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Demographic reconstruction from ancient DNA supports rapid extinction of the great auk.

ABSTRACT: The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.

SUBMITTER: Thomas JE

PROVIDER: S-EPMC6879203 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Demographic reconstruction from ancient DNA supports rapid extinction of the great auk.

Thomas Jessica E JE Carvalho Gary R GR Haile James J Rawlence Nicolas J NJ Martin Michael D MD Ho Simon Yw SY Sigfússon Arnór Þ AÞ Jósefsson Vigfús A VA Frederiksen Morten M Linnebjerg Jannie F JF Samaniego Castruita Jose A JA Niemann Jonas J Sinding Mikkel-Holger S MS Sandoval-Velasco Marcela M Soares André Er AE Lacy Robert R Barilaro Christina C Best Juila J Brandis Dirk D Cavallo Chiara C Elorza Mikelo M Garrett Kimball L KL Groot Maaike M Johansson Friederike F Lifjeld Jan T JT Nilson Göran G Serjeanston Dale D Sweet Paul P Fuller Errol E Hufthammer Anne Karin AK Meldgaard Morten M Fjeldså Jon J Shapiro Beth B Hofreiter Michael M Stewart John R JR Gilbert M Thomas P MTP Knapp Michael M

eLife 20191126

The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holoc ...[more]

PMID: 31767056

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Project description:Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the "Gymnomera"). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.].

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Demographic reconstruction from ancient DNA supports rapid extinction of the great auk.

Publications

Demographic reconstruction from ancient DNA supports rapid extinction of the great auk.

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