Common Methods for Phylogenetic Tree Construction and Their Implementation in R.

A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing phylogenetic trees, including distance methods, maximum parsimony, maximum likelihood, Bayesian inference, and tree-integration methods (supermatrix and supertree). Here we discuss the advantages, shortcomings, and applications of each method and offer relevant codes to construct phylogenetic trees from molecular data using packages and algorithms in R. This review aims to provide comprehensive guidance and reference for researchers seeking to construct phylogenetic trees while also promoting further development and innovation in this field. By offering a clear and concise overview of the different methods available, we hope to enable researchers to select the most appropriate approach for their specific research questions and datasets.

DNA Barcoding of Invasive Terrestrial Plant Species in India.

Invasive plants are known to cause biodiversity loss and pose a major risk to human health and environment. Identification of invasive plants and distinguishing them from native species has been relied on morphological examination. Stringent requirement of floral characters and decreasing number of expert taxonomists are making conventional morphology-based identification system tedious and resource-intensive. DNA barcoding may help in quick identification of invasive species if distinct sequence divergence pattern at various taxonomic levels is observed. The present work evaluates the utility of four molecular markers; rbcL, matK, their combination (rbcL + matK), and psbA-trnH for identification of 37 invasive plant species from India and also in distinguishing them from 97 native species. A psbA-trnH locus was found to be of restricted utility in this work as it was represented by the members of a single family. A hierarchical increase in K2P mean divergence across different taxonomic levels was found to be the maximum for matK alone followed by rbcL + matK and rbcL alone, respectively. NJ clustering analysis, however, confirmed the suitability of combined locus (rbcL + matK) over individual rbcL and matK as the DNA barcode. RbcL showed the lowest resolution power among the three markers studied. MatK exhibited much better performance compared to rbcL alone in identifying most of the species accurately although it failed to show monophyly of genus Dinebra. Two families; Asteraceae and Poaceae, remained polyphyletic in the trees constructed by all three markers. Combined locus (rbcL + matK) was found to be the most suitable marker as it raised the resolution power of both the markers and could identify more than 90% of genera correctly. Phylogenetic tree constructed by Maximum-Parsimony method using combined locus as a molecular marker exhibited the best resolution, thus, supporting the significance of two-locus combination of rbcL + matK for barcoding invasive plant species from India. Present study contributes to the global barcode data of invasive plant species by adding fifty-one new sequences to it. Effective barcoding of additional number of native as well as invasive plant species from India is possible using this dual locus if it is combined with one or more new molecular plastid markers. Expansion of barcode database with a focus on barcode performance optimisation to improve discrimination ability at species level can be undertaken in future.

Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph.

In many situations, it would be useful to know not just the best phylogenetic tree for a given data set, but the collection of high-quality trees. This goal is typically addressed using Bayesian techniques, however, current Bayesian methods do not scale to large data sets. Furthermore, for large data sets with relatively low signal one cannot even store every good tree individually, especially when the trees are required to be bifurcating. In this paper, we develop a novel object called the "history subpartition directed acyclic graph" (or "history sDAG" for short) that compactly represents an ensemble of trees with labels (e.g. ancestral sequences) mapped onto the internal nodes. The history sDAG can be built efficiently and can also be efficiently trimmed to only represent maximally parsimonious trees. We show that the history sDAG allows us to find many additional equally parsimonious trees, extending combinatorially beyond the ensemble used to construct it. We argue that this object could be useful as the "skeleton" of a more complete uncertainty quantification.

All quiet on the western front? The evolutionary history of monogeneans (Dactylogyridae: Cichlidogyrus, Onchobdella) infecting a West and Central African tribe of cichlid fishes (Chromidotilapiini).

