Reference genome and demographic history of the most endangered marine mammal, the vaquita

Abstract

The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large‐mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long‐read sequencing and long‐range scaffolding methods with long‐ and short‐read RNA sequencing to generate a near error‐free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome‐length autosome scaffolds and the X‐chromosome scaffold, with a scaffold N50 of 115 Mb. Genome‐wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long‐term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long‐term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

Gene duplications and gene loss in the epidermal differentiation complex during the evolutionary land-to-water transition of cetaceans

“…We investigated the EDC in species of cetaceans for which whole genome sequences had been published (Supplementary Tables S1 ). The study was focused on bottlenose dolphin ( Tursiops truncatus ) 23 , vaquita ( Phocoena sinus ) 24 , and minke whale ( Balaenoptera acutorostrata scammoni ) 25 (Supplementary Tables S2 - S4 ; Supplementary Fig. S1 - S3 ).…”

The genome of the Pyrenean desman and the effects of bottlenecks and inbreeding on the genomic landscape of an endangered species

“…A similar situation of a species surviving with an extremely low heterozygosity (14 SNPs/Mb) has been reported for the island fox of the San Nicolas population (Robinson et al, 2018 ). Although not with such low values, there are several other species with heterozygosity values that range between 100 and 120 SNPs/Mb (Figure S5 ; including the Iberian desmans from the western Pyrenees and Central System), in which it is likely that a similar mechanism of purging of lethal mutations occurred (Morin et al, 2020 ; Westbury et al, 2018 ). Further analysis of nonsynonymous substitutions and functional variation in populations of endangered species will be necessary to test these hypotheses.…”

An Economic Perspective on Policies to Save the Vaquita: Conservation Actions, Wildlife Trafficking, and the Structure of Incentives

“…and have persisted with low levels of genetic diversity but no signs of inbreeding depression (Taylor et al, 2019;Gulland et al, 2020;Morin et al, 2020;Rojas-Bracho et al, 2020). Yet, even if complete protection of these remaining vaquitas were guaranteed, recovery would take decades (Taylor et al, 2017.…”

“…The last best estimate from the area where vaquitas were most recently detected acoustically estimated 10 individuals, including 3 calves, and all appeared in good health (Rojas-Bracho et al, 2020). Ensuring protection of these surviving vaquitas from gillnets could still save the species (Jaramillo-Legorreta et al, 2019;Gulland et al, 2020;Morin et al, 2020;Rojas-Bracho et al, 2020).…”