Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.

1. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.. Bioinformatics 2009 Jul 15;25(14):1754-60.
   pubmed: 19451168doi: 10.1093/bioinformatics/btp324google scholar: lookup
2. Froese DG, Westgate JA, Reyes AV, Enkin RJ, Preece SJ. Ancient permafrost and a future, warmer Arctic.. Science 2008 Sep 19;321(5896):1648.
   pubmed: 18801991doi: 10.1126/science.1157525google scholar: lookup
3. Goto H, Ryder OA, Fisher AR, Schultz B, Kosakovsky Pond SL, Nekrutenko A, Makova KD. A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses.. Genome Biol Evol 2011;3:1096-106.
   pubmed: 21803766doi: 10.1093/gbe/evr067google scholar: lookup
4. Lorenzen ED, Nogués-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MT, Nielsen R, Ho SY, Goebel T, Graf KE, Byers D, Stenderup JT, Rasmussen M, Campos PF, Leonard JA, Koepfli KP, Froese D, Zazula G, Stafford TW Jr, Aaris-Sørensen K, Batra P, Haywood AM, Singarayer JS, Valdes PJ, Boeskorov G, Burns JA, Davydov SP, Haile J, Jenkins DL, Kosintsev P, Kuznetsova T, Lai X, Martin LD, McDonald HG, Mol D, Meldgaard M, Munch K, Stephan E, Sablin M, Sommer RS, Sipko T, Scott E, Suchard MA, Tikhonov A, Willerslev R, Wayne RK, Cooper A, Hofreiter M, Sher A, Shapiro B, Rahbek C, Willerslev E. Species-specific responses of Late Quaternary megafauna to climate and humans.. Nature 2011 Nov 2;479(7373):359-64.
   pubmed: 22048313doi: 10.1038/nature10574google scholar: lookup
5. Warmuth V, Eriksson A, Bower MA, Barker G, Barrett E, Hanks BK, Li S, Lomitashvili D, Ochir-Goryaeva M, Sizonov GV, Soyonov V, Manica A. Reconstructing the origin and spread of horse domestication in the Eurasian steppe.. Proc Natl Acad Sci U S A 2012 May 22;109(21):8202-6.
   pubmed: 22566639doi: 10.1073/pnas.1111122109google scholar: lookup
6. van Doorn NL, Wilson J, Hollund H, Soressi M, Collins MJ. Site-specific deamidation of glutamine: a new marker of bone collagen deterioration.. Rapid Commun Mass Spectrom 2012 Oct 15;26(19):2319-27.
   pubmed: 22956324doi: 10.1002/rcm.6351google scholar: lookup
7. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MC, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Lander ES, Lindblad-Toh K. Genome sequence, comparative analysis, and population genetics of the domestic horse.. Science 2009 Nov 6;326(5954):865-7.
   pubmed: 19892987doi: 10.1126/science.1178158google scholar: lookup
8. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Pääbo S. Genetic history of an archaic hominin group from Denisova Cave in Siberia.. Nature 2010 Dec 23;468(7327):1053-60.
   pubmed: 21179161doi: 10.1038/nature09710google scholar: lookup
9. Rohland N, Hofreiter M. Ancient DNA extraction from bones and teeth.. Nat Protoc 2007;2(7):1756-62.
   pubmed: 17641642doi: 10.1038/nprot.2007.247google scholar: lookup
10. Patterson N, Price AL, Reich D. Population structure and eigenanalysis.. PLoS Genet 2006 Dec;2(12):e190.
    pubmed: 17194218doi: 10.1371/journal.pgen.0020190google scholar: lookup
11. Lippold S, Matzke NJ, Reissmann M, Hofreiter M. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication.. BMC Evol Biol 2011 Nov 14;11:328.
    pubmed: 22082251doi: 10.1186/1471-2148-11-328google scholar: lookup
12. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools.. Bioinformatics 2009 Aug 15;25(16):2078-9.
    pubmed: 19505943doi: 10.1093/bioinformatics/btp352google scholar: lookup
13. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.. Syst Biol 2010 May;59(3):307-21.
    pubmed: 20525638doi: 10.1093/sysbio/syq010google scholar: lookup
14. Lindahl T. Instability and decay of the primary structure of DNA.. Nature 1993 Apr 22;362(6422):709-15.
    pubmed: 8469282doi: 10.1038/362709a0google scholar: lookup
15. Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Müller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis.. Science 2007 Jan 12;315(5809):207-12.
    pubmed: 17218520doi: 10.1126/science.1132894google scholar: lookup
16. Shimodaira H, Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection.. Bioinformatics 2001 Dec;17(12):1246-7.
    pubmed: 11751242doi: 10.1093/bioinformatics/17.12.1246google scholar: lookup
17. Sanderson MJ. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock.. Bioinformatics 2003 Jan 22;19(2):301-2.
    pubmed: 12538260doi: 10.1093/bioinformatics/19.2.301google scholar: lookup
18. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.. Nucleic Acids Res 2002 Jul 15;30(14):3059-66.
    pubmed: 12136088doi: 10.1093/nar/gkf436google scholar: lookup
19. Bowling AT, Zimmermann W, Ryder O, Penado C, Peto S, Chemnick L, Yasinetskaya N, Zharkikh T. Genetic variation in Przewalski's horses, with special focus on the last wild caught mare, 231 Orlitza III.. Cytogenet Genome Res 2003;102(1-4):226-34.
    pubmed: 14970708doi: 10.1159/000075754google scholar: lookup
20. Cappellini E, Jensen LJ, Szklarczyk D, Ginolhac A, da Fonseca RA, Stafford TW, Holen SR, Collins MJ, Orlando L, Willerslev E, Gilbert MT, Olsen JV. Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins.. J Proteome Res 2012 Feb 3;11(2):917-26.
    pubmed: 22103443doi: 10.1021/pr200721ugoogle scholar: lookup
21. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.. Gigascience 2012 Dec 27;1(1):18.
    pubmed: 23587118doi: 10.1186/2047-217X-1-18google scholar: lookup
22. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MT, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TF, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Pontén T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E. Ancient human genome sequence of an extinct Palaeo-Eskimo.. Nature 2010 Feb 11;463(7282):757-62.
    pubmed: 20148029doi: 10.1038/nature08835google scholar: lookup
23. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.. Nat Protoc 2009;4(1):44-57.
    pubmed: 19131956doi: 10.1038/nprot.2008.211google scholar: lookup
24. Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann KE, Kapranov P, Thompson JF, Zazula G, Froese D, Moltke I, Shapiro B, Hofreiter M, Al-Rasheid KA, Gilbert MT, Willerslev E. True single-molecule DNA sequencing of a pleistocene horse bone.. Genome Res 2011 Oct;21(10):1705-19.
    pubmed: 21803858doi: 10.1101/gr.122747.111google scholar: lookup
25. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified.. BMC Evol Biol 2006 Mar 24;6:29.
    pubmed: 16563161doi: 10.1186/1471-2148-6-29google scholar: lookup
26. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform.. Bioinformatics 2010 Mar 1;26(5):589-95.
    pubmed: 20080505doi: 10.1093/bioinformatics/btp698google scholar: lookup
27. Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S. A high-coverage genome sequence from an archaic Denisovan individual.. Science 2012 Oct 12;338(6104):222-6.
    pubmed: 22936568doi: 10.1126/science.1224344google scholar: lookup
28. Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing.. Cold Spring Harb Protoc 2010 Jun;2010(6):pdb.prot5448.
    pubmed: 20516186doi: 10.1101/pdb.prot5448google scholar: lookup
29. Weinstock J, Willerslev E, Sher A, Tong W, Ho SY, Rubenstein D, Storer J, Burns J, Martin L, Bravi C, Prieto A, Froese D, Scott E, Xulong L, Cooper A. Evolution, systematics, and phylogeography of pleistocene horses in the new world: a molecular perspective.. PLoS Biol 2005 Aug;3(8):e241.
    pubmed: 15974804doi: 10.1371/journal.pbio.0030241google scholar: lookup
30. Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SC, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM, Fleischer RC, Cooper A, Shapiro B, Orlando L. Mitochondrial phylogenomics of modern and ancient equids.. PLoS One 2013;8(2):e55950.
    pubmed: 23437078doi: 10.1371/journal.pone.0055950google scholar: lookup
31. Kelstrup CD, Young C, Lavallee R, Nielsen ML, Olsen JV. Optimized fast and sensitive acquisition methods for shotgun proteomics on a quadrupole orbitrap mass spectrometer.. J Proteome Res 2012 Jun 1;11(6):3487-97.
    pubmed: 22537090doi: 10.1021/pr3000249google scholar: lookup
32. Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.. Nat Biotechnol 2008 Dec;26(12):1367-72.
    pubmed: 19029910doi: 10.1038/nbt.1511google scholar: lookup
33. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7.. Mol Biol Evol 2012 Aug;29(8):1969-73.
    pubmed: 22367748doi: 10.1093/molbev/mss075google scholar: lookup
34. Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment.. J Proteome Res 2011 Apr 1;10(4):1794-805.
    pubmed: 21254760doi: 10.1021/pr101065jgoogle scholar: lookup
35. Smith CI, Chamberlain AT, Riley MS, Stringer C, Collins MJ. The thermal history of human fossils and the likelihood of successful DNA amplification.. J Hum Evol 2003 Sep;45(3):203-17.
    pubmed: 14580590doi: 10.1016/s0047-2484(03)00106-4google scholar: lookup
36. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees.. BMC Evol Biol 2007 Nov 8;7:214.
    pubmed: 17996036doi: 10.1186/1471-2148-7-214google scholar: lookup
37. Orlando L, Metcalf JL, Alberdi MT, Telles-Antunes M, Bonjean D, Otte M, Martin F, Eisenmann V, Mashkour M, Morello F, Prado JL, Salas-Gismondi R, Shockey BJ, Wrinn PJ, Vasil'ev SK, Ovodov ND, Cherry MI, Hopwood B, Male D, Austin JJ, Hänni C, Cooper A. Revising the recent evolutionary history of equids using ancient DNA.. Proc Natl Acad Sci U S A 2009 Dec 22;106(51):21754-9.
    pubmed: 20007379doi: 10.1073/pnas.0903672106google scholar: lookup
38. Nielsen R. Molecular signatures of natural selection.. Annu Rev Genet 2005;39:197-218.
    pubmed: 16285858doi: 10.1146/annurev.genet.39.073003.112420google scholar: lookup
39. Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, Campos PF, Samaniego JA, Gilbert MT, Willerslev E, Zhang G, Scofield RP, Holdaway RN, Bunce M. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils.. Proc Biol Sci 2012 Dec 7;279(1748):4724-33.
    pubmed: 23055061doi: 10.1098/rspb.2012.1745google scholar: lookup
40. Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L. mapDamage: testing for damage patterns in ancient DNA sequences.. Bioinformatics 2011 Aug 1;27(15):2153-5.
    pubmed: 21659319doi: 10.1093/bioinformatics/btr347google scholar: lookup
41. McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guérin G, Hasegawa T, Hill EW, Leeb T, Lindgren G, Penedo MC, Røed KH, Ryder OA, Swinburne JE, Tozaki T, Valberg SJ, Vaudin M, Lindblad-Toh K, Wade CM, Mickelson JR. A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies.. PLoS Genet 2012 Jan;8(1):e1002451.
    pubmed: 22253606doi: 10.1371/journal.pgen.1002451google scholar: lookup
42. Stamatakis A, Aberer AJ, Goll C, Smith SA, Berger SA, Izquierdo-Carrasco F. RAxML-Light: a tool for computing terabyte phylogenies.. Bioinformatics 2012 Aug 1;28(15):2064-6.
    pubmed: 22628519doi: 10.1093/bioinformatics/bts309google scholar: lookup
43. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.. Bioinformatics 2010 Aug 15;26(16):2069-70.
    pubmed: 20562413doi: 10.1093/bioinformatics/btq330google scholar: lookup
44. Achilli A, Olivieri A, Soares P, Lancioni H, Hooshiar Kashani B, Perego UA, Nergadze SG, Carossa V, Santagostino M, Capomaccio S, Felicetti M, Al-Achkar W, Penedo MC, Verini-Supplizi A, Houshmand M, Woodward SR, Semino O, Silvestrelli M, Giulotto E, Pereira L, Bandelt HJ, Torroni A. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication.. Proc Natl Acad Sci U S A 2012 Feb 14;109(7):2449-54.
    pubmed: 22308342doi: 10.1073/pnas.1111637109google scholar: lookup
45. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome.. Science 2010 May 7;328(5979):710-722.
    pubmed: 20448178doi: 10.1126/science.1188021google scholar: lookup
46. Hudson RR. Generating samples under a Wright-Fisher neutral model of genetic variation.. Bioinformatics 2002 Feb;18(2):337-8.
    pubmed: 11847089doi: 10.1093/bioinformatics/18.2.337google scholar: lookup
47. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses.. Am J Hum Genet 2007 Sep;81(3):559-75.
    pubmed: 17701901doi: 10.1086/519795google scholar: lookup
48. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.. Bioinformatics 2006 Nov 1;22(21):2688-90.
    pubmed: 16928733doi: 10.1093/bioinformatics/btl446google scholar: lookup
49. Ginolhac A, Vilstrup J, Stenderup J, Rasmussen M, Stiller M, Shapiro B, Zazula G, Froese D, Steinmann KE, Thompson JF, Al-Rasheid KA, Gilbert TM, Willerslev E, Orlando L. Improving the performance of true single molecule sequencing for ancient DNA.. BMC Genomics 2012 May 10;13:177.
    pubmed: 22574620doi: 10.1186/1471-2164-13-177google scholar: lookup
50. Stanke M, Steinkamp R, Waack S, Morgenstern B. AUGUSTUS: a web server for gene finding in eukaryotes.. Nucleic Acids Res 2004 Jul 1;32(Web Server issue):W309-12.
    pubmed: 15215400doi: 10.1093/nar/gkh379google scholar: lookup
51. Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S. Patterns of damage in genomic DNA sequences from a Neandertal.. Proc Natl Acad Sci U S A 2007 Sep 11;104(37):14616-21.
    pubmed: 17715061doi: 10.1073/pnas.0704665104google scholar: lookup
52. Miller W, Schuster SC, Welch AJ, Ratan A, Bedoya-Reina OC, Zhao F, Kim HL, Burhans RC, Drautz DI, Wittekindt NE, Tomsho LP, Ibarra-Laclette E, Herrera-Estrella L, Peacock E, Farley S, Sage GK, Rode K, Obbard M, Montiel R, Bachmann L, Ingólfsson O, Aars J, Mailund T, Wiig O, Talbot SL, Lindqvist C. Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.. Proc Natl Acad Sci U S A 2012 Sep 4;109(36):E2382-90.
    pubmed: 22826254doi: 10.1073/pnas.1210506109google scholar: lookup
53. Willerslev E, Cappellini E, Boomsma W, Nielsen R, Hebsgaard MB, Brand TB, Hofreiter M, Bunce M, Poinar HN, Dahl-Jensen D, Johnsen S, Steffensen JP, Bennike O, Schwenninger JL, Nathan R, Armitage S, de Hoog CJ, Alfimov V, Christl M, Beer J, Muscheler R, Barker J, Sharp M, Penkman KE, Haile J, Taberlet P, Gilbert MT, Casoli A, Campani E, Collins MJ. Ancient biomolecules from deep ice cores reveal a forested southern Greenland.. Science 2007 Jul 6;317(5834):111-4.
    pubmed: 17615355doi: 10.1126/science.1141758google scholar: lookup
54. Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program.. Brief Bioinform 2008 Jul;9(4):286-98.
