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ORIGINAL RESEARCH article

Front. Ecol. Evol.

Sec. Evolutionary and Population Genetics

Geographic distribution of genetic diversity of Heterocephalus glaber analyzed using whole genome sequencing and a chromosome-scale genome assembly

Provisionally accepted
Kevin M. WrightKevin M. Wright1Pranidhi SoodPranidhi Sood1Elena D. ZemlemerovaElena D. Zemlemerova2Danila S. KostinDanila S. Kostin2Nicole L. FongNicole L. Fong1Nelda YiNelda Yi1Andrea T. IrelandAndrea T. Ireland1Irene LamIrene Lam1Kaitlyn N. Hardell-LewisKaitlyn N. Hardell-Lewis1Megan SmithMegan Smith1Jackie VillaltaJackie Villalta1Calvin H. JanCalvin H. Jan1Margaret A. RoyMargaret A. Roy1David BotsteinDavid Botstein1Leonid A. LavrenchenkoLeonid A. Lavrenchenko2J. Graham RubyJ. Graham Ruby1*Rochelle BuffensteinRochelle Buffenstein3*
  • 1Calico Life Sciences LLC, South San Francisco, United States
  • 2Rossijskaa akademia nauk, Moscow, Russia
  • 3University of Illinois Chicago, Chicago, United States

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Naked mole-rats (Heterocephalus glaber) are a species of rodent endemic to the Horn of Africa, notable among mammals for their long lifespans, resistances to a variety of stresses, and eusocial mating behavior. Though their natural range extends across large portions of Kenya, Ethiopia, Somalia, and Djibouti, the large majority of genetic and genomic analyses focus on Kenyan specimens. Here, we constructed a chromosome-scale reference genome assembly for H. glaber, along with new reference assemblies of both the Damaraland mole-rat (Fukomys damarensis) and guinea pig (Cavia porcellus) genomes to aid annotation. We leveraged our H. glaber assembly, along with modern whole-genome sequencing, to characterize the genetic diversity of specimens deriving from Kenya, southern Ethiopia, and eastern Ethiopia. We found the Kenyan and southern Ethiopian specimens to be closely related to each other and highly diverged from eastern Ethiopian specimens. We also found specimens collected from nearby locations in southern Ethiopia to be more closely related to Kenyan specimens than to each other. This unexpected distribution of shared genetic diversity highlights the importance of local migration barriers to gene flow in wild H. glaber populations.

Keywords: naked mole-rat, Genome, population structure, polymorphism, genetic diversity

Received: 20 Aug 2025; Accepted: 28 Oct 2025.

Copyright: © 2025 Wright, Sood, Zemlemerova, Kostin, Fong, Yi, Ireland, Lam, Hardell-Lewis, Smith, Villalta, Jan, Roy, Botstein, Lavrenchenko, Ruby and Buffenstein. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
J. Graham Ruby, graham@calicolabs.com
Rochelle Buffenstein, rbuffen@uic.edu

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

Supplementary Material