Nucleotide variation and balancing selection at the<i>Ckma</i>gene in Atlantic cod: analysis with multiple merger coalescent models

Árnason, Einar; Halldórsdóttir, Katrín

doi:10.7717/peerj.786

Cited by 46 publications

(37 citation statements)

References 124 publications

(205 reference statements)

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“…Methods Population sampling We randomly sampled over 200 individual cod-fish from our large sample collection of greater than 20,000 Atlantic, Arctic and Pacific cod-fish individuals. 39,40 We stratified the sampling to cover the widest geographic range possible with our database. We sampled Pacific cod Gadus macrocephalus (Tilesius, 1810) (mnemonic: Gma) and walleye pollock Gadus chalcogrammus (Pallas, 1814) (Gch) from the Pacific Ocean.…”

Section: /28mentioning

confidence: 99%

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: /28mentioning

confidence: 99%

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

Halldórsdóttir

Árnason

2015

Preprint

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“…In contrast, microsatellite studies suggest range‐wide isolation by distance (O'Leary, Coughlan, Dillane, McCarthy, & Cross, 2007), and significant structure in waters off North America (e.g., Flemish cap, Bentzen, Taggart, Ruzzante, & Cook, 1996; inshore vs. offshore, Ruzzante, Taggart, Cook, & Goddard, 1996; Arctic populations, Hardie, Gillett, & Hutchings, 2006), Norway (Knutsen, Jorde, André, & Stenseth, 2003), and the North Sea (Hutchinson, Carvalho, & Rogers, 2001). Furthermore, genome scans of nuclear SNP markers have suggested the presence of local adaptation and temperature gradients at both large and small scales (Árnason & Halldórsdóttir, 2015; Berg et al., 2016; Bradbury et al., 2010, 2013; Nielsen et al., 2009). …”

Section: Introductionmentioning

confidence: 99%

“…the presence of local adaptation and temperature gradients at both large and small scales (Árnason & Halldórsdóttir, 2015;Berg et al, 2016;Bradbury et al, 2010Bradbury et al, , 2013Nielsen et al, 2009).…”

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confidence: 99%

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

Lait

Marshall

Carr

2018

Ecology and Evolution

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The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High‐resolution, whole‐genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans‐Atlantic comparisons (ΦST = .029–.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000–.060) or defined management stocks (ΦST = .000–.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans‐Atlantic phylogeography versus absence of such structure within various partitions of trans‐Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near‐identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153–.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200–250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.

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“…Multiple merger coalescent models, which are more general than the Kingman coalescent, include the -, -, and -coalescent (Irwin et al 2016). These have been developed since the early 2000s, and vary in how they handle multiple merger events as well as the number of descendants per lineage (Árnason and Halldórsdóttir 2015).…”

Section: Bottlenecks To Small Effective Population Sizementioning

confidence: 99%

Coalescent models at small effective population sizes and population declines are positively misleading

Lauterbur

2019

Preprint

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Population genetics employs two major models for conceptualizing genetic relationships among individuals – outcome-driven (coalescent) and process-driven (forward). These models are complementary, but the basic Kingman coalescent and its extensions make fundamental assumptions to allow analytical approximations: a constant effective population size much larger than the sample size. These make the probability of multiple coalescent events per generation negligible. Although these assumptions are often violated in species of conservation concern, conservation genetics often uses coalescent models of effective population sizes and trajectories in endangered species. Despite this, the effect of very small effective population sizes, and their interaction with bottlenecks and sample sizes, on such analyses of genetic diversity remains unexplored. Here, I use simulations to analyze the influence of small effective population size, population decline, and their relationship with sample size, on coalescent-based estimates of genetic diversity. Compared to forward process-based estimates, coalescent models significantly overestimate genetic diversity in oversampled populations with very small effective sizes. When sampled soon after a decline, coalescent models overestimate genetic diversity in small populations regardless of sample size. Such overestimates artificially inflate estimates of both bottleneck and population split times. For conservation applications with small effective population sizes, forward simulations that do not make population size assumptions are computationally tractable and should be considered instead of coalescent-based models. These findings underscore the importance of the theoretical basis of analytical techniques as applied to conservation questions.

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Nucleotide variation and balancing selection at theCkmagene in Atlantic cod: analysis with multiple merger coalescent models

Cited by 46 publications

References 124 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

Phylogeographic mitogenomics of Atlantic codGadus morhua: Variation in and among trans‐Atlantic, trans‐Laurentian, Northern cod, and landlocked fjord populations

Coalescent models at small effective population sizes and population declines are positively misleading

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