    pubmed: 18372315doi: 10.1093/bib/bbn013google scholar: lookup
55. Li H, Durbin R. Inference of human population history from individual whole-genome sequences.. Nature 2011 Jul 13;475(7357):493-6.
    pubmed: 21753753doi: 10.1038/nature10231google scholar: lookup

Citations

1. Vincelette A. The Characteristics, Distribution, Function, and Origin of Alternative Lateral Horse Gaits.. Animals (Basel) 2023 Aug 8;13(16).
   doi: 10.3390/ani13162557pubmed: 37627349google scholar: lookup
2. Musiał AD, Ropka-Molik K, Stefaniuk-Szmukier M, Myćka G, Bieniek A, Yasynetska N. Characteristic of Przewalski horses population from Askania-Nova reserve based on genetic markers.. Mol Biol Rep 2023 Aug;50(8):7121-7126.
   doi: 10.1007/s11033-023-08581-4pubmed: 37365410google scholar: lookup
3. Batcher K, Varney S, Raudsepp T, Jevit M, Dickinson P, Jagannathan V, Leeb T, Bannasch D. Ancient segmentally duplicated LCORL retrocopies in equids.. PLoS One 2023;18(6):e0286861.
   doi: 10.1371/journal.pone.0286861pubmed: 37289743google scholar: lookup
4. Reid BN, Star B, Pinsky ML. Detecting parallel polygenic adaptation to novel evolutionary pressure in wild populations: a case study in Atlantic cod (Gadus morhua).. Philos Trans R Soc Lond B Biol Sci 2023 Jul 17;378(1881):20220190.
   doi: 10.1098/rstb.2022.0190pubmed: 37246382google scholar: lookup
5. Piras FM, Cappelletti E, Abdelgadir WA, Salamon G, Vignati S, Santagostino M, Sola L, Nergadze SG, Giulotto E. A Satellite-Free Centromere in Equus przewalskii Chromosome 10.. Int J Mol Sci 2023 Feb 18;24(4).
   doi: 10.3390/ijms24044134pubmed: 36835543google scholar: lookup
6. Segawa T, Yonezawa T, Matsuzaki R, Mori H, Akiyoshi A, Navarro F, Fujita K, Aizen VB, Li Z, Mano S, Takeuchi N. Evolution of snow algae, from cosmopolitans to endemics, revealed by DNA analysis of ancient ice.. ISME J 2023 Apr;17(4):491-501.
   doi: 10.1038/s41396-023-01359-3pubmed: 36650274google scholar: lookup
7. Ren X, Liu Y, Zhao Y, Li B, Bai D, Bou G, Zhang X, Du M, Wang X, Bou T, Shen Y, Dugarjaviin M. Analysis of the Whole-Genome Sequences from an Equus Parent-Offspring Trio Provides Insight into the Genomic Incompatibilities in the Hybrid Mule.. Genes (Basel) 2022 Nov 23;13(12).
   doi: 10.3390/genes13122188pubmed: 36553455google scholar: lookup
8. Anderson LA. Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation.. Ecol Evol 2022 Dec;12(12):e9518.
   doi: 10.1002/ece3.9518pubmed: 36518622google scholar: lookup
9. Suminda GGD, Ghosh M, Son YO. The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research.. Life (Basel) 2022 Nov 15;12(11).
   doi: 10.3390/life12111893pubmed: 36431028google scholar: lookup
10. Turghan MA, Jiang Z, Niu Z. An Update on Status and Conservation of the Przewalski's Horse (Equus ferus przewalskii): Captive Breeding and Reintroduction Projects.. Animals (Basel) 2022 Nov 15;12(22).
    doi: 10.3390/ani12223158pubmed: 36428386google scholar: lookup
11. Wang Y, Hua X, Shi X, Wang C. Origin, Evolution, and Research Development of Donkeys.. Genes (Basel) 2022 Oct 25;13(11).
    doi: 10.3390/genes13111945pubmed: 36360182google scholar: lookup
12. Xu B, Yang G, Jiao B, Zhu H. Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication.. Front Genet 2022;13:944933.
    doi: 10.3389/fgene.2022.944933pubmed: 36276948google scholar: lookup
13. Gopalakrishnan S, Ebenesersdóttir SS, Lundstrøm IKC, Turner-Walker G, Moore KHS, Luisi P, Margaryan A, Martin MD, Ellegaard MR, Magnússon ÓÞ, Sigurðsson Á, Snorradóttir S, Magnúsdóttir DN, Laffoon JE, van Dorp L, Liu X, Moltke I, Ávila-Arcos MC, Schraiber JG, Rasmussen S, Juan D, Gelabert P, de-Dios T, Fotakis AK, Iraeta-Orbegozo M, Vågene ÅJ, Denham SD, Christophersen A, Stenøien HK, Vieira FG, Liu S, Günther T, Kivisild T, Moseng OG, Skar B, Cheung C, Sandoval-Velasco M, Wales N, Schroeder H, Campos PF, Guðmundsdóttir VB, Sicheritz-Ponten T, Petersen B, Halgunset J, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Willerslev E, Balloux F, Marques-Bonet T, Lalueza-Fox C, Nielsen R, Stefánsson K, Helgason A, Gilbert MTP. The population genomic legacy of the second plague pandemic.. Curr Biol 2022 Nov 7;32(21):4743-4751.e6.
    doi: 10.1016/j.cub.2022.09.023pubmed: 36182700google scholar: lookup
14. Bao W, Yu J, He Y, Liu M, Yang X. The diversity analysis and gene function prediction of intestinal bacteria in three equine species.. Front Microbiol 2022;13:973828.
    doi: 10.3389/fmicb.2022.973828pubmed: 36160217google scholar: lookup
15. Colleary C, O'Reilly S, Dolocan A, Toyoda JG, Chu RK, Tfaily MM, Hochella MF Jr, Nesbitt SJ. Using Macro- and Microscale Preservation in Vertebrate Fossils as Predictors for Molecular Preservation in Fluvial Environments.. Biology (Basel) 2022 Sep 2;11(9).
    doi: 10.3390/biology11091304pubmed: 36138783google scholar: lookup
16. Cirilli O, Machado H, Arroyo-Cabrales J, Barrón-Ortiz CI, Davis E, Jass CN, Jukar AM, Landry Z, Marín-Leyva AH, Pandolfi L, Pushkina D, Rook L, Saarinen J, Scott E, Semprebon G, Strani F, Villavicencio NA, Kaya F, Bernor RL. Evolution of the Family Equidae, Subfamily Equinae, in North, Central and South America, Eurasia and Africa during the Plio-Pleistocene.. Biology (Basel) 2022 Aug 24;11(9).
    doi: 10.3390/biology11091258pubmed: 36138737google scholar: lookup
17. Torres JM, Borja C, Gibert L, Ribot F, Olivares EG. Twentieth-Century Paleoproteomics: Lessons from Venta Micena Fossils.. Biology (Basel) 2022 Aug 6;11(8).
    doi: 10.3390/biology11081184pubmed: 36009810google scholar: lookup
18. Ullmann PV, Ash RD, Scannella JB. Taphonomic and Diagenetic Pathways to Protein Preservation, Part II: The Case of Brachylophosaurus canadensis Specimen MOR 2598.. Biology (Basel) 2022 Aug 5;11(8).
    doi: 10.3390/biology11081177pubmed: 36009804google scholar: lookup
19. Delsol N, Stucky BJ, Oswald JA, Reitz EJ, Emery KF, Guralnick R. Analysis of the earliest complete mtDNA genome of a Caribbean colonial horse (Equus caballus) from 16th-century Haiti.. PLoS One 2022;17(7):e0270600.
    doi: 10.1371/journal.pone.0270600pubmed: 35895670google scholar: lookup
20. Myćka G, Klecel W, Stefaniuk-Szmukier M, Jaworska J, Musiał AD, Ropka-Molik K. Mitochondrial Whole D-Loop Variability in Polish Draft Horses of Sztumski Subtype.. Animals (Basel) 2022 Jul 22;12(15).
    doi: 10.3390/ani12151870pubmed: 35892520google scholar: lookup
21. Cappelletti E, Piras FM, Sola L, Santagostino M, Abdelgadir WA, Raimondi E, Lescai F, Nergadze SG, Giulotto E. Robertsonian Fusion and Centromere Repositioning Contributed to the Formation of Satellite-free Centromeres During the Evolution of Zebras.. Mol Biol Evol 2022 Aug 3;39(8).
    doi: 10.1093/molbev/msac162pubmed: 35881460google scholar: lookup
22. Ghosh T, Kumar S, Sharma K, Kakati P, Sharma A, Mondol S. Consideration of genetic variation and evolutionary history in future conservation of Indian one-horned rhinoceros (Rhinoceros unicornis).. BMC Ecol Evol 2022 Jul 20;22(1):92.
    doi: 10.1186/s12862-022-02045-2pubmed: 35858827google scholar: lookup
23. Warinner C, Korzow Richter K, Collins MJ. Paleoproteomics.. Chem Rev 2022 Aug 24;122(16):13401-13446.
    doi: 10.1021/acs.chemrev.1c00703pubmed: 35839101google scholar: lookup
24. Garcia-Erill G, Jørgensen CHF, Muwanika VB, Wang X, Rasmussen MS, de Jong YA, Gaubert P, Olayemi A, Salmona J, Butynski TM, Bertola LD, Siegismund HR, Albrechtsen A, Heller R. Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes.. Mol Biol Evol 2022 Jul 2;39(7).
    doi: 10.1093/molbev/msac134pubmed: 35779009google scholar: lookup
25. Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding MS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, Fernandes DM, Ollivier M, Speidel L, Gopalakrishnan S, Westbury MV, Ramos-Madrigal J, Feuerborn TR, Reiter E, Gretzinger J, Münzel SC, Swali P, Conard NJ, Carøe C, Haile J, Linderholm A, Androsov S, Barnes I, Baumann C, Benecke N, Bocherens H, Brace S, Carden RF, Drucker DG, Fedorov S, Gasparik M, Germonpré M, Grigoriev S, Groves P, Hertwig ST, Ivanova VV, Janssens L, Jennings RP, Kasparov AK, Kirillova IV, Kurmaniyazov I, Kuzmin YV, Kosintsev PA, Lázničková-Galetová M, Leduc C, Nikolskiy P, Nussbaumer M, O'Drisceoil C, Orlando L, Outram A, Pavlova EY, Perri AR, Pilot M, Pitulko VV, Plotnikov VV, Protopopov AV, Rehazek A, Sablin M, Seguin-Orlando A, Storå J, Verjux C, Zaibert VF, Zazula G, Crombé P, Hansen AJ, Willerslev E, Leonard JA, Götherström A, Pinhasi R, Schuenemann VJ, Hofreiter M, Gilbert MTP, Shapiro B, Larson G, Krause J, Dalén L, Skoglund P. Grey wolf genomic history reveals a dual ancestry of dogs.. Nature 2022 Jul;607(7918):313-320.
    doi: 10.1038/s41586-022-04824-9pubmed: 35768506google scholar: lookup
26. Srigyan M, Bolívar H, Ureña I, Santana J, Petersen A, Iriarte E, Kırdök E, Bergfeldt N, Mora A, Jakobsson M, Abdo K, Braemer F, Smith C, Ibañez JJ, Götherström A, Günther T, Valdiosera C. Bioarchaeological evidence of one of the earliest Islamic burials in the Levant.. Commun Biol 2022 Jun 7;5(1):554.
    doi: 10.1038/s42003-022-03508-4pubmed: 35672445google scholar: lookup
27. Ntasi G, Palomo IR, Marino G, Piaz FD, Cappellini E, Birolo L, Petrone P. Molecular signatures written in bone proteins of 79 AD victims from Herculaneum and Pompeii.. Sci Rep 2022 May 27;12(1):8401.
    doi: 10.1038/s41598-022-12042-6pubmed: 35624181google scholar: lookup
28. Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Orlando L, Jiang Y. Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene.. Elife 2022 May 11;11.
    doi: 10.7554/eLife.73346pubmed: 35543411google scholar: lookup
29. Gömer A, Puff C, Reinecke B, Bracht S, Conze M, Baumgärtner W, Steinmann J, Feige K, Cavalleri JMV, Steinmann E, Todt D. Experimental cross-species infection of donkeys with equine hepacivirus and analysis of host immune signatures.. One Health Outlook 2022 May 9;4(1):9.
    doi: 10.1186/s42522-022-00065-ypubmed: 35527255google scholar: lookup
30. Polani S, Dean M, Lichter-Peled A, Hendrickson S, Tsang S, Fang X, Feng Y, Qiao W, Avni G, Kahila Bar-Gal G. Sequence Variant in the TRIM39-RPP21 Gene Readthrough is Shared Across a Cohort of Arabian Foals Diagnosed with Juvenile Idiopathic Epilepsy.. J Genet Mutat Disord 2022 Jan;1(1).
    pubmed: 35465405
31. Piras FM, Cappelletti E, Santagostino M, Nergadze SG, Giulotto E, Raimondi E. Molecular Dynamics and Evolution of Centromeres in the Genus Equus.. Int J Mol Sci 2022 Apr 10;23(8).
    doi: 10.3390/ijms23084183pubmed: 35457002google scholar: lookup
32. Dehasque M, Pečnerová P, Kempe Lagerholm V, Ersmark E, Danilov GK, Mortensen P, Vartanyan S, Dalén L. Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.. Genes (Basel) 2022 Apr 13;13(4).
    doi: 10.3390/genes13040687pubmed: 35456493google scholar: lookup
33. Zhang FL, Zhang SE, Sun YJ, Wang JJ, Shen W. Comparative Transcriptomics Uncover the Uniqueness of Oocyte Development in the Donkey.. Front Genet 2022;13:839207.
    doi: 10.3389/fgene.2022.839207pubmed: 35154289google scholar: lookup
34. Westbury MV, Barnett R, Sandoval-Velasco M, Gower G, Vieira FG, de Manuel M, Hansen AJ, Yamaguchi N, Werdelin L, Marques-Bonet T, Gilbert MTP, Lorenzen ED. A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives.. Open Res Eur 2021;1:25.
    doi: 10.12688/openreseurope.13104.2pubmed: 35098251google scholar: lookup
35. Aneli S, Saupe T, Montinaro F, Solnik A, Molinaro L, Scaggion C, Carrara N, Raveane A, Kivisild T, Metspalu M, Scheib CL, Pagani L. The Genetic Origin of Daunians and the Pan-Mediterranean Southern Italian Iron Age Context.. Mol Biol Evol 2022 Feb 3;39(2).
    doi: 10.1093/molbev/msac014pubmed: 35038748google scholar: lookup
36. Bennett EA, Weber J, Bendhafer W, Champlot S, Peters J, Schwartz GM, Grange T, Geigl EM. The genetic identity of the earliest human-made hybrid animals, the kungas of Syro-Mesopotamia.. Sci Adv 2022 Jan 14;8(2):eabm0218.
    doi: 10.1126/sciadv.abm0218pubmed: 35030024google scholar: lookup
37. Ullmann PV, Macauley K, Ash RD, Shoup B, Scannella JB. Taphonomic and Diagenetic Pathways to Protein Preservation, Part I: The Case of Tyrannosaurus rex Specimen MOR 1125.. Biology (Basel) 2021 Nov 17;10(11).
    doi: 10.3390/biology10111193pubmed: 34827186google scholar: lookup
38. Balcarcel AM, Geiger M, Clauss M, Sánchez-Villagra MR. The mammalian brain under domestication: Discovering patterns after a century of old and new analyses.. J Exp Zool B Mol Dev Evol 2022 Dec;338(8):460-483.
