The BPP program for species tree estimation and species delimitation

Current Zoology

Volumn 61, Issue 5, 2015, Pages 854-865

  Yang, Ziheng ^a,b  

^a China National Center for Bioinformation   (China)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

BPP; MCMC; Multispecies coalescent; Species delimitation; Species tree

Indexed keywords

EID: 84944395746     PISSN: 16745507     EISSN: None     Source Type: Journal    
DOI: 10.1093/czoolo/61.5.854     Document Type: Article

References (36)

1. Angelis K, dos Reis M, 2015. The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times. Curr. Zool. 61: 874-885.
2. Burgess R, Yang Z, 2008. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol. Biol. Evol. 25: 1979-1994.
3. Carstens BC, Pelletier TA, Reid NM, Satler JD, 2013. How to fail at species delimitation? Mol. Ecol. 22: 4369-4383.
4. Caviedes Solis I, Bouzid N, Banbury B, Leaché AD, 2015. Uprooting phylogenetic uncertainty in coalescent species delimitation: A meta-analysis of empirical studies. Curr. Zool. 61: 866-873.
5. Drummond AJ, Rambaut A, 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7: 214.
6. Edwards SV, 2009. Is a new and general theory of molecular systematics emerging? Evolution 63: 1-19.
7. Edwards SV, Liu L, Pearl DK, 2007. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. U.S.A. 104: 5936-5941.
8. Felsenstein J, 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376.
9. Fujita MK, Leaché AD, 2011. A coalescent perspective on delimiting and naming species: A reply to Bauer et al. Proc. R. Soc. Lond. B. Biol. Sci. 278: 493-495.
10. Fujita MK, Leaché AD, Burbrink FT, McGuire JA, Moritz C, 2012. Coalescent-based species delimitation in an integrative taxonomy. Trends Ecol. Evol. 27: 480-488.
11. Gatesy J, Springer MS, 2013. Concatenation versus coalescence versus "concatalescence". Proc. Natl. Acad. Sci. U.S.A. 110: E1179.
12. Green, P. J. 2003. Trans-dimensional Markov chain Monte Carlo. In: Green PJ, Hjort NL, Richardson S ed. Highly Structured Stochastic Systems. Oxford: Oxford University Press, 179- 196
13. Heled J, Drummond AJ, 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27: 570-580.
14. Hey J, 2010. Isolation with migration models for more than two populations. Mol. Biol. Evol. 27: 905-920.
15. Hobolth A, Christensen OF, Mailund T, Schierup MH, 2007. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet. 3: e7.
16. Jukes TH, Cantor CR, 1969. Evolution of protein molecules. In: Munro HN ed. Mammalian Protein Metabolism. New York: Academic Press, 21-123.
17. Kubatko LS, Carstens BC, Knowles LL, 2009. STEM: Species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25: 971-973.
18. Lanier HC, Knowles LL, 2012. Is recombination a problem for species-tree analyses? Syst. Biol. 61: 691-701.
19. Leaché AD, Fujita MK, 2010. Bayesian species delimitation in West African forest geckos Hemidactylus fasciatus. Proc. R. Soc. Lond. B. Biol. Sci. 277: 3071-3077.
20. Leaché AD, Harris RB, Rannala B, Yang Z, 2014. The influence of gene flow on Bayesian species tree estimation: A simulation study. Syst. Biol. 63: 17-30.
21. Liu L, Pearl DK, 2007. Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56: 504-514.
22. Liu L, Xi Z, Wu S, Davis C, Edwards SV, 2015. Estimating phylogenetic trees from genome-scale data. Ann. NY. Acad. Sci. doi: 10.1111/nyas.12747
23. Olave M, Sola E, Knowles LL, 2014. Upstream analyses create problems with DNA-based species delimitation. Syst. Biol. 63: 263-271.
24. Pelletier TA, Crisafulli C, Wagner S, Zellmer AJ, Carstens BC, 2015. Historical species distribution models predict species limits in Western Plethodon salamanders. Syst. Biol.: in press.
25. Rannala B, 2015. Species delimition and species tree estimation using multilocus sequence data. Curr. Zool. 61: 846-853.
26. Rannala B, Yang Z, 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656.
27. Rannala B, Yang Z, 2013. Improved reversible jump algorithms for Bayesian species delimitation. Genetics 194: 245-253.
28. Robert CP, Casella G, 2004. Monte Carlo Statistical Methods, 2nd edn. New York: Springer-Verlag.
29. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A et al., 2012. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61: 539-542.
30. Takahata N, Satta Y, Klein J, 1995. Divergence time and population size in the lineage leading to modern humans. Theor. Popul. Biol. 48: 198-221.
31. Yang Z, 2002. Likelihood and Bayes estimation of ancestral population sizes in Hominoids using data from multiple loci. Genetics 162: 1811-1823.
32. Yang Z, 2014. Molecular Evolution: A Statistical Approach. Oxford: Oxford University Press.
33. Yang Z, Rannala B, 2010. Bayesian species delimitation using multilocus sequence data. Proc. Natl. Acad. Sci. U.S.A. 107: 9264-9269.
34. Yang Z, Rannala B, 2014. Unguided species delimitation using DNA sequence data from multiple loci. Mol. Bio.l Evol. 31: 3125-3135.
35. Zhang C, D-X Zhang, Zhu T, Yang Z, 2011. Evaluation of a Bayesian coalescent method of species delimitation. Syst. Biol. 60: 747-761.
36. Zhou WW, Wen Y, Fu J, Xu YB, Jin JQ et al., 2012. Speciation in the Rana chensinensis species complex and its relationship to the uplift of the Qinghai-Tibetan Plateau. Mol. Ecol. 21: 960-973.