A Distance Method to Reconstruct Species Trees In the Presence of Gene Flow

One of the central tasks in evolutionary biology is to reconstruct the evolutionary relationships among species from sequence data, particularly from multilocus data. In the last ten years, many methods have been proposed to use the variance in the gene histories to estimate species trees by explicitly modeling deep coalescence. However, gene flow, another process that may produce gene history variance, has been less studied. In this paper, we propose a simple yet innovative method for species trees estimation in the presence of gene flow. Our method, called STEST (Species Tree Estimation from Speciation Times), constructs species tree estimates from pairwise speciation time or species divergence time estimates. By using methods that estimate speciation times in the presence of gene flow, (for example, M1 (Yang 2010) or SIM3s (Zhu and Yang 2012)), STEST is able to estimate species trees from data subject to gene flow. We develop two methods, called STEST (M1) and STEST (SIM3s), for this purpose. Additionally, we consider the method STEST (M0), which instead uses the M0 method (Yang 2002), a coalescent-based method that does not assume gene flow, to estimate speciation times. It is therefore devised to estimate species trees in the absence of gene flow. Our simulation studies show that STEST (M0) outperforms STEST(M1), STEST (SIM3s) and STEM in terms of estimation accuracy and outperfroms *BEAST in terms of running time when the degree of gene flow is small. STEST (M1) outperforms STEST (M0), STEST (SIM3s), STEM and *BEAST in term of estimation accuracy when the degree of gene flow is large. An empirical data set analyzed by these methods gives species tree estimates that are consistent with the previous results.