Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis

Molecular Biology and Evolution

Volumn 29, Issue 8, 2012, Pages 1917-1932

  Bryant, David ^a   Bouckaert, Remco ^b   Felsenstein, Joseph ^c   Rosenberg, Noah A ^d   Roychoudhury, Arindam ^e  

^a UNIVERSITY OF OTAGO   (New Zealand)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

^c UNIVERSITY OF WASHINGTON   (United States)

^d STANFORD UNIVERSITY   (United States)

^e Department of Medicine   (United States)

Author keywords

AFLP; effective population size; multispecies coalescent; SNAPP; SNP; species trees

Indexed keywords

ALGORITHM; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; BIALLELIC GENETIC MARKER; GENE LOCUS; GENETIC ANALYSIS; GENETIC MARKER; GENETIC VARIABILITY; NONHUMAN; PHYLOGENETIC TREE; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; ALLELES; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; COMPUTER SIMULATION; DATABASES, GENETIC; DIGITALIS; GENES, PLANT; GENETIC MARKERS; LIKELIHOOD FUNCTIONS; NEW ZEALAND; PHYLOGENY; SPECIES SPECIFICITY;

DIGITALIS (GENUS); OURISIA;

EID: 84864697376     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss086     Document Type: Article

References (51)

1. Bracewell R. 2000. The Fourier transform and its applications. New York: McGraw-Hill.
2. Bryant D, Moulton V. 2004. NeighborNet: an agglomerative algorithm for the construction of planar phylogenetic networks. Mol Biol Evol. 21:255-265.
3. Degnan JH, Rosenberg NA. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol. 24:332-340.
4. Degnan JH, Salter LA. 2005. Gene tree distributions under the coalescent process. Evolution 59:24-37.
5. Donnelly PJ, Kurtz TG. 1996. A countable representation of the Fleming-Viot measure-valued diffusion. Ann Appl Probab. 24:698-742.
6. Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320.
7. Drummond AJ, Rambaut A. 2007. Beast: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214.
8. Efromovich S, Kubatko LS. 2008. Coalescent time distributions in trees of arbitrary size. Stat Appl Genet Mol Biol. 7:2.
9. Ewens WJ. 2004. Mathematical population genetics. 2nd ed. New York: Springer.
10. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17:368-376.
11. Felsenstein J. 1988. Phylogenies and quantitative characters. Annu Rev Ecol Syst. 19:445-471.
12. Felsenstein J. 2004. Inferring phylogenies. Sunderland (MA): Sinauer Associates Inc. Gelman A, Rubin DB. 1992. Inference from iterative simulation using multiple sequences. Stat Sci. 7:457-472.
13. Griffiths RC, Jenkins PA, Song YS. 2008. Importance sampling and the two-locus model with subdivided population structure. Adv Appl Probab. 40:473-500.
14. Griffiths RC, Tavare S. 1997. Computational methods for the coalescent. In: Progress in population genetics and human evolution. Berlin (Germany): Springer-Verlag. p. 165-182.
15. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. 2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5:e1000695.
16. Hein J, Schierup MH, Wiuf C. 2005. Gene genealogies, variation and evolution: a primer in coalescent theory. Oxford: Oxford University Press.
17. Heled, J, Drummond, AJ. 2010. Bayesian inference of species trees from multilocus data. Mol Biol Evol. 27:570-580.
18. Hey J, Nielsen R. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A. 104:2785-2790.
19. Hudson RR. 1983. Testing the constant-rate neutral allele model with protein sequence data. Evolution 37:203-217.
20. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback J. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
21. Krauss SL. 2000. Accurate gene diversity estimates from amplified fragment length polymorphism (AFLP) markers. Mol Ecol. 9: 1241-1245.
22. Kubatko LS, Carstens BC, Knowles LL. 2009. Stem: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25:971-973.
23. 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.
24. Lundstrom R. 1990. Stochastic models and statistical methods for DNA sequence data [PhD thesis]. [Salt Lake City (UT)]: University of Utah.
25. Lynch M, Milligan BG. 1994. Analysis of population genetic structure with RAPD markers. Mol Ecol. 3:91-99.
26. Maddison WP, Maddison DR. 2010. Mesquite: a modular system for evolutionary analysis. Version 2.75. [cited 2012 Apr 12]. Available from: http://mesquiteproject.org
27. Meudt HM, Clarke AC. 2007. Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci. 12: 106-117.
28. Meudt HM, Lockhart PJ, Bryant D. 2009. Species delimitation and phylogeny of a New Zealand plant species radiation. BMC Evol Biol. 9:111.
29. Nei M. 1987. Molecular evolutionary genetics. New York: Columbia University Press.
30. Nielsen R. 1998. Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model. Theor Popul Biol. 53:143-151.
31. Nielsen R, Mountain JL, Huelsenbeck JP, Slatkin M. 1998. Maximumlikelihood estimation of population divergence times and population phylogeny in models without mutation. Evolution 52: 669-677.
32. Pamilo P, Nei M. 1988. Relationships between gene trees and species trees. Mol Biol Evol. 5:568-583.
33. Rambaut A, Drummond AJ. 2007. Tracer v1.4. Available from: Phttp://beast.bio.ed.ac.uk/Tracer
34. Rannala B, Yang ZH. 2003. Bayesian estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-56.
35. Ripley B. 1987. Stochastic simulation. New York: Wiley.
36. Rosenberg NA, Nordborg M. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet. 3:380-390.
37. RoyChoudhury A. 2006. Likelihood inference for population structure, using the coalescent [PhD thesis].
38. [Seattle (WA)]: University of Washington. RoyChoudhury A. 2011. Composite likelihood-based inferences on genetic data from dependent loci. J Math Biol. 62:65-80.
39. RoyChoudhury A, Felsenstein J, Thompson EA. 2008. A two-stage pruning algorithm for likelihood computation for a population tree. Genetics 180:1095-1105.
40. Sawyer SA, Dykhuizen DE, Hartl DL. 1987. Confidence interval for the number of selectively neutral amino acid polymorphisms. Proc Natl Acad Sci U S A. 84:6225-6228.
41. Schmelzer T, Trefethen LN. 2007. Evaluating matrix functions for exponential integrators via Carath?eodory-Fej?er approximation and contour integrals. Electron Trans Numer Anal. 29:1-18.
42. Sidje RB. 1998. Expokit: a software package for computing matrix exponentials. ACM Trans Math Softw. 24:130-156.
43. Siren J, Marttinen P, Corander J. 2010. Reconstructing population histories from single nucleotide polymorphism data. Mol Biol Evol. 28:673-683.
44. Slatkin M. 1996. Gene genealogies within mutant allelic classes. Genetics 143:579-587.
45. Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.
46. Takahata N. 1989. Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122:957-66.
47. Takahata N, Nei M. 1985. Gene genealogy and variance of interpopulational nucleotide differences. Genetics 110:325-344.
48. Tavar?e, S. 1984. Line-of-descent and genealogical processes, and their applications in population genetics models. Theor Popul Biol. 26:119-164.
49. Wakeley, J. 2009. Coalescent theory: an introduction. Greenwood Village (CO): Roberts and Company.
50. Wilson IJ, Weale ME, Balding DJ. 2003. Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities. J R Stat Soc A. 166:155-201.
51. Wu Y. 2011. Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution. 66:763-775.