Nuclear versus mitochondrial DNA: Evidence for hybridization in colobine monkeys

BMC Evolutionary Biology

Volumn 11, Issue 1, 2011, Pages

  Roos, Christian ^a   Zinner, Dietmar ^a   Kubatko, Laura S ^b   Schwarz, Christiane ^a   Yang, Mouyu ^a   Meyer, Dirk ^a   Nash, Stephen D ^c   Xing, Jinchuan ^d   Batzer, Mark A ^e   Brameier, Markus ^a   Leendertz, Fabian H ^f   Ziegler, Thomas ^a   Perwitasari Farajallah, Dyah ^g   Nadler, Tilo ^h   Walter, Lutz ^a   Osterholz, Martin ^a  

^a GERMAN PRIMATE CENTER   (Germany)

^b OHIO STATE UNIVERSITY   (United States)

^c STONY BROOK UNIVERSITY   (United States)

^d UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^e LOUISIANA STATE UNIVERSITY   (United States)

^f ROBERT KOCH INSTITUTE   (Germany)

^g BOGOR AGRICULTURAL UNIVERSITY   (Indonesia)

^h Cuc Phuong National Park   (Viet Nam)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKER; CHROMOSOME; EVOLUTIONARY BIOLOGY; HYBRIDIZATION; MITOCHONDRIAL DNA; PHYLOGENETICS; PLEISTOCENE; PRIMATE; SAMPLING; SOCIAL ORGANIZATION;

AFRICA; ASIA;

COLOBINAE; COLOBUS; PRIMATES; PROCOLOBUS; SEMNOPITHECUS; TRACHYPITHECUS;

MITOCHONDRIAL DNA;

ALU SEQUENCE; ANIMAL; ARTICLE; CELL NUCLEUS; CHROMOSOME MAP; CLASSIFICATION; COLOBINAE; DNA SEQUENCE; EVOLUTION; FEMALE; GENETICS; HYBRIDIZATION; MALE; PHYLOGENY; X CHROMOSOME; Y CHROMOSOME;

ALU ELEMENTS; ANIMALS; BIOLOGICAL EVOLUTION; CELL NUCLEUS; CHROMOSOME MAPPING; COLOBINAE; DNA, MITOCHONDRIAL; FEMALE; HYBRIDIZATION, GENETIC; MALE; PHYLOGENY; SEQUENCE ANALYSIS, DNA; X CHROMOSOME; Y CHROMOSOME;

EID: 79953097998     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-11-77     Document Type: Article

References (100)

