scholarly journals Bayesian Inference of Species Networks from Multilocus Sequence Data

2017 ◽  
Author(s):  
Chi Zhang ◽  
Huw A. Ogilvie ◽  
Alexei J. Drummond ◽  
Tanja Stadler
Keyword(s):  
Bayesian Inference ◽  
Gene Evolution ◽  
Sequence Data ◽  
Phylogenetic Network ◽  
Orthologous Gene ◽  
Reticulate Evolution ◽  
Gene Trees ◽  
Hybridization Event ◽  
Yeast Data ◽  
Species Evolution

AbstractReticulate species evolution, such as hybridization or introgression, is relatively common in nature. In the presence of reticulation, species relationships can be captured by a rooted phylogenetic network, and orthologous gene evolution can be modeled as bifurcating gene trees embedded in the species network. We present a Bayesian approach to jointly infer species networks and gene trees from multilocus sequence data. A novel birth-hybridization process is used as the prior for the species network, and we assume a multispecies network coalescent (MSNC) prior for the embedded gene trees. We verify the ability of our method to correctly sample from the posterior distribution, and thus to infer a species network, through simulations. To quantify the power of our method, we reanalyze two large datasets of genes from spruces and yeasts. For the three closely related spruces, we verify the previously suggested homoploid hybridization event in this clade; for the yeast data, we find extensive hybridization events. Our method is available within the BEAST 2 add-on SpeciesNetwork, and thus provides an extensible framework for Bayesian inference of reticulate evolution.

scholarly journals Phylogenomic analyses using genomes and transcriptomes do not resolve relationships among major clades in Phrymaceae

2021 ◽  
Author(s):  
Diego F. Morales-Briones ◽  
Nan Lin ◽  
Eileen Y. Huang ◽  
Dena L. Grossenbacher ◽  
James M. Sobel ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary Ecology ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Reticulate Evolution ◽  
Small Scale ◽  
Gene Trees ◽  
Network Analyses ◽  
Gene Tree Discordance ◽  
Close Relatives

Premise of the study: Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny for a stable taxonomy and for macroevolutionary comparisons. Methods: We sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and cloudogram, and carried out phylogenetic network analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distance, and gene duplication events. Key results: Most gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support the tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, polyphyly of Mimulus s.l. is strongly supported, and no particular reticulation event among the Phrymaceae tribes is well supported. Reticulation likely occurred among Erythranthe bicolor and close relatives. No ancient WGD event was detected in Phrymaceae. Instead, small-scale duplications are among potential drivers of macroevolutionary diversification of Phrymaceae. Conclusions: We show that analysis of reticulate evolution is sensitive to taxon sampling and methods used. We also demonstrate that genome-scale data do not always fully "resolve" phylogenetic relationships. They present rich opportunities to investigate reticulate evolution, and gene and genome evolution involved in lineage diversification and adaptation.

scholarly journals StarBeast3: Adaptive Parallelised Bayesian Inference of the Multispecies Coalescent

2021 ◽  
Author(s):  
Jordan Douglas ◽  
Cinthy L. Jiménez-Silva ◽  
Remco Bouckaert
Keyword(s):  
Bayesian Inference ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Gene Tree ◽  
Gene Trees ◽  
Multispecies Coalescent ◽  
Tree Inference ◽  
Synthetic Datasets ◽  
Set Up ◽  
The Cost

AbstractAs genomic sequence data becomes increasingly available, inferring the phylogeny of the species as that of concatenated genomic data can be enticing. However, this approach makes for a biased estimator of branch lengths and substitution rates and an inconsistent estimator of tree topology. Bayesian multispecies coalescent methods address these issues. This is achieved by embedding a set of gene trees within a species tree and jointly inferring both under a Bayesian framework. However, this approach comes at the cost of increased computational demand. Here, we introduce StarBeast3 – a software package for efficient Bayesian inference of the multispecies coalescent model via Markov chain Monte Carlo. We gain efficiency by introducing cutting-edge proposal kernels and adaptive operators, and StarBeast3 is particularly efficient when a relaxed clock model is applied. Furthermore, gene tree inference is parallelised, allowing the software to scale with the size of the problem. We validated our software and benchmarked its performance using three real and two synthetic datasets. Our results indicate that StarBeast3 is up to one-and-a-half orders of magnitude faster than StarBeast2, and therefore more than two orders faster than *BEAST, depending on the dataset and on the parameter, and is suitable for multispecies coalescent inference on large datasets (100+ genes). StarBeast3 is open-source and is easy to set up with a friendly graphical user interface.

