scholarly journals Integrated Likelihood for Phylogenomics under a No-Common-Mechanism Model

2018 ◽  
Author(s):  
Hunter Tidwell ◽  
Luay Nakhleh
Keyword(s):  
Sequence Data ◽  
Gene Tree ◽  
Branch Length ◽  
Biological Data ◽  
Common Mechanism ◽  
Sequence Evolution ◽  
Gene Trees ◽  
Species Trees ◽  
Integrated Likelihood ◽  
Species Phylogeny

The availability of genome-wide sequence data from a large number of species as well as data from multiple individuals within a species has ushered in the era of phylogenomics. In this era, species phylogeny inference is based on models of sequence evolution on gene trees as well as models of gene tree evolution within the branches of species phylogenies. Parsimony, likelihood, Bayesian, and distance methods have been introduced for species phylogeny inference based on such models. All methods, except for the parsimony ones, assume a common mechanism across all loci as captured by a single value of each branch length of the species phylogeny. In this paper, we propose a ``no common mechanism" (NCM) model, where every gene tree evolves according to its own parameters of the species phylogeny. An analogous model was proposed and explored, both mathematically and experimentally, for sites, or characters, in a sequence alignment in the context of the classical phylogeny problem. For example, a famous equivalence between the maximum parsimony and maximum likelihood phylogeny estimates was established under certain NCM models by Tuffley and Steel. Here we derive an analytically integrated likelihood of both species trees and networks given the gene trees of multiple loci under an NCM model. We demonstrate the performance of inference under this integrated likelihood on both simulated and biological data. The model presented here will afford opportunities for exploring connections among various methods for estimating species phylogenies from multiple, independent loci.

scholarly journals DEPP: Deep Learning Enables Extending Species Trees using Single Genes

2021 ◽  
Author(s):  
Yueyu Jiang ◽  
Metin Balaban ◽  
Qiyun Zhu ◽  
Siavash Mirarab
Keyword(s):  
Sequence Data ◽  
Single Gene ◽  
Query Sequence ◽  
Gene Tree ◽  
Species Tree ◽  
Metagenomic Data ◽  
Marker Genes ◽  
Sequence Evolution ◽  
Species Trees ◽  
Sample Identification

AbstractIdentifying samples in an evolutionary context is a fundamental step in the study of microbiome, and more broadly, biodiversity. Extending a reference phylogeny by placing new query sequences onto it has been increasingly used for sample identification and other applications. Existing phylogenetic placement methods have assumed that the query sequence is homologous to the data used to infer the reference phylogeny. Thus, they are designed to place data from a single gene onto a gene tree (e.g., they can place 16S sequences onto a 16S gene tree). While this assumption is reasonable, ultimately, sample identification is a question of identifying the species not individual genes. The placement of single gene data on a gene tree is therefore used as a proxy for a more ambitious goal: extending a species tree given sequence data from one or more gene. This goal poses difficult algorithmic questions. Nevertheless, a sufficiently accurate solution would not only improve sample identification using marker genes, it would also help achieving the long-standing goal of combining 16S and metagenomic data. We approach this problem using deep neural networks (DNN) and introduce a method called DEPP. Given a reference species tree and sequence data from one (or a handful of) genes, DEPP learns how to extend the species tree to include new species. DEPP does not rely on pre-specified models of sequence evolution or gene tree discordance; instead, it uses highly parameterized DNNs to learn both aspects from the data. We test DEPP both in simulations and on real microbial data and show high accuracy.

scholarly journals Phylogenetic signal is associated with the degree of variation in root-to-tip distances

2020 ◽  
Author(s):  
Mezzalina Vankan ◽  
Simon Y.W. Ho ◽  
Carolina Pardo-Diaz ◽  
David A. Duchêne
Keyword(s):  
Sequence Data ◽  
Phylogenetic Signal ◽  
Gene Tree ◽  
Phylogenetic Inference ◽  
Genomic Region ◽  
Published Data ◽  
Data Sets ◽  
Gene Trees ◽  
Species Trees ◽  
Data Set

AbstractThe phylogenetic information contained in sequence data is partly determined by the overall rate of nucleotide substitution in the genomic region in question. However, phylogenetic signal is affected by various other factors, such as heterogeneity in substitution rates across lineages. These factors might be able to predict the phylogenetic accuracy of any given gene in a data set. We examined the association between the accuracy of phylogenetic inference across genes and several characteristics of branch lengths in phylogenomic data. In a large number of published data sets, we found that the accuracy of phylogenetic inference from genes was consistently associated with their mean statistical branch support and variation in their gene tree root-to-tip distances, but not with tree length and stemminess. Therefore, a signal of constant evolutionary rates across lineages appears to be beneficial for phylogenetic inference. Identifying the causes of variation in root-to-tip lengths in gene trees also offers a potential way forward to increase congruence in the signal across genes and improve estimates of species trees from phylogenomic data sets.

