Inference of Gene Flow between Species under Misspecified Models

Huang, Jun; Thawornwattana, Yuttapong; Flouri, Tomáš; Mallet, James; Yang, Ziheng

doi:10.1093/molbev/msac237

Cited by 16 publications

(38 citation statements)

References 98 publications

(176 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The population inherits from each parent a proportion of genes, and inheritance proportions are assumed to be known. This punctual event is a simplified model for processes such as hybridization, horizontal gene transfer or gene flow, that can happen over a period of time [Huang et al, 2022].…”

Section: Methodsmentioning

confidence: 99%

Accounting for within-species variation in continuous trait evolution on a phylogenetic network

Teo

Rose

Bastide

et al. 2022

Preprint

View full text Add to dashboard Cite

Within-species variation may be the result of genetic variation, environmental variation or measurement error for example. In phylogenetic comparative studies, failing to account for intraspecific variation has many adverse effects, such as increased error to test hypotheses about evolutionary correlations, biased estimates of evolutionary rates, and inaccurate inference of the mode of evolution. These adverse effects were demonstrated in studies that considered a tree-like underlying phylogeny. Comparative methods on phylogenetic networks are still in their infancy. The impact of within-species variation on network-based methods has not been studied. Here, we extend the phylogenetic linear model available in the Julia package PhyloNetworks to account for within-species variation in the continuous response trait, assuming equal intraspecific variances across species. We show how inference based on the individual values can be reduced to a problem using species-level summaries, even when the within-species variance is estimated. Using simulations, we find that our method performs well under various settings, and is robust when intraspecific variances are unequal across species. When phenotypic correlations differ from evolutionary correlations, we find that estimates of evolutionary coefficients are pulled towards the phenotypic coefficients, for all methods we tested. Also, evolutionary rates are either underestimated or over-estimated, depending on the mismatch between phenotypic and evolutionary relationships. We applied our method to morphological and geographical data from Polemonium. We find a strong negative correlation of leaflet size with elevation, despite a positive correlation within species. Our method can explore the role of gene flow in trait evolution. We find marginal evidence for leaflet size being carried along in gene flow, supporting previous observations on the challenges of using individual continuous traits to infer inheritance weights at reticulations.

show abstract

Section: Methodsmentioning

confidence: 99%

Accounting for within-species variation in continuous trait evolution on a phylogenetic network

Teo

Rose

Bastide

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Interpreting and comparing these complex models is challenging because evolutionary processes are likely heterogeneous along the genome, and it is often unknown a priori if a model is misspecified (Huang et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

“…In practice, analyzing local ancestry often begins with imposing a particular model of admixture, then estimating parameters such as admixture times, selection coefficients, or effective population sizes (Gravel, 2012; Liang et al, 2022; Svedberg et al, 2021), which could be highly complex with many degrees of freedom. Interpreting and comparing these complex models is challenging because evolutionary processes are likely heterogeneous along the genome, and it is often unknown a priori if a model is misspecified (Huang et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Quantum entropy reveals chromosomal disorder of ancestry tracts in genetic admixture

Xiong

2023

Preprint

View full text Add to dashboard Cite

Ancestry tracts are contiguous haplotype blocks inherited from distinct groups of common ancestors. The genomic distribution of ancestry tracts (or local ancestry) provides rich information about evolutionary mechanisms shaping the genetic composition of hybrids. The correlation structure of ancestry tracts has been particularly useful in both empirical and theoretical studies, but there is a lack of descriptive measures operating on arbitrarily large genomic blocks to summarize this correlation structure without imposing too many assumptions about admixture. We here develop an approach inspired by quantum information theory to quantify this correlation structure. The key innovation is to represent local ancestry as quantum states, where less correlation in local ancestry leads to elevated quantum entropy. By leveraging a variety of entropy measures on local ancestry signals, we show that entropy is deeply connected to co-ancestry probabilities between and within haplotypes, so that ancestral recombination graphs become pivotal to the study of entropy dynamics in admixture. We use this approach to characterize a standard neutral admixture model with an arbitrary number of sources, and recover entropic laws governing the dynamics of ancestry tracts under recombination and genetic drift, which resembles the second law of thermodynamics. In application, entropy is well-defined on arbitrarily large genomic blocks with either phased or unphased local ancestry, and is insensitive to a small amount of noise. These properties are superior to simple statistics on ancestry tracts such as tract length and junction density. Finally, we construct an entropic index reflecting the degree of intermixing among ancestry tracts over a chromosomal block. This index confirms that the Z chromosome in a previously studied butterfly hybrid zone has the least potential of ancestry mixing, thus conforming to the "large-X/Z" effect in speciation. Together, we show that quantum entropy provides a useful framework for studying ancestry tract dynamics in both theories and real systems.

show abstract

Section: Introductionmentioning

confidence: 99%

“…Recent advances make it possible to model genomic evolution under the multispecies coalescent (MSC) framework and use full-likelihood methods to estimate the species tree and quantify introgression (Wen and Nakhleh 2018; Zhang et al 2018; Flouri et al 2020). Analyses of both simulated and real data demonstrate that this full-likelihood MSC approach is efficient, accurate, and robust to moderate levels of model violation (Huang et al 2022; Thawornwattana et al 2023). A major advantage over approximate methods is the ability to estimate parameters of the species tree and introgression events among branches precisely, including the strength and direction of introgression as well as species divergence times, introgression times and effective population sizes.…”

Section: Introductionmentioning

confidence: 99%

Major patterns in the introgression history ofHeliconiusbutterflies

Thawornwattana

Seixas

Yang

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Gene 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 inHeliconiusbutterflies 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.

show abstract

Inference of Gene Flow between Species under Misspecified Models

Cited by 16 publications

References 98 publications

Accounting for within-species variation in continuous trait evolution on a phylogenetic network

Accounting for within-species variation in continuous trait evolution on a phylogenetic network

Quantum entropy reveals chromosomal disorder of ancestry tracts in genetic admixture

Major patterns in the introgression history ofHeliconiusbutterflies

Contact Info

Product

Resources

About