MITOCHONDRIAL DNA IN<i>GASTEROSTEUS</i>AND PLEISTOCENE GLACIAL REFUGIUM ON THE QUEEN CHARLOTTE ISLANDS, BRITISH COLUMBIA

O’Reilly, P. T.; Reimchen, T. E.; Beech, Robin N.; Strobeck, Curtis

doi:10.1111/j.1558-5646.1993.tb02122.x

Cited by 61 publications

(3 citation statements)

References 48 publications

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“…Still, our inference of SC supports the hypothesis that smaller micro-refugia have persisted along the Pacific Coast [43,64]. In particular, the Haida Gwaii archipelago is known for high endemism, and its role as a refugium for mammals, invertebrates, and angiosperms is well established [64][65][66]. The divergence time inferred between populations from California and Haida Gwaii was relatively recent (39 KyA), in the range of inferred divergence times for bird species from the region [67] and in the time frame of the last interglacial period 55 to 25 KyA.…”

Section: Expansion From a Major Southern Refugium And Secondary Contasupporting

confidence: 86%

Section: Expansion From a Major Southern Refugium And Secondary Contasupporting

confidence: 85%

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Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

Rougemont

Moore

Leroy

et al. 2019

Preprint

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Understanding the impacts of current human activities on within-species genetic variation requires a thorough description of the historical factors that have shaped the genomic and geographical distribution of nucleotide diversity. Past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential under the nearly neutral theory. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncoryhnchus kisutch) to address three issues. First, we demonstrate that a single glacial refugium is the source of the majority of present-day genetic diversity, with minor but detectable inputs from secondary micro-refugia. We propose a scenario whereby several ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Following this expansion, we identify particular populations having undergone continuous declines in population size (Ne). Second, we combine multiple evidence from demographic modelling, analysis of recombination landscape, and genome-wide landscape of diversity to demonstrate that selection at linked sites and Hill-Robertson interference played a major role in shaping genetic diversity across the Coho salmon genome. Third, we demonstrate that this demographic history generated subtle differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations. Taken together, we found considerable support for the joint contributions of demographic history and linked selection in the load of deleterious mutations. We suggest that these inferences should be better integrated in conservation genetics of managed fish species which currently focuses largely on within-population adaptation. Author SummaryReconstruction of a species' past demographic history from genome-wide data allows understanding how historical factors interact with intrinsic genomic properties to shape the distribution of genetic diversity along its genome and its geographic range. Here, we combine genotyping-by-sequencing and whole genome sequence data with demographic modelling to address these issues in the Coho salmon, a Pacific salmon species with rapidly declining census size in some parts of its range, notably in the south. Our demographic reconstructions indicate a linear decrease in genetic diversity towards the north of the species range, supporting the hypothesis of a major southern refugia for the Coho salmon and a northern route of postglacial recolonization. Accordingly, the number of candidate deleterious homozygous derived mutations was higher in northern populations. Demographic modelling also suggested the existence of cryptic refugia that may have been missed with the use of simpler summary statistics. We further showed that the species' genome was shaped by linked selection and biased gene conv...

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Section: Expansion From a Major Southern Refugium And Secondary Contasupporting

confidence: 86%

Section: Expansion From a Major Southern Refugium And Secondary Contasupporting

confidence: 85%

Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

Rougemont

Moore

Leroy

et al. 2019

Preprint

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“…in 1993: he transplanted 100 adult stickleback from a large, deep, dystrophic, blackwater lake (Mayer Lake) with vertebrate-dominated predation into a small, shallow, eutrophic, previously unoccupied clearwater pond (Roadside Pond) dominated by invertebrate predators 41 . Mayer Lake contains some of the most derived freshwater stickleback, maximally divergent from the ancestral marine phenotype and occupying the extreme morphospace edge of the Haida Gwaii adaptive radiation 30 : 8-10 cm long, melanistic ‘giants’ with highly developed predator defence and adaptations to limnetic foraging 42,43 , low levels of phenotypic variance 31 but similar levels of genetic variation as other Haida Gwaii populations 34,44 . After evolving for 16 years in the new selective regime, six predator defence, four feeding morphology traits and eye size evolved in the expected direction (Fig.…”

mentioning

confidence: 99%

Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation

et al. 2018

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A substantial part of biodiversity is thought to have arisen from adaptive radiations in which one lineage rapidly diversified into multiple lineages specialized to many different niches. However, selection and drift reduce genetic variation during adaptation to new niches and may thus prevent or slow down further niche shifts. We tested whether rapid adaptation is still possible from a highly derived ecotype in the adaptive radiation of threespine stickleback on the Haida Gwaii archipelago, Western Canada. In a 19-year selection experiment, we let giant sticklebacks from a large blackwater lake evolve in a small clearwater pond without vertebrate predators. A total of 56 whole genomes from the experiment and 26 natural populations revealed that adaptive genomic change was rapid in many small genomic regions and encompassed 75% of the change between 12,000-year-old ecotypes. Genomic change was as fast as phenotypic change in defence and trophic morphology, and both were largely parallel between the short-term selection experiment and long-term natural adaptive radiation. Our results show that functionally relevant standing genetic variation can persist in derived radiation members, allowing adaptive radiations to unfold very rapidly.

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Living on the edge: Exploring the role of coastal refugia in the Alexander Archipelago of Alaska

Sawyer

MacDonald

Lessa

et al. 2019

Ecology and Evolution

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Although islands are of long‐standing interest to biologists, only a handful of studies have investigated the role of climatic history in shaping evolutionary diversification in high‐latitude archipelagos. In this study of the Alexander Archipelago (AA) of Southeast Alaska, we address the impact of glacial cycles on geographic genetic structure for three mammals co‐distributed along the North Pacific Coast. We examined variation in mitochondrial and nuclear loci for long‐tailed voles ( Microtus longicaudus ), northwestern deermice ( Peromyscus keeni ), and dusky shrews ( Sorex monticola ), and then tested hypotheses derived from Species Distribution Models, reconstructions of paleoshorelines, and island area and isolation. In all three species, we identified paleoendemic clades that likely originated in coastal refugia, a finding consistent with other paleoendemic lineages identified in the region such as ermine. Although there is spatial concordance at the regional level for endemism, finer scale spatial and temporal patterns are less clearly defined. Demographic expansion across the region for these distinctive clades is also evident and highlights the dynamic history of Late Quaternary contraction and expansion that characterizes high‐latitude species.

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MITOCHONDRIAL DNA INGASTEROSTEUSAND PLEISTOCENE GLACIAL REFUGIUM ON THE QUEEN CHARLOTTE ISLANDS, BRITISH COLUMBIA

Cited by 61 publications

References 48 publications

Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon

Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation

Living on the edge: Exploring the role of coastal refugia in the Alexander Archipelago of Alaska

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