    doi: 10.1002/jez.b.23105pubmed: 34813150google scholar: lookup
39. Wang L, Sheng G, Preick M, Hu S, Deng T, Taron UH, Barlow A, Hu J, Xiao B, Sun G, Song S, Hou X, Lai X, Hofreiter M, Yuan J. Ancient Mitogenomes Provide New Insights into the Origin and Early Introduction of Chinese Domestic Donkeys.. Front Genet 2021;12:759831.
    doi: 10.3389/fgene.2021.759831pubmed: 34721545google scholar: lookup
40. Sinding MS, Ciucani MM, Ramos-Madrigal J, Carmagnini A, Rasmussen JA, Feng S, Chen G, Vieira FG, Mattiangeli V, Ganjoo RK, Larson G, Sicheritz-Pontén T, Petersen B, Frantz L, Gilbert MTP, Bradley DG. Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos.. iScience 2021 Nov 19;24(11):103226.
    doi: 10.1016/j.isci.2021.103226pubmed: 34712923google scholar: lookup
41. Moltke I, Korneliussen TS, Seguin-Orlando A, Moreno-Mayar JV, LaPointe E, Billeck W, Willerslev E. Identifying a living great-grandson of the Lakota Sioux leader Tatanka Iyotake (Sitting Bull).. Sci Adv 2021 Oct 29;7(44):eabh2013.
    doi: 10.1126/sciadv.abh2013pubmed: 34705496google scholar: lookup
42. Bailleul AM, Zheng W, Horner JR, Hall BK, Holliday CM, Schweitzer MH. Evidence of proteins, chromosomes and chemical markers of DNA in exceptionally preserved dinosaur cartilage.. Natl Sci Rev 2020 Apr;7(4):815-822.
    doi: 10.1093/nsr/nwz206pubmed: 34692099google scholar: lookup
43. Zhu K, Du P, Xiong J, Ren X, Sun C, Tao Y, Ding Y, Xu Y, Meng H, Wang CC, Wen SQ. Comparative Performance of the MGISEQ-2000 and Illumina X-Ten Sequencing Platforms for Paleogenomics.. Front Genet 2021;12:745508.
    doi: 10.3389/fgene.2021.745508pubmed: 34671385google scholar: lookup
44. Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury JM, Gaunitz C, Chauvey L, Seguin-Orlando A, Der Sarkissian C, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregély T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel JC, Boudadi-Maligne M, Alvarez N, Germonpré M, Moskal-Del Hoyo M, Wilczyński J, Pospuła S, Lasota-Kuś A, Tunia K, Nowak M, Rannamäe E, Saarma U, Boeskorov G, Lōugas L, Kyselý R, Peške L, Bălășescu A, Dumitrașcu V, Dobrescu R, Gerber D, Kiss V, Szécsényi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsár G, Gál E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga JO, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Valenzuela Lamas S, Albizuri Canadell S, Nieto Espinet A, Iborra MP, Lira Garrido J, Rodríguez González E, Celestino S, Olària C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, Toleubaev A, Morgunova NL, Kuznetsova T, Lordkipanize D, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Clavel B, Lepetz S, Davoudi H, Mashkour M, Berezina NY, Stockhammer PW, Krause J, Haak W, Morales-Muñiz A, Benecke N, Hofreiter M, Ludwig A, Graphodatsky AS, Peters J, Kiryushin KY, Iderkhangai TO, Bokovenko NA, Vasiliev SK, Seregin NN, Chugunov KV, Plasteeva NA, Baryshnikov GF, Petrova E, Sablin M, Ananyevskaya E, Logvin A, Shevnina I, Logvin V, Kalieva S, Loman V, Kukushkin I, Merz I, Merz V, Sakenov S, Varfolomeyev V, Usmanova E, Zaibert V, Arbuckle B, Belinskiy AB, Kalmykov A, Reinhold S, Hansen S, Yudin AI, Vybornov AA, Epimakhov A, Berezina NS, Roslyakova N, Kosintsev PA, Kuznetsov PF, Anthony D, Kroonen GJ, Kristiansen K, Wincker P, Outram A, Orlando L. The origins and spread of domestic horses from the Western Eurasian steppes.. Nature 2021 Oct;598(7882):634-640.
    doi: 10.1038/s41586-021-04018-9pubmed: 34671162google scholar: lookup
45. Fogg JM, Judge AK, Stricker E, Chan HL, Zechiedrich L. Supercoiling and looping promote DNA base accessibility and coordination among distant sites.. Nat Commun 2021 Sep 28;12(1):5683.
    doi: 10.1038/s41467-021-25936-2pubmed: 34584096google scholar: lookup
46. Suchan T, Kusliy MA, Khan N, Chauvey L, Tonasso-Calvière L, Schiavinato S, Southon J, Keller M, Kitagawa K, Krause J, Bessudnov AN, Bessudnov AA, Graphodatsky AS, Valenzuela-Lamas S, Wilczyński J, Pospuła S, Tunia K, Nowak M, Moskal-delHoyo M, Tishkin AA, Pryor AJE, Outram AK, Orlando L. Performance and automation of ancient DNA capture with RNA hyRAD probes.. Mol Ecol Resour 2022 Apr;22(3):891-907.
    doi: 10.1111/1755-0998.13518pubmed: 34582623google scholar: lookup
47. Anžel A, Heider D, Hattab G. The visual story of data storage: From storage properties to user interfaces.. Comput Struct Biotechnol J 2021;19:4904-4918.
    doi: 10.1016/j.csbj.2021.08.031pubmed: 34527195google scholar: lookup
48. Reinecke B, Klöhn M, Brüggemann Y, Kinast V, Todt D, Stang A, Badenhorst M, Koeppel K, Guthrie A, Groner U, Puff C, de le Roi M, Baumgärtner W, Cavalleri JV, Steinmann E. Clinical Course of Infection and Cross-Species Detection of Equine Parvovirus-Hepatitis.. Viruses 2021 Jul 26;13(8).
    doi: 10.3390/v13081454pubmed: 34452320google scholar: lookup
49. Zacho CM, Bager MA, Margaryan A, Gravlund P, Galatius A, Rasmussen AR, Allentoft ME. Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes.. PLoS One 2021;16(8):e0256353.
    doi: 10.1371/journal.pone.0256353pubmed: 34424926google scholar: lookup
50. Segawa T, Yonezawa T, Mori H, Akiyoshi A, Allentoft ME, Kohno A, Tokanai F, Willerslev E, Kohno N, Nishihara H. Ancient DNA reveals multiple origins and migration waves of extinct Japanese brown bear lineages.. R Soc Open Sci 2021 Aug;8(8):210518.
    doi: 10.1098/rsos.210518pubmed: 34386259google scholar: lookup
51. Rossi C, Ruß-Popa G, Mattiangeli V, McDaid F, Hare AJ, Davoudi H, Laleh H, Lorzadeh Z, Khazaeli R, Fathi H, Teasdale MD, A'ali A, Stöllner T, Mashkour M, Daly KG. Exceptional ancient DNA preservation and fibre remains of a Sasanian saltmine sheep mummy in Chehrābād, Iran.. Biol Lett 2021 Jul;17(7):20210222.
    doi: 10.1098/rsbl.2021.0222pubmed: 34256582google scholar: lookup
52. Zeng L, Liu HQ, Tu XL, Ji CM, Gou X, Esmailizadeh A, Wang S, Wang MS, Wang MC, Li XL, Charati H, Adeola AC, Moshood Adedokun RA, Oladipo O, Olaogun SC, Sanke OJ, Godwin F M, Cecily Ommeh S, Agwanda B, Kasiiti Lichoti J, Han JL, Zheng HK, Wang CF, Zhang YP, Frantz LAF, Wu DD. Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation.. Zool Res 2021 Jul 18;42(4):450-460.
    doi: 10.24272/j.issn.2095-8137.2021.095pubmed: 34156172google scholar: lookup
53. Gacem S, Valverde A, Catalán J, Yánez Ortiz I, Soler C, Miró J. A New Approach of Sperm Motility Subpopulation Structure in Donkey and Horse.. Front Vet Sci 2021;8:651477.
    doi: 10.3389/fvets.2021.651477pubmed: 34113670google scholar: lookup
54. Patil AB, Vijay N. Repetitive genomic regions and the inference of demographic history.. Heredity (Edinb) 2021 Aug;127(2):151-166.
    doi: 10.1038/s41437-021-00443-8pubmed: 34002046google scholar: lookup
55. Kawasaki J, Kojima S, Mukai Y, Tomonaga K, Horie M. 100-My history of bornavirus infections hidden in vertebrate genomes.. Proc Natl Acad Sci U S A 2021 May 18;118(20).
    doi: 10.1073/pnas.2026235118pubmed: 33990470google scholar: lookup
56. Cirilli O, Pandolfi L, Rook L, Bernor RL. Evolution of Old World Equus and origin of the zebra-ass clade.. Sci Rep 2021 May 12;11(1):10156.
    doi: 10.1038/s41598-021-89440-9pubmed: 33980921google scholar: lookup
57. Arévalo-Soliz LM, Hardee CL, Fogg JM, Corman NR, Noorbakhsh C, Zechiedrich L. Improving therapeutic potential of non-viral minimized DNA vectors.. Cell Gene Ther Insights 2020 Nov;6(10):1489-1505.
    doi: 10.18609/cgti.2020.163pubmed: 33953961google scholar: lookup
58. Biller-Celander N, Shakun JD, McGee D, Wong CI, Reyes AV, Hardt B, Tal I, Ford DC, Lauriol B. Increasing Pleistocene permafrost persistence and carbon cycle conundrums inferred from Canadian speleothems.. Sci Adv 2021 Apr;7(18).
    doi: 10.1126/sciadv.abe5799pubmed: 33910910google scholar: lookup
59. Ramsøe A, Crispin M, Mackie M, McGrath K, Fischer R, Demarchi B, Collins MJ, Hendy J, Speller C. Assessing the degradation of ancient milk proteins through site-specific deamidation patterns.. Sci Rep 2021 Apr 8;11(1):7795.
    doi: 10.1038/s41598-021-87125-xpubmed: 33833277google scholar: lookup
60. Pinsky ML, Eikeset AM, Helmerson C, Bradbury IR, Bentzen P, Morris C, Gondek-Wyrozemska AT, Baalsrud HT, Brieuc MSO, Kjesbu OS, Godiksen JA, Barth JMI, Matschiner M, Stenseth NC, Jakobsen KS, Jentoft S, Star B. Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic.. Proc Natl Acad Sci U S A 2021 Apr 13;118(15).
    doi: 10.1073/pnas.2025453118pubmed: 33827928google scholar: lookup
61. Kusliy MA, Vorobieva NV, Tishkin AA, Makunin AI, Druzhkova AS, Trifonov VA, Iderkhangai TO, Graphodatsky AS. Traces of Late Bronze and Early Iron Age Mongolian Horse Mitochondrial Lineages in Modern Populations.. Genes (Basel) 2021 Mar 12;12(3).
    doi: 10.3390/genes12030412pubmed: 33809280google scholar: lookup
62. Fellows Yates JA, Lamnidis TC, Borry M, Andrades Valtueña A, Fagernäs Z, Clayton S, Garcia MU, Neukamm J, Peltzer A. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.. PeerJ 2021;9:e10947.
    doi: 10.7717/peerj.10947pubmed: 33777521google scholar: lookup
63. Kapp JD, Green RE, Shapiro B. A Fast and Efficient Single-stranded Genomic Library Preparation Method Optimized for Ancient DNA.. J Hered 2021 May 24;112(3):241-249.
    doi: 10.1093/jhered/esab012pubmed: 33768239google scholar: lookup
64. Callaway E. Million-year-old mammoth genomes shatter record for oldest ancient DNA.. Nature 2021 Feb;590(7847):537-538.
    doi: 10.1038/d41586-021-00436-xpubmed: 33597786google scholar: lookup
65. Roca AL. Million-year-old DNA provides a glimpse of mammoth evolution.. Nature 2021 Mar;591(7849):208-209.
    doi: 10.1038/d41586-021-00348-wpubmed: 33597773google scholar: lookup
66. van der Valk T, Pečnerová P, Díez-Del-Molino D, Bergström A, Oppenheimer J, Hartmann S, Xenikoudakis G, Thomas JA, Dehasque M, Sağlıcan E, Fidan FR, Barnes I, Liu S, Somel M, Heintzman PD, Nikolskiy P, Shapiro B, Skoglund P, Hofreiter M, Lister AM, Götherström A, Dalén L. Million-year-old DNA sheds light on the genomic history of mammoths.. Nature 2021 Mar;591(7849):265-269.
    doi: 10.1038/s41586-021-03224-9pubmed: 33597750google scholar: lookup
67. Saag L, Vasilyev SV, Varul L, Kosorukova NV, Gerasimov DV, Oshibkina SV, Griffith SJ, Solnik A, Saag L, D'Atanasio E, Metspalu E, Reidla M, Rootsi S, Kivisild T, Scheib CL, Tambets K, Kriiska A, Metspalu M. Genetic ancestry changes in Stone to Bronze Age transition in the East European plain.. Sci Adv 2021 Jan;7(4).
    doi: 10.1126/sciadv.abd6535pubmed: 33523926google scholar: lookup
68. Colleary C, Lamadrid HM, O'Reilly SS, Dolocan A, Nesbitt SJ. Molecular preservation in mammoth bone and variation based on burial environment.. Sci Rep 2021 Jan 29;11(1):2662.
    doi: 10.1038/s41598-021-81849-6pubmed: 33514821google scholar: lookup
69. Xavier C, Eduardoff M, Bertoglio B, Amory C, Berger C, Casas-Vargas A, Pallua J, Parson W. Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age.. Genes (Basel) 2021 Jan 22;12(2).
    doi: 10.3390/genes12020146pubmed: 33499220google scholar: lookup
70. Nedoluzhko AV, Rastorguev SM, Simonov E, Boulygina ES, Sharko FS, Tsygankova SV, Gabrielyan BK, Roubenyan HR, Levin BA. Two complete mitochondrial genomes of extinct form of the Sevan trout Salmo ischchan danilewskii.. Mitochondrial DNA B Resour 2017 Dec 21;3(1):40-41.
    doi: 10.1080/23802359.2017.1419096pubmed: 33474057google scholar: lookup
71. Keighley X, Bro-Jørgensen MH, Ahlgren H, Szpak P, Ciucani MM, Sánchez Barreiro F, Howse L, Gotfredsen AB, Glykou A, Jordan P, Lidén K, Olsen MT. Predicting sample success for large-scale ancient DNA studies on marine mammals.. Mol Ecol Resour 2021 May;21(4):1149-1166.
    doi: 10.1111/1755-0998.13331pubmed: 33463014google scholar: lookup
72. Egfjord AF, Margaryan A, Fischer A, Sjögren KG, Price TD, Johannsen NN, Nielsen PO, Sørensen L, Willerslev E, Iversen R, Sikora M, Kristiansen K, Allentoft ME. Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark.. PLoS One 2021;16(1):e0244872.
    doi: 10.1371/journal.pone.0244872pubmed: 33444387google scholar: lookup
73. Nedoluzhko AV, Sharko FS, Boulygina ES, Tsygankova SV, Slobodova NV, Gruzdeva NM, Rastorguev SM, Spasskaya NN, Maschenko EN. The complete mitochondrial genome of the extinct Pleistocene horse (Equus cf. lenensis) from Kotelny Island (New Siberian Islands, Russia) and its phylogenetic assessment.. Mitochondrial DNA B Resour 2019 Dec 13;5(1):243-245.
    doi: 10.1080/23802359.2019.1699877pubmed: 33366505google scholar: lookup
74. Fromm B, Tarbier M, Smith O, Marmol-Sanchez E, Dalen L, Gilbert TP, Friedlander MR. Ancient microRNA profiles of a 14,300-year-old canid samples confirm taxonomic origin and give glimpses into tissue-specific gene regulation from the Pleistocene.. RNA 2020 Dec 15;27(3):324-34.
