Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea

Steeves, Tammy E.; Holdaway, Richard N.; Hale, Marie L.; McLay, Emma; McAllan, Ian A W; Christian, Margaret; Hauber, Márk E.; Bunce, Michael

doi:10.1098/rsbl.2009.0478

Cited by 18 publications

(14 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Comparing ancient and modern DNA sequences using molecular techniques is a framework that has been used to decipher the population origin of species or lineages [4,5]. However, the DNA of most ancient samples is heavily degraded and its preservation depends deeply on different processes that take place after cellular death, including availability of water and changes to the environmental conditions in which bone or soft tissue preservation occurs [6].…”

Section: Introductionmentioning

confidence: 99%

Ancient DNA and the tropics: a rodent's tale

et al. 2014

View full text Add to dashboard Cite

Most genetic studies of Holocene fauna have been performed with ancient samples from dry and cold regions, in which preservation of fossils is facilitated and molecular damage is reduced. Ancient DNA work from tropical regions has been precluded owing to factors that limit DNA preservation (e.g. temperature, hydrolytic damage). We analysed ancient DNA from rodent jawbones identified as Ototylomys phyllotis, found in Holocene and Late Pleistocene stratigraphic layers from Loltú n, a humid tropical cave located in the Yucatan peninsula. We extracted DNA and amplified six short overlapping fragments of the cytochrome b gene, totalling 666 bp, which represents an unprecedented success considering tropical ancient DNA samples. We performed genetic, phylogenetic and divergence time analyses, combining sequences from ancient and modern O. phyllotis, in order to assess the ancestry of the Loltú n samples. Results show that all ancient samples fall into a unique clade that diverged prior to the divergence of the modern O. phyllotis, supporting it as a distinct Pleistocene form of the Ototylomys genus. Hence, this rodent's tale suggests that the sister group to modern O. phyllotis arose during the Miocene -Pliocene, diversified during the Pleistocene and went extinct in the Holocene.

show abstract

Section: Introductionmentioning

confidence: 99%

Ancient DNA and the tropics: a rodent's tale

et al. 2014

View full text Add to dashboard Cite

show abstract

“…However, reconstruction of past species ranges is not straightforward, due to major differences in sampling availability and data quality between modern‐day ecological studies and fossil, zooarchaeological or historical records (Turvey, ). One source of confusion arises from the increased tendency for palaeontological research to generate taxonomic inflation through overdescription, which has led to some locally extirpated populations of surviving species being erroneously described as distinct, supposedly extinct ‘species’ (see Pregill, and Steeves et al ., for examples), thus hindering accurate reconstruction of past species ranges and the magnitude of human‐caused biodiversity loss through misperception of ‘pseudo‐extinctions’.…”

Section: Introductionmentioning

confidence: 99%

Holocene range collapse of giant muntjacs and pseudo‐endemism in the Annamite large mammal fauna

Turvey

Hansford

Brace

et al. 2016

Journal of Biogeography

View full text Add to dashboard Cite

Aim To clarify the post-glacial biogeography of the Annamite and eastern Chinese ungulate faunas, and determine whether current understanding of Asian mammalian biogeography is biased by pseudo-extinctions and pseudo-endemism associated with a historical extinction filter.Location Modern-day specimens of giant muntjac (Muntiacus vuquangensis) from the Annamite Mountains of Laos and Vietnam were compared with zooarchaeological specimens of extinct giant muntjac (M. gigas) from eastern China, and with a reference sample of northern red muntjac (M. vaginalis) from China, Southeast Asia and South Asia.Methods We analysed a data set of antler measurements using Multivariate analyses of variance (MANOVAs), principal component analyses (PCAs) and scaling relationships, to quantify morphometric variation between extinct and living giant muntjacs in relation to variation shown by a different sympatric large-bodied muntjac species. We also attempted ancient biomolecule analysis of Holocene samples from China.Results Although the combined giant muntjac sample can be differentiated from the reference red muntjac sample in all of our multivariate morphometric analyses, no significant differences are shown between extinct and living giant muntjacs using any analyses, matching the pattern seen when comparing conspecific red muntjac samples from across the same geographical region.Main conclusions We find no support for recognizing extinct and living giant muntjacs as distinct taxa, and post-glacial populations from China and the Annamites should probably all be referred to M. gigas. The likely conspecificity of giant muntjacs across Eastern and Southeast Asia demonstrates that current-day Asian mammalian biogeography has been shaped by an extinction filter and challenges the idea that the Annamite region represents a cradle of evolution; instead, it may represent a refuge of diversity for some taxa, preserving remnant pseudo-endemic populations of species that have been extirpated across other parts of their former ranges.

show abstract

“…However, wider biogeographical trends and patterns of range collapse remain poorly understood (e.g. Fagan et al, 2005;Turvey et al, 2010), and ancient DNA studies have recently revised our understanding of spatial patterns of population extinction and connectivity for several seabird species (Boessenkool et al, 2009;Steeves et al, 2009;Ram ırez et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Late Holocene range collapse in a former British seabird species

Brace

Barnes

Kitchener

et al. 2014

Journal of Biogeography

View full text Add to dashboard Cite

Aim To determine the taxonomic identity of zooarchaeological gadfly petrel (Pterodroma) specimens from northern Europe, in order to investigate whether an unknown, now‐extinct Pterodroma species formerly occurred in this region, or whether extant north‐east Atlantic gadfly petrel populations now restricted to the Macaronesian Islands formerly had a much wider Holocene distribution. Location Zooarchaeological Pterodroma material from the Hebrides, Scotland, was compared with modern‐day material from the Madeira and Cape Verde archipelagos (Macaronesia) and a global Pterodroma sample. Methods We employed techniques for ancient DNA analysis to amplify mitochondrial cytochrome b sequence data from an Iron Age Scottish Pterodroma specimen. Bayesian phylogenetic analyses were applied to assess the phylogenetic relationship between these ancient sequence data and extant Pterodroma taxa. Results The Scottish Pterodroma sample is phylogenetically distinct from living Macaronesian populations and from all other extant Pterodroma taxa. Although it is phylogenetically placed outside any single Macaronesian taxon, it is most closely related to the P. feae–deserta complex, and the level of sequence divergence between the Scottish Pterodroma and Macaronesian populations is lower than that observed between any two extant global Pterodroma taxa. The extinct north Atlantic gadfly petrels are therefore not distinct at the species level from these surviving populations, and instead form part of the young evolutionary radiation represented today by recently divergent Pterodroma populations on Bugio and Cape Verde, which can all be interpreted as conspecific. Main conclusions Our results suggest that surviving Macaronesian P. feae–deserta populations represent the final remnant of a wider Holocene distribution of this species complex, with the Madeira and Cape Verde archipelagos constituting the final sanctuary of Pterodroma in the north Atlantic following late Holocene extirpation of more northerly colonies possibly associated with human‐mediated invasive mammal introduction across northern Europe. Macaronesia may therefore constitute a ‘museum’ of diversity rather than a ‘cradle’ of evolution for Atlantic Pterodroma.

show abstract

Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea

Cited by 18 publications

References 13 publications

Ancient DNA and the tropics: a rodent's tale

Ancient DNA and the tropics: a rodent's tale

Holocene range collapse of giant muntjacs and pseudo‐endemism in the Annamite large mammal fauna

Late Holocene range collapse in a former British seabird species

Contact Info

Product

Resources

About