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Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae
Department of Mathematics and Natural Sciences, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany;Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.ORCID iD: 0000-0003-0478-3930
Institute of Human Genetics, University Medical Center Leipzig, Leipzig, Germany;Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark;Research School of Biology, Australian National University, Canberra, ACT, Australia.
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA;Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha, India.
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2021 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 38, no 9, p. 3884-3897Article in journal (Refereed) Published
Abstract [en]

During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species: the bone-cracking spotted, striped, and brown hyenas, and the specialized insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. Here, we generated an aardwolf genome and analyzed it together with the remaining three species to reveal their evolutionary relationships, genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection, suggesting putative key adaptations to carrion and termite feeding, respectively. A family-wide expansion in olfactory receptor genes suggests that an acute sense of smell was a key early adaptation. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, putatively linked to their similarly slow decline in effective population size over the last ∼2 million years. High levels of genetic diversity and more stable population sizes through time are seen in the spotted hyena and aardwolf. Taken together, our findings highlight how ecological specialization can impact the evolutionary history, demographics, and adaptive genetic changes of an evolutionary lineage.

Place, publisher, year, edition, pages
2021. Vol. 38, no 9, p. 3884-3897
Keywords [en]
Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, adaptation, comparative genomics, genetic diversity, genome, hyena, phylogenomics
National Category
Evolutionary Biology
Research subject
Ecosystems and species history
Identifiers
URN: urn:nbn:se:nrm:diva-4482DOI: 10.1093/molbev/msab055OAI: oai:DiVA.org:nrm-4482DiVA, id: diva2:1618416
Funder
Australian Research Council, DE190100544
Note

We would like to thank Andrew Heidel, Pablo Santos, Marion East, Heribert Hofer, Oliver Hoener, Bettina Wachter, Simone Sommer, Martin Bens, and Matthias Platzer for providing the assembled spotted hyena transcriptome to aid in annotating the genomes. We also thank Dorina Menegheni and Bernd Senf for the transcriptome data transfer. We thank Armanda Bastos for allowing the use of her laboratory for the aardwolf DNA extractions. We also acknowledge sequencing support from the Swedish National Genomics Infrastructure (NGI) at the Science for Life Laboratory, which is funded by the Swedish Research Council and the Knut and Alice Wallenberg Foundation, and UPPMAX for access to computational infrastructure. Main funding for the project was provided through ERC consolidator grant # 310763 (Geneflow) to M.H. D.A.D. was funded by an Australian Research Council grant (DE190100544). D.L.D. is funded through “Clinician Scientist Programm, Medizinische Fakultät der Universität Leipzig.” A.W. is funded through “Leibniz Competition Fund (SAW-2018-IZW-3-EpiRank)”

Available from: 2021-12-09 Created: 2021-12-09 Last updated: 2021-12-09Bibliographically approved

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