The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection

Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa.     

iGTP: A software package for large-scale gene tree parsimony analysis

Background  

The ever-increasing wealth of genomic sequence information provides an unprecedented opportunity for large-scale phylogenetic analysis. However, species phylogeny inference is obfuscated by incongruence among gene trees due to evolutionary events such as gene duplication and loss, incomplete lineage sorting (deep coalescence), and horizontal gene transfer. Gene tree parsimony (GTP) addresses this issue by seeking a species tree that requires the minimum number of evolutionary events to reconcile a given set of incongruent gene trees. Despite its promise, the use of gene tree parsimony has been limited by the fact that existing software is either not fast enough to tackle large data sets or is restricted in the range of evolutionary events it can handle.     

A Primer to Molecular Phylogenetic Analysis in Plants

Reconstructing a tree of life by inferring evolutionary history is an important focus of evolutionary biology. Phylogenetic reconstructions also provide useful information for a range of scientific disciplines such as botany, zoology, phylogeography, archaeology and biological anthropology. Until the development of protein and DNA sequencing techniques in the 1960s and 1970s, phylogenetic reconstructions were based on fossil records and comparative morphological/physiological analyses. Since then, progress in molecular phylogenetics has compensated for some of the shortcomings of phenotype-based comparisons. Comparisons at the molecular level increase the accuracy of phylogenetic inference because there is no environmental influence on DNA/peptide sequences and evaluation of sequence similarity is not subjective. While the number of morphological/physiological characters that are sufficiently conserved for phylogenetic inference is limited, molecular data provide a large number of datapoints and enable comparisons from diverse taxa. Over the last 20 years, developments in molecular phylogenetics have greatly contributed to our understanding of plant evolutionary relationships. Regions in the plant nuclear and organellar genomes that are optimal for phylogenetic inference have been determined and recent advances in DNA sequencing techniques have enabled comparisons at the whole genome level. Sequences from the nuclear and organellar genomes of thousands of plant species are readily available in public databases, enabling researchers without access to molecular biology tools to investigate phylogenetic relationships by sequence comparisons using the appropriate nucleotide substitution models and tree building algorithms. In the present review, the statistical models and algorithms used to reconstruct phylogenetic trees are introduced and advances in the exploration and utilization of plant genomes for molecular phylogenetic analyses are discussed.     

TREEasy: An automated workflow to infer gene trees,species trees,and phylogenetic networks from multilocus data

Multilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user‐friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python—TREEasy—that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ‐Tree), species inference from concatenated data (with IQ‐Tree and RaxML‐NG), species tree inference from gene trees (with ASTRAL, MP‐EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the “WGD clade” of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology ( https://github.com/MaoYafei/TREEasy ).     

The enigmatic monotypic crab plover Dromas ardeola is closely related to pratincoles and coursers (Aves, Charadriiformes, Glareolidae)

The phylogenetic placement of the monotypic crab plover Dromasardeola (Aves, Charadriiformes) remains controversial. Phylogenetic analysis of anatomical and behavioral traits using phenetic and cladistic methods of tree inference have resulted in conflicting tree topologies, suggesting a close association of Dromas to members of different suborders and lineages within Charadriiformes. Here, we revisited the issue by applying Bayesian and parsimony methods of tree inference to 2,012 anatomical and 5,183 molecular characters to a set of 22 shorebird genera (including Turnix). Our results suggest that Bayesian analysis of anatomical characters does not resolve the phylogenetic relationship of shorebirds with strong statistical support. In contrast, Bayesian and parsimony tree inference from molecular data provided much stronger support for the phylogenetic relationships within shorebirds, and support a sister relationship of Dromas to Glareolidae (pratincoles and coursers), in agreement with previously published DNA-DNA hybridization studies.     

The identifiability of tree topology for phylogenetic models, including covarion and mixture models.

For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter. We establish tree identifiability for a number of phylogenetic models, including a covarion model and a variety of mixture models with a limited number of classes. The proof is based on the introduction of a more general model, allowing more states at internal nodes of the tree than at leaves, and the study of the algebraic variety formed by the joint distributions to which it gives rise. Tree identifiability is first established for this general model through the use of certain phylogenetic invariants.     

