Determination of the mutation rate in shark
General Genetics and Functional Genome Biology
Final Report Abstract
Sharks are members of one of the most basal vertebrate clades, the Chondrichthyans. They play important roles in the regulation and maintenance of a wide range of marine ecosystems. However, little is known about the evolutionary rate and adaptive potential of shark populations to counteract the threats of overfishing and habitat loss. How rapidly shark populations are able to cope with mounting ecological pressures and rebound from historically low population densities will ultimately depend on the genetic diversity within populations, a value that itself is dependent on the germline mutation rate µ. Another intriguing feature of sharks that we hypothesized to be at least partly connected to the endogenous mutation rate is the low incidence of cancers compared to other fish with whom the share their environment. Thus, the objective of our study was to determine this critical parameter and its impact on shark population genetics and evolution. We chose the most reliable method of de-novo mutation rate determination, direct determination of mutations from high throughput sequencing of the genomes of pair of sharks and their offspring. As target species we selected the Epaulette shark, Hemiscyllium ocellatum, because a full sib family was available. At first, a full-chromosome level assembly at haplotype resolution was generated as part of the Vertebrate Genome Project (VGP) and ascertained to fulfil the highest quality performance level. Then the genomes of all family members were sequenced, and novo-mutations determined. After PCR confirmation of the variants µ was estimated as 7x10-10 per base pair, per generation. This value, the first for the whole group of Chondrichthyans, is the lowest directly estimated mutation rate for any vertebrate clade. Considering that the somatic mutation rate correlates with the germline rate, an accordingly low spontaneous somatic rate (presumably also linked to a highly efficient DNA repair machinery), can explain a reduced susceptibility to develop neoplasms.. The extremely low mutation rate of sharks provides evidence that this basal vertebrate group is indeed a slowly evolving lineage whose ability to restore genetic diversity following a sustained population bottleneck may be hampered by this low rate. A low mutation rate evokes questions how sharks can maintain genetic diversity, evolve and adapt, in particular, in the anthropocene with its recently increasing threats of hostile ecological pressures. To better understand the impact of a low mutation rate on genetic diversity in shark populations we sequenced 61 individuals from wild populations of bamboo sharks. Determination of individual heterozygosity, population level genetic diversity and mutational load is expected to provide information for evaluating the evolutionary consequences of a low mutation rate and make inferences for a better understanding of shark biology.
Publications
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Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks. Nature Communications, 14(1).
Sendell-Price, Ashley T.; Tulenko, Frank J.; Pettersson, Mats; Kang, Du; Montandon, Margo; Winkler, Sylke; Kulb, Kathleen; Naylor, Gavin P.; Phillippy, Adam; Fedrigo, Olivier; Mountcastle, Jacquelyn; Balacco, Jennifer R.; Dutra, Amalia; Dale, Rebecca E.; Haase, Bettina; Jarvis, Erich D.; Myers, Gene; Burgess, Shawn M.; Currie, Peter D. ... & Schartl, Manfred