    doi: 10.1261/rna.078410.120pubmed: 33323528google scholar: lookup
75. Garrett Vieira F, Samaniego Castruita JA, Gilbert MTP. Using in silico predicted ancestral genomes to improve the efficiency of paleogenome reconstruction.. Ecol Evol 2020 Dec;10(23):12700-12709.
    doi: 10.1002/ece3.6925pubmed: 33304488google scholar: lookup
76. Guo X, He XX, Chen H, Wang ZC, Li HF, Wang JX, Wang MS, Jiang RS. Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses.. Zool Res 2021 Jan 18;42(1):43-50.
    doi: 10.24272/j.issn.2095-8137.2020.133pubmed: 33269825google scholar: lookup
77. Feuerborn TR, Palkopoulou E, van der Valk T, von Seth J, Munters AR, Pečnerová P, Dehasque M, Ureña I, Ersmark E, Lagerholm VK, Krzewińska M, Rodríguez-Varela R, Götherström A, Dalén L, Díez-Del-Molino D. Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.. BMC Genomics 2020 Nov 30;21(1):844.
    doi: 10.1186/s12864-020-07229-ypubmed: 33256612google scholar: lookup
78. Câmara RJF, Bueno BL, Resende CF, Balasuriya UBR, Sakamoto SM, Reis JKPD. Viral Diseases that Affect Donkeys and Mules.. Animals (Basel) 2020 Nov 25;10(12).
    doi: 10.3390/ani10122203pubmed: 33255568google scholar: lookup
79. Kvist L, Honka J, Niskanen M, Liedes O, Aspi J. Selection in the Finnhorse, a native all-around horse breed.. J Anim Breed Genet 2021 Mar;138(2):188-203.
    doi: 10.1111/jbg.12524pubmed: 33226152google scholar: lookup
80. Vorobieva NV, Makunin AI, Druzhkova AS, Kusliy MA, Trifonov VA, Popova KO, Polosmak NV, Molodin VI, Vasiliev SK, Shunkov MV, Graphodatsky AS. High genetic diversity of ancient horses from the Ukok Plateau.. PLoS One 2020;15(11):e0241997.
    doi: 10.1371/journal.pone.0241997pubmed: 33180850google scholar: lookup
81. Drake JL, Whitelegge JP, Jacobs DK. First sequencing of ancient coral skeletal proteins.. Sci Rep 2020 Nov 10;10(1):19407.
    doi: 10.1038/s41598-020-75846-4pubmed: 33173075google scholar: lookup
82. Ramos-Madrigal J, Sinding MS, Carøe C, Mak SST, Niemann J, Samaniego Castruita JA, Fedorov S, Kandyba A, Germonpré M, Bocherens H, Feuerborn TR, Pitulko VV, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Larson G, Frantz LAF, Willerslev E, Meldgaard M, Petersen B, Sicheritz-Ponten T, Bachmann L, Wiig Ø, Hansen AJ, Gilbert MTP, Gopalakrishnan S. Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages.. Curr Biol 2021 Jan 11;31(1):198-206.e8.
    doi: 10.1016/j.cub.2020.10.002pubmed: 33125870google scholar: lookup
83. Ababaikeri B, Abduriyim S, Tohetahong Y, Mamat T, Ahmat A, Halik M. Whole-genome sequencing of Tarim red deer (Cervus elaphus yarkandensis) reveals demographic history and adaptations to an arid-desert environment.. Front Zool 2020;17:31.
    doi: 10.1186/s12983-020-00379-5pubmed: 33072165google scholar: lookup
84. Klumplerova M, Splichalova P, Oppelt J, Futas J, Kohutova A, Musilova P, Kubickova S, Vodicka R, Orlando L, Horin P. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae.. BMC Genomics 2020 Sep 30;21(1):677.
    doi: 10.1186/s12864-020-07089-6pubmed: 32998693google scholar: lookup
85. Bokelmann L, Glocke I, Meyer M. Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples.. Genome Res 2020 Oct;30(10):1449-1457.
    doi: 10.1101/gr.263863.120pubmed: 32963029google scholar: lookup
86. Guimaraes S, Arbuckle BS, Peters J, Adcock SE, Buitenhuis H, Chazin H, Manaseryan N, Uerpmann HP, Grange T, Geigl EM. Ancient DNA shows domestic horses were introduced in the southern Caucasus and Anatolia during the Bronze Age.. Sci Adv 2020 Sep;6(38).
    doi: 10.1126/sciadv.abb0030pubmed: 32938680google scholar: lookup
87. Peyrégne S, Peter BM. AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination.. Genome Biol 2020 Sep 15;21(1):246.
    doi: 10.1186/s13059-020-02123-ypubmed: 32933569google scholar: lookup
88. Saidi-Mehrabad A, Neuberger P, Cavaco M, Froese D, Lanoil B. Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples.. Sci Rep 2020 Aug 31;10(1):14295.
    doi: 10.1038/s41598-020-71234-0pubmed: 32868827google scholar: lookup
89. He Z, Dai X, Beaumont M, Yu F. Detecting and Quantifying Natural Selection at Two Linked Loci from Time Series Data of Allele Frequencies with Forward-in-Time Simulations.. Genetics 2020 Oct;216(2):521-541.
    doi: 10.1534/genetics.120.303463pubmed: 32826299google scholar: lookup
90. Sinding MS, Gopalakrishnan S, Ramos-Madrigal J, de Manuel M, Pitulko VV, Kuderna L, Feuerborn TR, Frantz LAF, Vieira FG, Niemann J, Samaniego Castruita JA, Carøe C, Andersen-Ranberg EU, Jordan PD, Pavlova EY, Nikolskiy PA, Kasparov AK, Ivanova VV, Willerslev E, Skoglund P, Fredholm M, Wennerberg SE, Heide-Jørgensen MP, Dietz R, Sonne C, Meldgaard M, Dalén L, Larson G, Petersen B, Sicheritz-Pontén T, Bachmann L, Wiig Ø, Marques-Bonet T, Hansen AJ, Gilbert MTP. Arctic-adapted dogs emerged at the Pleistocene-Holocene transition.. Science 2020 Jun 26;368(6498):1495-1499.
    doi: 10.1126/science.aaz8599pubmed: 32587022google scholar: lookup
91. Bishop RP, Kappmeyer LS, Onzere CK, Odongo DO, Githaka N, Sears KP, Knowles DP, Fry LM. Equid infective Theileria cluster in distinct 18S rRNA gene clades comprising multiple taxa with unusually broad mammalian host ranges.. Parasit Vectors 2020 May 19;13(1):261.
    doi: 10.1186/s13071-020-04131-0pubmed: 32430015google scholar: lookup
92. Santagostino M, Piras FM, Cappelletti E, Del Giudice S, Semino O, Nergadze SG, Giulotto E. Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective.. Int J Mol Sci 2020 Apr 18;21(8).
    doi: 10.3390/ijms21082838pubmed: 32325780google scholar: lookup
93. Dehasque M, Ávila-Arcos MC, Díez-Del-Molino D, Fumagalli M, Guschanski K, Lorenzen ED, Malaspinas AS, Marques-Bonet T, Martin MD, Murray GGR, Papadopulos AST, Therkildsen NO, Wegmann D, Dalén L, Foote AD. Inference of natural selection from ancient DNA.. Evol Lett 2020 Apr;4(2):94-108.
    doi: 10.1002/evl3.165pubmed: 32313686google scholar: lookup
94. Al Abri MA, Holl HM, Kalla SE, Sutter NB, Brooks SA. Whole genome detection of sequence and structural polymorphism in six diverse horses.. PLoS One 2020;15(4):e0230899.
    doi: 10.1371/journal.pone.0230899pubmed: 32271776google scholar: lookup
95. Welker F, Ramos-Madrigal J, Gutenbrunner P, Mackie M, Tiwary S, Rakownikow Jersie-Christensen R, Chiva C, Dickinson MR, Kuhlwilm M, de Manuel M, Gelabert P, Martinón-Torres M, Margvelashvili A, Arsuaga JL, Carbonell E, Marques-Bonet T, Penkman K, Sabidó E, Cox J, Olsen JV, Lordkipanidze D, Racimo F, Lalueza-Fox C, Bermúdez de Castro JM, Willerslev E, Cappellini E. The dental proteome of Homo antecessor.. Nature 2020 Apr;580(7802):235-238.
    doi: 10.1038/s41586-020-2153-8pubmed: 32269345google scholar: lookup
96. Yi L, Dalai M, Su R, Lin W, Erdenedalai M, Luvsantseren B, Chimedtseren C, Wang Z, Hasi S. Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features.. BMC Genomics 2020 Jan 31;21(1):108.
    doi: 10.1186/s12864-020-6495-2pubmed: 32005147google scholar: lookup
97. Mather N, Traves SM, Ho SYW. A practical introduction to sequentially Markovian coalescent methods for estimating demographic history from genomic data.. Ecol Evol 2020 Jan;10(1):579-589.
    doi: 10.1002/ece3.5888pubmed: 31988743google scholar: lookup
98. Nedoluzhko AV, Sharko FS, Tsygankova SV, Boulygina ES, Barmintseva AE, Krasivskaya AA, Ibragimova AS, Gruzdeva NM, Rastorguev SM, Mugue NS. Molecular phylogeny of one extinct and two critically endangered Central Asian sturgeon species (genus Pseudoscaphirhynchus) based on their mitochondrial genomes.. Sci Rep 2020 Jan 20;10(1):722.
    doi: 10.1038/s41598-020-57581-ypubmed: 31959974google scholar: lookup
99. Barlow A, Hartmann S, Gonzalez J, Hofreiter M, Paijmans JLA. Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates.. Genes (Basel) 2020 Jan 2;11(1).
    doi: 10.3390/genes11010050pubmed: 31906474google scholar: lookup
100. Zyoud SH, Fuchs-Hanusch D. Mapping of climate change research in the Arab world: a bibliometric analysis.. Environ Sci Pollut Res Int 2020 Jan;27(3):3523-3540.
     doi: 10.1007/s11356-019-07100-ypubmed: 31865588google scholar: lookup
101. Hübler R, Key FM, Warinner C, Bos KI, Krause J, Herbig A. HOPS: automated detection and authentication of pathogen DNA in archaeological remains.. Genome Biol 2019 Dec 16;20(1):280.
     doi: 10.1186/s13059-019-1903-0pubmed: 31842945google scholar: lookup
102. Martchenko D, Chikhi R, Shafer ABA. Genome Assembly and Analysis of the North American Mountain Goat (Oreamnos americanus) Reveals Species-Level Responses to Extreme Environments.. G3 (Bethesda) 2020 Feb 6;10(2):437-442.
     doi: 10.1534/g3.119.400747pubmed: 31806764google scholar: lookup
103. McHugo GP, Dover MJ, MacHugh DE. Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics.. BMC Biol 2019 Dec 2;17(1):98.
     doi: 10.1186/s12915-019-0724-7pubmed: 31791340google scholar: lookup
104. Harrison JB, Sunday JM, Rogers SM. Predicting the fate of eDNA in the environment and implications for studying biodiversity.. Proc Biol Sci 2019 Nov 20;286(1915):20191409.
     doi: 10.1098/rspb.2019.1409pubmed: 31744434google scholar: lookup
105. Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era.. Anim Genet 2019 Dec;50(6):569-597.
     doi: 10.1111/age.12857pubmed: 31568563google scholar: lookup
106. Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, Fotakis AK, Lyon D, Moreno-Mayar JV, Bukhsianidze M, Rakownikow Jersie-Christensen R, Mackie M, Ginolhac A, Ferring R, Tappen M, Palkopoulou E, Dickinson MR, Stafford TW Jr, Chan YL, Götherström A, Nathan SKSS, Heintzman PD, Kapp JD, Kirillova I, Moodley Y, Agusti J, Kahlke RD, Kiladze G, Martínez-Navarro B, Liu S, Sandoval Velasco M, Sinding MS, Kelstrup CD, Allentoft ME, Orlando L, Penkman K, Shapiro B, Rook L, Dalén L, Gilbert MTP, Olsen JV, Lordkipanidze D, Willerslev E. Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.. Nature 2019 Oct;574(7776):103-107.
     doi: 10.1038/s41586-019-1555-ypubmed: 31511700google scholar: lookup
107. Orlando L, Librado P. Origin and Evolution of Deleterious Mutations in Horses.. Genes (Basel) 2019 Aug 28;10(9).
     doi: 10.3390/genes10090649pubmed: 31466279google scholar: lookup
108. Beeson SK, Mickelson JR, McCue ME. Exploration of fine-scale recombination rate variation in the domestic horse.. Genome Res 2019 Oct;29(10):1744-1752.
     doi: 10.1101/gr.243311.118pubmed: 31434677google scholar: lookup
109. Castaneda C, Juras R, Khanshour A, Randlaht I, Wallner B, Rigler D, Lindgren G, Raudsepp T, Cothran EG. Population Genetic Analysis of the Estonian Native Horse Suggests Diverse and Distinct Genetics, Ancient Origin and Contribution from Unique Patrilines.. Genes (Basel) 2019 Aug 20;10(8).
     doi: 10.3390/genes10080629pubmed: 31434327google scholar: lookup
110. Fawcett JA, Sato F, Sakamoto T, Iwasaki WM, Tozaki T, Innan H. Genome-wide SNP analysis of Japanese Thoroughbred racehorses.. PLoS One 2019;14(7):e0218407.
     doi: 10.1371/journal.pone.0218407pubmed: 31339891google scholar: lookup
111. Lan TM, Lin Y, Njaramba-Ngatia J, Guo XS, Li RG, Li HM, Kumar-Sahu S, Wang X, Yang XJ, Guo HB, Xu WH, Kristiansen K, Liu H, Xu YC. Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data.. Genes (Basel) 2019 Jul 5;10(7).
     doi: 10.3390/genes10070509pubmed: 31284503google scholar: lookup
112. Liu X, Zhang Y, Li Y, Pan J, Wang D, Chen W, Zheng Z, He X, Zhao Q, Pu Y, Guan W, Han J, Orlando L, Ma Y, Jiang L. EPAS1 Gain-of-Function Mutation Contributes to High-Altitude Adaptation in Tibetan Horses.. Mol Biol Evol 2019 Nov 1;36(11):2591-2603.
     doi: 10.1093/molbev/msz158pubmed: 31273382google scholar: lookup
113. Wang Y, Gao S, Zhao Y, Chen WH, Shao JJ, Wang NN, Li M, Zhou GX, Wang L, Shen WJ, Xu JT, Deng WD, Wang W, Chen YL, Jiang Y. Allele-specific expression and alternative splicing in horse×donkey and cattle×yak hybrids.. Zool Res 2019 Jul 18;40(4):293-304.
     doi: 10.24272/j.issn.2095-8137.2019.042pubmed: 31271004google scholar: lookup
114. Eisenhofer R, Cooper A. A new home for microbes.. Elife 2019 Jun 21;8.
     doi: 10.7554/eLife.48493pubmed: 31223116google scholar: lookup
115. Saitta ET, Liang R, Lau MC, Brown CM, Longrich NR, Kaye TG, Novak BJ, Salzberg SL, Norell MA, Abbott GD, Dickinson MR, Vinther J, Bull ID, Brooker RA, Martin P, Donohoe P, Knowles TD, Penkman KE, Onstott T. Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities.. Elife 2019 Jun 18;8.