Distinguishing coevolution from covicariance in an obligate pollination mutualism: asynchronous divergence in Joshua tree and its pollinators

Obligate pollination mutualisms--in which both plants and their pollinators are reliant upon one another for reproduction--represent some of the most remarkable coevolutionary interactions in the natural world. The intimacy and specificity of these interactions have led to the prediction that the plants and their pollinators may be prone to cospeciation driven by coevolution. Several studies have identified patterns of phylogenetic congruence that are consistent with this prediction, but it is difficult to determine the evolutionary process that underlies these patterns. Phylogenetic congruence might also be produced by extrinsic factors, such as a shared biogeographic history. We examine the biogeographic history of a putative case of codivergence in the obligate pollination mutualism between Joshua trees (Yucca brevifolia) and two sister species of pollinating yucca moths (Tegeticula spp.) We employ molecular phylogenetic methods and coalescent-based approaches, in combination with relaxed-clock estimates of absolute rates of molecular evolution, to analyze multi-locus sequence data from more than 30 populations of Y. brevifolia and its pollinators. The results indicate that the moth species diverged significantly (p < 0.01) more recently than their corresponding host populations, suggesting that the apparent codivergence is not an artifact of a shared biogeographic history.     

Phenotypic characters of static homology increase phylogenetic stability under direct optimization of otherwise dynamic homology characters

Direct optimization of unaligned sequence characters provides a natural framework to explore the sensitivity of phylogenetic hypotheses to variation in analytical parameters. Phenotypic data, when combined into such analyses, are typically analyzed with static homology correspondences unlike the dynamic homology sequence data. Static homology characters may be expected to constrain the direct optimization and thus, potentially increase the similarity of phylogenetic hypotheses under different cost sets. However, whether a total-evidence approach increases the phylogenetic stability or not remains empirically largely unexplored. Here, I studied the impact of static homology data on sensitivity using six empirical data sets composed of several molecular markers and phenotypic data. The inclusion of static homology phenotypic data increased the average stability of phylogenetic hypothesis in five out of the six data sets. To investigate if any static homology characters would have similar effect, the analyses were repeated with randomized phenotypic data, and with one of the molecular markers fixed as static homology characters. These analyses had, on average, almost no effect on the phylogenetic stability, although the randomized phenotypic data sometimes resulted in even higher stability than empirical phenotypic data. The impact was related to the strength of the phylogenetic signal in the phenotypic data: higher average jackknife support of the phenotypic tree correlated with stronger stabilizing effect in the total-evidence analysis. Phenotypic data with a strong signal made the total-evidence trees topologically more similar to the phenotypic trees, thus, they constrained the dynamic homology correspondences of the sequence data. Characters that increase phylogenetic stability are particularly valuable for phylogenetic inference. These results indicate an important role and additive value of phenotypic data in increasing the stability of phylogenetic hypotheses in total-evidence analyses.     

Are monophyly and synapomorphy the same or different? Revisiting the role of morphology in phylogenetics

Species are groups of organisms, marked out by reproductive (replicative) properties. Monophyletic taxa are groups of species, marked out by synapomorphies. In Nelson’s analysis, monophyly and synapomorphy are identical relations. Monophyly and synapomorphy, however, are not equivalent relations. Monophyly is epistemically not accessible, whereas synapomorphy is epistemically accessible through character analysis. Monophyly originates with speciation, the two sister‐species that come into being through the splitting of the ancestral species lineage forming a monophyletic taxon at the lowest level of inclusiveness. Synapomorphy provides the empirical evidence for monophyly, inferred from character analysis in the context of a three‐taxon statement. If synapomorphy and monophyly were equivalent, phylogenetic systematists should find a single tree, instead of multiple equally parsimonious trees. Understanding synapomorphy as the relevant evidence for phylogenetic inference reveals a category mistake in contemporary phylogenetics: the treatment of morphological characters mapped onto molecular trees as synapomorphies and homoplasies. The mapping of morphological characters onto nodes of a molecular tree results in an empirically empty procedure for synapomorphy discovery. Morphological synapomorphies and homoplasies can only be discovered by morphological and combined analyses. The use of morphology in phylogenetic inference in general is defended by examples from Laurales and Squamata in particular. To make empirical evidence scientifically relevant in order to search for concordance, or dis‐concordance, of phylogenetic signal, is certainly more fruitful for phylogenetics than the uncritical mapping of morphological traits on a molecular scaffold. © The Willi Hennig Society 2010.     

A numerical analysis of isoelectric focused keratin monomers: Affinities of some western indian ocean green geckos

This is a case study in the numerical analysis of intra- and interspecific differences in isoelectric focused proteins. The proteins are epidermal keratin monomers extracted and characterized by relatively novel porocedures. The numerical analysis of the biochemical data by principal component analysis indicates the relatives similarity of the populations whilst Wagner trees were computed to hypothesize their phylogeny. The character states of the tree nodes (‘ancestors’) are deduced and the phylgenetic tree is fitted directly onto the ordination diagram. In this way evolutionary divargence, convergence and extent of change can be readily visualize. Little convergence exists in this biochemical data set, there being close agreement between the phenetic and phylogenetic analyses. The existence of three species is indicated and this contradicts some facets of the conventional classification.     

Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions

The desire to infer the evolutionary history of a group of species should be more viable now that a considerable amount of multilocus molecular data is available. However, the current molecular phylogenetic paradigm still reconstructs gene trees to represent the species tree. Further, commonly used methods of combining data, such as the concatenation method, are known to be inconsistent in some circumstances. In this paper, we propose a Bayesian hierarchical model to estimate the phylogeny of a group of species using multiple estimated gene tree distributions, such as those that arise in a Bayesian analysis of DNA sequence data. Our model employs substitution models used in traditional phylogenetics but also uses coalescent theory to explain genealogical signals from species trees to gene trees and from gene trees to sequence data, thereby forming a complete stochastic model to estimate gene trees, species trees, ancestral population sizes, and species divergence times simultaneously. Our model is founded on the assumption that gene trees, even of unlinked loci, are correlated due to being derived from a single species tree and therefore should be estimated jointly. We apply the method to two multilocus data sets of DNA sequences. The estimates of the species tree topology and divergence times appear to be robust to the prior of the population size, whereas the estimates of effective population sizes are sensitive to the prior used in the analysis. These analyses also suggest that the model is superior to the concatenation method in fitting these data sets and thus provides a more realistic assessment of the variability in the distribution of the species tree that may have produced the molecular information at hand. Future improvements of our model and algorithm should include consideration of other factors that can cause discordance of gene trees and species trees, such as horizontal transfer or gene duplication.     

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

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.     

利用DNA序列构建系统树的方法介绍

利用DNA序列进行系统发生分析是分子进化研究的必要手段。构建系统树的方法有距离法、简约法、最大似然法以及贝叶斯推断法等。要解决特定的系统发生问题,首先要挑选合理的分类群及序列,尽量减少数据的偏倚,然后选择构树方法,最后还要对结果进行评价并给出进化学上的解释。本文讨论了挑选数据的原则及存在的问题,介绍了几种构树方法的基本原理及步骤,并列举了它们的优缺点。Abstract: Construction of phylogenetic trees is a key means in molecular evolutionary studies. The methods of constructing phylogenetic trees include the distance-based methods, parsimony, maximum likelihood, and Bayesian inference methods. To resolve a special problem about phylogeny, several notices are necessary: first, to select the reasonable data at less bias as possible; second, to choose the proper method to reconstruct phylogenetic tree; third, to evaluate the conclusions and explain them on the field of evolution. The present paper provides a brief introduction of the principles of data selection and tree-construction methods, and discusses about their advantage and disadvantage points.     

Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analysing fungal environmental samples

Fungi associated with seeds of tropical trees pervasively affect seed survival and germination, and thus are an important, but understudied, component of forest ecology. Here, we examine the diversity and evolutionary origins of fungi isolated from seeds of an important pioneer tree (Cecropia insignis, Cecropiaceae) following burial in soil for five months in a tropical moist forest in Panama. Our approach, which relied on molecular sequence data because most isolates did not sporulate in culture, provides an opportunity to evaluate several methods currently used to analyse environmental samples of fungi. First, intra- and interspecific divergence were estimated for the nu-rITS and 5.8S gene for four genera of Ascomycota that are commonly recovered from seeds. Using these values we estimated species boundaries for 527 isolates, showing that seed-associated fungi are highly diverse, horizontally transmitted, and genotypically congruent with some foliar endophytes from the same site. We then examined methods for inferring the taxonomic placement and phylogenetic relationships of these fungi, evaluating the effects of manual versus automated alignment, model selection, and inference methods, as well as the quality of BLAST-based identification using GenBank. We found that common methods such as neighbor-joining and Bayesian inference differ in their sensitivity to alignment methods; analyses of particular fungal genera differ in their sensitivity to alignments; and numerous and sometimes intricate disparities exist between BLAST-based versus phylogeny-based identification methods. Lastly, we used our most robust methods to infer phylogenetic relationships of seed-associated fungi in four focal genera, and reconstructed ancestral states to generate preliminary hypotheses regarding the evolutionary origins of this guild. Our results illustrate the dynamic evolutionary relationships among endophytic fungi, pathogens, and seed-associated fungi, and the apparent evolutionary distinctiveness of saprotrophs. Our study also elucidates the diversity, taxonomy, and ecology of an important group of plant-associated fungi and highlights some of the advantages and challenges inherent in the use of ITS data for environmental sampling of fungi.     