scholarly journals How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example

2022 ◽  
Vol 12 ◽  
Author(s):  
Martha Kandziora ◽  
Petr Sklenář ◽  
Filip Kolář ◽  
Roswitha Schmickl
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Species Tree ◽  
Secondary Contact ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Phylogenetic Discordance ◽  
Gene Tree Discordance ◽  
High Degree

A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus Loricaria to shed light on the potential sources of phylogenetic discordance and generated a phylogenetic hypothesis. By accounting for paralogy during gene tree inference, we generated a species tree based on hundreds of nuclear loci, using Hyb-Seq, and a plastome phylogeny obtained from off-target reads during target enrichment. We observed a high degree of gene tree discordance, which we found implausible at first sight, because the genus did not show evidence of hybridization in previous studies. We used various phylogenomic analyses (trees and networks) as well as the D-statistics to test for ILS and hybridization, which we developed into a workflow on how to tackle phylogenetic discordance in recent radiations. We found strong evidence for ILS and hybridization within the genus Loricaria. Low genetic differentiation was evident between species located in different Andean cordilleras, which could be indicative of substantial introgression between populations, promoted during Pleistocene glaciations, when alpine habitats shifted creating opportunities for secondary contact and hybridization.

scholarly journals Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

2020 ◽  
Author(s):  
Matthew H Van Dam ◽  
James B Henderson ◽  
Lauren Esposito ◽  
Michelle Trautwein
Keyword(s):  
Marine Invertebrates ◽  
Phylogenetic Analyses ◽  
Single Gene ◽  
Gene Tree ◽  
Single Copy ◽  
Species Tree ◽  
Bootstrap Support ◽  
Gene Trees ◽  
Species Trees ◽  
Tree Reconstruction

Abstract Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.]

scholarly journals Terraces in Gene Tree Reconciliation-Based Species Tree Inference

2020 ◽  
Author(s):  
Michael J. Sanderson ◽  
Michelle M. McMahon ◽  
Mike Steel
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Solution Space ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Data Set ◽  
Tree Reconciliation ◽  
The Impact

AbstractTerraces in phylogenetic tree space are sets of trees with identical optimality scores for a given data set, arising from missing data. These were first described for multilocus phylogenetic data sets in the context of maximum parsimony inference and maximum likelihood inference under certain model assumptions. Here we show how the mathematical properties that lead to terraces extend to gene tree - species tree problems in which the gene trees are incomplete. Inference of species trees from either sets of gene family trees subject to duplication and loss, or allele trees subject to incomplete lineage sorting, can exhibit terraces in their solution space. First, we show conditions that lead to a new kind of terrace, which stems from subtree operations that appear in reconciliation problems for incomplete trees. Then we characterize when terraces of both types can occur when the optimality criterion for tree search is based on duplication, loss or deep coalescence scores. Finally, we examine the impact of assumptions about the causes of losses: whether they are due to imperfect sampling or true evolutionary deletion.

scholarly journals Phylogenomic terraces: presence and implication in species tree estimation from gene trees

2020 ◽  
Author(s):  
Ishrat Tanzila Farah ◽  
Md Muktadirul Islam ◽  
Kazi Tasnim Zinat ◽  
Atif Hasan Rahman ◽  
Md Shamsuzzoha Bayzid
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Species Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Lineage Sorting ◽  
Deep Coalescence ◽  
Tree Estimation ◽  
Tree Space ◽  
Multiple Species

AbstractSpecies tree estimation from multi-locus dataset is extremely challenging, especially in the presence of gene tree heterogeneity across the genome due to incomplete lineage sorting (ILS). Summary methods have been developed which estimate gene trees and then combine the gene trees to estimate a species tree by optimizing various optimization scores. In this study, we have formalized the concept of “phylogenomic terraces” in the species tree space, where multiple species trees with distinct topologies may have exactly the same optimization score (quartet score, extra lineage score, etc.) with respect to a collection of gene trees. We investigated the presence and implication of terraces in species tree estimation from multi-locus data by taking ILS into account. We analyzed two of the most popular ILS-aware optimization criteria: maximize quartet consistency (MQC) and minimize deep coalescence (MDC). Methods based on MQC are provably statistically consistent, whereas MDC is not a consistent criterion for species tree estimation. Our experiments, on a collection of dataset simulated under ILS, indicate that MDC-based methods may achieve competitive or identical quartet consistency score as MQC but could be significantly worse than MQC in terms of tree accuracy – demonstrating the presence and affect of phylogenomic terraces. This is the first known study that formalizes the concept of phylogenomic terraces in the context of species tree estimation from multi-locus data, and reports the presence and implications of terraces in species tree estimation under ILS.