1. AG Davies JF Oates, Colobine Monkeys - Their Ecology, Behaviour and Evolution Cambridge: Cambridge University Press 1994
2. CP Groves, Primate Taxonomy Washington DC: Smithsonian Institution Press 2001
3. CP Groves, A Theory of Human and Primate Evolution Oxford: Clarendon Press 1989
4. NG Jablonski, Natural History of the Doucs and Snub-Nosed Monkeys New Jersey: World Scientific Publishing Company 1998
5. Primate evolution - in and out of Africa. NG Jablonski, Curr Biol 1999 9 119 R122 10.1016/S0960-9822(99)80077-3 10074435
6. Primate evolution - in and out of Africa. CB Stewart TR Disotell, Curr Biol 1999 9 120 R122
7. Primate evolution - in and out of Africa. YP Zhang OA Ryder, Curr Biol 1999 9 119 R120 10.1016/S0960-9822(99)80077-3 10215416
8. Mitochondrial data support an odd-nosed colobine clade. KN Sterner RL Raaum YP Zhang CB Stewart TR Disotell, Mol Phylogenet Evol 2006 40 1 7 10.1016/j.ympev.2006.01.017 16500120 (Pubitemid 43903645)
9. Phylogenetic position of the langur genera Semnopithecus and Trachypithecus among Asian colobines, and genus affiliations of their species groups. M Osterholz L Walter C Roos, BMC Evol Biol 2008 8 58 10.1186/1471-2148-8-58 18298809
10. Phylogenetic incongruence between nuclear and mitochondrial markers in the Asian colobines and the evolution of the langurs and leaf monkeys. N Ting AJ Tosi Y Li YP Zhang TR Disotell, Mol Phylogenet Evol 2008 46 466 474 10.1016/j.ympev.2007.11.008 18180172
11. JR Napier PH Napier, A Handbook of Living Primates London: Academic Press 1967
12. FS Szalay E Delson, Evolutionary History of the Primates New York: Academic Press 1979
13. The role of hybridization on evolution. NH Barton, Mol Ecol 2001 10 551 568 10.1046/j.1365-294x.2001.01216.x 11298968
14. Gene trees and species trees are not the same. R Nichols, Trends Ecol Evol 2001 16 358 364 10.1016/S0169-5347(01)02203-0 11403868 (Pubitemid 32525776)
15. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. D Funk K Omland, Ann Rev Ecol Evol Syst 2003 34 397 423 10.1146/annurev.ecolsys.34.011802.132421 (Pubitemid 38171425)
16. JC Avise, Molecular Markers, Natural History, and Evolution Sunderland, MA: Sinauer Associates 2004
17. Hybridization and adaptive radiation. O Seehausen, Trends Ecol Evol 2004 19 198 207 10.1016/j.tree.2004.01.003 16701254 (Pubitemid 38355799)
18. Is homoplasy or lineage sorting the source of incongruent mtDNA and nuclear gene trees in the stiff-tailed ducks (Nomonyx-Oxyyura)? K McCracken M Sorenson, Syst Biol 2005 54 35 55 10.1080/10635150590910249 15805009 (Pubitemid 40441161)
19. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. DA Pollard VN Iyer AM Moses MB Eisen, PLoS Genet 2006 2 173 10.1371/journal.pgen.0020173 17132051
20. Reticulate phylogeny of gastropod-shell-breeding cichlids from Lake Tanganyika - the result of repeated introgressive hybridization. S Koblmüller N Duftner KM Sefc M Aibara M Stipacek M Blanc B Egger C Sturmbauer, BMC Evol Biol 2007 7 7 17254340
21. How good are deep phylogenetic trees? H Philippe J Laurent, Curr Opin Genetics Dev 1998 8 616 623 10.1016/S0959-437X(98)80028-2 (Pubitemid 28558522)
22. Gene flow and species delimitation. RJ Petit L Excoffier, Trends Ecol Evol 2009 24 386 393 10.1016/j.tree.2009.02.011 19409650
23. A mobile element based phylogeny of Old World monkeys. J Xing H Wang K Han DA Ray CH Huang LG Chemnick CB Stewart TR Disotell OA Ryder MA Batzer, Mol Phylogenet Evol 2005 37 872 880 10.1016/j.ympev.2005.04.015 15936216 (Pubitemid 41597796)
24. A human-specific subfamily of Alu sequences. MA Batzer PL Deininger, Genomics 1991 9 481 487 10.1016/0888-7543(91)90414-A 1851725
