Biology subjects

Thawornwattana, Y.

Publications and source records attributed to Thawornwattana, Y..

4 recordsLinked to original sources

bioRxiv2024

Inference of continuous gene flow between species under misspecified models

Gene flow between species is increasingly recognized as an important evolutionary process with potential adaptive consequences. Recent methodological advances make it possible to infer different modes of gene flow from genome-scale data, including pulse introgression at a specific time and continuous gene flow over an extended time period. However, it remains challenging to infer the history of species divergence and between-species gene flow from genomic sequence data. As a result, models used in real data analysis may often be misspecified, potentially leading to incorrect biological interpretations. Here, we characterize biases in parameter estimation under continuous migration models using a combination of asymptotic analysis and posterior inference from simulated datasets. When sequence data are generated under a pulse introgression model, isolation-with-initial-migration models assuming no recent gene flow are able to better recover gene flow with less bias than models that assume recent gene flow. When gene flow is assigned to an incorrect branch in the phylogeny, there may be large biases associated with the migration rate and species divergence times. When the direction of gene flow is incorrectly assumed, we may still detect gene flow if it is recent and between non-sister species but not when it is ancestral and between sister species. Overall, the impact of model misspecification is local in the species phylogeny. The pulse introgression model appears to be more robust to model misspecification and is preferable in real data analysis over the continuous migration model unless there is substantive evidence for continuous gene flow.

evolutionary biology↗

bioRxiv2023

Major patterns in the introgression history of Heliconius butterflies

AO_SCPLOWBSTRACTC_SCPLOWGene flow between species is an important evolutionary process that can facilitate adaptation and lead to species diversification. It also makes reconstruction of species relationships difficult. Here, we use the full-likelihood multispecies coalescent (MSC) approach to estimate species phylogeny and major introgression events in Heliconius butterflies from whole-genome sequence data. We obtain a robust estimate of species branching order among major clades in the genus, including the "melpomene-silvaniform" group, which shows extensive historical and on-going gene flow. We obtain chromosome-level estimates of key parameters in the species phylogeny, including species divergence times, present-day and ancestral population sizes as well as the direction, timing, and intensity of gene flow. Our analysis leads to a phylogeny with introgression events that differ from those obtained in previous studies. We find that H. aoede most likely represents the earliest-branching lineage of the genus and that "silvaniform" species are paraphyletic within the melpomene-silvaniform group. Our phylogeny provides new, parsimonious histories for the origins of key traits in Heliconius, including pollen feeding and an inversion involved in wing pattern mimicry. Our results demonstrate the power and feasibility of the full-likelihood MSC approach for estimating species phylogeny and key population parameters despite extensive gene flow. The methods used here should be useful for analysis of other difficult species groups with high rates of introgression.

evolutionary biology↗

bioRxiv2023

Inferring the direction of introgression using genomic sequence data

Genomic data are informative about the history of species divergence and interspecific gene flow, including the direction, timing, and strength of gene flow. However, gene flow in opposite directions generates similar patterns in multilocus sequence data, such as reduced sequence divergence between the hybridizing species. As a result, inference of the direction of gene flow is challenging. Here we investigate the information about the direction of gene flow present in genomic sequence data using likelihood-based methods under the multispecies-coalescent-with-introgression (MSci) model. We analyze the case of two species, and use simulation to examine cases with three or four species. We find that it is easier to infer gene flow from a small population to a large one than in the opposite direction, and easier to infer inflow (gene flow from outgroup species to an ingroup species) than outflow (gene flow from an ingroup species to an outgroup species). It is also easier to infer gene flow if there is a longer time of separate evolution between the initial divergence and subsequent introgression. When introgression is assumed to occur in the wrong direction, the time of introgression tends to be correctly estimated and the Bayesian test of gene flow is often significant, while estimates of introgression probability can be even greater than the true probability. We analyze genomic sequences from Heliconius butterflies to demonstrate that typical genomic datasets are informative about the direction of interspecific gene flow, as well as its timing and strength.

evolutionary biology↗

bioRxiv2021

Complex introgression history of the erato-sara clade of Heliconius butterflies

AO_SCPLOWBSTRACTC_SCPLOWIntrogressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species makes estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood analysis methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ full-likelihood methods under the multispecies coalescent (MSC) model with and without gene flow to analyze the genomic data from six members of the erato-sara clade of Heliconius butterflies and infer the species phylogeny and cross-species introgression events. The methods naturally accommodate random fluctuations in genealogical history across the genome due to deep coalescence. To avoid heterozygote phasing errors in haploid sequences commonly produced by genome assembly methods, we process and compile unphased diploid sequence alignments and use analytical methods to average over uncertainties in heterozygote phase resolution. There is robust evidence for introgression across the genome, both among distantly related species deep in the phylogeny and between sister species in shallow parts of the tree. We obtain chromosome-specific estimates of key population parameters such as introgression directions, times and probabilities, as well as species divergence times and population sizes for modern and ancestral species. We confirm ancestral gene flow between the sara clade and an ancestral population of H. telesiphe, a likely hybrid speciation origin for H. hecalesia, and gene flow between sister species H. erato and H. himera. Inferred introgression among ancestral species also explains the history of two chromosomal inversions deep in the phylogeny of the group. This study illustrates how a full-likelihood approach based on the multispecies coalescent makes it possible to extract rich historical information of species divergence and gene flow from genomic data.

evolutionary biology↗