Who, Where, What, Wren? Using Ancient DNA to Examine the Veracity of Museum Specimen Data: A Case Study of the New Zealand Rock Wren (Xenicus gilviventris)

Verry, Alexander J. F.; Scarsbrook, Lachie; Scofield, R. Paul; Tennyson, Alan J. D.; Weston, Kerry A.; Robertson, Bruce C.; Rawlence, Nicolas J.

doi:10.3389/fevo.2019.00496

Cited by 10 publications

(7 citation statements)

References 51 publications

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“…library indexing and hybridisation capture enrichment) were undertaken within a separate modern genetics laboratory. Ancient DNA extraction followed Verry et al . (2019).…”

Section: Methodsmentioning

confidence: 99%

Ancient mitogenomes reveal evidence for the late Miocene dispersal of mergansers to the Southern Hemisphere

Rawlence,

Verry,

Cole

et al. 2023

Preprint

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Mergansers are riverine and coastal piscivorous ducks that are widespread throughout North America and Eurasia but uncommon in the Southern Hemisphere. One species occurs in South America and at least two extinct species from New Zealand. It has been proposed that Southern Hemisphere mergansers were founded by independent dispersal events from the Northern Hemisphere. However, some morphological and behavioural evidence suggests that Southern Hemisphere mergansers may be closely related to one another. They share several characteristics that differ from Northern Hemisphere mergansers (e.g., non-migratory vs. migratory, sexual monochromatism vs. sexual dichromatism, long vs. short pair bonds). We sequenced complete mitogenomes from the Brazilian merganser and an extinct merganser from New Zealand—the Auckland Island merganser. Our results show the Brazilian and Auckland Island mergansers form a monophyletic clade with the common merganser, and that a sister relationship between Southern Hemisphere mergansers cannot be rejected. We cannot exclude the possibility that the Brazilian and Auckland Island mergansers descend from a single dispersal event from the Northern Hemisphere at least seven million years ago. Nuclear (palaeo)genomic data may help to resolve the relationship between living and extinct mergansers, including merganser fossils from New Zealand that have not been subjected to palaeogenetic analysis.

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“…library indexing and hybridisation capture enrichment) were undertaken within a separate modern genetics laboratory. Ancient DNA extraction followed Verry et al . (2019).…”

Section: Methodsmentioning

confidence: 99%

Ancient mitogenomes reveal evidence for the late Miocene dispersal of mergansers to the Southern Hemisphere

Rawlence,

Verry,

Cole

et al. 2023

Preprint

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“…library indexing and hybridisation capture enrichment) were undertaken within a separate modern genetics laboratory. Ancient DNA extractions from bone followed Rohland et al (2010), while ancient DNA extractions from toepad tissue followed Verry et al (2019). DNA extracts were screened for endogenous mitochondrial DNA via PCR of an 85 bp fragment of 12S using the primers 12Shf and 12SKr (Cooper et al, 2001) and/or a 199 bp fragment of the control region using Takdloop1 and Takdloop4 ; see Supporting Information for details).…”