25. SINEs. N Okada, Curr Opin Genet Dev 1991 1 498 504 10.1016/S0959-437X(05) 80198-4 1668310
26. SINE insertions: powerful tools for molecular systematics. AM Shedlock N Okada, Bioessays 2000 22 148 160 10.1002/(SICI)1521-1878(200002)22:2<148:: AID-BIES6>3.0.CO;2-Z 10655034 (Pubitemid 30092081)
27. Identity by descent and DNA sequence variation of human SINE and LINE elements. AH Salem DA Ray MA Batzer, Cytogenet Genome Res 2005 108 63 72 10.1159/000080803 15545717 (Pubitemid 39555522)
28. Primate phylogeny: molecular evidence from retroposons. J Schmitz C Roos H Zischler, Cytogenet Genome Res 2005 108 26 37 10.1159/000080799 15545713 (Pubitemid 39551765)
29. Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. LN Van de Lagemaat L Gagnier P Medstrand DL Mager, Genome Res 2005 15 1243 1249 10.1101/gr.3910705 16140992 (Pubitemid 41247914)
30. SINEs of a nearly perfect character. DA Ray J Xing AH Salem MA Batzer, Syst Biol 2006 55 928 935 10.1080/10635150600865419 17345674
31. SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates. J Schmitz M Ohme H Zischler, Genetics 2001 157 777 784 11156996 (Pubitemid 32165033)
32. Alu elements and hominid phylogenetics. AH Salem DA Ray J Xing PA Callinan JS Myers DJ Hedges RK Garber DJ Witherspoon LB Jorde MA Batzer, Proc Natl Acad Sci USA 2003 22 12787 12791 10.1073/pnas.2133766100 (Pubitemid 37339977)
33. Primate jumping genes elucidate strepsirrhine phylogeny. C Roos J Schmitz H Zischler, Proc Natl Acad Sci USA 2004 101 10650 10654 10.1073/pnas.0403852101 15249661 (Pubitemid 38955797)
34. Alu insertion loci and platyrrhine primate phylogeny. DA Ray J Xing DJ Hedges MA Hall ME Laborde BA Anders BR White N Stoilova JD Fowlkes KE Landry LG Chemnick OA Ryder MA Batzer, Mol Phylogenet Evol 2005 35 117 126 10.1016/j.ympev.2004.10.023 15737586 (Pubitemid 40281407)
35. A SINE-based dichotomous key for primate identification. SW Herke J Xing DA Ray JW Zimmermann R Cordaux MA Batzer, Gene 2007 390 39 51 10.1016/j.gene.2006.08.015 17056208 (Pubitemid 46241740)
36. A mobile element based evolutionary history of guenons (Tribe Cercopithecini). J Xing H Wang Y Zhang DA Ray AJ Tosi TR Disotell MA Batzer, BMC Biol 2007 5 5 10.1186/1741-7007-5-5 17266768
37. Mobile DNA elements in primate and human evolution. J Xing DJ Witherspoon DA Ray MA Batzer LB Jorde, Am J Phys Anthropol 2007 45 Suppl 2 19 10.1002/ajpa.20722 18046749
38. Retropositional events consolidate the branching order among New World monkey genera. M Osterholz L Walter C Roos, Mol Phylogenet Evol 2009 50 507 513 10.1016/j.ympev.2008.12.014 19135536
39. Phylogeny of macaques (Cercopithecidae: Macaca) based on Alu elements. J Li K Han J Xing HS Kim J Rogers OA Ryder T Disotell B Yue MA Batzer, Gene 2009 448 242 249 10.1016/j.gene.2009.05.013 19497354
40. Identifying hybridization events in the presence of coalescence via model selection. LS Kubatko, Syst Biol 2009 58 478 488 10.1093/sysbio/syp055 20525602
41. KP Burnham DR Anderson, Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach New York: Springer 2002
42. Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence. M Goodman CA Porter J Czelusniak SL Page H Schneider J Shoshani G Gunnell CP Groves, Mol Phylogenet Evol 1998 9 585 598 10.1006/mpev.1998.0495 9668008 (Pubitemid 128351494)
43. Catarrhine primate divergence dates estimated from complete mitochondrial genomes: concordance with fossil and nuclear DNA evidence. RL Raaum KN Sterner CM Noviello CB Stewart TR Disotell, J Hum Evol 2005 48 237 257 10.1016/j.jhevol.2004.11.007 15737392 (Pubitemid 40301117)
