Inferences from tip-calibrated phylogenies: a review and a practical guide

Molecular Ecology
Adrien Rieux, François Balloux

Abstract

Molecular dating of phylogenetic trees is a growing discipline using sequence data to co-estimate the timing of evolutionary events and rates of molecular evolution. All molecular-dating methods require converting genetic divergence between sequences into absolute time. Historically, this could only be achieved by associating externally derived dates obtained from fossil or biogeographical evidence to internal nodes of the tree. In some cases, notably for fast-evolving genomes such as viruses and some bacteria, the time span over which samples were collected may cover a significant proportion of the time since they last shared a common ancestor. This situation allows phylogenetic trees to be calibrated by associating sampling dates directly to the sequences representing the tips (terminal nodes) of the tree. The increasing availability of genomic data from ancient DNA extends the applicability of such tip-based calibration to a variety of taxa including humans, extinct megafauna and various microorganisms which typically have a scarce fossil record. The development of statistical models accounting for heterogeneity in different aspects of the evolutionary process while accommodating very large data sets (e.g. whole genomes) has...Continue Reading

References

Dec 29, 1998·Molecular Biology and Evolution·J L ThorneI S Painter
Jun 16, 1999·Journal of Molecular Evolution·P L Bollyky, E C Holmes
Jun 10, 2000·Science·B KorberT Bhattacharya
Jun 23, 2001·Molecular Biology and Evolution·A DrummondA G Rodrigo
Mar 1, 2003·Nature Reviews. Genetics·Lindell Bromham, David Penny
Jan 9, 2004·Advances in Parasitology·Alexei DrummondAndrew Rambaut
Nov 30, 2004·Science·Beth ShapiroAlan Cooper
Oct 14, 2005·Molecular Biology and Evolution·Daniel H Huson, David Bryant
May 11, 2006·PLoS Biology·Alexei J DrummondAndrew Rambaut
May 17, 2006·Trends in Ecology & Evolution·John J Welch, Lindell Bromham
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Jun 15, 2007·Systematic Biology·Simon Y W HoAlexei J Drummond
Jul 7, 2007·Science·Eske WillerslevMatthew J Collins
Sep 6, 2007·Biology Letters·Simon Y W HoRobin G Allaby
Nov 13, 2007·BMC Evolutionary Biology·Alexei J Drummond, Andrew Rambaut
Apr 18, 2008·Molecular Biology and Evolution·Cadhla RamsdenUNKNOWN VGDN Consortium
May 27, 2008·Trends in Ecology & Evolution·Craig D MillarDavid M Lambert
Jun 11, 2008·Proceedings of the National Academy of Sciences of the United States of America·M Thomas P GilbertStephan C Schuster
Jul 26, 2008·Molecular Biology and Evolution·Erik AxelssonRasmus Nielsen
Sep 6, 2008·Microbiology and Molecular Biology Reviews : MMBR·Colin R ParrishPeter Daszak
Nov 6, 2008·Molecular Biology and Evolution·Brenna M HennJoanna L Mountain
Nov 13, 2008·Molecular Biology and Evolution·Andrew RambautBeth Shapiro
May 13, 2009·Science·Christophe FraserUNKNOWN WHO Rapid Pandemic Assessment Collaboration
Jul 18, 2009·Science·Adrian W BriggsSvante Pääbo
Sep 9, 2009·Molecular Ecology·Miguel Navascués, Brent C Emerson
Nov 20, 2009·Proceedings of the National Academy of Sciences of the United States of America·M BunceA Cooper
Feb 12, 2010·Journal of the Royal Society, Interface·J Conrad StackBryan T Grenfell
Mar 26, 2010·Molecular Biology and Evolution·Mathias StillerMichael Knapp
Apr 7, 2010·Molecular Biology and Evolution·Cadhla FirthAndrew Rambaut
May 19, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Simon D W Frost, Erik M Volz
Jun 8, 2010·Bioinformatics·Thibaut JombartStéphane Dray
Jul 27, 2010·Trends in Ecology & Evolution·Robert LanfearLindell Bromham
Oct 5, 2010·Molecular Biology and Evolution·Beth ShapiroAndrew Rambaut
Apr 13, 2011·Molecular Ecology Resources·Simon Y W Ho, Beth Shapiro
Jun 16, 2011·Heredity·C S Smukowski, M A F Noor
Jul 12, 2011·Molecular Ecology·Simon Y W HoAlan Cooper
Oct 14, 2011·Nature·Kirsten I BosJohannes Krause
Feb 10, 2012·Molecular Biology and Evolution·Robert LanfearStephane Guindon

❮ Previous
Next ❯

Citations

Oct 26, 2016·Molecular Ecology Resources·Adrien Rieux, Camilo E Khatchikian
Oct 21, 2016·PLoS Biology·Priya MoorjaniMolly Przeworski
Jan 29, 2017·Molecular Ecology·Loren RiesebergKaren Chambers
Dec 20, 2017·Scientific Reports·James A Fellows YatesJohannes Krause
May 12, 2018·Science·Simon J O'HanlonMatthew C Fisher
Jun 27, 2018·Systematic Biology·Sebastian DucheneAlexei J Drummond
Apr 14, 2018·Scientific Reports·Ning ZhangDebashish Bhattacharya
Apr 28, 2019·Applied and Environmental Microbiology·Mathieu VanhoveRodrigo P P Almeida
Jul 6, 2019·Molecular Biology and Evolution·Fanny WegnerJudith Breuer
Sep 13, 2019·PLoS Pathogens·Fabrizio MenardoSebastien Gagneux
Dec 16, 2017·Biological Reviews of the Cambridge Philosophical Society·Lindell BromhamSimon Y W Ho
Jan 18, 2020·PLoS Computational Biology·Sayaka MiuraSudhir Kumar
Nov 8, 2019·Molecular Biology and Evolution·Lucy van DorpCarles Lalueza-Fox
Feb 27, 2020·Nature Reviews. Microbiology·Matthew C Fisher, Trenton W J Garner
Jun 20, 2018·BMC Evolutionary Biology·Sebastian DucheneKathryn E Holt
Jul 10, 2019·Annual Review of Microbiology·Kirsten I BosJohannes Krause
Jun 20, 2020·Science·Simon Y W Ho, Sebastián Duchêne
Nov 30, 2018·Biological Reviews of the Cambridge Philosophical Society·Byron B LamontZhaogui Yan
Dec 4, 2019·BMC Evolutionary Biology·Yang FangYulong Niu
May 18, 2018·BMC Evolutionary Biology·K Jun TongSimon Y W Ho
Jan 5, 2018·PLoS Pathogens·Zoe Patterson RossHendrik N Poinar
May 20, 2017·Annual Review of Phytopathology·Coralie PicardGaël Thébaud
Sep 9, 2020·Molecular Biology and Evolution·Sebastian DucheneGuy Baele
Mar 20, 2021·Trends in Microbiology·Danielle J IngleSebastian Duchene
Aug 17, 2020·Current Biology : CB·Kerttu MajanderVerena J Schuenemann
Sep 29, 2021·PLoS Genetics·Jessica K CallandSamuel K Sheppard

❮ Previous
Next ❯

Software Mentioned

beast

Related Concepts

Related Feeds

Ancient DNA

Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, but are notoriously difficult to analyze due to molecular damage and exogenous dna contamination. Discover the latest research on Ancient DNA here.