     doi: 10.7554/eLife.46205pubmed: 31210129google scholar: lookup
116. Saag L, Laneman M, Varul L, Malve M, Valk H, Razzak MA, Shirobokov IG, Khartanovich VI, Mikhaylova ER, Kushniarevich A, Scheib CL, Solnik A, Reisberg T, Parik J, Saag L, Metspalu E, Rootsi S, Montinaro F, Remm M, Mägi R, D'Atanasio E, Crema ER, Díez-Del-Molino D, Thomas MG, Kriiska A, Kivisild T, Villems R, Lang V, Metspalu M, Tambets K. The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East.. Curr Biol 2019 May 20;29(10):1701-1711.e16.
     doi: 10.1016/j.cub.2019.04.026pubmed: 31080083google scholar: lookup
117. Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, McCrory Constantz C, Gamba C, Al-Rasheid KAS, Albizuri S, Alfarhan AH, Allentoft M, Alquraishi S, Anthony D, Baimukhanov N, Barrett JH, Bayarsaikhan J, Benecke N, Bernáldez-Sánchez E, Berrocal-Rangel L, Biglari F, Boessenkool S, Boldgiv B, Brem G, Brown D, Burger J, Crubézy E, Daugnora L, Davoudi H, de Barros Damgaard P, de Los Ángeles de Chorro Y de Villa-Ceballos M, Deschler-Erb S, Detry C, Dill N, do Mar Oom M, Dohr A, Ellingvåg S, Erdenebaatar D, Fathi H, Felkel S, Fernández-Rodríguez C, García-Viñas E, Germonpré M, Granado JD, Hallsson JH, Hemmer H, Hofreiter M, Kasparov A, Khasanov M, Khazaeli R, Kosintsev P, Kristiansen K, Kubatbek T, Kuderna L, Kuznetsov P, Laleh H, Leonard JA, Lhuillier J, Liesau von Lettow-Vorbeck C, Logvin A, Lõugas L, Ludwig A, Luis C, Arruda AM, Marques-Bonet T, Matoso Silva R, Merz V, Mijiddorj E, Miller BK, Monchalov O, Mohaseb FA, Morales A, Nieto-Espinet A, Nistelberger H, Onar V, Pálsdóttir AH, Pitulko V, Pitskhelauri K, Pruvost M, Rajic Sikanjic P, Rapan Papeša A, Roslyakova N, Sardari A, Sauer E, Schafberg R, Scheu A, Schibler J, Schlumbaum A, Serrand N, Serres-Armero A, Shapiro B, Sheikhi Seno S, Shevnina I, Shidrang S, Southon J, Star B, Sykes N, Taheri K, Taylor W, Teegen WR, Trbojević Vukičević T, Trixl S, Tumen D, Undrakhbold S, Usmanova E, Vahdati A, Valenzuela-Lamas S, Viegas C, Wallner B, Weinstock J, Zaibert V, Clavel B, Lepetz S, Mashkour M, Helgason A, Stefánsson K, Barrey E, Willerslev E, Outram AK, Librado P, Orlando L. Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series.. Cell 2019 May 30;177(6):1419-1435.e31.
     doi: 10.1016/j.cell.2019.03.049pubmed: 31056281google scholar: lookup
118. Stahlschmidt MC, Collin TC, Fernandes DM, Bar-Oz G, Belfer-Cohen A, Gao Z, Jakeli N, Matskevich Z, Meshveliani T, Pritchard JK, McDermott F, Pinhasi R. Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia.. Sci Rep 2019 Apr 29;9(1):6628.
     doi: 10.1038/s41598-019-43147-0pubmed: 31036834google scholar: lookup
119. Barnett R, Sinding MS, Vieira FG, Mendoza MLZ, Bonnet M, Araldi A, Kienast I, Zambarda A, Yamaguchi N, Henschel P, Gilbert MTP. No longer locally extinct? Tracing the origins of a lion (Panthera leo) living in Gabon.. Conserv Genet 2018;19(3):611-618.
     doi: 10.1007/s10592-017-1039-2pubmed: 31007636google scholar: lookup
120. Yan L, Zhang M, Tang L, Ente M, Ma X, Chu H, Li K, Hu D, Zhang D. First reports of nasal and traumatic myiasis infection in endangered Przewalski's horses (Equus ferus przewalskii).. Int J Parasitol Parasites Wildl 2019 Aug;9:21-24.
     doi: 10.1016/j.ijppaw.2019.03.018pubmed: 30976513google scholar: lookup
121. Yamagata K, Nagai K, Miyamoto H, Anzai M, Kato H, Miyamoto K, Kurosaka S, Azuma R, Kolodeznikov II, Protopopov AV, Plotnikov VV, Kobayashi H, Kawahara-Miki R, Kono T, Uchida M, Shibata Y, Handa T, Kimura H, Hosoi Y, Mitani T, Matsumoto K, Iritani A. Signs of biological activities of 28,000-year-old mammoth nuclei in mouse oocytes visualized by live-cell imaging.. Sci Rep 2019 Mar 11;9(1):4050.
     doi: 10.1038/s41598-019-40546-1pubmed: 30858410google scholar: lookup
122. Novak BJ. De-Extinction.. Genes (Basel) 2018 Nov 13;9(11).
     doi: 10.3390/genes9110548pubmed: 30428542google scholar: lookup
123. Wiemann J, Fabbri M, Yang TR, Stein K, Sander PM, Norell MA, Briggs DEG. Fossilization transforms vertebrate hard tissue proteins into N-heterocyclic polymers.. Nat Commun 2018 Nov 9;9(1):4741.
     doi: 10.1038/s41467-018-07013-3pubmed: 30413693google scholar: lookup
124. Yoon SH, Lee W, Ahn H, Caetano-Anolles K, Park KD, Kim H. Origin and spread of Thoroughbred racehorses inferred from complete mitochondrial genome sequences: Phylogenomic and Bayesian coalescent perspectives.. PLoS One 2018;13(9):e0203917.
     doi: 10.1371/journal.pone.0203917pubmed: 30216366google scholar: lookup
125. Zhu H, Gifford RJ, Murcia PR. Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes.. J Virol 2018 Dec 1;92(23).
     doi: 10.1128/JVI.00927-18pubmed: 30209175google scholar: lookup
126. Ney G, Frederick K, Schul J. A Post-pleistocene Calibrated Mutation Rate from Insect Museum Specimens.. PLoS Curr 2018 Jul 13;10.
     doi: 10.1371/currents.tol.aba557de56be881793261f7e1565cf35pubmed: 30116653google scholar: lookup
127. Janečka JE, Davis BW, Ghosh S, Paria N, Das PJ, Orlando L, Schubert M, Nielsen MK, Stout TAE, Brashear W, Li G, Johnson CD, Metz RP, Zadjali AMA, Love CC, Varner DD, Bellott DW, Murphy WJ, Chowdhary BP, Raudsepp T. Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes.. Nat Commun 2018 Jul 27;9(1):2945.
     doi: 10.1038/s41467-018-05290-6pubmed: 30054462google scholar: lookup
128. Leonardi M, Boschin F, Giampoudakis K, Beyer RM, Krapp M, Bendrey R, Sommer R, Boscato P, Manica A, Nogues-Bravo D, Orlando L. Late Quaternary horses in Eurasia in the face of climate and vegetation change.. Sci Adv 2018 Jul;4(7):eaar5589.
     doi: 10.1126/sciadv.aar5589pubmed: 30050986google scholar: lookup
129. Metzger J, Rau J, Naccache F, Bas Conn L, Lindgren G, Distl O. Genome data uncover four synergistic key regulators for extremely small body size in horses.. BMC Genomics 2018 Jun 25;19(1):492.
     doi: 10.1186/s12864-018-4877-5pubmed: 29940849google scholar: lookup
130. Zhang C, Ni P, Ahmad HI, Gemingguli M, Baizilaitibei A, Gulibaheti D, Fang Y, Wang H, Asif AR, Xiao C, Chen J, Ma Y, Liu X, Du X, Zhao S. Detecting the Population Structure and Scanning for Signatures of Selection in Horses (Equus caballus) From Whole-Genome Sequencing Data.. Evol Bioinform Online 2018;14:1176934318775106.
     doi: 10.1177/1176934318775106pubmed: 29899660google scholar: lookup
131. Tunstall T, Kock R, Vahala J, Diekhans M, Fiddes I, Armstrong J, Paten B, Ryder OA, Steiner CC. Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells.. Genome Res 2018 Jun;28(6):780-788.
     doi: 10.1101/gr.227603.117pubmed: 29798851google scholar: lookup
132. Muntané G, Farré X, Rodríguez JA, Pegueroles C, Hughes DA, de Magalhães JP, Gabaldón T, Navarro A. Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis.. Mol Biol Evol 2018 Aug 1;35(8):1990-2004.
     doi: 10.1093/molbev/msy105pubmed: 29788292google scholar: lookup
133. Tong KJ, Duchêne DA, Duchêne S, Geoghegan JL, Ho SYW. A comparison of methods for estimating substitution rates from ancient DNA sequence data.. BMC Evol Biol 2018 May 16;18(1):70.
     doi: 10.1186/s12862-018-1192-3pubmed: 29769015google scholar: lookup
134. Panda D, Molla KA, Baig MJ, Swain A, Behera D, Dash M. DNA as a digital information storage device: hope or hype?. 3 Biotech 2018 May;8(5):239.
     doi: 10.1007/s13205-018-1246-7pubmed: 29744271google scholar: lookup
135. de Barros Damgaard P, Martiniano R, Kamm J, Moreno-Mayar JV, Kroonen G, Peyrot M, Barjamovic G, Rasmussen S, Zacho C, Baimukhanov N, Zaibert V, Merz V, Biddanda A, Merz I, Loman V, Evdokimov V, Usmanova E, Hemphill B, Seguin-Orlando A, Yediay FE, Ullah I, Sjögren KG, Iversen KH, Choin J, de la Fuente C, Ilardo M, Schroeder H, Moiseyev V, Gromov A, Polyakov A, Omura S, Senyurt SY, Ahmad H, McKenzie C, Margaryan A, Hameed A, Samad A, Gul N, Khokhar MH, Goriunova OI, Bazaliiskii VI, Novembre J, Weber AW, Orlando L, Allentoft ME, Nielsen R, Kristiansen K, Sikora M, Outram AK, Durbin R, Willerslev E. The first horse herders and the impact of early Bronze Age steppe expansions into Asia.. Science 2018 Jun 29;360(6396).
     doi: 10.1126/science.aar7711pubmed: 29743352google scholar: lookup
136. Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R, Paillot R, Bryant N, Vaudin M, Librado P, Orlando L. Improved de novo genomic assembly for the domestic donkey.. Sci Adv 2018 Apr;4(4):eaaq0392.
     doi: 10.1126/sciadv.aaq0392pubmed: 29740610google scholar: lookup
137. Nergadze SG, Piras FM, Gamba R, Corbo M, Cerutti F, McCarter JGW, Cappelletti E, Gozzo F, Harman RM, Antczak DF, Miller D, Scharfe M, Pavesi G, Raimondi E, Sullivan KF, Giulotto E. Birth, evolution, and transmission of satellite-free mammalian centromeric domains.. Genome Res 2018 Jun;28(6):789-799.
     doi: 10.1101/gr.231159.117pubmed: 29712753google scholar: lookup
138. Zhang Z, Jia Y, Almeida P, Mank JE, van Tuinen M, Wang Q, Jiang Z, Chen Y, Zhan K, Hou S, Zhou Z, Li H, Yang F, He Y, Ning Z, Yang N, Qu L. Whole-genome resequencing reveals signatures of selection and timing of duck domestication.. Gigascience 2018 Apr 1;7(4).
     doi: 10.1093/gigascience/giy027pubmed: 29635409google scholar: lookup
139. Dias GM, Bidault A, Le Chevalier P, Choquet G, Der Sarkissian C, Orlando L, Medigue C, Barbe V, Mangenot S, Thompson CC, Thompson FL, Jacq A, Pichereau V, Paillard C. Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs.. Front Microbiol 2018;9:227.
     doi: 10.3389/fmicb.2018.00227pubmed: 29515533google scholar: lookup
140. Welker F. Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment.. BMC Evol Biol 2018 Feb 20;18(1):23.
     doi: 10.1186/s12862-018-1141-1pubmed: 29463217google scholar: lookup
141. Kumar R, Patil RD. Cryptic etiopathological conditions of equine nervous system with special emphasis on viral diseases.. Vet World 2017 Dec;10(12):1427-1438.
     doi: 10.14202/vetworld.2017.1427-1438pubmed: 29391683google scholar: lookup
142. Moreno-Mayar JV, Potter BA, Vinner L, Steinrücken M, Rasmussen S, Terhorst J, Kamm JA, Albrechtsen A, Malaspinas AS, Sikora M, Reuther JD, Irish JD, Malhi RS, Orlando L, Song YS, Nielsen R, Meltzer DJ, Willerslev E. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans.. Nature 2018 Jan 11;553(7687):203-207.
     doi: 10.1038/nature25173pubmed: 29323294google scholar: lookup
143. Segawa T, Takeuchi N, Fujita K, Aizen VB, Willerslev E, Yonezawa T. Demographic analysis of cyanobacteria based on the mutation rates estimated from an ancient ice core.. Heredity (Edinb) 2018 Jun;120(6):562-573.
     doi: 10.1038/s41437-017-0040-3pubmed: 29302050google scholar: lookup
144. Mays HL Jr, Hung CM, Shaner PJ, Denvir J, Justice M, Yang SF, Roth TL, Oehler DA, Fan J, Rekulapally S, Primerano DA. Genomic Analysis of Demographic History and Ecological Niche Modeling in the Endangered Sumatran Rhinoceros Dicerorhinus sumatrensis.. Curr Biol 2018 Jan 8;28(1):70-76.e4.
     doi: 10.1016/j.cub.2017.11.021pubmed: 29249659google scholar: lookup
145. Soraggi S, Wiuf C, Albrechtsen A. Powerful Inference with the D-Statistic on Low-Coverage Whole-Genome Data.. G3 (Bethesda) 2018 Feb 2;8(2):551-566.
     doi: 10.1534/g3.117.300192pubmed: 29196497google scholar: lookup
146. Heintzman PD, Zazula GD, MacPhee R, Scott E, Cahill JA, McHorse BK, Kapp JD, Stiller M, Wooller MJ, Orlando L, Southon J, Froese DG, Shapiro B. A new genus of horse from Pleistocene North America.. Elife 2017 Nov 28;6.
     doi: 10.7554/eLife.29944pubmed: 29182148google scholar: lookup
147. Rifkin RF, Potgieter M, Ramond JB, Cowan DA. Ancient oncogenesis, infection and human evolution.. Evol Appl 2017 Dec;10(10):949-964.
     doi: 10.1111/eva.12497pubmed: 29151852google scholar: lookup
148. Metcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E, Amir A, Willerslev E, Knight R, McKenzie V, Orlando L. Evaluating the impact of domestication and captivity on the horse gut microbiome.. Sci Rep 2017 Nov 14;7(1):15497.
     doi: 10.1038/s41598-017-15375-9pubmed: 29138485google scholar: lookup
149. Mackie M, Hendy J, Lowe AD, Sperduti A, Holst M, Collins MJ, Speller CF. Preservation of the metaproteome: variability of protein preservation in ancient dental calculus.. Sci Technol Archaeol Res 2017;3(1):74-86.
     doi: 10.1080/20548923.2017.1361629pubmed: 29098079google scholar: lookup
150. Washburn JD, Schnable JC, Conant GC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC. Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses.. Sci Rep 2017 Oct 19;7(1):13528.
     doi: 10.1038/s41598-017-13236-zpubmed: 29051622google scholar: lookup
151. Gim JA, Kim HS. Identification and Expression Analyses of Equine Endogenous Retroviruses in Horses.. Mol Cells 2017 Oct;40(10):796-804.
     doi: 10.14348/molcells.2017.0141pubmed: 29047258google scholar: lookup
152. Beichman AC, Phung TN, Lohmueller KE. Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories.. G3 (Bethesda) 2017 Nov 6;7(11):3605-3620.