scholarly journals On the independent loci assumption in phylogenomic studies

2016 ◽  
Author(s):  
W. Bryan Jennings
Keyword(s):  
Homologous Recombination ◽  
Population Size ◽  
Effective Population Size ◽  
Gene Tree ◽  
Gene Trees ◽  
Species Trees ◽  
Long Term Effects ◽  
Effective Population ◽  
Independent Assortment

AbstractStudies using multi-locus coalescent methods to infer species trees or historical demographic parameters usually require the assumption that the gene tree for each locus (or SNP) is genealogically independent from the gene trees of other sampled loci. In practice, however, researchers have used two different criteria to delimit independent loci in phylogenomic studies. The first criterion, which directly addresses the condition of genealogical independence of sampled loci, considers the long-term effects of homologous recombination and effective population size on linkage between two loci. In contrast, the second criterion, which only considers the single-generation effects of recombination in the meioses of individuals, identifies sampled loci as being independent of each other if they undergo Mendelian independent assortment. Methods that use these criteria to estimate the number of independent loci per genome as well as intra-chromosomal “distance thresholds” that can be used to delimit independent loci in phylogenomic datasets are reviewed. To compare the efficacy of each criterion, they are applied to two species (an invertebrate and vertebrate) for which relevant genetic and genomic data are available. Although the independent assortment criterion is relatively easy to apply, the results of this study show that it is overly conservative and therefore its use would unfairly restrict the sizes of phylogenomic datasets. It is therefore recommended that researchers only refer to genealogically independent loci when discussing the independent loci assumption in phylogenomics and avoid using terms that may conflate this assumption with independent assortment. Moreover, whenever feasible, researchers should use methods for delimiting putatively independent loci that take into account both homologous recombination and effective population size (i.e., long-term effective recombination).

scholarly journals Species tree-aware simultaneous reconstruction of gene and domain evolution

2018 ◽  
Author(s):  
Sayyed Auwn Muhammad ◽  
Bengt Sennblad ◽  
Jens Lagergren
Keyword(s):  
Sequence Alignment ◽  
Gene Tree ◽  
Phylogenetic Reconstruction ◽  
Gene Families ◽  
Species Tree ◽  
Biological Data ◽  
Sequence Evolution ◽  
Multiple Sequence ◽  
Alignment Algorithms ◽  
Tandem Duplications

AbstractMost genes are composed of multiple domains, with a common evolutionary history, that typically perform a specific function in the resulting protein. As witnessed by many studies of key gene families, it is important to understand how domains have been duplicated, lost, transferred between genes, and rearranged. Analogously to the case of evolutionary events affecting entire genes, these domain events have large consequences for phylogenetic reconstruction and, in addition, they create considerable obstacles for gene sequence alignment algorithms, a prerequisite for phylogenetic reconstruction.We introduce the DomainDLRS model, a hierarchical, generative probabilistic model containing three levels corresponding to species, genes, and domains, respectively. From a dated species tree, a gene tree is generated according to the DL model, which is a birth-death model generalized to occur in a dated tree. Then, from the dated gene tree, a pre-specified number of dated domain trees are generated using the DL model and the molecular clock is relaxed, effectively converting edge times to edge lengths. Finally, for each domain tree and its lengths, domain sequences are generated for the leaves based on a selected model of sequence evolution.For this model, we present a MCMC-based inference framework called DomainDLRS that takes a dated species tree together with a multiple sequence alignment for each domain family as input and outputs an estimated posterior distribution over reconciled gene and domain trees. By requiring aligned domains rather than genes, our framework evades the problem of aligning full-length genes that have been exposed to domain duplications, in particular non-tandem domain duplications. We show that DomainDLRS performs better than MrBayes on synthetic data and that it outperforms MrBayes on biological data. We analyse several zincfinger genes and show that most domain duplications have been tandem duplications, some involving two or more domains, but non-tandem duplications have also been common.

scholarly journals Whole-Genome Analyses Resolve the Phylogeny of Flightless Birds (Palaeognathae) in the Presence of an Empirical Anomaly Zone

2019 ◽  
Vol 68 (6) ◽  
pp. 937-955 ◽  
Author(s):  
Alison Cloutier ◽  
Timothy B Sackton ◽  
Phil Grayson ◽  
Michele Clamp ◽  
Allan J Baker ◽  
...  
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Estimation Error ◽  
Gene Tree ◽  
Species Tree ◽  
Tree Topology ◽  
Whole Genome ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Genome Analyses

Abstract Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totaling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4274 CR1 retroelements identified from multispecies whole-genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other nonostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations and topology tests indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.

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