-Barreiro, F, Gopalakrishnan, S, Ramos-Madrigal, J, Westbury, MV, de Manuel, M, Margaryan, A, Ciucani, MM, Vieira, FG, Patramanis, Y, Kalthoff, DC, Timmons, Z, Sicheritz-Pontén, T, Dalén, L, Ryder, OA, Zhang, G, Marques-Bonet, T, Moodley, Y & Gilbert, MTP 2021, 'Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)', Molecular Ecology, vol. 30, no. 23, pp. 6355-6369. https://doi.org/10.1111/mec.16043

APA

Sánchez-Barreiro, F., Gopalakrishnan, S., Ramos-Madrigal, J., Westbury, M. V., de Manuel, M., Margaryan, A., Ciucani, M. M., Vieira, F. G., Patramanis, Y., Kalthoff, D. C., Timmons, Z., Sicheritz-Pontén, T., Dalén, L., Ryder, O. A., Zhang, G., Marques-Bonet, T., Moodley, Y., & Gilbert, M. T. P. (2021). Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum). Molecular Ecology, 30(23), 6355-6369. https://doi.org/10.1111/mec.16043

Vancouver

Sánchez-Barreiro F, Gopalakrishnan S, Ramos-Madrigal J, Westbury MV, de Manuel M, Margaryan A et al. Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum). Molecular Ecology. 2021;30(23):6355-6369. https://doi.org/10.1111/mec.16043

Author

Sánchez-Barreiro, Fatima ; Gopalakrishnan, Shyam ; Ramos-Madrigal, Jazmín ; Westbury, Michael V. ; de Manuel, Marc ; Margaryan, Ashot ; Ciucani, Marta M. ; Vieira, Filipe G. ; Patramanis, Yannis ; Kalthoff, Daniela C. ; Timmons, Zena ; Sicheritz-Pontén, Thomas ; Dalén, Love ; Ryder, Oliver A. ; Zhang, Guojie ; Marques-Bonet, Tomas ; Moodley, Yoshan ; Gilbert, M. Thomas P. / Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum). In: Molecular Ecology. 2021 ; Vol. 30, No. 23. pp. 6355-6369.

Bibtex

@article{fbb6465aade648eab6528be1d5cc1e3b,
title = "Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)",
abstract = "Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.",
keywords = "conservation genomics, genomic erosion, northern white rhinoceros, population decline, southern white rhinoceros, SEQUENCE, ANCIENT, FORMAT",
author = "Fatima S{\'a}nchez-Barreiro and Shyam Gopalakrishnan and Jazm{\'i}n Ramos-Madrigal and Westbury, {Michael V.} and {de Manuel}, Marc and Ashot Margaryan and Ciucani, {Marta M.} and Vieira, {Filipe G.} and Yannis Patramanis and Kalthoff, {Daniela C.} and Zena Timmons and Thomas Sicheritz-Pont{\'e}n and Love Dal{\'e}n and Ryder, {Oliver A.} and Guojie Zhang and Tomas Marques-Bonet and Yoshan Moodley and Gilbert, {M. Thomas P.}",
year = "2021",
doi = "10.1111/mec.16043",
language = "English",
volume = "30",
pages = "6355--6369",
journal = "Molecular Ecology",
issn = "0962-1083",
publisher = "Wiley-Blackwell",
number = "23",

}

RIS

TY - JOUR

T1 - Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)

AU - Sánchez-Barreiro, Fatima

AU - Gopalakrishnan, Shyam

AU - Ramos-Madrigal, Jazmín

AU - Westbury, Michael V.

AU - de Manuel, Marc

AU - Margaryan, Ashot

AU - Ciucani, Marta M.

AU - Vieira, Filipe G.

AU - Patramanis, Yannis

AU - Kalthoff, Daniela C.

AU - Timmons, Zena

AU - Sicheritz-Pontén, Thomas

AU - Dalén, Love

AU - Ryder, Oliver A.

AU - Zhang, Guojie

AU - Marques-Bonet, Tomas

AU - Moodley, Yoshan

AU - Gilbert, M. Thomas P.

PY - 2021

Y1 - 2021

N2 - Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.

AB - Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.

KW - conservation genomics

KW - genomic erosion

KW - northern white rhinoceros

KW - population decline

KW - southern white rhinoceros

KW - SEQUENCE

KW - ANCIENT

KW - FORMAT

U2 - 10.1111/mec.16043

DO - 10.1111/mec.16043

M3 - Journal article

C2 - 34176179

VL - 30

SP - 6355

EP - 6369

JO - Molecular Ecology

JF - Molecular Ecology

SN - 0962-1083

IS - 23

ER -

ID: 274275903