     doi: 10.1534/g3.117.300259pubmed: 28893846google scholar: lookup
153. Mohandesan E, Fitak RR, Corander J, Yadamsuren A, Chuluunbat B, Abdelhadi O, Raziq A, Nagy P, Stalder G, Walzer C, Faye B, Burger PA. Mitogenome Sequencing in the Genus Camelus Reveals Evidence for Purifying Selection and Long-term Divergence between Wild and Domestic Bactrian Camels.. Sci Rep 2017 Aug 30;7(1):9970.
     doi: 10.1038/s41598-017-08995-8pubmed: 28855525google scholar: lookup
154. Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MS, Kuderna LFK, Zhang W, Fu S, Vieira FG, Germonpré M, Bocherens H, Fedorov S, Petersen B, Sicheritz-Pontén T, Marques-Bonet T, Zhang G, Jiang H, Gilbert MTP. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing.. Gigascience 2017 Aug 1;6(8):1-13.
     doi: 10.1093/gigascience/gix049pubmed: 28854615google scholar: lookup
155. Barrón-Ortiz CI, Rodrigues AT, Theodor JM, Kooyman BP, Yang DY, Speller CF. Cheek tooth morphology and ancient mitochondrial DNA of late Pleistocene horses from the western interior of North America: Implications for the taxonomy of North American Late Pleistocene Equus.. PLoS One 2017;12(8):e0183045.
     doi: 10.1371/journal.pone.0183045pubmed: 28817644google scholar: lookup
156. Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA, Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V, Kalbfleisch T, Leeb T, Lindgren G, Lopes MS, Mach N, da Câmara Machado A, MacLeod JN, McCoy A, Metzger J, Penedo C, Polani S, Rieder S, Tammen I, Tetens J, Thaller G, Verini-Supplizi A, Wade CM, Wallner B, Orlando L, Mickelson JR, McCue ME. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds.. BMC Genomics 2017 Jul 27;18(1):565.
     doi: 10.1186/s12864-017-3943-8pubmed: 28750625google scholar: lookup
157. Sawafuji R, Cappellini E, Nagaoka T, Fotakis AK, Jersie-Christensen RR, Olsen JV, Hirata K, Ueda S. Proteomic profiling of archaeological human bone.. R Soc Open Sci 2017 Jun;4(6):161004.
     doi: 10.1098/rsos.161004pubmed: 28680659google scholar: lookup
158. Gopalakrishnan S, Samaniego Castruita JA, Sinding MS, Kuderna LFK, Räikkönen J, Petersen B, Sicheritz-Ponten T, Larson G, Orlando L, Marques-Bonet T, Hansen AJ, Dalén L, Gilbert MTP. The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics.. BMC Genomics 2017 Jun 29;18(1):495.
     doi: 10.1186/s12864-017-3883-3pubmed: 28662691google scholar: lookup
159. Zaucha J, Heddle JG. Resurrecting the Dead (Molecules).. Comput Struct Biotechnol J 2017;15:351-358.
     doi: 10.1016/j.csbj.2017.05.002pubmed: 28652896google scholar: lookup
160. Thomas JE, Carvalho GR, Haile J, Martin MD, Castruita JAS, Niemann J, Sinding MS, Sandoval-Velasco M, Rawlence NJ, Fuller E, Fjeldså J, Hofreiter M, Stewart JR, Gilbert MTP, Knapp M. An ‛Aukward' Tale: A Genetic Approach to Discover the Whereabouts of the Last Great Auks.. Genes (Basel) 2017 Jun 15;8(6).
     doi: 10.3390/genes8060164pubmed: 28617333google scholar: lookup
161. Meyer M, Palkopoulou E, Baleka S, Stiller M, Penkman KEH, Alt KW, Ishida Y, Mania D, Mallick S, Meijer T, Meller H, Nagel S, Nickel B, Ostritz S, Rohland N, Schauer K, Schüler T, Roca AL, Reich D, Shapiro B, Hofreiter M. Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution.. Elife 2017 Jun 6;6.
     doi: 10.7554/eLife.25413pubmed: 28585920google scholar: lookup
162. Buckley M, Warwood S, van Dongen B, Kitchener AC, Manning PL. A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination.. Proc Biol Sci 2017 May 31;284(1855).
     doi: 10.1098/rspb.2017.0544pubmed: 28566488google scholar: lookup
163. Elsner J, Hofreiter M, Schibler J, Schlumbaum A. Ancient mtDNA diversity reveals specific population development of wild horses in Switzerland after the Last Glacial Maximum.. PLoS One 2017;12(5):e0177458.
     doi: 10.1371/journal.pone.0177458pubmed: 28542345google scholar: lookup
164. Kistler L, Ware R, Smith O, Collins M, Allaby RG. A new model for ancient DNA decay based on paleogenomic meta-analysis.. Nucleic Acids Res 2017 Jun 20;45(11):6310-6320.
     doi: 10.1093/nar/gkx361pubmed: 28486705google scholar: lookup
165. Cucchi T, Mohaseb A, Peigné S, Debue K, Orlando L, Mashkour M. Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies.. R Soc Open Sci 2017 Apr;4(4):160997.
     doi: 10.1098/rsos.160997pubmed: 28484618google scholar: lookup
166. Warinner C, Herbig A, Mann A, Fellows Yates JA, Weiß CL, Burbano HA, Orlando L, Krause J. A Robust Framework for Microbial Archaeology.. Annu Rev Genomics Hum Genet 2017 Aug 31;18:321-356.
     doi: 10.1146/annurev-genom-091416-035526pubmed: 28460196google scholar: lookup
167. Lefébure T, Morvan C, Malard F, François C, Konecny-Dupré L, Guéguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Sarkissian C, Charrier NP, Eme D, Mermillod-Blondin F, Duret L, Vieira C, Orlando L, Douady CJ. Less effective selection leads to larger genomes.. Genome Res 2017 Jun;27(6):1016-1028.
     doi: 10.1101/gr.212589.116pubmed: 28424354google scholar: lookup
168. Kumar V, Lammers F, Bidon T, Pfenninger M, Kolter L, Nilsson MA, Janke A. The evolutionary history of bears is characterized by gene flow across species.. Sci Rep 2017 Apr 19;7:46487.
     doi: 10.1038/srep46487pubmed: 28422140google scholar: lookup
169. Glocke I, Meyer M. Extending the spectrum of DNA sequences retrieved from ancient bones and teeth.. Genome Res 2017 Jul;27(7):1230-1237.
     doi: 10.1101/gr.219675.116pubmed: 28408382google scholar: lookup
170. Bösl E. [aDNA Research From a Historical Perspective].. NTM 2017 Mar;25(1):99-142.
     doi: 10.1007/s00048-017-0168-5pubmed: 28389681google scholar: lookup
171. Viļuma A, Mikko S, Hahn D, Skow L, Andersson G, Bergström TF. Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology.. Sci Rep 2017 Mar 31;7:45518.
     doi: 10.1038/srep45518pubmed: 28361880google scholar: lookup
172. Welker F, Smith GM, Hutson JM, Kindler L, Garcia-Moreno A, Villaluenga A, Turner E, Gaudzinski-Windheuser S. Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae.. PeerJ 2017;5:e3033.
     doi: 10.7717/peerj.3033pubmed: 28316883google scholar: lookup
173. Froese D, Stiller M, Heintzman PD, Reyes AV, Zazula GD, Soares AE, Meyer M, Hall E, Jensen BJ, Arnold LJ, MacPhee RD, Shapiro B. Fossil and genomic evidence constrains the timing of bison arrival in North America.. Proc Natl Acad Sci U S A 2017 Mar 28;114(13):3457-3462.
     doi: 10.1073/pnas.1620754114pubmed: 28289222google scholar: lookup
174. Faerman M, Bar-Gal GK, Boaretto E, Boeskorov GG, Dokuchaev NE, Ermakov OA, Golenishchev FN, Gubin SV, Mintz E, Simonov E, Surin VL, Titov SV, Zanina OG, Formozov NA. DNA analysis of a 30,000-year-old Urocitellus glacialis from northeastern Siberia reveals phylogenetic relationships between ancient and present-day arctic ground squirrels.. Sci Rep 2017 Feb 16;7:42639.
     doi: 10.1038/srep42639pubmed: 28205612google scholar: lookup
175. Braud M, Magee DA, Park SD, Sonstegard TS, Waters SM, MacHugh DE, Spillane C. Genome-Wide microRNA Binding Site Variation between Extinct Wild Aurochs and Modern Cattle Identifies Candidate microRNA-Regulated Domestication Genes.. Front Genet 2017;8:3.
     doi: 10.3389/fgene.2017.00003pubmed: 28197171google scholar: lookup
176. Palacio P, Berthonaud V, Guérin C, Lambourdière J, Maksud F, Philippe M, Plaire D, Stafford T, Marsolier-Kergoat MC, Elalouf JM. Genome data on the extinct Bison schoetensacki establish it as a sister species of the extant European bison (Bison bonasus).. BMC Evol Biol 2017 Feb 10;17(1):48.
     doi: 10.1186/s12862-017-0894-2pubmed: 28187706google scholar: lookup
177. Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA.. Syst Biol 2017 Jan 1;66(1):e1-e29.
     doi: 10.1093/sysbio/syw059pubmed: 28173586google scholar: lookup
178. Hansen HB, Damgaard PB, Margaryan A, Stenderup J, Lynnerup N, Willerslev E, Allentoft ME. Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum.. PLoS One 2017;12(1):e0170940.
     doi: 10.1371/journal.pone.0170940pubmed: 28129388google scholar: lookup
179. Schroeter ER, DeHart CJ, Cleland TP, Zheng W, Thomas PM, Kelleher NL, Bern M, Schweitzer MH. Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein.. J Proteome Res 2017 Feb 3;16(2):920-932.
     doi: 10.1021/acs.jproteome.6b00873pubmed: 28111950google scholar: lookup
180. Seersholm FV, Pedersen MW, Søe MJ, Shokry H, Mak SS, Ruter A, Raghavan M, Fitzhugh W, Kjær KH, Willerslev E, Meldgaard M, Kapel CM, Hansen AJ. DNA evidence of bowhead whale exploitation by Greenlandic Paleo-Inuit 4,000 years ago.. Nat Commun 2016 Nov 8;7:13389.
     doi: 10.1038/ncomms13389pubmed: 27824339google scholar: lookup
181. Walter S, Rasche A, Moreira-Soto A, Pfaender S, Bletsa M, Corman VM, Aguilar-Setien A, García-Lacy F, Hans A, Todt D, Schuler G, Shnaiderman-Torban A, Steinman A, Roncoroni C, Veneziano V, Rusenova N, Sandev N, Rusenov A, Zapryanova D, García-Bocanegra I, Jores J, Carluccio A, Veronesi MC, Cavalleri JMV, Drosten C, Lemey P, Steinmann E, Drexler JF. Differential Infection Patterns and Recent Evolutionary Origins of Equine Hepaciviruses in Donkeys.. J Virol 2017 Jan 1;91(1).
     doi: 10.1128/JVI.01711-16pubmed: 27795428google scholar: lookup
182. Librado P, Fages A, Gaunitz C, Leonardi M, Wagner S, Khan N, Hanghøj K, Alquraishi SA, Alfarhan AH, Al-Rasheid KA, Der Sarkissian C, Schubert M, Orlando L. The Evolutionary Origin and Genetic Makeup of Domestic Horses.. Genetics 2016 Oct;204(2):423-434.
     doi: 10.1534/genetics.116.194860pubmed: 27729493google scholar: lookup
183. Demarchi B, Hall S, Roncal-Herrero T, Freeman CL, Woolley J, Crisp MK, Wilson J, Fotakis A, Fischer R, Kessler BM, Rakownikow Jersie-Christensen R, Olsen JV, Haile J, Thomas J, Marean CW, Parkington J, Presslee S, Lee-Thorp J, Ditchfield P, Hamilton JF, Ward MW, Wang CM, Shaw MD, Harrison T, Domínguez-Rodrigo M, MacPhee R, Kwekason A, Ecker M, Kolska Horwitz L, Chazan M, Kröger R, Thomas-Oates J, Harding JH, Cappellini E, Penkman K, Collins MJ. Protein sequences bound to mineral surfaces persist into deep time.. Elife 2016 Sep 27;5.
     doi: 10.7554/eLife.17092pubmed: 27668515google scholar: lookup
184. Welker F, Hajdinjak M, Talamo S, Jaouen K, Dannemann M, David F, Julien M, Meyer M, Kelso J, Barnes I, Brace S, Kamminga P, Fischer R, Kessler BM, Stewart JR, Pääbo S, Collins MJ, Hublin JJ. Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne.. Proc Natl Acad Sci U S A 2016 Oct 4;113(40):11162-11167.
     doi: 10.1073/pnas.1605834113pubmed: 27638212google scholar: lookup
185. Hanghøj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L. Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX.. Mol Biol Evol 2016 Dec;33(12):3284-3298.
     doi: 10.1093/molbev/msw184pubmed: 27624717google scholar: lookup
186. Parker GJ, Leppert T, Anex DS, Hilmer JK, Matsunami N, Baird L, Stevens J, Parsawar K, Durbin-Johnson BP, Rocke DM, Nelson C, Fairbanks DJ, Wilson AS, Rice RH, Woodward SR, Bothner B, Hart BR, Leppert M. Demonstration of Protein-Based Human Identification Using the Hair Shaft Proteome.. PLoS One 2016;11(9):e0160653.
     doi: 10.1371/journal.pone.0160653pubmed: 27603779google scholar: lookup
187. Extance A. How DNA could store all the world's data.. Nature 2016 Sep 1;537(7618):22-4.
     doi: 10.1038/537022apubmed: 27582204google scholar: lookup
188. Mikšík I, Sedláková P, Pataridis S, Bortolotti F, Gottardo R. Proteins and their modifications in a medieval mummy.. Protein Sci 2016 Nov;25(11):2037-2044.
     doi: 10.1002/pro.3024pubmed: 27543755google scholar: lookup
189. O'Sullivan NJ, Teasdale MD, Mattiangeli V, Maixner F, Pinhasi R, Bradley DG, Zink A. A whole mitochondria analysis of the Tyrolean Iceman's leather provides insights into the animal sources of Copper Age clothing.. Sci Rep 2016 Aug 18;6:31279.
     doi: 10.1038/srep31279pubmed: 27537861google scholar: lookup
190. Solazzo C, Courel B, Connan J, van Dongen BE, Barden H, Penkman K, Taylor S, Demarchi B, Adam P, Schaeffer P, Nissenbaum A, Bar-Yosef O, Buckley M. Identification of the earliest collagen- and plant-based coatings from Neolithic artefacts (Nahal Hemar cave, Israel).. Sci Rep 2016 Aug 9;6:31053.
     doi: 10.1038/srep31053pubmed: 27503740google scholar: lookup
191. Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV. Toward high-resolution population genomics using archaeological samples.. DNA Res 2016 Aug;23(4):295-310.
     doi: 10.1093/dnares/dsw029pubmed: 27436340google scholar: lookup
192. Yang J, Li WR, Lv FH, He SG, Tian SL, Peng WF, Sun YW, Zhao YX, Tu XL, Zhang M, Xie XL, Wang YT, Li JQ, Liu YG, Shen ZQ, Wang F, Liu GJ, Lu HF, Kantanen J, Han JL, Li MH, Liu MJ. Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments.. Mol Biol Evol 2016 Oct;33(10):2576-92.
     doi: 10.1093/molbev/msw129pubmed: 27401233google scholar: lookup
193. Cleland TP, Schroeter ER, Feranec RS, Vashishth D. Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for palaeoproteomics.. Proc Biol Sci 2016 Jun 15;283(1832).
