Ancient mitochondrial genomes recovered from small vertebrate bones through minimally destructive DNA extraction: Phylogeography of the New Zealand gecko genus Hoplodactylus. 2023

Lachie Scarsbrook, and Alexander J F Verry, and Kerry Walton, and Rodney A Hitchmough, and Nicolas J Rawlence
Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand.

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.

UI MeSH Term Description Entries
D008116 Lizards Reptiles within the order Squamata that generally possess limbs, moveable EYELIDS, and EXTERNAL EAR openings, although there are some species which lack one or more of these structures. Chameleons,Geckos,Chameleon,Gecko,Lizard
D009520 New Zealand A group of islands in the southwest Pacific. Its capital is Wellington. It was discovered by the Dutch explorer Abel Tasman in 1642 and circumnavigated by Cook in 1769. Colonized in 1840 by the New Zealand Company, it became a British crown colony in 1840 until 1907 when colonial status was terminated. New Zealand is a partly anglicized form of the original Dutch name Nieuw Zeeland, new sea land, possibly with reference to the Dutch province of Zeeland. (From Webster's New Geographical Dictionary, 1988, p842 & Room, Brewer's Dictionary of Names, 1992, p378)
D010802 Phylogeny The relationships of groups of organisms as reflected by their genetic makeup. Community Phylogenetics,Molecular Phylogenetics,Phylogenetic Analyses,Phylogenetic Analysis,Phylogenetic Clustering,Phylogenetic Comparative Analysis,Phylogenetic Comparative Methods,Phylogenetic Distance,Phylogenetic Generalized Least Squares,Phylogenetic Groups,Phylogenetic Incongruence,Phylogenetic Inference,Phylogenetic Networks,Phylogenetic Reconstruction,Phylogenetic Relatedness,Phylogenetic Relationships,Phylogenetic Signal,Phylogenetic Structure,Phylogenetic Tree,Phylogenetic Trees,Phylogenomics,Analyse, Phylogenetic,Analysis, Phylogenetic,Analysis, Phylogenetic Comparative,Clustering, Phylogenetic,Community Phylogenetic,Comparative Analysis, Phylogenetic,Comparative Method, Phylogenetic,Distance, Phylogenetic,Group, Phylogenetic,Incongruence, Phylogenetic,Inference, Phylogenetic,Method, Phylogenetic Comparative,Molecular Phylogenetic,Network, Phylogenetic,Phylogenetic Analyse,Phylogenetic Clusterings,Phylogenetic Comparative Analyses,Phylogenetic Comparative Method,Phylogenetic Distances,Phylogenetic Group,Phylogenetic Incongruences,Phylogenetic Inferences,Phylogenetic Network,Phylogenetic Reconstructions,Phylogenetic Relatednesses,Phylogenetic Relationship,Phylogenetic Signals,Phylogenetic Structures,Phylogenetic, Community,Phylogenetic, Molecular,Phylogenies,Phylogenomic,Reconstruction, Phylogenetic,Relatedness, Phylogenetic,Relationship, Phylogenetic,Signal, Phylogenetic,Structure, Phylogenetic,Tree, Phylogenetic
D004247 DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D004272 DNA, Mitochondrial Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins. Mitochondrial DNA,mtDNA
D000072441 DNA, Ancient DNA isolated from fossils or other ancient specimens. Ancient DNA
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D054629 Genome, Mitochondrial The genetic complement of MITOCHONDRIA as represented in their DNA. Mitochondrial Genome,Genomes, Mitochondrial,Mitochondrial Genomes
D055114 X-Ray Microtomography X-RAY COMPUTERIZED TOMOGRAPHY with resolution in the micrometer range. MicroCT,Microcomputed Tomography,X-Ray Micro-CAT Scans,X-Ray Micro-CT,X-Ray Micro-CT Scans,X-Ray Micro-Computed Tomography,X-Ray Microcomputed Tomography,X-ray MicroCT,Xray Micro-CT,Xray MicroCT,Micro-CAT Scan, X-Ray,Micro-CAT Scans, X-Ray,Micro-CT Scan, X-Ray,Micro-CT Scans, X-Ray,Micro-CT, X-Ray,Micro-CT, Xray,Micro-CTs, X-Ray,Micro-CTs, Xray,Micro-Computed Tomography, X-Ray,MicroCT, X-ray,MicroCT, Xray,MicroCTs,MicroCTs, X-ray,MicroCTs, Xray,Microcomputed Tomography, X-Ray,Microtomography, X-Ray,Scan, X-Ray Micro-CAT,Scan, X-Ray Micro-CT,Scans, X-Ray Micro-CAT,Scans, X-Ray Micro-CT,Tomography, Microcomputed,Tomography, X-Ray Micro-Computed,Tomography, X-Ray Microcomputed,X Ray Micro CAT Scans,X Ray Micro CT,X Ray Micro CT Scans,X Ray Micro Computed Tomography,X Ray Microcomputed Tomography,X Ray Microtomography,X ray MicroCT,X-Ray Micro-CAT Scan,X-Ray Micro-CT Scan,X-Ray Micro-CTs,X-ray MicroCTs,Xray Micro CT,Xray Micro-CTs,Xray MicroCTs
D058974 Phylogeography A field of study concerned with the principles and processes governing the geographic distributions of genealogical lineages, especially those within and among closely related species. (Avise, J.C., Phylogeography: The History and Formation of Species. Harvard University Press, 2000) Phylogenetic Biogeography,Biogeography, Phylogenetic

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