Section: Ancient Takahē and Moho Mitochondrial Genome Sequencingmentioning

confidence: 99%

Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahē and moho

Verry,

Mas‐Carrió,

Gibb

et al. 2023

Molecular Ecology

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Many avian species endemic to Aotearoa New Zealand were driven to extinction or reduced to relict populations following successive waves of human arrival, due to hunting, habitat destruction and the introduction of mammalian predators. Among the affected species were the large flightless South Island takahē (Porphyrio hochstetteri) and the moho (North Island takahē; P. mantelli), with the latter rendered extinct and the former reduced to a single relictual population. Little is known about the evolutionary history of these species prior to their decline and/or extinction. Here we sequenced mitochondrial genomes from takahē and moho subfossils (12 takahē and 4 moho) and retrieved comparable sequence data from takahē museum skins (n = 5) and contemporary individuals (n = 17) to examine the phylogeny and recent evolutionary history of these species. Our analyses suggest that prehistoric takahē populations lacked deep phylogeographic structure, in contrast to moho, which exhibited significant spatial genetic structure, albeit based on limited sample sizes (n = 4). Temporal genetic comparisons show that takahē have lost much of their mitochondrial genetic diversity, likely due to a sudden demographic decline soon after human arrival (~750 years ago). Time‐calibrated phylogenetic analyses strongly support a sister species relationship between takahē and moho, suggesting these flightless taxa diverged around 1.5 million years ago, following a single colonisation of New Zealand by a flighted Porphyrio ancestor approximately 4 million years ago. This study highlights the utility of palaeogenetic approaches for informing the conservation and systematic understanding of endangered species whose ranges have been severely restricted by anthropogenic impacts.

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“…Conversely, shallow genetic divergence between the remaining North Island and northern South Island populations of H. duvaucelii implies widespread population connectivity during periods of eustatically low sea levels (up to 130 m; Lewis et al, 1994); with subsequent isolation (0.32-1.03 and 0.47-1.48 Ma respectively) facilitating increased haplotype diversity both within and between monophyletic island groups. The paraphyly of Hongiora (Alderman Islands) and Korapuki (Mercury Islands) Island populations, however, presents a possible exception to this simple isolation model, with discordance reflecting either recent population connectivity independent of adjacent islands (or incomplete lineage sorting), an undocumented historical translocation or incorrect locality information (repeatedly documented in historical collections; Rawlence et al, 2014;Verry et al, 2019). Erroneous collection records may also explain the unexpected affinities between a "Waitomo" subfossil specimen and the Great Barrier Island population (Figures 3 and 4).…”

Section: Repeated Inundation Of This Region Throughout the Pleistocen...mentioning

confidence: 99%

Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: Phylogeography of the New Zealand gecko genus Hoplodactylus

et al. 2022

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Methodological and technological improvements are continually revolutionizing the field of ancient DNA. Most ancient DNA extraction methods require the partial (or complete) destruction of finite museum specimens, which disproportionately impacts small or fragmentary subfossil remains, and future analyses. We present a minimally destructive ancient DNA extraction method optimized for small vertebrate remains. We applied this method to detect lost mainland genetic diversity in the large New Zealand diplodactylid gecko genus Hoplodactylus, which is presently restricted to predator‐free island and mainland sanctuaries. We present the first mitochondrial genomes for New Zealand diplodactylid geckos, recovered from 19 modern, six historical/archival (1898–2011) and 16 Holocene Hoplodactylus duvaucelii sensu latu specimens, and one modern Woodworthia sp. specimen. No obvious damage was observed in post‐extraction micro‐computed tomography reconstructions. All “large gecko” specimens examined from extinct populations were found to be conspecific with extant Hoplodactylus species, suggesting their large relative size evolved only once in the New Zealand diplodactylid radiation. Phylogenetic analyses of Hoplodactylus samples recovered two genetically (and morphologically) distinct North and South Island clades, probably corresponding to distinct species. Finer phylogeographical structuring within Hoplodactylus spp. highlighted the impacts of Late Cenozoic biogeographical barriers, including the opening and closure of Pliocene marine straits, fluctuations in the size and suitability of glacial refugia, and eustatic sea‐level change. Recent mainland extinction obscured these signals from the modern tissue‐derived data. These results highlight the utility of minimally destructive DNA extraction in genomic analyses of less well studied small vertebrate taxa, and the conservation of natural history collections.

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Who, Where, What, Wren? Using Ancient DNA to Examine the Veracity of Museum Specimen Data: A Case Study of the New Zealand Rock Wren (Xenicus gilviventris)

Cited by 10 publications

References 51 publications

Ancient mitogenomes reveal evidence for the late Miocene dispersal of mergansers to the Southern Hemisphere

Ancient mitogenomes reveal evidence for the late Miocene dispersal of mergansers to the Southern Hemisphere

Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahē and moho

Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: Phylogeography of the New Zealand gecko genus Hoplodactylus

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