     doi: 10.1098/rspb.2016.0593pubmed: 27306052google scholar: lookup
194. Mohandesan E, Speller CF, Peters J, Uerpmann HP, Uerpmann M, De Cupere B, Hofreiter M, Burger PA. Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel.. Mol Ecol Resour 2017 Mar;17(2):300-313.
     doi: 10.1111/1755-0998.12551pubmed: 27289015google scholar: lookup
195. Krause J, Pääbo S. Genetic Time Travel.. Genetics 2016 May;203(1):9-12.
     doi: 10.1534/genetics.116.187856pubmed: 27183562google scholar: lookup
196. O'Connor A, Wills MA. Measuring Stratigraphic Congruence Across Trees, Higher Taxa, and Time.. Syst Biol 2016 Sep;65(5):792-811.
     doi: 10.1093/sysbio/syw039pubmed: 27155010google scholar: lookup
197. Schrimpf R, Gottschalk M, Metzger J, Martinsson G, Sieme H, Distl O. Screening of whole genome sequences identified high-impact variants for stallion fertility.. BMC Genomics 2016 Apr 14;17:288.
     doi: 10.1186/s12864-016-2608-3pubmed: 27079378google scholar: lookup
198. Burger PA. The history of Old World camelids in the light of molecular genetics.. Trop Anim Health Prod 2016 Jun;48(5):905-13.
     doi: 10.1007/s11250-016-1032-7pubmed: 27048619google scholar: lookup
199. Zhirnov V, Zadegan RM, Sandhu GS, Church GM, Hughes WL. Nucleic acid memory.. Nat Mater 2016 Apr;15(4):366-70.
     doi: 10.1038/nmat4594pubmed: 27005909google scholar: lookup
200. McLean BS, Bell KC, Dunnum JL, Abrahamson B, Colella JP, Deardorff ER, Weber JA, Jones AK, Salazar-Miralles F, Cook JA. Natural history collections-based research: progress, promise, and best practices.. J Mammal 2016 Jan 20;97(1):287-297.
     doi: 10.1093/jmammal/gyv178pubmed: 26989266google scholar: lookup
201. Chang D, Shapiro B. Using ancient DNA and coalescent-based methods to infer extinction.. Biol Lett 2016 Feb;12(2):20150822.
     doi: 10.1098/rsbl.2015.0822pubmed: 26864783google scholar: lookup
202. Bayerova Z, Janova E, Matiasovic J, Orlando L, Horin P. Positive selection in the SLC11A1 gene in the family Equidae.. Immunogenetics 2016 May;68(5):353-64.
     doi: 10.1007/s00251-016-0905-2pubmed: 26846480google scholar: lookup
203. Kanda K, Pflug JM, Sproul JS, Dasenko MA, Maddison DR. Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing.. PLoS One 2015;10(12):e0143929.
     doi: 10.1371/journal.pone.0143929pubmed: 26716693google scholar: lookup
204. Imsland F, McGowan K, Rubin CJ, Henegar C, Sundström E, Berglund J, Schwochow D, Gustafson U, Imsland P, Lindblad-Toh K, Lindgren G, Mikko S, Millon L, Wade C, Schubert M, Orlando L, Penedo MC, Barsh GS, Andersson L. Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses.. Nat Genet 2016 Feb;48(2):152-8.
     doi: 10.1038/ng.3475pubmed: 26691985google scholar: lookup
205. dos Reis M, Donoghue PC, Yang Z. Bayesian molecular clock dating of species divergences in the genomics era.. Nat Rev Genet 2016 Feb;17(2):71-80.
     doi: 10.1038/nrg.2015.8pubmed: 26688196google scholar: lookup
206. Kader A, Li Y, Dong K, Irwin DM, Zhao Q, He X, Liu J, Pu Y, Gorkhali NA, Liu X, Jiang L, Li X, Guan W, Zhang Y, Wu DD, Ma Y. Population Variation Reveals Independent Selection toward Small Body Size in Chinese Debao Pony.. Genome Biol Evol 2015 Dec 3;8(1):42-50.
     doi: 10.1093/gbe/evv245pubmed: 26637467google scholar: lookup
207. Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover CA, Lorente-Galdos B, Nedoluzhko A, Boulygina E, Tsygankova S, Neuditschko M, Jagannathan V, Thèves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Sicheritz-Ponten T, Popov R, Grigoriev S, Alekseev AN, Rubin EM, McCue M, Rieder S, Leeb T, Tikhonov A, Crubézy E, Slatkin M, Marques-Bonet T, Nielsen R, Willerslev E, Kantanen J, Prokhortchouk E, Orlando L. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments.. Proc Natl Acad Sci U S A 2015 Dec 15;112(50):E6889-97.
     doi: 10.1073/pnas.1513696112pubmed: 26598656google scholar: lookup
208. Cleland TP, Schroeter ER, Zamdborg L, Zheng W, Lee JE, Tran JC, Bern M, Duncan MB, Lebleu VS, Ahlf DR, Thomas PM, Kalluri R, Kelleher NL, Schweitzer MH. Mass Spectrometry and Antibody-Based Characterization of Blood Vessels from Brachylophosaurus canadensis.. J Proteome Res 2015 Dec 4;14(12):5252-62.
     doi: 10.1021/acs.jproteome.5b00675pubmed: 26595531google scholar: lookup
209. Bruford MW, Ginja C, Hoffmann I, Joost S, Orozco-terWengel P, Alberto FJ, Amaral AJ, Barbato M, Biscarini F, Colli L, Costa M, Curik I, Duruz S, Ferenčaković M, Fischer D, Fitak R, Groeneveld LF, Hall SJ, Hanotte O, Hassan FU, Helsen P, Iacolina L, Kantanen J, Leempoel K, Lenstra JA, Ajmone-Marsan P, Masembe C, Megens HJ, Miele M, Neuditschko M, Nicolazzi EL, Pompanon F, Roosen J, Sevane N, Smetko A, Štambuk A, Streeter I, Stucki S, Supakorn C, Telo Da Gama L, Tixier-Boichard M, Wegmann D, Zhan X. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025.. Front Genet 2015;6:314.
     doi: 10.3389/fgene.2015.00314pubmed: 26539210google scholar: lookup
210. Park SD, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.. Genome Biol 2015 Oct 26;16:234.
     doi: 10.1186/s13059-015-0790-2pubmed: 26498365google scholar: lookup
211. Metzger J, Karwath M, Tonda R, Beltran S, Águeda L, Gut M, Gut IG, Distl O. Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses.. BMC Genomics 2015 Oct 9;16:764.
     doi: 10.1186/s12864-015-1977-3pubmed: 26452642google scholar: lookup
212. Duchemin W, Daubin V, Tannier E. Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence.. BMC Genomics 2015;16 Suppl 10(Suppl 10):S9.
     doi: 10.1186/1471-2164-16-S10-S9pubmed: 26450112google scholar: lookup
213. Brinkmann J, Koudelka T, Keppler JK, Tholey A, Schwarz K, Thaller G, Tetens J. Characterization of an Equine α-S2-Casein Variant Due to a 1.3 kb Deletion Spanning Two Coding Exons.. PLoS One 2015;10(10):e0139700.
     doi: 10.1371/journal.pone.0139700pubmed: 26444874google scholar: lookup
214. Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jónsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, Petersen B, Ginolhac A, Seguin-Orlando A, Magnussen K, Fages A, Gamba C, Lorente-Galdos B, Polani S, Steiner C, Neuditschko M, Jagannathan V, Feh C, Greenblatt CL, Ludwig A, Abramson NI, Zimmermann W, Schafberg R, Tikhonov A, Sicheritz-Ponten T, Willerslev E, Marques-Bonet T, Ryder OA, McCue M, Rieder S, Leeb T, Slatkin M, Orlando L. Evolutionary Genomics and Conservation of the Endangered Przewalski's Horse.. Curr Biol 2015 Oct 5;25(19):2577-83.
     doi: 10.1016/j.cub.2015.08.032pubmed: 26412128google scholar: lookup
215. Huang H, Rabosky DL. Sex-linked genomic variation and its relationship to avian plumage dichromatism and sexual selection.. BMC Evol Biol 2015 Sep 16;15:199.
     doi: 10.1186/s12862-015-0480-4pubmed: 26377432google scholar: lookup
216. Huang J, Zhao Y, Bai D, Shiraigol W, Li B, Yang L, Wu J, Bao W, Ren X, Jin B, Zhao Q, Li A, Bao S, Bao W, Xing Z, An A, Gao Y, Wei R, Bao Y, Bao T, Han H, Bai H, Bao Y, Zhang Y, Daidiikhuu D, Zhao W, Liu S, Ding J, Ye W, Ding F, Sun Z, Shi Y, Zhang Y, Meng H, Dugarjaviin M. Donkey genome and insight into the imprinting of fast karyotype evolution.. Sci Rep 2015 Sep 16;5:14106.
     doi: 10.1038/srep14106pubmed: 26373886google scholar: lookup
217. Moon S, Lee JW, Shin D, Shin KY, Kim J, Choi IY, Kim J, Kim H. A Genome-wide Scan for Selective Sweeps in Racing Horses.. Asian-Australas J Anim Sci 2015 Nov;28(11):1525-31.
     doi: 10.5713/ajas.14.0696pubmed: 26333666google scholar: lookup
218. Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, de Barros Damgaard P, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C, Seguin-Orlando A, Malmström H, Stafford T Jr, Shringarpure SS, Moreno-Estrada A, Karmin M, Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CPE, Ponce de León MS, Smith CI, Grimes V, Pike KA, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF, Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.. Science 2015 Aug 21;349(6250):aab3884.
     doi: 10.1126/science.aab3884pubmed: 26198033google scholar: lookup
219. Fitak RR, Mohandesan E, Corander J, Burger PA. The de novo genome assembly and annotation of a female domestic dromedary of North African origin.. Mol Ecol Resour 2016 Jan;16(1):314-24.
     doi: 10.1111/1755-0998.12443pubmed: 26178449google scholar: lookup
220. Zhang Y, Cao QS, Rubenstein DI, Zang S, Songer M, Leimgruber P, Chu H, Cao J, Li K, Hu D. Water Use Patterns of Sympatric Przewalski's Horse and Khulan: Interspecific Comparison Reveals Niche Differences.. PLoS One 2015;10(7):e0132094.
     doi: 10.1371/journal.pone.0132094pubmed: 26161909google scholar: lookup
221. Bertolini F, Scimone C, Geraci C, Schiavo G, Utzeri VJ, Chiofalo V, Fontanesi L. Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms.. PLoS One 2015;10(7):e0131925.
     doi: 10.1371/journal.pone.0131925pubmed: 26151450google scholar: lookup
222. Jones MR, Good JM. Targeted capture in evolutionary and ecological genomics.. Mol Ecol 2016 Jan;25(1):185-202.
     doi: 10.1111/mec.13304pubmed: 26137993google scholar: lookup
223. Seguin-Orlando A, Gamba C, Sarkissian C, Ermini L, Louvel G, Boulygina E, Sokolov A, Nedoluzhko A, Lorenzen ED, Lopez P, McDonald HG, Scott E, Tikhonov A, Stafford TW Jr, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Shapiro B, Willerslev E, Prokhortchouk E, Orlando L. Pros and cons of methylation-based enrichment methods for ancient DNA.. Sci Rep 2015 Jul 2;5:11826.
     doi: 10.1038/srep11826pubmed: 26134828google scholar: lookup
224. Rebolledo-Mendez J, Hestand MS, Coleman SJ, Zeng Z, Orlando L, MacLeod JN, Kalbfleisch T. Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads.. PLoS One 2015;10(6):e0126852.
     doi: 10.1371/journal.pone.0126852pubmed: 26107638google scholar: lookup
225. Hestand MS, Kalbfleisch TS, Coleman SJ, Zeng Z, Liu J, Orlando L, MacLeod JN. Annotation of the Protein Coding Regions of the Equine Genome.. PLoS One 2015;10(6):e0124375.
     doi: 10.1371/journal.pone.0124375pubmed: 26107351google scholar: lookup
226. Damgaard PB, Margaryan A, Schroeder H, Orlando L, Willerslev E, Allentoft ME. Improving access to endogenous DNA in ancient bones and teeth.. Sci Rep 2015 Jun 17;5:11184.
     doi: 10.1038/srep11184pubmed: 26081994google scholar: lookup
227. Allentoft ME, Sikora M, Sjögren KG, Rasmussen S, Rasmussen M, Stenderup J, Damgaard PB, Schroeder H, Ahlström T, Vinner L, Malaspinas AS, Margaryan A, Higham T, Chivall D, Lynnerup N, Harvig L, Baron J, Della Casa P, Dąbrowski P, Duffy PR, Ebel AV, Epimakhov A, Frei K, Furmanek M, Gralak T, Gromov A, Gronkiewicz S, Grupe G, Hajdu T, Jarysz R, Khartanovich V, Khokhlov A, Kiss V, Kolář J, Kriiska A, Lasak I, Longhi C, McGlynn G, Merkevicius A, Merkyte I, Metspalu M, Mkrtchyan R, Moiseyev V, Paja L, Pálfi G, Pokutta D, Pospieszny Ł, Price TD, Saag L, Sablin M, Shishlina N, Smrčka V, Soenov VI, Szeverényi V, Tóth G, Trifanova SV, Varul L, Vicze M, Yepiskoposyan L, Zhitenev V, Orlando L, Sicheritz-Pontén T, Brunak S, Nielsen R, Kristiansen K, Willerslev E. Population genomics of Bronze Age Eurasia.. Nature 2015 Jun 11;522(7555):167-72.
     doi: 10.1038/nature14507pubmed: 26062507google scholar: lookup
228. Zakeri B, Lu TK. DNA nanotechnology: new adventures for an old warhorse.. Curr Opin Chem Biol 2015 Oct;28:9-14.
     doi: 10.1016/j.cbpa.2015.05.020pubmed: 26056949google scholar: lookup
229. Richards S. It's more than stamp collecting: how genome sequencing can unify biological research.. Trends Genet 2015 Jul;31(7):411-21.
     doi: 10.1016/j.tig.2015.04.007pubmed: 26003218google scholar: lookup
230. Cleland TP, Schroeter ER, Schweitzer MH. Biologically and diagenetically derived peptide modifications in moa collagens.. Proc Biol Sci 2015 Jun 7;282(1808):20150015.
     doi: 10.1098/rspb.2015.0015pubmed: 25972464google scholar: lookup
231. Legrand R, Tiret L, Abitbol M. Two recessive mutations in FGF5 are associated with the long-hair phenotype in donkeys.. Genet Sel Evol 2014 Sep 25;46(1):65.
     doi: 10.1186/s12711-014-0065-5pubmed: 25927731google scholar: lookup
232. Terhorst J, Schlötterer C, Song YS. Multi-locus analysis of genomic time series data from experimental evolution.. PLoS Genet 2015 Apr;11(4):e1005069.
     doi: 10.1371/journal.pgen.1005069pubmed: 25849855google scholar: lookup
233. Welker F, Collins MJ, Thomas JA, Wadsley M, Brace S, Cappellini E, Turvey ST, Reguero M, Gelfo JN, Kramarz A, Burger J, Thomas-Oates J, Ashford DA, Ashton PD, Rowsell K, Porter DM, Kessler B, Fischer R, Baessmann C, Kaspar S, Olsen JV, Kiley P, Elliott JA, Kelstrup CD, Mullin V, Hofreiter M, Willerslev E, Hublin JJ, Orlando L, Barnes I, MacPhee RD. Ancient proteins resolve the evolutionary history of Darwin's South American ungulates.. Nature 2015 Jun 4;522(7554):81-4.
