Evolutionary Biology

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Understanding Discordance Between Species Trees and Gene Trees




Phylogenetic inferences from genomic data consist of many loci. Each locus is assumed to evolve independently because recombination breaks linkage between loci. Independent loci can therefore have distinct evolutionary histories and cause gene tree species tree incongruence. For example, the following scenarios can cause incongruent gene trees: (a) simple population genetic processes (i.e., the coalescent), (b) migration and thus gene-flow between species/populations , and (c) gene-duplication and gene-loss. Even though, gene-tree discordance is a major challenge in species-tree estimation, its identification also provides key information about biological processes. Our first key question is the estimation of species trees when the underlying gene trees are discordant. Specifically, we are working on more realistic models that incorporate different causes of gene-tree incongruence such as the multispecies coalescent with migration model. This work also entails new algorithm development and theory design for more efficient computation of species trees from thousands of gene trees. Our second key question is the estimation of divergence times under complex gene-tree histories (e.g., Martin and Höhna 2018, Martin et al. 2017). Gene trees are older than species/population divergence under a multispecies coalescent model, but gene trees are younger than species/population divergence in the presence of migration. This problem is exacerbated for young species. Thus, we aim to obtain improved and robust estimated of divergences times using our new developments on a multispecies coalescent with migration model. Finally, this multispecies coalescent with migration model could be used for improved species delimitation in the presence of migration.


  • CH Martin and S Höhna: New evidence for the recent divergence of Devil’s Hole pupfish and the plausibility of elevated mutation rates in endangered taxa. Molecular Ecology, 2018, 27:831-838
  • CH Martin, S Höhna, JE Crawford, BJ Turner, EJ Richards and LH Simons: The complex effects of demographic history on the estimation of substitution rate: concatenated gene analysis results in no more than 2-fold overestimation. Proceedings of the Royal Society B, 2017, 284: 20170537