干旱区生态环境知识资源中心(Arid): Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA

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DOI	10.1002/ece3.6082
	Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA
	Moore, Grace 1,2; Tessler, Michael 2; Cunningham, Seth W.2; Betancourt, Julio 3; Harbert, Robert 2,4
通讯作者	Harbert, Robert
来源期刊	ECOLOGY AND EVOLUTION
ISSN	2045-7758
出版年	2020
卷号	10 期号:5 页码:2530-2544
英文摘要	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.
英文关键词	ancient DNA metagenomics Neotoma paleoecology
类型	Article
语种	英语
国家	USA
开放获取类型	Green Published, gold
收录类别	SCI-E
WOS记录号	WOS:000514401800001
WOS关键词	MOLECULAR ANALYSIS ; ATACAMA DESERT ; RODENT MIDDENS ; SMALL MAMMALS ; GROUND SLOTH ; ARIZONA ; HOLOCENE ; HISTORY ; PLANT ; DIET
WOS类目	Ecology ; Evolutionary Biology
WOS研究方向	Environmental Sciences & Ecology ; Evolutionary Biology
来源机构	United States Geological Survey
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/314371
作者单位	1.Smith Coll, Northampton, MA 01063 USA; 2.Amer Museum Nat Hist, Sackler Inst Comparat Genom, New York, NY 10024 USA; 3.USGS, Reston, VA USA; 4.Stonehill Coll, Easton, MA 02357 USA
推荐引用方式 GB/T 7714	Moore, Grace,Tessler, Michael,Cunningham, Seth W.,et al. Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA[J]. United States Geological Survey,2020,10(5):2530-2544.
APA	Moore, Grace,Tessler, Michael,Cunningham, Seth W.,Betancourt, Julio,&Harbert, Robert.(2020).Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA.ECOLOGY AND EVOLUTION,10(5),2530-2544.
MLA	Moore, Grace,et al."Paleo-metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA".ECOLOGY AND EVOLUTION 10.5(2020):2530-2544.