Resolving the phylogenetic position of Darwin's extinct ground sloth (Mylodon darwinii ) using mitogenomic and nuclear exon data

Proceedings. Biological Sciences
F DelsucHendrik N Poinar

Abstract

Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first collected its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12 880-year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient subfossil, probably the result of the dry and cold conditions prevailing within the cave. Accordingly, taxonomic assessment of our shotgun metagenomic data showed a very high percentage of endogenous DNA with 22% of the assembled metagenomic contigs assigned to Xenarthra. Additionally, we enriched over 15 kb of sequence data from seven nuclear exons, using target sequence capture designed against a wide xenarthran dataset. Phylogenetic and dating analyses of the mitogenomic dataset including all extant species of xenarthrans and the assembled nuclear supermatrix unambiguously place Mylodon darwinii as the sister-group of modern two-fingered sloths, from which it diverged around 22 million years ago. These congruent results from both the mitochondrial and nuclear data support the diphyly of the two modern sloth lineages, impl...Continue Reading

References

Jan 9, 1996·Proceedings of the National Academy of Sciences of the United States of America·M HössS Pääbo
Feb 13, 2001·Molecular Phylogenetics and Evolution·A D GreenwoodS Pääbo
Sep 25, 2002·Molecular Biology and Evolution·Frédéric DelsucEmmanuel J P Douzery
Dec 1, 2004·Annual Review of Genetics·Svante PääboMichael Hofreiter
Jan 22, 2005·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jun 19, 2009·Bioinformatics·Nicolas LartillotSamuel Blanquart
Jun 3, 2010·Cold Spring Harbor Protocols·Matthias Meyer, Martin Kircher
Feb 4, 2011·Proceedings. Biological Sciences·Guillaume BilletXavier Valentin
Jun 7, 2011·Annals of Anatomy = Anatomischer Anzeiger : Official Organ of the Anatomische Gesellschaft·Andrew A ClackHendrik N Poinar
Jun 22, 2011·Genome Research·Daniel H HusonStephan C Schuster
Oct 4, 2011·BMC Bioinformatics·Brian D OndovAdam M Phillippy
Nov 30, 2011·Molecular Phylogenetics and Evolution·Frédéric DelsucAlexandre Hassanin
Feb 10, 2012·Molecular Biology and Evolution·Robert LanfearStephane Guindon
Feb 24, 2012·Systematic Biology·Fredrik RonquistJohn P Huelsenbeck
Mar 30, 2012·Proceedings. Biological Sciences·Céline BonJean-Marc Elalouf
Jun 19, 2012·Molecular Phylogenetics and Evolution·Johanna L A PaijmansMichael Hofreiter
Jun 29, 2012·Molecular Ecology·David P L Toews, Alan Brelsford
Apr 25, 2013·Bioinformatics·Hákon JónssonLudovic Orlando
Feb 18, 2014·Molecular Biology and Evolution·Jacob M EnkHendrik N Poinar
Mar 13, 2014·Molecular Ecology·C Der SarkissianL Orlando
Jul 11, 2014·Proceedings of the National Academy of Sciences of the United States of America·Tracy A HeathTanja Stadler
Aug 8, 2014·Nucleic Acids Research·Gabriel RenaudJanet Kelso
Dec 20, 2014·Journal of Human Evolution·Logan KistlerGeorge H Perry
Mar 13, 2015·Biology Letters·Clio Der SarkissianLudovic Orlando
Jun 4, 2015·Molecular Biology and Evolution·Peter D HeintzmanBeth Shapiro
Nov 12, 2015·Molecular Biology and Evolution·Gillian C GibbFrédéric Delsuc
Feb 18, 2016·Genome Biology and Evolution·Graham J SlaterAlex D Greenwood
Feb 26, 2016·Current Biology : CB·Frédéric DelsucHendrik N Poinar
Mar 26, 2016·Methods : a Companion to Methods in Enzymology·Dinghua LiTak-Wah Lam

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Citations

Jun 7, 2019·Nature Ecology & Evolution·Samantha PressleeRoss D E MacPhee
Mar 20, 2019·Molecular Phylogenetics and Evolution·Maxime CourcellePierre-Henri Fabre
Apr 30, 2021·Genome Biology·Giulio FormentiUNKNOWN Vertebrate Genomes Project Consortium

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Datasets Mentioned

BETA
SP57
SRR2007674

Methods Mentioned

BETA
Illumina sequencing
Illumina shotgun sequencing
PCR

Software Mentioned

MAFFT
y SS
P F inder
egablast
r B ayes
BWA
rona
bpcomp
cutadapt
AB

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