Comparative population genomics reveals key barriers to dispersal in Southern Ocean penguins

Clucas, Gemma V.; Younger, Jane L.; Kao, Damian; Emmerson, Louise; Southwell, Colin; Wienecke, Bárbara; Rogers, Alex D.; Bost, Charles A.; Miller, Gary D.; Polito, Michael J.; Lelliott, Patrick M.; Handley, Jonathan; Crofts, Sarah; Phillips, Richard A.; Dünn, Michael J.; Miller, Karen J.; Hart, Tom

doi:10.1111/mec.14896

Cited by 41 publications

(62 citation statements)

References 112 publications

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“…Despite the apparent homogeneity of the Southern Ocean it harbours geographically structured populations of many species and is a hotbed for adaptation (see examples given in Rogers, 2007 and Moon, Chown & Fraser, 2017). For example, pelagic versus coastal niche, and oceanographic fronts, shape the range, dispersal potential and consequently genetic structuring among Southern Ocean penguin populations (Clucas et al, 2018). Our findings of structure between Antarctic and all other killer whales, in addition to previous findings of structure between Antarctic types B1, B2 and C (Foote et al, 2016) are therefore consistent with patterns in other Antarctic taxa.…”

Section: Discussionsupporting

confidence: 90%

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

Foote

Martin

Louis

et al. 2019

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Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global dataset of killer whale genomes in a rare attempt to elucidate global population structure in a non-human species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during post-glacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations.Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

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Section: Discussionsupporting

confidence: 90%

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

Foote

Martin

Louis

et al. 2019

Preprint

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“…The APF is a nonphysical barrier that could produce genetic differentiation (e.g., toothfish and penguin spp. ; Clucas et al, ; Frugone et al, ; Shaw, Arkhipkin, & Al‐Khairulla, ; Vianna et al, ), but there is little evidence that the APF is a barrier to flying seabirds like white‐chinned petrels; rather, we see gene flow between islands that lie either side of the APF (Falkland Islands and South Georgia; Figure ). Glacial cycles have had profound influences on the distribution of other Southern Ocean species (penguins, elephant seals Mirounga leonina ; Durvillaea kelp, Catharacta skuas; Clucas et al, ; de Bruyn et al, ; Fraser, Nikula, Spencer, & Waters, ; Frugone et al, ; Ritz et al, ; Vianna et al, ), and white‐chinned petrels appear to be highly philopatric, like most seabirds (Schreiber & Burger, ; Warham, ).…”

Section: Discussionmentioning

confidence: 73%

“…ACC is the Antarctic Circumpolar Current, or west-wind drift (ACC arrows and fronts drawn from Orsi & Harris, 2015;Orsi, Whitworth, & Nowlin, 1995), and seaice maximum is the mean September extent (AAD, 2017). Oceanographic zones are STZ subtropical zone; SAZ subantarctic zone; PFZ polar frontal zone; and AZ Antarctic Zone [Colour figure can be viewed at wileyonlinelibrary.com] and coastal shelf waters) compared with species that forage mostly inshore (Burg & Croxall, 2001;Clucas et al, 2018), and white-chinned petrels forage over very large distances in polar-temperate waters (e.g. Rollinson et al, 2018).…”

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confidence: 99%

“…toothfish and penguin spp. ;Clucas et al, 2018;Frugone et al, 2018; TA B L E 4 Genetic differentiation of white-chinned petrels between island groups (F ST , island-pair comparisons) based on the data set of 60Bold highlights comparisons among breeding sites within ocean basins. Breeding islands: ANT, Antipodes; AKL, Auckland; CBL, Campbell; PEI, Prince Edwards; CRZ, Crozet; FKL, Falklands; SG, South Georgia.…”

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confidence: 99%

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Genomics detects population structure within and between ocean basins in a circumpolar seabird: The white‐chinned petrel

et al. 2019

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The Southern Ocean represents a continuous stretch of circumpolar marine habitat, but the potential physical and ecological drivers of evolutionary genetic differentiation across this vast ecosystem remain unclear. We tested for genetic structure across the full circumpolar range of the white‐chinned petrel (Procellaria aequinoctialis) to unravel the potential drivers of population differentiation and test alternative population differentiation hypotheses. Following range‐wide comprehensive sampling, we applied genomic (genotyping‐by‐sequencing or GBS; 60,709 loci) and standard mitochondrial‐marker approaches (cytochrome b and first domain of control region) to quantify genetic diversity within and among island populations, test for isolation by distance, and quantify the number of genetic clusters using neutral and outlier (non‐neutral) loci. Our results supported the multi‐region hypothesis, with a range of analyses showing clear three‐region genetic population structure, split by ocean basin, within two evolutionary units. The most significant differentiation between these regions confirmed previous work distinguishing New Zealand and nominate subspecies. Although there was little evidence of structure within the island groups of the Indian or Atlantic oceans, a small set of highly‐discriminatory outlier loci could assign petrels to ocean basin and potentially to island group, though the latter needs further verification. Genomic data hold the key to revealing substantial regional genetic structure within wide‐ranging circumpolar species previously assumed to be panmictic.

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“…Despite the apparent homogeneity of the Southern Ocean, it harbours geographically structured populations of many species and is a hotbed for adaptation (see examples given in Rogers, ; Moon, Chown, & Fraser, ). For example, pelagic versus coastal niche, and oceanographic fronts, shape the range, dispersal potential and consequently genetic structuring among Southern Ocean penguin populations (Clucas et al, ). Our findings of structure between Antarctic and all other killer whales, in addition to previous findings of structure between Antarctic types B1, B2 and C (Foote et al, ) are therefore consistent with patterns in other Antarctic taxa.…”

Section: Discussionmentioning

confidence: 99%

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

et al. 2019

View full text Add to dashboard Cite

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree‐like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non‐Antarctic lineages is further driven by ancestry segments with up to four‐fold older coalescence time than the genome‐wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome‐wide data to sample the variation in ancestry within individuals.

show abstract

Comparative population genomics reveals key barriers to dispersal in Southern Ocean penguins

Cited by 41 publications

References 112 publications

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

Genomics detects population structure within and between ocean basins in a circumpolar seabird: The white‐chinned petrel

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

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