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Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA

Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted an...

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Autores principales: Moore, Grace, Tessler, Michael, Cunningham, Seth W., Betancourt, Julio, Harbert, Robert
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069311/
https://www.ncbi.nlm.nih.gov/pubmed/32184999
http://dx.doi.org/10.1002/ece3.6082
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author Moore, Grace
Tessler, Michael
Cunningham, Seth W.
Betancourt, Julio
Harbert, Robert
author_facet Moore, Grace
Tessler, Michael
Cunningham, Seth W.
Betancourt, Julio
Harbert, Robert
author_sort Moore, Grace
collection PubMed
description Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C(14) years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI “nt” database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well‐preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.
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spelling pubmed-70693112020-03-17 Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA Moore, Grace Tessler, Michael Cunningham, Seth W. Betancourt, Julio Harbert, Robert Ecol Evol Original Research Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C(14) years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI “nt” database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well‐preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power. John Wiley and Sons Inc. 2020-02-20 /pmc/articles/PMC7069311/ /pubmed/32184999 http://dx.doi.org/10.1002/ece3.6082 Text en © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
Moore, Grace
Tessler, Michael
Cunningham, Seth W.
Betancourt, Julio
Harbert, Robert
Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA
title Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA
title_full Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA
title_fullStr Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA
title_full_unstemmed Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA
title_short Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA
title_sort paleo‐metagenomics of north american fossil packrat middens: past biodiversity revealed by ancient dna
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069311/
https://www.ncbi.nlm.nih.gov/pubmed/32184999
http://dx.doi.org/10.1002/ece3.6082
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