Phylogenetic Problems Research Articles

Gentrius: Generating Trees Compatible With a Set of Unrooted Subtrees and its Application to Phylogenetic Terraces.

For a set of binary unrooted subtrees generating all binary unrooted trees compatible with them, i.e. generating their stand, is one of the classical problems in phylogenetics. Here, we introduce Gentrius-an efficient algorithm to tackle this task. The algorithm has a direct application in practice. Namely, Gentrius generates phylogenetic terraces-topologically distinct, equally scoring trees due to missing data. Despite stand generation being computationally intractable, we showed on simulated and biological datasets that Gentrius generates stands with millions of trees in feasible time. We exemplify that depending on the distribution of missing data across species and loci and the inferred phylogeny, the number of equally optimal terrace trees varies tremendously. The strict consensus tree computed from them displays all the branches unaffected by the pattern of missing data. Thus, by solving the problem of stand generation, in practice Gentrius provides an important systematic assessment of phylogenetic trees inferred from incomplete data. Furthermore, Gentrius can aid theoretical research by fostering understanding of tree space structure imposed by missing data.

Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations.

In both statistical genetics and phylogenetics, a major goal is to identify correlations between genetic loci or other aspects of the phenotype or environment and a focal trait. In these 2 fields, there are sophisticated but disparate statistical traditions aimed at these tasks. The disconnect between their respective approaches is becoming untenable as questions in medicine, conservation biology, and evolutionary biology increasingly rely on integrating data from within and among species, and once-clear conceptual divisions are becoming increasingly blurred. To help bridge this divide, we lay out a general model describing the covariance between the genetic contributions to the quantitative phenotypes of different individuals. Taking this approach shows that standard models in both statistical genetics (e.g., genome-wide association studies; GWAS) and phylogenetic comparative biology (e.g., phylogenetic regression) can be interpreted as special cases of this more general quantitative-genetic model. The fact that these models share the same core architecture means that we can build a unified understanding of the strengths and limitations of different methods for controlling for genetic structure when testing for associations. We develop intuition for why and when spurious correlations may occur analytically and conduct population-genetic and phylogenetic simulations of quantitative traits. The structural similarity of problems in statistical genetics and phylogenetics enables us to take methodological advances from one field and apply them in the other. We demonstrate by showing how a standard GWAS technique-including both the genetic relatedness matrix (GRM) as well as its leading eigenvectors, corresponding to the principal components of the genotype matrix, in a regression model-can mitigate spurious correlations in phylogenetic analyses. As a case study, we re-examine an analysis testing for coevolution of expression levels between genes across a fungal phylogeny and show that including eigenvectors of the covariance matrix as covariates decreases the false positive rate while simultaneously increasing the true positive rate. More generally, this work provides a foundation for more integrative approaches for understanding the genetic architecture of phenotypes and how evolutionary processes shape it.

Reliable estimation of tree branch lengths using deep neural networks.

A phylogenetic tree represents hypothesized evolutionary history for a set of taxa. Besides the branching patterns (i.e., tree topology), phylogenies contain information about the evolutionary distances (i.e. branch lengths) between all taxa in the tree, which include extant taxa (external nodes) and their last common ancestors (internal nodes). During phylogenetic tree inference, the branch lengths are typically co-estimated along with other phylogenetic parameters during tree topology space exploration. There are well-known regions of the branch length parameter space where accurate estimation of phylogenetic trees is especially difficult. Several novel studies have recently demonstrated that machine learning approaches have the potential to help solve phylogenetic problems with greater accuracy and computational efficiency. In this study, as a proof of concept, we sought to explore the possibility of machine learning models to predict branch lengths. To that end, we designed several deep learning frameworks to estimate branch lengths on fixed tree topologies from multiple sequence alignments or its representations. Our results show that deep learning methods can exhibit superior performance in some difficult regions of branch length parameter space. For example, in contrast to maximum likelihood inference, which is typically used for estimating branch lengths, deep learning methods are more efficient and accurate. In general, we find that our neural networks achieve similar accuracy to a Bayesian approach and are the best-performing methods when inferring long branches that are associated with distantly related taxa. Together, our findings represent a next step toward accurate, fast, and reliable phylogenetic inference with machine learning approaches.

Phylogenetic and Comparative Genomics Study of Papilionidae Based on Mitochondrial Genomes.

