• New non-destructive DNA method opens opp

    From ScienceDaily@1:317/3 to All on Tue Apr 5 22:30:38 2022
    New non-destructive DNA method opens opportunities

    Date:
    April 5, 2022
    Source:
    University of Otago
    Summary:
    A new method of obtaining ancient genomic data without damaging
    source material has been developed, creating new opportunities
    for museum and archaeological collections worldwide.



    FULL STORY ==========================================================================
    A new method of obtaining ancient genomic data without damaging source
    material has been developed by University of Otago researchers, creating
    new opportunities for museum and archaeological collections worldwide.


    ========================================================================== "Ancient DNA doesn't have to be destructive," says lead author Lachie Scarsbrook. "Our new method allows the reconstruction of genetic whakapapa without destroying the very bone that's kept its secrets for thousands of years." The research, published in the international journal Molecular Ecology, presents a new method of obtaining genomic data from small
    vertebrate remains that causes no visible damage to the underlying bone.

    "This will not only facilitate analyses on materials in museum collections
    that are either too small to be destructively sampled, but also more
    rare and valuable materials, both culturally and scientifically," Mr
    Scarsbrook says.

    The study, undertaken when Mr Scarsbrook was completing a Master of
    Science in the Department of Zoology, used contemporary and extinct
    populations of Hoplodactylus geckos as a case study, and represents the
    first mitochondrial genomes obtained for any New Zealand lizard.

    The newly sequenced DNA data allowed researchers to understand and show
    how tectonic activity, climate change and human impact have influenced Duvaucel's gecko (Hoplodactylus duvauceli) populations regionally within
    New Zealand.



    ========================================================================== "Deep splits between North and South Island populations reflect long-term isolation prior to the formation of Cook Strait, while South Island
    populations show genetic breaks geographically consistent with maximum ice coverage during the height of the last Ice Age," Mr Scarsbrook explains.

    "The significant loss of genetic diversity in both North and South
    Island populations is testament to the impact of humans and introduced predators. Our research is having meaningful and direct impacts on the conservation management of Duvaucel's gecko." Supervisor and co-author
    of the study, Dr Nic Rawlence of the Otago Palaeogenetics Laboratory
    says that one of the upshots of this research is that knowledge of New Zealand's geckos at the time of human arrival is now a clean slate.

    "It was previously thought that you could only distinguish between bones
    of different gecko species on the basis of size, but amazingly CT scans
    and ancient DNA showed that we could in fact distinguish different
    geckos using shape alone -- size got thrown out with the bathwater,"
    Dr Rawlence says.



    ==========================================================================
    "It turns out size doesn't matter after all, meaning what we know
    about New Zealand's geckos at the time of human arrival is now a palaeontological clean slate." Currently completing his DPhil in the Palaeogenomics and Bio-Archaeology Research Network at the University
    of Oxford, Mr Scarsbrook says the research also speaks to the process
    involved with making scientific progress.

    "We first attempted to obtain mitochondrial genomes using a different
    method, and after months of time in the laboratory, we failed to produce
    usable data." "After going back to the drawing board and making some
    changes we achieved our goal, which just goes to show that perseverance
    in the face of failure is key if you're going to help make scientific advancements." Dr Rawlence says the continuing research programme will
    use these new techniques to reconstruct the lost ecological history of
    New Zealand's gecko and skinks (where size-based identifications have confounded scientists), and frogs and tuatara, in partnership with the Department of Conservation and M?ori iwi.

    "The long-term conservation of finite specimens is of huge concern to
    curators globally, so what Lachie has developed will not only unlock
    molecular secrets but potentially vast swaths of natural history and archaeological collections globally to similar genetic analysis."

    ========================================================================== Story Source: Materials provided by University_of_Otago. Note: Content
    may be edited for style and length.


    ========================================================================== Journal Reference:
    1. Lachie Scarsbrook, Alexander J. F. Verry, Kerry Walton, Rodney A.

    Hitchmough, Nicolas J. Rawlence. Ancient mitochondrial genomes
    recovered from small vertebrate bones through minimally destructive
    DNA extraction: Phylogeography of the New Zealand gecko genus
    Hoplodactylus. Molecular Ecology, 2022; DOI: 10.1111/mec.16434 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2022/04/220405084557.htm

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