Inferring Phylogenetic Networks Using PhyloNet

Wen, Dingqiao; Yun, Yun; Zhu, Jiafan; Nakhleh, Luay

doi:10.1101/238071

Cited by 64 publications

(110 citation statements)

References 33 publications

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“…Mosquito dataset re-analysis. Our re-analysis of the 18-taxon dataset published by Neafsey et al [46] confirmed the historical introgression in the Anopheles phylogeny that was detected by Fontaine et al [51] and Wen et al [52] by analyzing a smaller 6-taxon was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.…”

Section: Empirical Studysupporting

confidence: 82%

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Fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data

Hejase

Vandepol

Bonito

et al. 2017

Preprint

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An emerging discovery in phylogenomics is that interspecific gene flow has played a major role in the evolution of many different organisms. To what extent is the Tree of Life not truly a tree reflecting strict “vertical” divergence, but rather a more general graph structure known as a phylogenetic network which also captures “horizontal”gene flow? The answer to this fundamental question not only depends upon densely sampled and divergent genomic sequence data, but also compu-tational methods which are capable of accurately and efficiently inferring phylogenetic networks from large-scale genomic sequence datasets. Re-cent methodological advances have attempted to address this gap. How-ever, in the 2016 performance study of Hejase and Liu, state-of-the-art methods fell well short of the scalability requirements of existing phy-logenomic studies.The methodological gap remains: how can phylogenetic networks be ac-curately and efficiently inferred using genomic sequence data involving many dozens or hundreds of taxa? In this study, we address this gap by proposing a new phylogenetic divide-and-conquer method which we call FastNet. We conduct a performance study involving a range of evolu-tionary scenarios, and we demonstrate that FastNet outperforms state-of-the-art methods in terms of computational efficiency and topological accuracy.

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Section: Empirical Studysupporting

confidence: 82%

“…The two-reticulation species phylogeny inferred by FastNet(MPL) is shown in Figure 3, where reticulations are visualized in a manner similar to [13]. (shown as Figure 1C in [51]) and the MLE-inferred species phylogeny reported by Wen et al [52], both of which were inferred using the 6-taxon Fontaine et al…”

Section: Empirical Studymentioning

confidence: 99%

Fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data

Hejase

Vandepol

Bonito

et al. 2017

Preprint

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“…Strictly bifurcating trees may not adequately depict evolutionary history when gene flow and hybridization are prevalent (Solís‐Lemus & Ané, ; Wen, Yu, Zhu, Nakhleh, & Posada, ; Yu & Nakhleh, ). Using SNaQ, we found hybridization within the sampled taxa of the C. triseriatus group to be relatively rare.…”

Section: Discussionmentioning

confidence: 99%

“…Interest in phylogenomic networks continues to increase as more evidence accumulates suggesting that both incomplete lineage sorting and reticulation/hybridization may be a common component of the evolutionary history of several groups (Solís‐Lemus & Ané, ; Solís‐Lemus et al, ; Wen et al, ). Unfortunately, many of these explicit network methods are computationally demanding (Than, Ruths, & Nakhleh, ), necessitating the use of some type of approximation.…”

Section: Discussionmentioning

confidence: 99%

“…Unfortunately, many of these explicit network methods are computationally demanding (Than, Ruths, & Nakhleh, ), necessitating the use of some type of approximation. New pseudolikelihood methods such as SNaQ and similar techniques in the PhyloNet package (Yu & Nakhleh, ; Wen et al, ) show promise for analysing large phylogenomic data sets. Combining tree‐based and network‐based phylogenomic methods, each with their own strengths and weaknesses, will likely provide the most robust conclusions regarding evolutionary history.…”

Section: Discussionmentioning

confidence: 99%

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Cryptic diversity in the Mexican highlands: Thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)

Blair

Bryson

Linkem

et al. 2018

Molecular Ecology Resources

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With the continued adoption of genome‐scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent‐based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent‐based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent‐based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.

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Differences in flowering time maintain species boundaries in a continental radiation ofViburnum

Spriggs

Schlutius

Eaton

et al. 2019

American J of Botany

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Premise We take an integrative approach in assessing how introgression and Pleistocene climate fluctuations have shaped the diversification of the core Lentago clade of Viburnum, a group of five interfertile species with broad areas of sympatry. We specifically tested whether flowering time plays a role in maintaining species isolation. Methods RAD‐seq data for 103 individuals were used to infer the species relationships and the genetic structure within each species. Flowering times were compared among species on the basis of historical flowering dates documented by herbarium specimens. Results Within each species, we found a strong relationship between flowering date and latitude, such that southern populations flower earlier than northern ones. In areas of sympatry, the species flower in sequence rather than simultaneously, with flowering dates offset by ≥9 d for all species pairs. In two cases it appears that the offset in flowering times is an incidental consequence of adaptation to differing climates, but in the recently diverged sister species V. prunifolium and V. rufidulum, we find evidence that reinforcement led to reproductive character displacement. Long‐term trends suggest that the two northern‐most species are flowering earlier in response to recent climate change. Conclusions We argue that speciation in the Lentago clade has primarily occurred through ecological divergence of allopatric populations, but differences in flowering time were essential to maintain separation of incipient species when they came into secondary contact. This combination of factors may underlie diversification in many other plant clades.

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Inferring Phylogenetic Networks Using PhyloNet

Cited by 64 publications

References 33 publications

Fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data

Fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data

Cryptic diversity in the Mexican highlands: Thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus)

Differences in flowering time maintain species boundaries in a continental radiation ofViburnum

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