Most species of Papilionidae are large and beautiful ornamental butterflies. They are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology but present numerous unresolved phylogenetic problems. Complete mitochondrial genomes (mitogenomes) have been widely used in phylogenetic studies of butterflies, but mitogenome knowledge within the family Papilionidae is limited, and its phylogeny is far from resolved. In this study, we first report the mitogenome of Byasa confusa from the subfamily Papilioninae of Papilionidae. The mitogenome of B. confusa is 15,135 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an AT-rich control region (CR), closely mirroring the genomic structure observed in related butterfly species. Comparative analysis of 77 Papilionidae mitogenomes shows gene composition and order to be identical to that of an ancestral insect, and the AT bias, Ka/Ks, and relative synonymous codon usage (RSCU) are all consistent with that of other reported butterfly mitogenomes. We conducted phylogenetic analyses using maximum-likelihood (ML) and Bayesian-inference (BI) methods, with 77 Papilionidae species as ingroups and two species of Nymphalidae and Lycaenidae as outgroups. The phylogenetic analysis indicated that B. confusa were clustered within Byasa. The phylogenetic trees show the monophyly of the subfamily Papilioninae and the tribes Leptocircini, Papilionini, and Troidini. The data supported the following relationships in tribe level on Papilioninae: (((Troidini + Papilionini) + Teinopalpini) + Leptocircini). The divergence time analysis suggests that Papilionidae originated in the late Creataceous. Overall, utilizing the largest number of Papilionidae mitogenomes sequenced to date, with the current first exploration in a phylogenetic analysis on Papilionidae (including four subfamilies), this study comprehensively reveals the mitogenome characteristics and mitogenome-based phylogeny, providing information for further studies on the mitogenome, phylogeny, evolution, and taxonomic revision of the Papilionidae family.

Relationships Among the Bryophytes and Vascular Plants: A Case Study in Deep-Time Reconstruction

Relationships of the three bryophyte lineages (liverworts, mosses, and hornworts) to vascular plants is a pivotal question in the study of the origin and evolution of land plants. In recent decades, this question has been subjected to intense phylogenetic analyses using morphological characters, multigene DNA sequences, and genome structural characters. A tentative consensus, reached ten years ago, suggested that bryophytes are a paraphyletic group, with liverworts being sister to all other land plants and hornworts being sister to vascular plants. However, several more recent nuclear phylogenomic studies have concluded that bryophytes represent a monophyletic group that is sister to vascular plants. A discussion is presented here on strengths and weaknesses of different types of characters (morphological traits, nucleotide sequences, and genome structural arrangements) and their suitability for resolving deep phylogenetic relationships. Moreover, several criteria for credible phylogenetic reconstruction are proposed. Strong statistical support for reconstructed relationships should be derived from high-quality, independent characters selected for suitability to the particular question being addressed. The relationships inferred in a study should be congruent with those from as many other lines of phylogenetic evidence as possible. Any incongruities should be explicable by well-understood biological mechanisms. It is concluded that the relationships of the three bryophyte lineages to vascular plants should currently be viewed as unresolved. This is a difficult phylogenetic problem; the land plants underwent a rapid radiation a long time ago. Yet, further exploration of analytical methods and careful choice of characters should lead to the eventual elucidation of diversification patterns among early land plants.

Macroecological correlates of Darwinian shortfalls across terrestrial vertebrates.

Most described species have not been explicitly included in phylogenetic trees-a problem named the Darwinian shortfall-owing to a lack of molecular and/or morphological data, thus hampering the explicit incorporation of evolution into large-scale biodiversity analyses. We investigate potential drivers of the Darwinian shortfall in tetrapods, a group in which at least one-third of described species still lack phylogenetic data, thus necessitating the imputation of their evolutionary relationships in fully sampled phylogenies. We show that the number of preserved specimens in scientific collections is the main driver of phylogenetic knowledge accumulation, highlighting the major role of biological collections in unveiling novel biodiversity data and the importance of continued sampling efforts to reduce knowledge gaps. Additionally, large-bodied and wide-ranged species, as well as terrestrial and aquatic amphibians and reptiles, are phylogenetically better known. Future efforts should prioritize phylogenetic research on organisms that are narrow-ranged, small-bodied and underrepresented in scientific collections, such as fossorial species. Addressing the Darwinian shortfall will be imperative for advancing our understanding of evolutionary drivers shaping biodiversity patterns and implementing comprehensive conservation strategies.