Pitfalls of heterogeneous processes for phylogenetic reconstruction

Different genes often have different phylogenetic histories. Even within regions having the same phylogenetic history, the mutation rates often vary. We investigate the prospects of phylogenetic reconstruction when all the characters are generated from the same tree topology, but the branch lengths vary (with possibly different tree shapes). Furthering work of Kolaczkowski and Thornton (2004, Nature 431: 980-984) and Chang (1996, Math. Biosci. 134: 189-216), we show examples where maximum likelihood (under a homogeneous model) is an inconsistent estimator of the tree. We then explore the prospects of phylogenetic inference under a heterogeneous model. In some models, there are examples where phylogenetic inference under any method is impossible - despite the fact that there is a common tree topology. In particular, there are nonidentifiable mixture distributions, i.e., multiple topologies generate identical mixture distributions. We address which evolutionary models have nonidentifiable mixture distributions and prove that the following duality theorem holds for most DNA substitution models. The model has either: (i) nonidentifiability - two different tree topologies can produce identical mixture distributions, and hence distinguishing between the two topologies is impossible; or (ii) linear tests - there exist linear tests which identify the common tree topology for character data generated by a mixture distribution. The theorem holds for models whose transition matrices can be parameterized by open sets, which includes most of the popular models, such as Tamura-Nei and Kimura's 2-parameter model. The duality theorem relies on our notion of linear tests, which are related to Lake's linear invariants.     

Escaping from the Felsenstein Zone by Detecting Long Branches in Phylogenetic Data

Long branches in a true phylogeny tend to disrupt hierarchical character covariation (phylogenetic signal) in the distribution of traits among organisms. The distortion of hierarchical structure in character-state matrices can lead to errors in the estimation of phylogenetic relationships and inconsistency of methods of phylogenetic inference. Examination of trees distorted by long-branch attraction will not reveal the identities of problematic taxa, in part because the distortion can mask long branches by reducing inferred branch lengths and through errors in branching order. Here we present a simple method for the detection of taxa whose placement in evolutionary trees is made difficult by the effects of long-branch attraction. The method is an extension of a tree-independent conceptual framework of phylogenetic data exploration (RASA). Taxa that are likely to attract are revealed because long branches leave distinct footprints in the distribution of character states among taxa, and these traces can be directly observed in the error structure of the RASA regression. Problematic taxa are identified using a new diagnostic plot called the taxon variance plot, in which the apparent cladistic and phenetic variances contributed by individual taxa are compared. The procedure for identifying long edges employs algorithms solved in polynomial time and can be applied to morphological, molecular, and mixed characters. The efficacy of the method is demonstrated using simulated evolution and empirical evidence of long branches in a set of recently published sequences. We show that the accuracy of evolutionary trees can be improved by detecting and combating the potentially misleading influences of long-branch taxa.     

Adequacy of numerical taxonomic methods: Further experiments using simulated data

The adequacy of various phenetic and phylogenetic estimation methods was evaluated using simulated data sets. Two parsimony programs were used to construct maximum parsimony trees (WAGNER 78 and HENNIG 86). The CAFCA program was used to perform group-compatibility analysis. Four UPGMA clustering strategies were employed. The simulation model GENESIS was used to generate data sets under different evolutionary conditions. The effects of input parameters and tree properties on the accuracy of the estimated trees were evaluated. UPGMA based on product moment correlations of unstandardized characters appeared to perform best, under all evolutionary conditions tested. The effect of input parameters on the accuracy was not very significant. Among the tree statistics the stemminess of the true tree appeared to be the most important estimator of accuracy.     

Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family Pontederiaceae

Most plant phylogenetic inference has used DNA sequence data from the plastid genome. This genome represents a single genealogical sample with no recombination among genes, potentially limiting the resolution of evolutionary relationships in some contexts. In contrast, nuclear DNA is inherently more difficult to employ for phylogeny reconstruction because major mutational events in the genome, including polyploidization, gene duplication, and gene extinction can result in homologous gene copies that are difficult to identify as orthologs or paralogs. Gene tree parsimony (GTP) can be used to infer the rooted species tree by fitting gene genealogies to species trees while simultaneously minimizing the estimated number of duplications needed to reconcile conflicts among them. Here, we use GTP for five nuclear gene families and a previously published plastid data set to reconstruct the phylogenetic backbone of the aquatic plant family Pontederiaceae. Plastid-based phylogenetic studies strongly supported extensive paraphyly of Eichhornia (one of the four major genera) but also depicted considerable ambiguity concerning the true root placement for the family. Our results indicate that species trees inferred from the nuclear genes (alone and in combination with the plastid data) are highly congruent with gene trees inferred from plastid data alone. Consideration of optimal and suboptimal gene tree reconciliations place the root of the family at (or near) a branch leading to the rare and locally restricted E. meyeri. We also explore methods to incorporate uncertainty in individual gene trees during reconciliation by considering their individual bootstrap profiles and relate inferred excesses of gene duplication events on individual branches to whole-genome duplication events inferred for the same branches. Our study improves understanding of the phylogenetic history of Pontederiaceae and also demonstrates the utility of GTP for phylogenetic analysis.     

Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives

To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based "supergene" approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred.