The use of archived tags in retrospective genetic analysis of fish

Bonanomi, Sara; Therkildsen, Nina Overgaard; Hedeholm, Rasmus; Hemmer‐Hansen, Jakob; Nielsen, Einar Eg

doi:10.1111/1755-0998.12211

Cited by 5 publications

(4 citation statements)

References 25 publications

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“…There is normal Mendelian segregation of variants within the truebreeding hybrid species (such as the PanI AA, AB, and BB on LG01). This addresses the contradictory results regarding in-termediate forms 23 and has implications for the interpretation of the relative importance of these groups (e.g., the contribution of the different Greenland ecotypes to the Icelandic population 31,35 and vice versa). .…”

Section: Resultsmentioning

confidence: 89%

“…23 A study of other genomic islands suggests cryptic speciation and extensive hybridization producing F 1 hybrids and few, if any, F 2 and back-crossed individuals. 8 Thus, if the coastal and frontal types are reproductively isolated, as has been suggested, 7,30,31 the intermediates are an enigma: is most of the population composed of sterile hybrids, as implied by the lack of F 2 and back-crossed individuals 8 ? This is hardly a tenable proposition.…”

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confidence: 99%

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Whole-genome sequencing uncovers cryptic and hybrid species among Atlantic and Pacific cod-fish

Halldórsdóttir

Árnason

2015

Preprint

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Speciation often involves the splitting of a lineage and the adaptation of daughter lineages to different environments. It may also involve the merging of divergent lineages, thus creating a stable homoploid hybrid species 1 that constructs a new ecological niche by transgressing 2 the ecology of the parental types. Hybrid speciation may also contribute to enigmatic and cryptic biodiversity in the sea. 3,4 The enigmatic walleye pollock, which is not a pollock at all but an Atlantic cod that invaded the Pacific 3.8 Mya, 5 differs considerably from its presumed closest relatives, the Pacific and Atlantic cod. Among the Atlantic cod, shallow-water coastal and deep-water migratory frontal ecotypes are associated with highly divergent genomic islands; 6, 7 however, intermediates remain an enigma. 8 Here, we performed whole-genome sequencing of over 200 individuals using up to 33 million SNPs based on genotype likelihoods 9 and showed that the evolutionary status of walleye pollock is a hybrid species: it is a hybrid between Arctic cod and Atlantic cod that transgresses the ecology of its parents. For the first time, we provide decisive evidence that the Atlantic cod coastal and frontal ecotypes are separate species that hybridized, leading to a true-breeding hybrid species that differs ecologically from its parents. We refute monophyly and dichotomous branching of these taxa, and stress the importance of looking beyond branching trees at admixture and hybridity. Our study demonstrates the power of whole-genome sequencing and population genomics in providing deep insights into fundamental processes of speciation. Our study was a starting point for further work aimed at examining the criteria of hybrid speciation, 10 selection, sterility and structural chromosomal variation 11 among cod-fish, which are among the most important fish stocks in the world. The hybrid nature of both the walleye pollock and Atlantic cod raises the question concerning the extent to which very profitable fisheries 12, 13 depend on hybrid vigour. Our results have implications for management of marine resources in times of rapid climate change. 14, 15

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Section: Resultsmentioning

confidence: 89%

mentioning

confidence: 99%

Whole-genome sequencing uncovers cryptic and hybrid species among Atlantic and Pacific cod-fish

Halldórsdóttir

Árnason

2015

Preprint

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“…Historical specimens from museum or other institutional collections are valuable sources of information representing organisms that may be difficult or impossible to sample in contemporary populations (Holmes et al., 2016). Most studies that use historical specimens for phylogenetic reconstruction tend to focus on larger‐bodied species that are recently extinct (Anmarkrud & Lifjeld, 2017; Bunce et al., 2009; Mitchell et al., 2014; Sharko et al., 2019), well‐studied groups (Billerman & Walsh, 2019; Jarvis et al., 2014) and organisms of economic importance (Bonanomi et al., 2014; Larson et al., 2007; Larsson et al., 2019). Only recently have we begun to see an increase in such reports on invertebrate and other small‐bodied taxa (e.g., Cruaud et al., 2019; Der Sarkissian et al., 2017; Kistenich et al., 2019; Sproul & Maddison, 2017).…”

Section: Introductionmentioning

confidence: 99%

A molecular phylogeny of historical and contemporary specimens of an under‐studied micro‐invertebrate group

Orr

Sannum

Boessenkool

et al. 2020

Ecology and Evolution

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“…However, the growing number of studies that successfully extracted DNA from archived scales and otoliths (Nielsen and Hansen 2008; Bonanomi et al. 2014) raised the prospect that spine samples could be used to retroactively characterize the genetic composition of the New York Bight fishery.…”

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confidence: 99%

Stock Composition of the Historical New York Bight Atlantic Sturgeon Fishery Revealed through Microsatellite Analysis of Archived Spines

White¹,

Johnson

Lubinski

et al. 2021

Mar Coast Fish

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A targeted commercial fishery for Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus once operated in the New York Bight, where it was assumed that most harvested Atlantic Sturgeon were natal to the Hudson River population. However, more recent evidence suggests that the fishery may have been targeting a mixed‐stock aggregation, in which case harvested Atlantic Sturgeon could have been comprised of individuals from multiple populations throughout the species’ range. Although there is now a moratorium on Atlantic Sturgeon harvest in the New York Bight, modern molecular approaches provide an opportunity to use archived tissues to perform a retrospective mixed‐stock analysis on the fishery. Genomic DNA extracted from archived fin spines from 80 Atlantic Sturgeon collected nearly 30 years ago suggests that the fishery primarily harvested individuals from the Hudson River population. However, based on individual‐based assignment tests, our results indicate that the fishery also harvested individuals from at least eight other populations located throughout the species’ range. This study highlights how archival hard parts that were previously used for age and growth analyses can be employed for retrospective genetic analyses. Further, because the New York Bight harbors relatively high concentrations of Atlantic Sturgeon, the study shows how localized management decisions can influence Atlantic Sturgeon conservation at rangewide scales. When integrated with more recent knowledge of species ecology, these analyses can be used to evaluate the efficacy of previous management strategies and understand the effects of historical processes on contemporary demography.

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The use of archived tags in retrospective genetic analysis of fish

Cited by 5 publications

References 25 publications

Whole-genome sequencing uncovers cryptic and hybrid species among Atlantic and Pacific cod-fish

Whole-genome sequencing uncovers cryptic and hybrid species among Atlantic and Pacific cod-fish

A molecular phylogeny of historical and contemporary specimens of an under‐studied micro‐invertebrate group

Stock Composition of the Historical New York Bight Atlantic Sturgeon Fishery Revealed through Microsatellite Analysis of Archived Spines

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