scholarly journals Inference of Species Phylogenies from Bi-allelic Markers Using Pseudo-likelihood

2018 ◽  
Author(s):  
Jiafan Zhu ◽  
Luay Nakhleh
Keyword(s):  
Network Inference ◽  
Sequence Data ◽  
Phylogenetic Network ◽  
Simulated Data ◽  
Biological Data ◽  
Phylogenetic Networks ◽  
Gene Trees ◽  
Multispecies Coalescent ◽  
Pseudo Likelihood ◽  
Computational Bottleneck

AbstractMotivationPhylogenetic networks represent reticulate evolutionary histories. Statistical methods for their inference under the multispecies coalescent have recently been developed. A particularly powerful approach uses data that consist of bi-allelic markers (e.g., single nucleotide polymorphism data) and allows for exact likelihood computations of phylogenetic networks while numerically integrating over all possible gene trees per marker. While the approach has good accuracy in terms of estimating the network and its parameters, likelihood computations remain a major computational bottleneck and limit the method’s applicability.ResultsIn this paper, we first demonstrate why likelihood computations of networks take orders of magnitude more time when compared to trees. We then propose an approach for inference of phylo-genetic networks based on pseudo-likelihood using bi-allelic markers. We demonstrate the scalability and accuracy of phylogenetic network inference via pseudo-likelihood computations on simulated data. Furthermore, we demonstrate aspects of robustness of the method to violations in the underlying assumptions of the employed statistical model. Finally, we demonstrate the application of the method to biological data. The proposed method allows for analyzing larger data sets in terms of the numbers of taxa and reticulation events. While pseudo-likelihood had been proposed before for data consisting of gene trees, the work here uses sequence data directly, offering several advantages as we discuss.AvailabilityThe methods have been implemented in PhyloNet (http://bioinfocs.rice.edu/phylonet)[email protected], [email protected]

Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

2019 ◽  
Vol 44 (4) ◽  
pp. 930-942
Author(s):  
Geraldine A. Allen ◽  
Luc Brouillet ◽  
John C. Semple ◽  
Heidi J. Guest ◽  
Robert Underhill
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Morphological Evidence ◽  
South American ◽  
New Combinations ◽  
The North ◽  
Hybridization Event ◽  
Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

scholarly journals Ranking top-k trees in tree-based phylogenetic networks

2019 ◽  
Author(s):  
Momoko Hayamizu ◽  
Kazuhisa Makino
Keyword(s):  
Optimal Algorithm ◽  
Linear Time ◽  
Fundamental Problem ◽  
Phylogenetic Network ◽  
Reticulate Evolution ◽  
Interesting Property ◽  
Biological Data ◽  
Phylogenetic Networks ◽  
Linear Delay ◽  
Algorithmic Problems

Abstract 'Tree-based' phylogenetic networks provide a mathematically-tractable model for representing reticulate evolution in biology. Such networks consist of an underlying 'support tree' together with arcs between the edges of this tree. However, a tree-based network can have several such support trees, and this leads to a variety of algorithmic problems that are relevant to the analysis of biological data. Recently, Hayamizu (arXiv:1811.05849 [math.CO]) proved a structure theorem for tree-based phylogenetic networks and obtained linear-time and linear-delay algorithms for many basic problems on support trees, such as counting, optimisation, and enumeration. In the present paper, we consider the following fundamental problem in statistical data analysis: given a tree-based phylogenetic network $N$ whose arcs are associated with probability, create the top-$k$ support tree ranking for $N$ by their likelihood values. We provide a linear-delay (and hence optimal) algorithm for the problem and thus reveal the interesting property of tree-based phylogenetic networks that ranking top-$k$ support trees is as computationally easy as picking $k$ arbitrary support trees.

scholarly journals Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts

2019 ◽  
Author(s):  
Joshua I Brian ◽  
Simon K Davy ◽  
Shaun P Wilkinson
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Reticulate Evolution ◽  
Next Generation Sequencing Data ◽  
Putative Hybrid ◽  
Its2 Region ◽  
Sequencing Data ◽  
Lineage Sorting ◽  
Evolutionary Potential ◽  
Unbiased Test

Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondria; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of Next Generation Sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.