     doi: 10.1038/nature14249pubmed: 25799987google scholar: lookup
234. Der Sarkissian C, Vilstrup JT, Schubert M, Seguin-Orlando A, Eme D, Weinstock J, Alberdi MT, Martin F, Lopez PM, Prado JL, Prieto A, Douady CJ, Stafford TW, Willerslev E, Orlando L. Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids.. Biol Lett 2015 Mar;11(3).
     doi: 10.1098/rsbl.2014.1058pubmed: 25762573google scholar: lookup
235. Delsuc F, Tilak MK. Naked but not Hairless: the pitfalls of analyses of molecular adaptation based on few genome sequence comparisons.. Genome Biol Evol 2015 Feb 20;7(3):768-74.
     doi: 10.1093/gbe/evv036pubmed: 25714745google scholar: lookup
236. Koepfli KP, Paten B, O'Brien SJ. The Genome 10K Project: a way forward.. Annu Rev Anim Biosci 2015;3:57-111.
     doi: 10.1146/annurev-animal-090414-014900pubmed: 25689317google scholar: lookup
237. Parks M, Lambert D. Impacts of low coverage depths and post-mortem DNA damage on variant calling: a simulation study.. BMC Genomics 2015 Jan 23;16(1):19.
     doi: 10.1186/s12864-015-1219-8pubmed: 25613391google scholar: lookup
238. Steinrücken M, Bhaskar A, Song YS. A NOVEL SPECTRAL METHOD FOR INFERRING GENERAL DIPLOID SELECTION FROM TIME SERIES GENETIC DATA.. Ann Appl Stat 2014 Dec;8(4):2203-2222.
     doi: 10.1214/14-aoas764pubmed: 25598858google scholar: lookup
239. McMahon BJ, Teeling EC, Höglund J. How and why should we implement genomics into conservation?. Evol Appl 2014 Nov;7(9):999-1007.
     doi: 10.1111/eva.12193pubmed: 25553063google scholar: lookup
240. Sang Y, Blecha F. Alternatives to antibiotics in animal agriculture: an ecoimmunological view.. Pathogens 2014 Dec 29;4(1):1-19.
     doi: 10.3390/pathogens4010001pubmed: 25551290google scholar: lookup
241. Cleland TP, Vashishth D. Bone protein extraction without demineralization using principles from hydroxyapatite chromatography.. Anal Biochem 2015 Mar 1;472:62-6.
     doi: 10.1016/j.ab.2014.12.006pubmed: 25535955google scholar: lookup
242. Froese D. The curious case of the Arctic mastodons.. Proc Natl Acad Sci U S A 2014 Dec 30;111(52):18405-6.
     doi: 10.1073/pnas.1422018112pubmed: 25535342google scholar: lookup
243. Jun J, Cho YS, Hu H, Kim HM, Jho S, Gadhvi P, Park KM, Lim J, Paek WK, Han K, Manica A, Edwards JS, Bhak J. Whole genome sequence and analysis of the Marwari horse breed and its genetic origin.. BMC Genomics 2014;15 Suppl 9(Suppl 9):S4.
     doi: 10.1186/1471-2164-15-S9-S4pubmed: 25521865google scholar: lookup
244. Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M, Seguin-Orlando A, Korneliussen TS, Velazquez AM, Stenderup J, Hoover CA, Rubin CJ, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, MacHugh DE, Kalbfleisch T, MacLeod JN, Rubin EM, Sicheritz-Ponten T, Andersson L, Hofreiter M, Marques-Bonet T, Gilbert MT, Nielsen R, Excoffier L, Willerslev E, Shapiro B, Orlando L. Prehistoric genomes reveal the genetic foundation and cost of horse domestication.. Proc Natl Acad Sci U S A 2014 Dec 30;111(52):E5661-9.
     doi: 10.1073/pnas.1416991111pubmed: 25512547google scholar: lookup
245. Der Sarkissian C, Allentoft ME, Ávila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernández R, da Fonseca R, Ginolhac A, Hansen AJ, Jónsson H, Korneliussen T, Margaryan A, Martin MD, Moreno-Mayar JV, Raghavan M, Rasmussen M, Velasco MS, Schroeder H, Schubert M, Seguin-Orlando A, Wales N, Gilbert MT, Willerslev E, Orlando L. Ancient genomics.. Philos Trans R Soc Lond B Biol Sci 2015 Jan 19;370(1660):20130387.
     doi: 10.1098/rstb.2013.0387pubmed: 25487338google scholar: lookup
246. Parks M, Subramanian S, Baroni C, Salvatore MC, Zhang G, Millar CD, Lambert DM. Ancient population genomics and the study of evolution.. Philos Trans R Soc Lond B Biol Sci 2015 Jan 19;370(1660):20130381.
     doi: 10.1098/rstb.2013.0381pubmed: 25487332google scholar: lookup
247. Teasdale MD, van Doorn NL, Fiddyment S, Webb CC, O'Connor T, Hofreiter M, Collins MJ, Bradley DG. Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing.. Philos Trans R Soc Lond B Biol Sci 2015 Jan 19;370(1660):20130379.
     doi: 10.1098/rstb.2013.0379pubmed: 25487331google scholar: lookup
248. Malmström H, Linderholm A, Skoglund P, Storå J, Sjödin P, Gilbert MT, Holmlund G, Willerslev E, Jakobsson M, Lidén K, Götherström A. Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process.. Philos Trans R Soc Lond B Biol Sci 2015 Jan 19;370(1660):20130373.
     doi: 10.1098/rstb.2013.0373pubmed: 25487325google scholar: lookup
249. Hagelberg E, Hofreiter M, Keyser C. Introduction. Ancient DNA: the first three decades.. Philos Trans R Soc Lond B Biol Sci 2015 Jan 19;370(1660):20130371.
     doi: 10.1098/rstb.2013.0371pubmed: 25487324google scholar: lookup
250. Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L. Speciation with gene flow in equids despite extensive chromosomal plasticity.. Proc Natl Acad Sci U S A 2014 Dec 30;111(52):18655-60.
     doi: 10.1073/pnas.1412627111pubmed: 25453089google scholar: lookup
251. Korneliussen TS, Albrechtsen A, Nielsen R. ANGSD: Analysis of Next Generation Sequencing Data.. BMC Bioinformatics 2014 Nov 25;15(1):356.
     doi: 10.1186/s12859-014-0356-4pubmed: 25420514google scholar: lookup
252. Aerts JW, Röling WF, Elsaesser A, Ehrenfreund P. Biota and biomolecules in extreme environments on Earth: implications for life detection on Mars.. Life (Basel) 2014 Oct 13;4(4):535-65.
     doi: 10.3390/life4040535pubmed: 25370528google scholar: lookup
253. Ghosh S, Qu Z, Das PJ, Fang E, Juras R, Cothran EG, McDonell S, Kenney DG, Lear TL, Adelson DL, Chowdhary BP, Raudsepp T. Copy number variation in the horse genome.. PLoS Genet 2014 Oct;10(10):e1004712.
     doi: 10.1371/journal.pgen.1004712pubmed: 25340504google scholar: lookup
254. Harris K, Sheehan S, Kamm JA, Song YS. Decoding coalescent hidden Markov models in linear time.. Res Comput Mol Biol 2014;8394:100-114.
     doi: 10.1007/978-3-319-05269-4_8pubmed: 25340178google scholar: lookup
255. Brandt LØ, Schmidt AL, Mannering U, Sarret M, Kelstrup CD, Olsen JV, Cappellini E. Species identification of archaeological skin objects from Danish bogs: comparison between mass spectrometry-based peptide sequencing and microscopy-based methods.. PLoS One 2014;9(9):e106875.
     doi: 10.1371/journal.pone.0106875pubmed: 25260035google scholar: lookup
256. Overballe-Petersen S, Willerslev E. Horizontal transfer of short and degraded DNA has evolutionary implications for microbes and eukaryotic sexual reproduction.. Bioessays 2014 Oct;36(10):1005-10.
     doi: 10.1002/bies.201400035pubmed: 25143190google scholar: lookup
257. Martiniano R, Coelho C, Ferreira MT, Neves MJ, Pinhasi R, Bradley DG. Genetic evidence of African slavery at the beginning of the trans-Atlantic slave trade.. Sci Rep 2014 Aug 8;4:5994.
     doi: 10.1038/srep05994pubmed: 25104065google scholar: lookup
258. Nedoluzhko AV, Boulygina ES, Sokolov AS, Tsygankova SV, Gruzdeva NM, Rezepkin AD, Prokhortchouk EB. Analysis of the Mitochondrial Genome of a Novosvobodnaya Culture Representative using Next-Generation Sequencing and Its Relation to the Funnel Beaker Culture.. Acta Naturae 2014 Apr;6(2):31-5.
     pubmed: 25093108
259. Metzger J, Tonda R, Beltran S, Agueda L, Gut M, Distl O. Next generation sequencing gives an insight into the characteristics of highly selected breeds versus non-breed horses in the course of domestication.. BMC Genomics 2014 Jul 4;15(1):562.
     doi: 10.1186/1471-2164-15-562pubmed: 24996778google scholar: lookup
260. Gorbunova V, Seluanov A, Zhang Z, Gladyshev VN, Vijg J. Comparative genetics of longevity and cancer: insights from long-lived rodents.. Nat Rev Genet 2014 Aug;15(8):531-40.
     doi: 10.1038/nrg3728pubmed: 24981598google scholar: lookup
261. Molak M, Suchard MA, Ho SY, Beilman DW, Shapiro B. Empirical calibrated radiocarbon sampler: a tool for incorporating radiocarbon-date and calibration error into Bayesian phylogenetic analyses of ancient DNA.. Mol Ecol Resour 2015 Jan;15(1):81-6.
     doi: 10.1111/1755-0998.12295pubmed: 24964386google scholar: lookup
262. Skoglund P, Sjödin P, Skoglund T, Lascoux M, Jakobsson M. Investigating population history using temporal genetic differentiation.. Mol Biol Evol 2014 Sep;31(9):2516-27.
     doi: 10.1093/molbev/msu192pubmed: 24939468google scholar: lookup
263. Hipsley CA, Müller J. Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology.. Front Genet 2014;5:138.
     doi: 10.3389/fgene.2014.00138pubmed: 24904638google scholar: lookup
264. Huang J, Zhao Y, Shiraigol W, Li B, Bai D, Ye W, Daidiikhuu D, Yang L, Jin B, Zhao Q, Gao Y, Wu J, Bao W, Li A, Zhang Y, Han H, Bai H, Bao Y, Zhao L, Zhai Z, Zhao W, Sun Z, Zhang Y, Meng H, Dugarjaviin M. Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype.. Sci Rep 2014 May 14;4:4958.
     doi: 10.1038/srep04958pubmed: 24828444google scholar: lookup
265. Finno CJ, Bannasch DL. Applied equine genetics.. Equine Vet J 2014 Sep;46(5):538-44.
     doi: 10.1111/evj.12294pubmed: 24802051google scholar: lookup
266. Schubert M, Ermini L, Der Sarkissian C, Jónsson H, Ginolhac A, Schaefer R, Martin MD, Fernández R, Kircher M, McCue M, Willerslev E, Orlando L. Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.. Nat Protoc 2014 May;9(5):1056-82.
     doi: 10.1038/nprot.2014.063pubmed: 24722405google scholar: lookup
267. Callaway E. Human evolution: The Neanderthal in the family.. Nature 2014 Mar 27;507(7493):414-6.
     doi: 10.1038/507414apubmed: 24670743google scholar: lookup
268. Gold DA, Robinson J, Farrell AB, Harris JM, Thalmann O, Jacobs DK. Attempted DNA extraction from a Rancho La Brea Columbian mammoth (Mammuthus columbi): prospects for ancient DNA from asphalt deposits.. Ecol Evol 2014 Feb;4(4):329-36.
     doi: 10.1002/ece3.928pubmed: 24634719google scholar: lookup
269. Veeramah KR, Hammer MF. The impact of whole-genome sequencing on the reconstruction of human population history.. Nat Rev Genet 2014 Mar;15(3):149-62.
     doi: 10.1038/nrg3625pubmed: 24492235google scholar: lookup
270. Chambers GK, Curtis C, Millar CD, Huynen L, Lambert DM. DNA fingerprinting in zoology: past, present, future.. Investig Genet 2014 Feb 3;5(1):3.
     doi: 10.1186/2041-2223-5-3pubmed: 24490906google scholar: lookup
271. Bona A, Papai Z, Maasz G, Toth GA, Jambor E, Schmidt J, Toth C, Farkas C, Mark L. Mass spectrometric identification of ancient proteins as potential molecular biomarkers for a 2000-year-old osteogenic sarcoma.. PLoS One 2014;9(1):e87215.
     doi: 10.1371/journal.pone.0087215pubmed: 24475253google scholar: lookup
272. Meyer M, Fu Q, Aximu-Petri A, Glocke I, Nickel B, Arsuaga JL, Martínez I, Gracia A, de Castro JM, Carbonell E, Pääbo S. A mitochondrial genome sequence of a hominin from Sima de los Huesos.. Nature 2014 Jan 16;505(7483):403-6.
     doi: 10.1038/nature12788pubmed: 24305051google scholar: lookup
273. Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, Jones PA, Hoover CA, Tikhonov A, Prokhortchouk E, Rubin EM, Sandelin A, Gilbert MT, Krogh A, Willerslev E, Orlando L. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome.. Genome Res 2014 Mar;24(3):454-66.
     doi: 10.1101/gr.163592.113pubmed: 24299735google scholar: lookup
274. Schweitzer MH, Zheng W, Cleland TP, Goodwin MB, Boatman E, Theil E, Marcus MA, Fakra SC. A role for iron and oxygen chemistry in preserving soft tissues, cells and molecules from deep time.. Proc Biol Sci 2014 Jan 22;281(1775):20132741.
     doi: 10.1098/rspb.2013.2741pubmed: 24285202google scholar: lookup
275. Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW Jr, Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Mägi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T, Villems R, Nielsen R, Jakobsson M, Willerslev E. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans.. Nature 2014 Jan 2;505(7481):87-91.
     doi: 10.1038/nature12736pubmed: 24256729google scholar: lookup
276. Overballe-Petersen S, Harms K, Orlando LA, Mayar JV, Rasmussen S, Dahl TW, Rosing MT, Poole AM, Sicheritz-Ponten T, Brunak S, Inselmann S, de Vries J, Wackernagel W, Pybus OG, Nielsen R, Johnsen PJ, Nielsen KM, Willerslev E. Bacterial natural transformation by highly fragmented and damaged DNA.. Proc Natl Acad Sci U S A 2013 Dec 3;110(49):19860-5.
     doi: 10.1073/pnas.1315278110pubmed: 24248361google scholar: lookup
277. Seguin-Orlando A, Schubert M, Clary J, Stagegaard J, Alberdi MT, Prado JL, Prieto A, Willerslev E, Orlando L. Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.. PLoS One 2013;8(10):e78575.
     doi: 10.1371/journal.pone.0078575pubmed: 24205269google scholar: lookup
278. Callaway E. Proteins help solve taxonomy riddle.. Nature 2013 Nov 7;503(7474):18-9.
     doi: 10.1038/503018apubmed: 24201261google scholar: lookup
279. Dabney J, Knapp M, Glocke I, Gansauge MT, Weihmann A, Nickel B, Valdiosera C, García N, Pääbo S, Arsuaga JL, Meyer M. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.. Proc Natl Acad Sci U S A 2013 Sep 24;110(39):15758-63.
     doi: 10.1073/pnas.1314445110pubmed: 24019490google scholar: lookup
280. Millar CD, Lambert DM. Ancient DNA: Towards a million-year-old genome.. Nature 2013 Jul 4;499(7456):34-5.
     doi: 10.1038/nature12263pubmed: 23803770google scholar: lookup