Genomic and population viability analyses predict extinction risk in the most endangered marine mammal, the vaquita (Phocoena sinus)
Authors: Jacqueline Robinson 1; Christopher Kyriazis 2; Sergio Nigenda-Morales 3; Annabel Beichman 4; Lorenzo Rojas-Bracho 5; Kelly Robertson 6; Michael Fontaine 7,8,9; Robert Wayne 2; Kirk Lohmueller 2,10; Barbara Taylor 6; Phillip Morin 6
Affiliations: 1) Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; 2) Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA; 3) Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav), Irapuato, Guanajuato, Mexico; 4) Department of Genome Sciences, University of Washington, Seattle, WA; 5) PNUD-Sinergia en la Comisión Nacional de Áreas Naturales Protegidas, Ensenada, BC, Mexico; 6) Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA; 7) MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France; 8) Centre de Recherche en Écologie et Évolution de la Santé (CREES), Montpellier, France; 9) Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands; 10) Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
Keywords: Ecological & conservation genetics
Anthropogenic pressures are driving species declines across the globe. Given limited conservation resources, a key question in cases of severe decline is whether recovery is possible, or if it is likely to be impeded by genetic factors such as inbreeding depression. Predicting the threat of inbreeding depression remains challenging, particularly for non-model species for which genetic and pedigree information is often limited or unavailable. A potential solution is to use genomic data to infer the genetic and demographic parameters needed to predict extinction risk through population viability analysis. We applied this framework to model extinction risk in the critically endangered vaquita porpoise (Phocoena sinus), which has declined to ~10 remaining individuals following decades of excess mortality from gillnet fishing in the Gulf of California, Mexico. We analyzed whole genome sequences from 20 vaquitas to investigate the impacts of the recent population decline, infer the species' demographic history, and examine deleterious variation in comparison with other cetaceans. We then integrated this genomic and demographic information into stochastic, individual-based simulations to quantify the vaquita's recovery potential. We find that the recent catastrophic decline has not yet impacted vaquita genomes, but that vaquitas nonetheless contain extremely low diversity and an excess of homozygous deleterious mutations due to long-term small population size. However, as a result of this naturally low diversity, vaquita genomes also contain very few segregating deleterious mutations, implying fitness may not decline under future inbreeding that is inevitable in any recovery scenario. We confirm this prediction through simulations of population dynamics over the next 50 years, which suggest that inbreeding depression in vaquitas is likely to be weak, and recovery is possible if bycatch mortality from gillnets is immediately halted. However, even modest rates of continuing bycatch result in an appreciable extinction risk, underscoring the importance of enforcing gillnet limits to avert the vaquita's extinction. Our results provide hope for vaquita recovery and highlight the applicability of genomic data in conservation.