Anatomy of a species tree

Transcription

1 Anatomy of a species tree T 1 Size of current and ancestral Populations (N) N Confidence in branches of species tree t/2n = 1 coalescent unit T 2 Branch lengths and divergence times of species & populations (t/2n)

2 Hierarchical nature of phylogeny Liu, Yu, Kubatko, Pearl and Edwards Mol. Phyl. Evol. 53:

3 Deep coalescence vs. branch length heterogeneity Edwards Evolution 63:1-19

4 The multispecies coalescent model in context Genetics Population genetics Phylogenetics Isolation-migration and network coalescent models Species tree inference via multispecies coalescent model Concatenation Key assumption of the MSC: conditional independence of loci (mediated by recombination) not presence of incomplete lineage sorting Edwards et al Mol. Phyl. Evol. 94:

5 Controversies surrounding species tree methods

6 Posterior probability Posterior of species tree Do species tree methods require discordance of gene trees? Simulation: all gene trees are topologically congruent with the species tree Sequences analyzed with BEST. DATA SET 1 (100% Matching) bp bp 1000bp Number of loci 8 species, 1 allele per species Castillo et al. 2010

7 30 gene trees from Australian finches P. acuticauda P. hecki P. cincta Jennings & Edwards (2005) Evolution 59,

8 Species trees from gene trees Bayesian Estimation of Species Trees = The BEST method species tree gene trees 1. Define an approximate species tree as a prior for gene trees 2. Estimate posterior of species tree f (S D) using a birth-death prior on species tree and likelihoods of gene tree vectors from step 1 using coalescent theory. Liu and Pearl Species trees from gene trees: reconstructing posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56 (May):

9 Bayesian hierarchical model (Liu and Pearl) Bayesian Estimation of Species Trees = The BEST method (ha ha!) Likelihood of sequence data given gene trees and substitution model Prior on substitution parameters birth-death prior on species tree Estimated posterior of species tree f (S,G,λ D) = Likelihood of sequence data given gene trees and substitution model f (D G,λ) f (λ) f (G S) f (S) f (D) Likelihood of gene tree distributions given species tree Probability of the sequence data (impossible to know) Liu, L Bioinformatics 24:

10 Australo-Papuan Fairy Wrens - Maluridae Splendid Fairywren (Malurus) Striated Grasswren (Amytornis) Superb Fairywren (Malurus) Southern Emu-wren (Stipiturus)

11 Exploring incomplete lineage sorting through species tree methods Full Coalescent Model (BEST) Liu and Pearl 2007 Systematic Biology 56: Average Rank of Gene Trees (STAR) Heterogeneous Set of gene trees Minimize discordance in posterior probability of gene trees (BUCKy) Ané et al 2007 Molecular Biology and Evolution 24: Minimizing Deep Coalescence (MDC) Maddison and Knowles Syst. Biol. 55: Liu et al 2009 Systematic Biology 58: Concatenation (MrBayes)

12 Maximum (pseudo) likelihood method for species trees Rooted gene tree triplets (topologies only) A B C B A C A B C 1.0 species tree A B C Prooportion τ/θ 0 Liu, Li & Edwards BMC Evol. Biol.

13 Species Tree Web Server: STRAW

14 Summarizing variation in gene trees Compare taxon pairs via 1) Ranks 2) coalescence times 3) minimum divergences

15 Species Trees from Average Ranks of Coalescence Times (STAR) Multilocus sequences Distance tree Estimate rooted gene trees Distance matrix Average ranks of coalescence times Liu, Yu, Pearl, Edwards (2009) Syst. Biol.doi: /sysbi

16 Calculating a STAR tree Liu, Yu, Kubatko, Pearl and Edwards Mol. Phyl. Evol. 53:

17 PHYBASE: Constructing, manipulating and evaluating species trees Liu & Yu Bioinformatics 26:

18 Uses of phybase Conduct multilocus bootstrap Estimate STAR, STEAC and Maximum Trees Calculate likelihood of species trees given gene trees Simulate gene trees (ultrametric and variable rates) and DNA sequences

19 Likelihood of gene trees given a species tree Liu, Yu, Kubatko, Pearl and Edwards Mol. Phyl. Evol. 53:

20 Multilocus bootstrap Sample loci at random with replacement Pseudomatrix 1 Pseudomatrix 2 Pseudomatrix 3 Then sample sites within loci with replacement, just as in the normal bootstrap. Seo, T.-K Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data. Mol. Biol. Evol. 25:

21 Phybase phyml Phybase B A B C Pipeline for STAR/STEAC trees in phybase Multilocus bootstrap (b replicates) A Make matrix of gene trees C A B C n n gene trees n species, l loci for each replicate l Make gene trees for all b*l single gene matrices b replicates Phybase or other program Consensus STAR tree

22 The anomaly zone Species tree Gene tree probabilities Gene trees

23 Phylogenetic analysis in the anomaly zone Liu, L., et al Syst Biol 58:

24 The multispecies coalescent applies to ancient as well as recent divergences internode length in coalescent units (τ/θ) Pleistocene Probability of inconguence is the same in both cases!! Think: short, not recent Absolute time in the past (τ/θ) K/T boundary

25 Mammal data set 37 ingroup taxa (placental mammals) 758 genes from Orthomam database 447 genes passed filtering Total ~1.38 Mb per species, avg. ~3.1 kb/gene Gene trees made via RaxML and best-fit substitution model MP-EST and STAR method ML and Bayesian supermatrix analysis

26 Conflict between concatenation and species tree approaches Song et al PNAS

27 Large diversity of gene trees in mammal data set Densitree analysis of 440 scaled gene tree topologies

28 Phylogenomic subsampling Phylogenomic subsampling Random subsampling of loci Ordered addition of loci Comparing stability of phylogenetic methods or datasets Assessing the effect of evolutionary rate on phylogenetic analysis Assessing the effect of missing data on phylogenetic analysis Edwards 2016 Zoologica Scripta

29 More genes = more support MP-EST STAR 100 Tree shrews-primates Horse-Dog Whales-(Horse/Dog) Average* bootstrap support *10 replicates per number of genes random sampling from pool of 447 genes Number of genes Song et al PNAS

30 Concatenation: more genes = strong but conflicting support for clades Tree shrews-primates Whales-(Horse/Dog) < 90%, < 0.9 Whales-Bats Tree shrews-rodents Bats-(Horse/Dog) coalescence concatenation coalescence concatenation MP-EST STAR Bayesian ML MP-EST STAR Bayesian ML Number of genes Number of genes Number of taxa Number of taxa 10 replicates (gene sets) per box, random sampling from pool of 447 genes Song et al PNAS

31 Multispecies coalescent model explains ~77% of gene tree variation Song et al PNAS

32 Gene tree distributions consistent with multispecies coalescent model* *Model predicts equal frequencies of minority gene trees

33 Misconceptions about species tree methods Species tree methods require discordance among gene trees FALSE Species tree methods don t acknowledge gene tree estimation error FALSE Species tree methods attribute all gene tree heterogeneity to incomplete lineage sorting TRUE and FALSE