Owing to the largely unexplored diversity of metazoan parasites, their speciation mechanisms and the circumstances under which such speciation occurs - in allopatry or sympatry - remain vastly understudied. Cichlids and their monogenean flatworm parasites have previously served as a study system for macroevolutionary processes, e.g., for the role of East African host radiations on parasite communities. Here, we investigate the diversity and evolution of the poorly explored monogeneans infecting a West and Central African lineage of cichlid fishes: Chromidotilapiini, which is the most species-rich tribe of cichlids in this region. We screened gills of 149 host specimens (27 species) from natural history collections and measured systematically informative characters of the sclerotised attachment and reproductive organs of the parasites. Ten monogenean species (Dactylogyridae: Cichlidogyrus and Onchobdella) were found, eight of which are newly described and one redescribed herein. The phylogenetic positions of chromidotilapiines-infecting species of Cichlidogyrus were inferred through a parsimony analysis of the morphological characters. Furthermore, we employed machine learning algorithms to detect morphological features associated with the main lineages of Cichlidogyrus. Although the results of these experimental algorithms remain inconclusive, the parsimony analysis indicates that West and Central African lineages of Cichlidogyrus and Onchobdella are monophyletic, unlike the paraphyletic host lineages. Several instances of host sharing suggest occurrences of intra-host speciation (sympatry) and host switching (allopatry). Some morphological variation was recorded that may also indicate the presence of species complexes. We conclude that collection material can provide important insights on parasite evolution despite the lack of well-preserved DNA material.

Title: À l'Ouest, rien de nouveau ? L'histoire évolutive des monogènes (Dactylogyridae : Cichlidogyrus, Onchobdella) infectant une tribu de poissons cichlidés (Chromidotilapiini) d'Afrique occidentale et centrale. Abstract: En raison de la nature largement inexplorée de la diversité des parasites métazoaires, leurs mécanismes de spéciation et les circonstances dans lesquelles cette spéciation se produit­allopatrie ou sympatrie­restent très peu étudiés. Les cichlidés et leurs parasites Plathelminthes monogènes ont déjà servi de modèle pour l'étude des processus macro-évolutifs, par exemple pour le rôle des radiations d'hôtes de l'Afrique de l'Est sur les communautés de parasites. Ici, nous étudions la diversité et l'évolution des monogènes peu étudiées qui infestent une lignée de poissons cichlidés d'Afrique occidentale et centrale : les Chromidotilapiini, qui est la tribu de cichlidés la plus riche en espèces dans cette région. Nous avons examiné les branchies de 149 spécimens hôtes (27 espèces) provenant de musées d'histoire naturelle et mesuré systématiquement les caractères informatifs des pièces sclérifiées du hapteur et des organes copulateurs des parasites. Dix espèces de monogènes (Dactylogyridae : Cichlidogyrus et Onchobdella) ont été trouvées ; huit sont nouvelles pour la science et une est redécrite. Les positions phylogénétiques des espèces de Cichlidogyrus infectant les chromidotilapiines ont été déduites par une analyse de parcimonie des caractères morphologiques. En outre, nous avons utilisé des algorithmes d'apprentissage automatique pour détecter les caractéristiques morphologiques associées aux principales lignées de Cichlidogyrus. Bien que les résultats de ces algorithmes expérimentaux restent peu concluants, l'analyse de parcimonie indique que les lignées de Cichlidogyrus et d'Onchobdella de l'Afrique de l'Ouest et Central sont monophylétiques, contrairement aux lignées d'hôtes qui sont paraphylétiques. Plusieurs cas de partage d'hôtes suggèrent des occurrences de spéciation synxénique (sympatrie) et de changement d'hôte (allopatrie). Certaines variations morphologiques ont été enregistrées et peuvent également indiquer la présence de complexes d'espèces. Nous concluons donc que le matériel de collection peut fournir des informations importantes sur l'évolution des parasites malgré le manque d'ADN exploitable.

Maximum parsimony reconciliation in the DTLOR model.

BACKGROUND: Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of reconciliation, a gene family may enter the species tree from the outside. Moreover, within the genome, genes are often rearranged, causing them to move to new syntenic regions. RESULTS: We extend the DTL model to account for two events that commonly arise in the evolution of microbes: origin of a gene from outside the sampled species tree and rearrangement of gene syntenic regions. We describe an efficient algorithm for maximum parsimony reconciliation in this new DTLOR model and then show how it can be extended to account for non-binary gene trees to handle uncertainty in gene tree topologies. Finally, we describe preliminary experimental results from the integration of our algorithm into the existing xenoGI tool for reconstructing the histories of genomic islands in closely related bacteria. CONCLUSIONS: Reconciliation in the DTLOR model can offer new insights into the evolution of microbes that is not currently possible under the DTL model.