44. Molecular phylogeny and biogeography of langurs and leaf monkeys of South Asia (Primates: Colobinae). KP Karanth L Singh RV Collura CB Stewart, Mol Phylogenet Evol 2008 46 683 694 10.1016/j.ympev.2007.11.026 18191589
45. Mitochondrial relationships and divergence dates of the African colobines: evidence of Miocene origins for the living colobus monkeys. N Ting, J Hum Evol 2008 55 312 325 10.1016/j.jhevol.2008.02.011 18423802
46. Colobus and leaf monkeys. D Brandon-Jones, Encylopedia of Mammals London: George Allen and Unwin, MacDonald ID, 1984 398 408
47. Cladistic analysis of cercopithecid relationships. E Strasser E Delson, J Hum Evol 1987 16 81 99 10.1016/0047-2484(87)90061-3
48. Dispersal and philopatry. AE Pusey C Packer, Primate Societies Chicago: University of Chicago Press, Smuts BB, Cheney DL, Seyfarth RM, Wrangham RW, Struhsaker TT, 1987 250 266
49. Primate evolution - in and out of Africa. CB Stewart TR Disotell, Curr Biol 1998 8 582 R588 10.1016/S0960-9822(07)00367-3 9707399
50. Land movements and species dispersal. PJ Whybrow, The Cambridge Encyclopedia of Human Evolution Cambridge: Cambridge University Press, Jones S, Martin RE, Pilbeam D, 1992 169 173
51. Classification and evolution of Asian colobines. YZ Peng RL Pan N Jablonski, Folia Primatol 1993 60 106 117 10.1159/000156680 8335288
52. Mitochondrial evidence for multiple radiations in the evolutionary history of small apes. VN Thinh AR Mootnick T Geissmann M Li T Ziegler M Agil P Moisson T Nadler L Walter C Roos, BMC Evol Biol 2010 10 74 10.1186/1471-2148-10- 74 20226039
53. The geography of mammals and rivers in mainland Southeast Asia. E Meijaard CP Groves, Primate Biogeography New York: Springer, Lehman SM, Fleagle JG, 2006 305 329 full-text
54. Distorted drainage basins as markers of crustal strain east of the Himalayas. B Hallet P Molnar, J Geophys Res 2001 106 13697 13709 10.1029/2000JB900335
55. The phanerozoic record of global sea-level change. KG Miller MA Kominz JV Browning JD Wright GS Mountain ME Katz PJ Sugarman BS Cramer N Christie-Blick SF Pekar, Science 2005 310 1293 1298 10.1126/science.1116412 16311326 (Pubitemid 41698854)
56. Phylogenetic relationships and morphometric affinities of the Arunachal macaque Macaca munzala, a newly described primate from Arunachal Pradesh, northeastern India. D Chakraborty U Ramakrishnan J Panor C Mishra A Sinha, Mol Phylogenet Evol 2007 44 838 849 10.1016/j.ympev.2007.04.007 17548213 (Pubitemid 47061435)
57. C Darwin, On the Origin of Species by Means of Natural Selection or the Preservation of Favoured Races in the Struggle of Life London: John Murray 1859
58. E Mayr, Animal Species and Evolution Cambridge, MA: Belknap Press 1963
59. Natural hybridization in primates: one evolutionary mechanism. ML Arnold A Meyer, Zoology 2006 109 261 276 10.1016/j.zool.2006.03.006 16945512 (Pubitemid 44572717)
60. The strange blood: natural hybridization in primates. D Zinner ML Arnold C Roos, Evol Anthropol 12287173
61. Hybridization in large-bodied New World primates. L Cortés-Ortiz TF Duda Jr D Canales-Espinosa F Garcia-Orduna E Rodriguez-Luna E Bermingham, Genetics 2007 176 2421 2425 17603105 (Pubitemid 47360670)
62. The complex evolutionary history of gorillas: insights from genomic data. O Thalmann A Fischer F Lankester S Pääbo L Vigilant, Mol Biol Evol 2007 24 146 158 10.1093/molbev/msl160 17065595 (Pubitemid 46026290)
63. Comparing chromosomal and mitochondrial phylogenies of sportive lemurs (genus Lepilemur, Primates). Y Rumpler S Warter M Hauwy JL Fausser C Roos D Zinner, Chromosome Res 2008 16 1143 1158 10.1007/s10577-008-1265-z 19067195
