Today's project. Test input data Six alignments (from six independent markers) of Curcuma species

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DNA sequences II Analyses of multiple sequence data datasets, incongruence tests, gene trees vs. species tree reconstruction, networks, detection of hybrid species

DNA sequences II Test of congruence of multiple alignments [ILD test, Concaterpillar] Visualization of gene tree incongruences using NeighbourNet [Splitstree] Reconstruction of species tree under multicoalescent model [*BEAST] Reconstruction of species network (ILS/hybridization) [Phylonet]

Today's project 1) Evaluation of congruence of multiple sequence alignment 2) Identification of individuals that causing incongruence 3) Reconstruct of species tree 4) Reconstruction of species network AIMS: understand causes and consequences of differences between datasets choose the correct method for reconstruction of species phylogeny Test input data Six alignments (from six independent markers) of Curcuma species

Gene trees vs. Species tree

(In)congruence of gene trees (alignments)

Ancestral polymorphism ~ incomplete lineage sorting (ILS) ~ deep coalescence

Vizualization of conflicting datasets NeighborNet- http://www.splitstree.org/ distance based method powerful tool for conflict/hybrids detection

Test of gene trees (dataset) incongruence Incongruence length difference (ILD) test (Farris et al., 1994) Test of homogeneity of datasets, H0: datasets are congruent Parsimony-based compares the length of the tree inferred from the combined data set to the combined length of the trees inferred for each locus in the data set rather outdated and questionable (e.g. Leigh, 2008) Shimodaira-Hasegawa (SH) test (Shimodaira, 2002) Maximum-likelihood based determine whether individual markers reject the tree inferred from the concatenation of all markers also questionable (e.g. Leigh, 2008)

Test of gene trees (dataset) incongruence Concaterpillar (Leigh, 2008) Test gene tree topology and branch length Maximum-likelihood based Can handle many markers in single analysis Running only on Linux/Mac CONGRUENCE TEST SELECTION might depends on the aims of the study, quality of data and amount of markers to be compared. READ more about it, if you need it for your studies!

Species tree reconstruction X Concatenating multiple alignments into single one --> analysing the data as a single locus? Likely results in wrong topology (Kubatko & Degnan, 2007) MDC minimize deep coalescence Parsimony based methods Do not take into account ILS Multispecies coalescence models (Heled and Drummond, 2010) ML or Bayesian based searches Accurate, powerful but not modeling hybridization just recently... several models taking into account ILS & hybridization ML or Bayesian based searches

Species tree using multispecies coalescens *BEAST (Heled and Drummond, 2010) Bayesian inference of the species tree model Do not allow for gene flow between studied species Based on alignments of multiple markers that can lead to different topology due to ILS

BEAST software cross-platform program for Bayesian analysis of molecular sequences using MCMC *BEAST is one of the modules valuable online support google groups, tutorials http://beast.bio.ed.ac.uk Sister tool - BEAST2

Species Networks Models allowing for ILS and gene flow complex Only few models useful as an exploratory tool for multiple species PhyloNet software https://bioinfo.cs.rice.edu/phylonet Different tools to reconstruct networks Exploratory species network reconstruction using Maximum pseudolikelihood approach Models user defined number of hybridization events

Species network visualization Dendroscope, http://dendroscope.org/

Project 1) Evaluation of congruence of multiple sequence alignment 2) Identification of individuals that causing incongruence 3) Reconstruct of species tree 4) Reconstruction of species network AIMS: understand causes and consequences of differences between datasets choose the correct method for reconstruction of species phylogeny.follow THE MANUAL and comes with question/comments to us! HAVE FUN!

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