The Complexity and Phylogenetic Continuity of Laughter and Smiles in Hominids.

Laughter and smiles are often, but not always, associated with positive affect. These expressions of humans help to promote social relationships as well as the development of cognitive and socio-emotional skills and they may have a positive impact on health and well-being, hereby covering a selection of fitness-relevant benefits. Both laughter and smiles of positive affect also occur early in human development and across cultures, suggesting deep roots in human biology. The present work provides an evolutionary reconstruction of the evolution of human laughter and smiles of positive affect in form and function, based on the principle of maximum parsimony. According to the Complexity and Continuity Hypothesis, human laughter and smiles of positive affect must have evolved within the context of play from ancestral species. Furthermore, ancestral ape laughter and their open-mouth faces must already have been complex in form and function and changed over time via categorically different phylogenetic pathways to become characteristic, effective, and pervasive behaviors of everyday social interactions in humans.

Bipartite molecular approach for species delimitation and resolving cryptic speciation of Exobasidium vexans within the Exobasidium genus.

Exobasidium vexans, a basidiomycete pathogen, is the causal organism of blister blight disease in tea. The molecular identification of the pathogen remains a challenge due to the limited availability of genomic data in sequence repositories and cryptic speciation within its genus Exobasidium. In this study, the nuclear internal transcribed spacer rDNA region (ITS) based DNA barcode was developed for E. vexans, to address the problem of molecular identification within the background of cryptic speciation. The isolation of E. vexans strain was confirmed through morphological studies followed by molecular identification utilizing the developed ITS barcode. Phylogenetic analysis based on Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) confirmed the molecular identification of the pathogen as E. vexans strain. Further, BI analysis using BEAST mediated the estimation of the divergence time and evolutionary relationship of E. vexans within genus Exobasidium. The speciation process followed the Yule diversification model wherein the genus Exobasidium is approximated to have diverged in the Paleozoic era. The study thus sheds light on the molecular barcode-based species delimitation and evolutionary relationship of E. vexans within its genus Exobasidium.

Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants?

Whilst substantial research effort has been placed on understanding the interactions of plant proteins with their molecular partners, relatively few studies in plants - by contrast to work in other organisms - address how these interactions evolve. It is thought that ancestral proteins were more promiscuous than modern proteins and that specificity often evolved following gene duplication and subsequent functional refining. However, ancestral protein resurrection studies have found that some modern proteins have evolved de novo from ancestors lacking those functions. Intriguingly, the new interactions evolved as a consequence of just a few mutations and, as such, acquisition of new functions appears to be neither difficult nor rare, however, only a few of them are incorporated into biological processes before they are lost to subsequent mutations. Here, we detail the approach of ancestral sequence reconstruction (ASR), providing a primer to reconstruct the sequence of an ancestral gene. We will present case studies from a range of different eukaryotes before discussing the few instances where ancestral reconstructions have been used in plants. As ASR is used to dig into the remote evolutionary past, we will also present some alternative genetic approaches to investigate molecular evolution on shorter timescales. We argue that the study of plant secondary metabolism is particularly well suited for ancestral reconstruction studies. Indeed, its ancient evolutionary roots and highly diverse landscape provide an ideal context in which to address the focal issue around the emergence of evolutionary novelties and how this affects the chemical diversification of plant metabolism.

Assessing topological congruence among concatenation-based phylogenomic approaches in empirical datasets.

