Genomic Flatlining in the Endangered Island Fox.
Genetic studies of rare and endangered species often focus on defining and preserving genetically distinct populations, especially those having unique adaptations [1, 2]. Much less attention is directed at understanding the landscape of deleterious variation, an insidious consequence of geographic isolation and the inefficiency of natural selection to eliminate harmful variants in small populations [3-5]. With population sizes of many vertebrates decreasing and isolation increasing through habitat fragmentation and loss, understanding the extent and nature of deleterious variation in small populations is essential for predicting and enhancing population persistence. The Channel Island fox (Urocyon littoralis) is a dwarfed species that inhabits six of California's Channel Islands and is derived from the mainland gray fox (U. cinereoargenteus). These isolated island populations have persisted for thousands of years at extremely small population sizes [6, 7] and, consequently, are a model for testing ideas about the accumulation of deleterious variation in small populations under natural conditions. Analysis of complete genome sequence data from island foxes shows a dramatic decrease in genome-wide variation and a sharp increase in the homozygosity of deleterious variants. The San Nicolas Island population has a near absence of variation, demonstrating a unique genetic flatlining that is punctuated by heterozygosity hotspots, enriched for olfactory receptor genes and other genes with high levels of ancestral variation. These findings question the generality of the small-population paradigm that maintains substantial genetic variation is necessary for short- and long-term persistence.
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Jacqueline A
JA
Robinson
Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Diego
D
Ortega-Del Vecchyo
Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China.
Zhenxin
Z
Fan
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Bernard Y
BY
Kim
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
Bridgett M
BM
vonHoldt
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Clare D
CD
Marsden
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Kirk E
KE
Lohmueller
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: rwayne@ucla.edu.
Robert K
RK
Wayne
D000818:Animals; D002140:California; D003710:Demography; D056727:Endangered Species; D005589:Foxes / Q000235:genetics*; D014644:Genetic Variation / Q000502:physiology*; D023281:Genomics; D005838:Genotype; D062312:Islands