TY - JOUR

T1 - Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size

AU - Hempel, Elisabeth

AU - Faith, J. Tyler

AU - Preick, Michaela

AU - de Jager, Deon

AU - Barish, Scott

AU - Hartmann, Stefanie

AU - Grau, José H.

AU - Moodley, Yoshan

AU - Gedman, Gregory

AU - Pirovich, Kathleen Morrill

AU - Bibi, Faysal

AU - Kalthoff, Daniela C.

AU - Bocklandt, Sven

AU - Lamm, Ben

AU - Dalén, Love

AU - Westbury, Michael V.

AU - Hofreiter, Michael

N1 - Publisher Copyright: © 2024 The Authors

PY - 2024

Y1 - 2024

N2 - Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability.123456 Moreover, small population size may promote gene flow with congeners and outbreeding depression.78910111213 Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40× nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa,1415 populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat.161718 However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in ∼AD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (∼1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species’ unique traits.

AB - Low genomic diversity is generally indicative of small population size and is considered detrimental by decreasing long-term adaptability.123456 Moreover, small population size may promote gene flow with congeners and outbreeding depression.78910111213 Here, we examine the connection between habitat availability, effective population size (Ne), and extinction by generating a 40× nuclear genome from the extinct blue antelope (Hippotragus leucophaeus). Historically endemic to the relatively small Cape Floristic Region in southernmost Africa,1415 populations were thought to have expanded and contracted across glacial-interglacial cycles, tracking suitable habitat.161718 However, we found long-term low Ne, unaffected by glacial cycles, suggesting persistence with low genomic diversity for many millennia prior to extinction in ∼AD 1800. A lack of inbreeding, alongside high levels of genetic purging, suggests adaptation to this long-term low Ne and that human impacts during the colonial era (e.g., hunting and landscape transformation), rather than longer-term ecological processes, were central to its extinction. Phylogenomic analyses uncovered gene flow between roan (H. equinus) and blue antelope, as well as between roan and sable antelope (H. niger), approximately at the time of divergence of blue and sable antelope (∼1.9 Ma). Finally, we identified the LYST and ASIP genes as candidates for the eponymous bluish pelt color of the blue antelope. Our results revise numerous aspects of our understanding of the interplay between genomic diversity and evolutionary history and provide the resources for uncovering the genetic basis of this extinct species’ unique traits.

KW - bluebuck

KW - coat color

KW - extinction

KW - gene flow

KW - genetic load

KW - heterozygosity

KW - Hippotragus leucophaeus

KW - paleogenomics

KW - PSMC

KW - South Africa

U2 - 10.1016/j.cub.2024.03.051

DO - 10.1016/j.cub.2024.03.051

M3 - Journal article

C2 - 38614080

AN - SCOPUS:85191484860

VL - 34

SP - 2020-2029.e6

JO - Current Biology

JF - Current Biology

SN - 0960-9822

IS - 9

ER -