Assessing the effect of methodological decisions on the resulting hypotheses is critical in phylogenetics. Recent studies have focused on evaluating how model selection, orthology definition and confounding factors affect phylogenomic results. Here, we compare the results of three concatenated phylogenetic methods (Maximum Likelihood, ML; Bayesian Inference, BI; Maximum Parsimony, MP) in 157 empirical phylogenomic datasets. The resulting trees were very similar, with 96.7% of all nodes shared between BI and ML (90.6% for ML-MP and 89.1% for BI-MP). Differing nodes were predominantly those of lower support. The main conclusions of most of the studies agreed for the three phylogenetic methods and the discordance involved nodes considered as recalcitrant problems in systematics. The differences between methods were proportionally larger in datasets that analyze the relationships at higher taxonomic levels (particularly phyla and kingdoms), and independent of the number of characters included in the datasets. Note: a spanish version of this article is available in the Supplementary material (Supplementary material online).

Comparison of Different Reweighting Approaches for the Calculation of Conformational Variability of Macromolecules from Molecular Simulations.

Conformational variability and heterogeneity are crucial determinants of the function of biological macromolecules. The possibility of accessing this information experimentally suffers from severe under-determination of the problem, since there are a few experimental observables to be accounted for by a (potentially) infinite number of available conformational states. Several computational methods have been proposed over the years in order to circumvent this theoretically insurmountable obstacle. A large share of these strategies is based on reweighting an initial conformational ensemble which arises from, for example, molecular simulations of different qualities and levels of theory. In this work, we compare the outcome of three reweighting approaches based on radically different views of the conformational heterogeneity problem, namely Maximum Entropy, Maximum Parsimony and Maximum Occurrence, and we do so using the same experimental data. In this comparison we find both expected as well as unexpected similarities.

Most Parsimonious Likelihood Exhibits Multiple Optima for Compatible Characters.

Maximum likelihood estimators are a popular method for scoring phylogenetic trees to best explain the evolutionary histories of biomolecular sequences. In 1994, Steel showed that, given an incompatible set of binary characters and a fixed tree topology, there exist multiple sets of branch lengths that are optima of the maximum average likelihood estimator. Since parsimony techniques-another popular method of scoring evolutionary trees-tend to exhibit favorable behavior on data compatible with the tree, Steel asked if the same is true for likelihood estimators, or if multiple optima can occur for compatible sequences. We show that, despite exhibiting behavior similar to parsimony, multiple local optima can occur for compatible characters for the most parsimonious likelihood estimator. We caution that thorough understanding of likelihood criteria is necessary before they are used to analyze biological data.

Osteological Re-Assessment and Taxonomic Revision of "Tanius laiyangensis" (Ornithischia: Hadrosauroidea) from the Upper Cretaceous of Shandong, China.

Tanius is the earliest named ornithischian genus from China. Since 1929, three species of this genus, namely T. sinensis (the type species), "T. chingkankouensis" and "T. laiyangensis", have been reported based on remains from the Wangshi Group of Shandong, China, and were previously recognized as hadrosaurines. Following the recent achievement of consensus on the phylogenetic placement of T. sinensis outside Hadrosauridae, the assignments of the "T. chingkankouensis" and "T. laiyangensis" material of hadrosaurid origin to the genus Tanius become problematic. Related taxonomic issues of "T. laiyangensis" therefore need re-appraisals. Here, we provide an overall taxonomic revision of "T. laiyangensis" from the Jingangkou Formation of northeast Shandong, by means of approaches of comparative anatomy, phylogeny and geometric morphometrics. Our osteological comparisons confirm the hadrosaurine affinity of "T. laiyangensis", given the presence of a suite of characters largely typical of Hadrosaurinae in the single specimen (i.e., a nearly complete sacrum and a partial right ilium), including a dorsoventrally narrow central plate of the ilium with the depth/length ratio <0.80. In the proposed phylogenetic framework, "T. laiyangensis" is inferred to be a member of Kritosaurini within Hadrosaurinae, as the sister taxon to Secernosaurus koerneri. The relative warp analysis on the lateral outline of the supraacetabular process also reveals a close resemblance of shape between the two species. Based on these different lines of evidence and considering no identification of any diagnostic characters from the specimen, we argue that the "T. laiyangensis" material comes from an indeterminate kritosaurin hadrosaurine in Asia. Anat Rec, 303:790-800, 2020. © 2019 Wiley Periodicals, Inc.