64. Elucidating geological and biological processes underlying the diversification of Sulawesi tarsiers. S Merker C Driller D Perwitasari- Farajallah J Pamungkas H Zischler, Proc Natl Acad Sci USA 2009 106 8459 8464 10.1073/pnas.0900319106 19451646
65. Mitochondrial phylogeography of baboons (Papio spp.) - indication for introgressive hybridization? D Zinner LF Groeneveld C Keller C Roos, BMC Evol Biol 2009 9 83 10.1186/1471-2148-9-83 19389236
66. Is the new primate genus Rungwecebus a baboon? D Zinner ML Arnold C Roos, PLoS ONE 2009 4 4859 10.1371/journal.pone.0004859 19295908
67. The mosaic that is our genome. S Pääbo, Nature 2003 421 409 412 12540910 (Pubitemid 36157943)
68. Genetic evidence for complex speciation of humans and chimpanzees. N Patterson DJ Richter S Gnerre ES Lander D Reich, Nature 2006 441 1103 1108 10.1038/nature04789 16710306 (Pubitemid 43990725)
69. A draft sequence of the Neandertal genome. RE Green J Krause AW Briggs T Maricic U Stenzel M Kircher N Patterson H Li W Zhai MH Fritz NF Hansen EY Durand AS Malaspinas JD Jensen T Marques-Bonet C Alkan K Prüfer M Meyer HA Burbano JM Good R Schultz A Aximu-Petri A Butthof B Höber B Höffner M Siegemund A Weihmann C Nusbaum ES Lander C Russ N Novod J Affourtit M Egholm C Verna P Rudan D Brajkovic Z Kucan I Gusic VB Doronichev LV Golovanova C Lalueza-Fox M de la Rasilla J Fortea A Rosas RW Schmitz PL Johnson EE Eichler D Falush E Birney JC Mullikin M Slatkin R Nielsen J Kelso M Lachmann D Reich S Pääbo, Science 2010 328 710 722 10.1126/science.1188021 20448178
70. DL Swofford, PAUP* Phylogenetic Analysis using Parsimony (*and other Methods), Version 4 Sunderland, MA: Sinauer Associates 2003
71. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. H Kishino M Hasegawa, J Mol Evol 1989 29 170 179 10.1007/BF02100115 2509717 (Pubitemid 19206089)
72. Rapid sequence evolution of the mammalian sex-determining gene SRY. LS Whitfield R Lovell-Badge PN Goodfellow, Nature 1993 364 713 715 10.1038/364713a0 8355783 (Pubitemid 23273122)
73. The place of Callimico goeldii in the callithrichine phylogenetic tree: evidence from von Willebrand factor gene intron 11 sequences. R Chaves I Sampaio MP Schneider H Schneider SL Page M Goodman, Mol Phylogenet Evol 1999 13 392 404 10.1006/mpev.1999.0658 10603266 (Pubitemid 129499347)
74. Y chromsome conserved anchored tagged sequences (YCATS) for the analysis of mammalian male-specific DNA. L Hellborg H Ellegren, Mol Ecol 2003 12 283 291 10.1046/j.1365-294X.2003.01702.x 12492896 (Pubitemid 36108124)
75. X-chromosomal window into the evolutionary history of the guenons (Primates: Cercopithecini). AJ Tosi KM Detwiler TR Disotell, Mol Phylogenet Evol 2005 36 58 66 10.1016/j.ympev.2005.01.009 15904856 (Pubitemid 40722091)
76. Geneious, version 4.6.1. AJ Drummond M Kearse J Heled R Moir T Thierer B Ashton A Wilson S Stones-Havas, 2009 http://www.geneious.com
77. Automatic annotation of organellar genomes with DOGMA. SK Wyman RK Jansen JL Boore, Bioinformatics 2004 20 3252 3255 10.1093/bioinformatics/bth352 15180927 (Pubitemid 39619219)
78. MAFFT version 5: improvement in accuracy of multiple sequence alignment. K Katoh K Kuma H Toh T Miyata, Nucleic Acids Res 2005 33 511 518 10.1093/nar/gki198 15661851 (Pubitemid 40360980)
79. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. J Castresana, Mol Biol Evol 2000 17 540 552 10742046 (Pubitemid 30210700)
80. Mesquite: a modular system for evolutionary analysis, version 2.6. WP Maddison DR Maddison, 2009 http://mesquite.org
81. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence data sets under the maximum likelihood criterion. DJ Zwickl, PhD thesis Texas University, Austin 2006
