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The DOI matches its Crossref record; 19 of the 19 references it cites were found in a registry or an index.

A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA

Shapiro, B., Hofreiter, M.·2014·Science
DOI 10.1126/science.1236573
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Abstract

Background: After three decades of research aimed at recovering DNA from preserved remains, the field of ancient DNA is moving rapidly toward the sequencing and analysis of complete paleogenomes. These data provide a means to better understand evolutionary processes through time, including inference of ancient demography and admixture between lineages, as well as adaptive evolution within populations. Advances: Key advances enabling a paleogenomic perspective include improvements in DNA extraction and library preparation, as well as methods to enrich ancient libraries for targeted loci. These methods have made it possible to isolate ancient DNA from a far wider range of preservation environments than has been assumed to be attainable, including extending the temporal reach of ancient DNA back to nearly 1 million years. Outlook: Although relatively few paleogenomes have been published to date, their number is rising rapidly, and it is increasingly clear that the range of specimens from which paleogenomes could be produced is much larger than has been assumed previously. As more data become available, including genomic data from living organisms, the capacity to use paleogenomic data to infer evolutionary change through time will continue to expand, particularly with respect to the evolution of populations and the link between genotype and phenotype.

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  • Parameters maximizing mapping specificity and sensitivity depend on the evolutionary distance to the reference genome used, DNA fragment size and the amount of post-mortem damage.

    “Parameters maximizing mapping specificity and sensitivity can be identified using aDNA read simulators such as 16 gargammel 180 , and depend on the evolutionary distance to the reference genome used, DNA fragment size and the amount of post-mortem damage 111,181-184 .”

    From Ancient DNA analysis (2021) · cites this paper as [182]

    In “Hominin Paleogenomics,” the review says very short fragments are difficult to map unambiguously; Fig. 3 says increasing evolutionary distance reduces the proportion of reads mappable to a reference genome. Our copy does not state that mapping parameters maximizing specificity and sensitivity depend on post-mortem damage, or identify such optimal parameters. Page numbers were not supplied for these passages. (LLM, conf=0.84)

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Metadata

Authors
Shapiro, B., & Hofreiter, M.
Affiliations
  • Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
  • Department of Biology, The University of York, Wentworth Way, York YO10 5DD, UK.
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2014-01-24
Volume
343
Issue
6169
ISSN
  • 0036-8075
  • 1095-9203
DOI
10.1126/science.1236573
Cited by
192
References
19
Language
en

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