An efficient exact algorithm for computing all pairwise distances between reconciliations in the duplication-transfer-loss model.

BACKGROUND: Maximum parsimony reconciliation in the duplication-transfer-loss model is widely used in studying the evolutionary histories of genes and species and in studying coevolution of parasites and their hosts and pairs of symbionts. While efficient algorithms are known for finding maximum parsimony reconciliations, the number of reconciliations can grow exponentially in the size of the trees. An understanding of the space of maximum parsimony reconciliations is necessary to determine whether a single reconciliation can adequately represent the space or whether multiple representative reconciliations are needed. RESULTS: We show that for any instance of the reconciliation problem, the distribution of pairwise distances can be computed exactly by an efficient polynomial-time algorithm with respect to several different distance metrics. We describe the algorithm, analyze its asymptotic worst-case running time, and demonstrate its utility and viability on a large biological dataset. CONCLUSIONS: This result provides new insights into the structure of the space of maximum parsimony reconciliations. These insights are likely to be useful in the wide range of applications that employ reconciliation methods.

Hierarchical clustering of maximum parsimony reconciliations.

BACKGROUND: Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and species and genes. While efficient algorithms are known for finding maximum parsimony reconciliations, the number of such reconciliations can be exponential in the size of the trees. Since these reconciliations can differ substantially from one another, making inferences from any one reconciliation may lead to conclusions that are not supported, or may even be contradicted, by other maximum parsimony reconciliations. Therefore, there is a need to find small sets of best representative reconciliations when the space of solutions is large and diverse. RESULTS: We provide a general framework for hierarchical clustering the space of maximum parsimony reconciliations. We demonstrate this framework for two specific linkage criteria, one that seeks to maximize the average support of the events found in the reconciliations in each cluster and the other that seeks to minimize the distance between reconciliations in each cluster. We analyze the asymptotic worst-case running times and provide experimental results that demonstrate the viability and utility of this approach. CONCLUSIONS: The hierarchical clustering algorithm method proposed here provides a new approach to find a set of representative reconciliations in the potentially vast and diverse space of maximum parsimony reconciliations.

Quantifying the extent of morphological homoplasy: A phylogenetic analysis of 490 characters in Drosophila.

Homoplasy is a fundamental phenomenon in evolutionary biology but an appraisal of its extent at the morphological level is still lacking. Here, we analyzed the evolution of 490 morphological characters conceptualized among 56 drosophilid species. We found that two thirds of morphological changes were homoplastic and that the level of homoplasy depended on the stage of development and the type of the organ, with the adult terminalia being the least homoplastic. In spite of its predominance at the character change level, homoplasy accounts for only ∼13% of between species similarities in pairwise comparisons. These results provide empirical insights on the limits of morphological changes and the frequency of recurrent evolution.

On the uniqueness of the maximum parsimony tree for data with up to two substitutions: An extension of the classic Buneman theorem in phylogenetics.

One of the main aims of phylogenetics is the reconstruction of the correct evolutionary tree when data concerning the underlying species set are given. These data typically come in the form of DNA, RNA or protein alignments, which consist of various characters (also often referred to as sites). Often, however, tree reconstruction methods based on criteria like maximum parsimony may fail to provide a unique tree for a given dataset, or, even worse, reconstruct the 'wrong' tree (i.e. a tree that differs from the one that generated the data). On the other hand it has long been known that if the alignment consists of all the characters that correspond to edges of a particular tree, i.e. they all require exactly k=1 substitution to be realized on that tree, then this tree will be recovered by maximum parsimony methods. This is based on Buneman's theorem in mathematical phylogenetics. It is the goal of the present manuscript to extend this classic result as follows: We prove that if an alignment consists of all characters that require exactly k=2 substitutions on a particular tree, this tree will always be the unique maximum parsimony tree (and we also show that this can be generalized to characters which require at most k=2 substitutions). In particular, this also proves a conjecture based on a recently published observation by Goloboff et al. affirmatively for the special case of k=2.

A Third Strike Against Perfect Phylogeny.

