Reference genome and demographic history of the most endangered marine mammal, the vaquita
Phillip A Morin,
Frederick I Archer,
Catherine D Avila,
Jennifer R Balacco,
Yury V Bukhman,
Julie A Fronczek,
Frances M.D. Gulland,
Mads Peter Heide-Jørgensen,
Marlys L. Houck,
Ann C Misuraca,
Jacqueline A. Robinson,
Teri K Rowles,
Oliver A. Ryder,
Cynthia R Smith,
Barbara L. Taylor,
Randall S Wells,
Erich D Jarvis
Posted 28 May 2020
bioRxiv DOI: 10.1101/2020.05.27.098582
Posted 28 May 2020
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 resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. 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 analyzed 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 5000 (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. ### Competing Interest Statement The authors have declared no competing interest.
- Downloaded 1,150 times
- Download rankings, all-time:
- Site-wide: 21,648
- In genomics: 2,034
- Year to date:
- Site-wide: 56,784
- Since beginning of last month:
- Site-wide: 95,142
Downloads over time
Distribution of downloads per paper, site-wide
- 27 Nov 2020: The website and API now include results pulled from medRxiv as well as bioRxiv.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!