Additions to the microfungi in Taiwan: introducing Pseudorobillarda camelliae-sinensis sp. nov., (Pseudorobillardaceae) and new host records of pleosporalean taxa in mountainous habitats

Phytotaxa ◽  
2021 ◽  
Vol 516 (2) ◽  
Author(s):  
ACHALA R. RATHNAYAKA ◽  
K.W. THILINI CHETHANA ◽  
DANUSHKA S. TENNAKOON ◽  
SAISAMORN LUMYONG ◽  
KEVIN D. HYDE
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Sequence Data ◽  
Similar Species ◽  
New Host ◽  
Mountain Ranges ◽  
Mountain Habitats ◽  
Phylogenetic Affinities ◽  
New Host Records

A novel taxon, Pseudorobillarda camelliae-sinensis (Pseudorobillardaceae) and new host records of pleosporalean taxa viz. Neopyrenochaeta triseptatispora (Neopyrenochaetaceae), Ramusculicola thailandica (Teichosporaceae) and Vaginatispora palmae (Lophiostomataceae) resulted from our investigation of plant-associated microfungi in Alishan and Fenghuang Mountain ranges in Taiwan. These taxa were isolated from dicotyledonous hosts of Bignoniaceae, Caprifoliaceae, Meliaceae and Moraceae. Maximum likelihood and Bayesian inference analyses were performed using combined SSU, LSU, ITS, tef1-α and rpb2 sequence data to clarify the phylogenetic affinities of taxa. The newly described taxa of the current study are accompanied by comprehensive descriptions, micrographs and comparisons with similar species. In addition, the importance of exploiting fungi from mountain habitats in Taiwan is discussed.

Species delimitation of Hymenasplenium obliquissimum group (Aspleniaceae) in southwestern China

Phytotaxa ◽  
2021 ◽  
Vol 480 (1) ◽  
pp. 29-44
Author(s):  
GUO-CHENG ZHANG ◽  
HUA-FENG HONG ◽  
GE-HONG CHEN ◽  
SHU-GANG LU ◽  
YAN-FEN CHANG
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Reticulate Evolution ◽  
Southwestern China ◽  
Natural Classification ◽  
Ploidy Levels ◽  
Dna Sequence Data ◽  
Taxonomic Implications ◽  
Taxonomic Approach ◽  
Locus Classicus

The Hymenasplenium obliquissimum group contains the widespread H. obliquissimum and several geographically restricted species, including H. retusulum, H. wuliangshanense, H. latidens, H. changputungense, H. quercicola, H. szechuanense, H. furfuraceum, H. adiantifrons, and H. filipes. However, the taxonomy of this group is still unclear and needs to be revised because some entities were treated infraspecifically or as synonyms and the validation of some species still needs to be assessed. To formulate a natural classification and investigate the relationships in this group, we collected and studied specimens of species related to the H. obliquissimum group and obtained specimens of species described by Ching at their locus classicus in southwestern China. An integrative taxonomic approach was taken to delimit species in the group using cytological, morphological, and DNA sequence data. Specifically, in the phylogenetic analyses, the H. obliquissimum group was recovered as a monophyletic group, comprising five principal chloroplast lineages. Based on our inferences, we provided taxonomic implications of chloroplast lineages discovered in this study and suggested possible reticulate evolution in the H. obliquissimum group which was interpreted by the incongruence of chloroplast and nuclear phylogenies. Further studies to strengthen the taxonomic of taxa especially those with the co-existence of different ploidy levels are still warranted.

Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Ran Li ◽  
Wenbao Zhuang ◽  
Congcong Wang ◽  
Hamed El-Serehy ◽  
Saleh A. Al-Farraj ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Trees ◽  
Ssu Rrna Gene ◽  
Anaerobic Ciliate ◽  
Pr China

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.

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