Perfect phylogenies are fundamental in the study of evolutionary trees because they capture the situation when each evolutionary trait emerges only once in history; if such events are believed to be rare, then by Occam's Razor such parsimonious trees are preferable as a hypothesis of evolution. A classical result states that 2-state characters permit a perfect phylogeny precisely if each subset of 2 characters permits one. More recently, it was shown that for 3-state characters the same property holds but for size-3 subsets. A long-standing open problem asked whether such a constant exists for each number of states. More precisely, it has been conjectured that for any fixed number of states $r$ there exists a constant $f(r)$ such that a set of $r$-state characters $C$ has a perfect phylogeny if and only if every subset of at most $f(r)$ characters has a perfect phylogeny. Informally, the conjecture states that checking fixed-size subsets of characters is enough to correctly determine whether input data permits a perfect phylogeny, irrespective of the number of characters in the input. In this article, we show that this conjecture is false. In particular, we show that for any constant $t$, there exists a set $C$ of $8$-state characters such that $C$ has no perfect phylogeny, but there exists a perfect phylogeny for every subset of at most $t$ characters. Moreover, there already exists a perfect phylogeny when ignoring just one of the characters, independent of which character you ignore. This negative result complements the two negative results ("strikes") of Bodlaender et al. (1992,2000). We reflect on the consequences of this third strike, pointing out that while it does close off some routes for efficient algorithm development, many others remain open.

Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony.

In phylogenetic studies, biologists often wish to estimate the ancestral discrete character state at an interior vertex v of an evolutionary tree T from the states that are observed at the leaves of the tree. A simple and fast estimation method-maximum parsimony-takes the ancestral state at v to be any state that minimises the number of state changes in T required to explain its evolution on T. In this paper, we investigate the reconstruction accuracy of this estimation method further, under a simple symmetric model of state change, and obtain a number of new results, both for 2-state characters, and r-state characters ([Formula: see text]). Our results rely on establishing new identities and inequalities, based on a coupling argument that involves a simpler 'coin toss' approach to ancestral state reconstruction.

Statistical Inconsistency of Maximum Parsimony for k-Tuple-Site Data.

One of the main aims of phylogenetics is to reconstruct the "Tree of Life." In this respect, different methods and criteria are used to analyze DNA sequences of different species and to compare them in order to derive the evolutionary relationships of these species. Maximum parsimony is one such criterion for tree reconstruction, and it is the one which we will use in this paper. However, it is well known that tree reconstruction methods can lead to wrong relationship estimates. One typical problem of maximum parsimony is long branch attraction, which can lead to statistical inconsistency. In this work, we will consider a blockwise approach to alignment analysis, namely the so-called k-tuple analyses. For four taxa, it has already been shown that k-tuple-based analyses are statistically inconsistent if and only if the standard character-based (site-based) analyses are statistically inconsistent. So, in the four-taxon case, going from individual sites to k-tuples does not lead to any improvement. However, real biological analyses often consider more than only four taxa. Therefore, we analyze the case of five taxa for 2- and 3-tuple-site data and consider alphabets with two and four elements. We show that the equivalence of single-site data and k-tuple-site data then no longer holds. Even so, we can show that maximum parsimony is statistically inconsistent for k-tuple-site data and five taxa.

Finding a most parsimonious or likely tree in a network with respect to an alignment.

Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant phylogenetic signals that were not present in the input. Here we show that, given a multiple alignment A for a set of taxa X and a rooted phylogenetic network N whose leaves are labelled by X, it is NP-hard to locate a most parsimonious phylogenetic tree displayed by N (with respect to A) even when the level of N-the maximum number of reticulation nodes within a biconnected component-is 1 and A contains only 2 distinct states. (If, additionally, gaps are allowed the problem becomes APX-hard.) We also show that under the same conditions, and assuming a simple binary symmetric model of character evolution, finding a most likely tree displayed by the network is NP-hard. These negative results contrast with earlier work on parsimony in which it is shown that if A consists of a single column the problem is fixed parameter tractable in the level. We conclude with a discussion of why, despite the NP-hardness, both the parsimony and likelihood problem can likely be well-solved in practice.