Literature DB >> 28173586

Evolutionary Patterns and Processes: Lessons from Ancient DNA.

Michela Leonardi1, Pablo Librado1, Clio Der Sarkissian1, Mikkel Schubert1, Ahmed H Alfarhan2, Saleh A Alquraishi2, Khaled A S Al-Rasheid2, Cristina Gamba1, Eske Willerslev1,2, Ludovic Orlando1,3.   

Abstract

Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.

Entities:  

Keywords:  Ancient DNA; metagenomics; palaeogenomics; population genomics; temporal sampling

Mesh：

Substances：

Year:  2017        PMID： 28173586      PMCID： PMC5410953          DOI： 10.1093/sysbio/syw059

Source DB:  PubMed          Journal:  Syst Biol        ISSN： 1063-5157            Impact factor:   9.160


  244 in total

1.  On the number of segregating sites in genetical models without recombination.

Authors:  G A Watterson
Journal:  Theor Popul Biol       Date:  1975-04       Impact factor: 1.570

2.  A Bayesian phylogenetic method to estimate unknown sequence ages.

Authors:  Beth Shapiro; Simon Y W Ho; Alexei J Drummond; Marc A Suchard; Oliver G Pybus; Andrew Rambaut
Journal:  Mol Biol Evol       Date:  2010-10-01       Impact factor: 16.240

3.  Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?

Authors:  James Haile; Richard Holdaway; Karen Oliver; Michael Bunce; M Thomas P Gilbert; Rasmus Nielsen; Kasper Munch; Simon Y W Ho; Beth Shapiro; Eske Willerslev
Journal:  Mol Biol Evol       Date:  2007-01-25       Impact factor: 16.240

4.  Statistical assignment of DNA sequences using Bayesian phylogenetics.

Authors:  Kasper Munch; Wouter Boomsma; John P Huelsenbeck; Eske Willerslev; Rasmus Nielsen
Journal:  Syst Biol       Date:  2008-10       Impact factor: 15.683

5.  Genetic discontinuity between local hunter-gatherers and central Europe's first farmers.

Authors:  B Bramanti; M G Thomas; W Haak; M Unterlaender; P Jores; K Tambets; I Antanaitis-Jacobs; M N Haidle; R Jankauskas; C-J Kind; F Lueth; T Terberger; J Hiller; S Matsumura; P Forster; J Burger
Journal:  Science       Date:  2009-09-03       Impact factor: 47.728

6.  Testing for ancient admixture between closely related populations.

Authors:  Eric Y Durand; Nick Patterson; David Reich; Montgomery Slatkin
Journal:  Mol Biol Evol       Date:  2011-02-15       Impact factor: 16.240

7.  Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques.

Authors:  Torsten Günther; Cristina Valdiosera; Helena Malmström; Irene Ureña; Ricardo Rodriguez-Varela; Óddny Osk Sverrisdóttir; Evangelia A Daskalaki; Pontus Skoglund; Thijessen Naidoo; Emma M Svensson; José María Bermúdez de Castro; Eudald Carbonell; Michael Dunn; Jan Storå; Eneko Iriarte; Juan Luis Arsuaga; José-Miguel Carretero; Anders Götherström; Mattias Jakobsson
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-08       Impact factor: 11.205

Review 8.  Human migrations and population structure: what we know and why it matters.

Authors:  David B Goldstein; Lounès Chikhi
Journal:  Annu Rev Genomics Hum Genet       Date:  2002-04-15       Impact factor: 8.929

Review 9.  Revising the human mutation rate: implications for understanding human evolution.

Authors:  Aylwyn Scally; Richard Durbin
Journal:  Nat Rev Genet       Date:  2012-09-11       Impact factor: 53.242

10.  Efficient moment-based inference of admixture parameters and sources of gene flow.

Authors:  Mark Lipson; Po-Ru Loh; Alex Levin; David Reich; Nick Patterson; Bonnie Berger
Journal:  Mol Biol Evol       Date:  2013-05-24       Impact factor: 16.240
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  23 in total

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Authors:  Jennifer C French; Philip Riris; Javier Fernandéz-López de Pablo; Sergi Lozano; Fabio Silva
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-11-30       Impact factor: 6.237

2.  Estimation of Natural Selection and Allele Age from Time Series Allele Frequency Data Using a Novel Likelihood-Based Approach.

Authors:  Zhangyi He; Xiaoyang Dai; Mark Beaumont; Feng Yu
Journal:  Genetics       Date:  2020-08-07       Impact factor: 4.562

Review 3.  Fostering Responsible Research on Ancient DNA.

Authors:  Jennifer K Wagner; Chip Colwell; Katrina G Claw; Anne C Stone; Deborah A Bolnick; John Hawks; Kyle B Brothers; Nanibaa' A Garrison
Journal:  Am J Hum Genet       Date:  2020-08-06       Impact factor: 11.025

4.  A new model for ancient DNA decay based on paleogenomic meta-analysis.

Authors:  Logan Kistler; Roselyn Ware; Oliver Smith; Matthew Collins; Robin G Allaby
Journal:  Nucleic Acids Res       Date:  2017-06-20       Impact factor: 16.971

Review 5.  Harnessing ancient genomes to study the history of human adaptation.

Authors:  Stephanie Marciniak; George H Perry
Journal:  Nat Rev Genet       Date:  2017-09-11       Impact factor: 53.242

Review 6.  Peopling of the Americas as inferred from ancient genomics.

Authors:  Eske Willerslev; David J Meltzer
Journal:  Nature       Date:  2021-06-16       Impact factor: 49.962

Review 7.  Sometimes hidden but always there: the assumptions underlying genetic inference of demographic histories.

Authors:  Liisa Loog
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-11-30       Impact factor: 6.237

8.  Performance and automation of ancient DNA capture with RNA hyRAD probes.

Authors:  Tomasz Suchan; Mariya A Kusliy; Naveed Khan; Loreleï Chauvey; Laure Tonasso-Calvière; Stéphanie Schiavinato; John Southon; Marcel Keller; Keiko Kitagawa; Johannes Krause; Alexander N Bessudnov; Alexander A Bessudnov; Alexander S Graphodatsky; Silvia Valenzuela-Lamas; Jarosław Wilczyński; Sylwia Pospuła; Krzysztof Tunia; Marek Nowak; Magdalena Moskal-delHoyo; Alexey A Tishkin; Alexander J E Pryor; Alan K Outram; Ludovic Orlando
Journal:  Mol Ecol Resour       Date:  2021-10-15       Impact factor: 8.678

Review 9.  Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.

Authors:  Anja Spang; Tara A Mahendrarajah; Pierre Offre; Courtney W Stairs
Journal:  Genome Biol Evol       Date:  2022-05-31       Impact factor: 4.065

10.  Human mobility at Tell Atchana (Alalakh), Hatay, Turkey during the 2nd millennium BC: Integration of isotopic and genomic evidence.

Authors:  Tara Ingman; Stefanie Eisenmann; Eirini Skourtanioti; Murat Akar; Jana Ilgner; Guido Alberto Gnecchi Ruscone; Petrus le Roux; Rula Shafiq; Gunnar U Neumann; Marcel Keller; Cäcilia Freund; Sara Marzo; Mary Lucas; Johannes Krause; Patrick Roberts; K Aslıhan Yener; Philipp W Stockhammer
Journal:  PLoS One       Date:  2021-06-30       Impact factor: 3.240
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