82. Bayesian inference of phylogeny and its impact on evolutionary biology. JP Huelsenbeck F Ronquist R Nielsen JP Bollback, Science 2001 294 2310 2314 10.1126/science.1065889 11743192 (Pubitemid 33140548)
83. MrBayes 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 1572 1574 10.1093/bioinformatics/btg180 12912839 (Pubitemid 37038874)
84. Modeltest: testing the model of DNA substitution. D Posada KA Crandall, Bioinformatics 1998 14 817 818 10.1093/bioinformatics/14.9.817 9918953 (Pubitemid 28552116)
85. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. H Shimodaira M Hasegawa, Mol Biol Evol 1999 16 1114 1116 (Pubitemid 29368141)
86. Relaxed phylogenetics and dating with confidence. AJ Drummond SYW Ho MJ Phillips A Rambaut, PLoS Biol 2006 4 88 10.1371/journal.pbio.0040088 16683862
87. BEAST: Bayesian evolutionary analysis by sampling trees. AJ Drummond A Rambaut, BMC Evol Biol 2007 7 214 10.1186/1471-2148-7-214 17996036
88. Geology and palaeontology of the Upper Miocene Toros-Menalla hominid locality, Chad. P Vignaud P Duringer HT Mackaye A Likius C Blondel JR Boisserie L De Bonis V Eisenmann ME Etienne D Geraads F Guy T Lehmann F Lihoreau N Lopez-Martinez C Mourer-Chauviré O Otero JC Rage M Schuster L Viriot A Zazzo M Brunet, Nature 2002 418 152 155 10.1038/nature00880 12110881 (Pubitemid 34773763)
89. New material of the earliest hominid from the Upper Miocene of Chad. M Brunet F Guy D Pilbeam DE Lieberman A Likius HT Mackaye MS Ponce de Leán CP Zollokofer P Vignaud, Nature 2005 434 752 755 10.1038/nature03392 15815627 (Pubitemid 40558371)
90. Cosmogenic nuclide dating of Sahelanthropus tchadensis and Australopithecus bahrelghazali: Mio-Pliocene hominids from Chad. AE Lebatard DL Bourlès P Duringer M Jolivet R Braucher J Carcaillet M Schuster N Arnaud P Monié F Lihoreau A Likius HT Mackaye P Vignaud M Brunet, Proc Natl Acad Sci USA 2008 105 3226 3231 10.1073/pnas.0708015105 18305174 (Pubitemid 351723535)
91. The hominoid radiation in Asia. J Kelley, The Primate Fossil Record Cambridge: Cambridge University Press, Hartwig WC, 2002 369 384
92. Evolution of Theropithecus in the Turkana Basin. MG Leakey, Theropithecus, the Rise and Fall of a Primate Genus Cambridge: Cambridge University Press, Jablonski NG, 1993 85 124 full-text
93. Cercopithecinae. E Delson, Encyclopedia of Human Evolution and Prehistory New York: Garland Publishing Inc, Delson E, Tattersall I, Van Couvering JA, Brooks AS, 2000 166 171 2000
94. The Victoriapithecidae, Cercopithecoidea. BR Benefit ML McCrossin, The Primate Fossil Record Cambridge: Cambridge University Press, Hartwig WC, 2002 241 253
95. The phylogenetic position of Moropithecus. NM Young L MacLatchy, J Hum Evol 2004 46 163 184 10.1016/j.jhevol.2003.11.002 14871561
96. New Oligocene primate from Saudi Arabia and the divergence of apes and Old World monkeys. IS Zalmout WJ Sanders LM MacLatchy GF Gunnell YA Al-Mufarreh MA Ali AAH Nasser AM Al-Masari SA Al-Sobhi AO Nadhra AH Matari JA Wilson PD Gingerich, Nature 2010 466 360 365 10.1038/nature09094 20631798
97. Tracer: MCMC trace analysis tool, version 1.4.1. A Rambaut AJ Drummond, Institute of Evolutionary Biology, University of Edinburgh 2007 http://tree.bio.ed.ac.uk/software/tracer/
98. FigTree: Tree figure drawing tool, version 1.2.2. A Rambaut, Institute of Evolutionary Biology, University of Edinburgh 2008 http://tree.bio.ed.ac.uk/ software/figtree/
99. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Z Yang, Genetics 2002 162 1811 1823 12524351 (Pubitemid 36114665)
100. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. LS Kubatko BC Carstens LL Knowles, Bioinformatics 2009 25 971 973 10.1093/bioinformatics/btp079 19211573