A species tree for three species (A, B, C) with a gene tree for 12 sequences running inside it to illustrate the gene-tree node-age move and the gene-tree SPR move. In summary, in both introgression scenarios of models D and 2H, where SNaQ and Hyde are inapplicable, Bpp appears to be a well-behaved method, providing reliable estimates of introgression probabilities as well as species divergence and introgression times. Model 2H (fig. There are four speciation nodes (R,S,U,V) and two hybridization nodes (H1 and H2). We ran the MCMC without any constraint, but the MCMC sample was preprocessed, with Θ replaced by Θ′ if the sampled value for φX>0.5, before the posterior summary was generated. By accommodating gene flow and providing more reliable estimates of evolutionary parameters, the model may also be used in heuristic species delimitation (Jackson et al.
Maximum Likelihood (3S) Estimates of Migration Rate (M = Nm) and Bayesian (Bpp) Estimates of Introgression Probability (φ) from the Anopheles Genomic Data.
We simulated and analyzed data using Bpp under two models: model D of figure 1 with bidirectional introgression between species A and B and the model of figure 2 (referred to as model 2H), with three species and two introgression events. Note that both φ and M reflect long-term effective gene flow, after the filtering of introgressed alleles by natural selection. We also sampled three sequences per locus to form data triplets for analysis using the maximum likelihood (ML) program 3S (Thawornwattana et al.
Then θA, θB, and θC, as well as θH1l, θH1r, θH2l, and θH2r, are unidentifiable.
Parameter estimates under model A from the two small data sets were similar to those in Zhang et al.
Martin SH, Dasmahapatra KK, Nadeau NJ, Salazar C, Walters JR, Simpson F, Blaxter M, Manica A, Mallet J, Jiggins CD. The sequence length was 500 sites. Summary methods such as SNaQ use outgroups to root the tree without the need for the molecular clock.
The remaining part of the gene tree is called the backbone. The priors were τ0∼ IG(3,0.004), θ∼IG(3,0.003), and φ∼U(0,1). 2018a, supplementary table S3, Supplementary Material online, GAR and RQO). The data were then analyzed using the three programs to estimate φ (supplementary fig. We show that these errors, as well as two nucleotide sorting methods used in the analysis of Amborella, have little impact on the conclusions of those papers. 2008), as (A–C): ((A,(C)H)S,(H,B)T)R and (D): ((A,Y)X,(X,B)Y)R. The φ estimate under model C was 0.53, with the 95% highest posterior density (HPD) CI to be 0.36–0.71. In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the multispecies coalescent (MSC) model in phylogenomics, popularly known as “species tree” methods.
Overall, the three methods had similar performance in estimating φ. 2018) for the IM model, and *beast (Zhang et al. 2015; Thawornwattana et al. We used two values of φ (0.1 and 0.5) and two values of θ (0.001 and 0.01), applied to all populations. Here we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity.
The multispecies coalescent provides a natural framework for accommodating ancestral genetic polymorphism and coalescent processes that can cause different genomic regions to have different genealogical histories.
Change node ages on gene trees using a sliding window.
The Multilocus Multispecies Coalescent: A Flexible New Model of Gene Family Evolution, School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Institut des Sciences de l’Evolution, Université Montpellier. Change τs on the species tree using a variant of the rubber-band algorithm (Rannala and Yang 2003). To reconcile the estimates from the two models, note that M is the expected number of migrants per generation, so that even a small M may mean a large number of migrants accumulated over many generations. We prune off its parent node y. However, if there are no branches on the backbone passing the population of node a, the reattachment point has to be in an ancestral species (in which there exists at least one branch on the backbone) and tL has to be greater.
As the role of the mutation model in Bpp is to correct for multiple hits at the same site and as the simulated sequences are highly similar, the choice of the mutation model is unimportant. Most methods are designed to test for the presence of gene flow (hybridization or migration) (Degnan 2018). (2012) on mammals and Xi et al. Then, we let branch y′*–a′ go through H2l or H2r according to their probabilities. We used models A and C of figure 1. It does not appear computationally feasible to apply those programs to realistically sized data sets, with more than 200 loci, say.
We acknowledge these previously reported errors in recent phylogenomic data sets, but disapprove of S&G’s excessively combative and taunting tone. We suggest that model C should be preferred, because of its biological plausibility. The models implemented here (fig. Suppose we prune off branch y′–a′ in figure 2 and the new age is ty′*>τR. We reanalyzed sequence data concerning the origin of the purple cone spruce Picea purpurea (P) from the Qinghai–Tibet Plateau, hypothesized to have originated through homoploid hybridization between P. wilsonii (W) and P. likiangensis (L) (Sun et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, Long-term m5C methylome dynamics parallel phenotypic adaptation in the cyanobacterium, Genomic Targets of Positive Selection in Giant Mice from Gough Island, Natural selection on the phase-separation properties of FUS during 160 million years of mammalian evolution, Divergence and Remarkable Diversity of the Y Chromosome in Guppies, Discovery of ongoing selective sweeps within, About the Society for Molecular Biology and Evolution, Appendix: Extended Newick Notation for the MSci Model, multispecies coalescent with introgression, https://github.com/brannala/NetworkMSCSimulations, http://creativecommons.org/licenses/by/4.0/, Receive exclusive offers and updates from Oxford Academic, Copyright © 2020 Society for Molecular Biology and Evolution. In fact, although both concatenation and MSC models clearly perform well in regions of tree space with long branches and little incomplete lineage sorting (ILS), simulations reveal the erratic behavior of concatenation when subjected to data subsampling and its tendency to produce spuriously confident yet conflicting results in regions of parameter space where MSC models still perform well. Step 6. This move may cause large changes to the flags even though it does not change the gene-tree topology.
Although limited to three sequences, 3S can use tens of thousands of loci and each run took a few minutes.
Population size parameters (θs) for modern species A and B were well estimated even with 100 loci, as was θR for the root, but θX for species X (branch X-R) and θY (for branch Y-R) were more poorly estimated (supplementary fig. The model is represented as ((A,(B)Y)X,(X)Y)R.
The number of replicates was 10. Arguably Θ and Θ′ have the same biological interpretations concerning the relatedness of the sequences sampled from A and B. We note that Bpp has several advantages.
Change θs on the species tree using a sliding window. 2016), butterflies (Martin et al. When the data set gets larger, particularly with more loci in the data set, the posterior for parameters becomes spiky, which in general leads to a deterioration of MCMC mixing efficiency, so that a greater number of MCMC iterations become necessary to produce estimates with acceptable precision. If the priors on φX and φY are symmetrical, say beta(α,α), the posterior density will satisfy f(Θ|X)=f(Θ′|X) for all X. The branches were drawn to reflect the posterior means of divergence/introgression times (τs) from Bpp, with node bars showing the 95% HPD intervals, whereas posterior means of population sizes (θs) are shown along the branches. Those proposals 1) change node ages on gene trees, 2) change gene-tree topologies using subtree pruning and regrafting (SPR), 3) change θs on the species tree using sliding windows, 4) change τs on the species tree using a variant of the rubber-band algorithm (Rannala and Yang 2003), 5) changing all node ages on the species tree and gene trees using a multiplier, and 6) change the introgression probabilities φs using sliding windows.
Data were generated using the “simulate” option of Bpp. Here, we note an interesting unidentifiability issue with model D of figure 1. The complexity of those models means that large data sets with hundreds or thousands of loci may be necessary to obtain reliable parameter estimates, as indicated by our analyses of both simulated and real data.
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