The genus Syllis Savigny in Lamarck, 1818 (Annelida: Syllidae: Syllinae) from Australia (Fourth part)

Syllis Savigny in Lamarck, 1818, the type genus of Syllidae, is the largest and most diverse within the family. This genus presents many taxonomic, biogeographic, and phylogenetic problems due mainly to the lack of molecular data and morphological synapomorphies for many of the species, but also due to poor or inadequate descriptions. In order to improve our understanding of the genus, we have undertaken a morphological revision of Australian species, based on type material and material collected over years by the Australian Museum. This is the fourth paper dealing with this genus. Nine species are herein described, of which five are new records for Australia: Syllis ergeni Çinar, 2005; S. patersoni Soto, San Martín & Lucas, 2020; S. valida Grube, 1857; S. violacea Grube, 1870; and S. ypsiloides Aguado, San Martín & ten Hove, 2008. Three species already known from Australia are redescribed: S. heronislandensis (Hartmann-Schröder, 1991) n. comb.; S. parturiens Haswell, 1920; and S. cf. schmardiana Haswell, 1886. Syllis gantheaumensis (Hartmann-Schröder, 1979) n. comb. is raised to species level, since it was originally described as a subspecies of Typosyllis filidentata Hartmann-Schröder, 1962. We include an addendum with a list of species already treated in the previous papers on this genus, as well as some new synonymies after revision of types: Typosyllis (Typosyllis) gerhardi Hartmann-Schröder, 1980 and T. (T.) guildertonensis Hartmann-Schröder, 1979, as synonymous of Syllis busseltonensis (Hartmann-Schröder, 1982); T. (T.) raygeorgei Hartmann-Schröder, 1979 as synonymous of S. hyalina Grube, 1863; T. (T.) rockinghamensis Hartmann-Schröder, 1983 and T. (T.) pseudopapillata Hartmann-Schröder, 1991 as synonymous of S. pharobroomensis (Hartmann-Schröder, 1979). We also include a discussion of the genus and a key to Australian species.

The tree-child network inference problem for line trees and the shortest common supersequence problem for permutation strings

One strategy for inference of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the trees. This approach capitalizes on exceptional tools available for inferring phylogenetic trees from biomolecular sequences. Since the vast space of phylogenetic networks poses difficulties in obtaining comprehensive sampling, the researchers switch their attention to inferring tree-child networks from multiple phylogenetic trees, where in a tree-child network each non-leaf node must have at least one child that is an indegree-one node. Three results are obtained in this work: (1) The shortest common supersequence problem remains NP-hard even for permutation strings. (2) Derived from the first result, the tree-child network inference problem is also established as NP-hard even for line trees (also known as caterpillar trees). (3) The parsimonious tree-child networks that display all the line trees are the same as those displaying all the binary trees and their hybridization number is Θ(n3) for n taxa.

Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region.

Equisetum is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. Equisetum is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails (Equisetum, Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in Equisetum remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of Equisetum, and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of Equisetum. The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of Equisetum plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes accD and ycf1 can be used as potential DNA barcodes for the identification and phylogeny of the genus Equisetum. Twelve photosynthesis-related genes were specifically selected in Equisetum. Comparative genomic analyses implied divergent evolutionary patterns between Equisetum and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between Equisetum and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between Equisetum species, and also provide genomic resources for the study of Equisetum systematics and evolution.

Learning From an Artificial Neural Network in Phylogenetics.

We show that an iterative ansatz of deep learning and human intelligence guided simplification may lead to surprisingly simple solutions for a difficult problem in phylogenetics. Distinguishing Farris and Felsenstein trees is a longstanding problem in phylogenetic tree reconstruction. The Artificial Neural Network F-zoneNN solves this problem for 4-taxon alignments evolved under the Jukes-Cantor model. It distinguishes between Farris and Felsenstein trees, but owing to its complexity, lacks transparency in its mechanism of discernment. Based on the simplification of F-zoneNN and alignment properties we constructed the function FarFelDiscerner. In contrast to F-zoneNN, FarFelDiscerner's decision process is understandable. Moreover, FarFelDiscerner is significantly simpler than F-zoneNN. Despite its simplicity this function infers the tree-type almost perfectly on noise-free data, and also performs well on simulated noisy alignments of finite length. We applied FarFelDiscerner to the historical Holometabola alignments where it places Strepsiptera with beetles, concordant with the current scientific view.

A new centrohelid heliozoan, Pterocystis polycristalepis sp. nov., and taxonomic and phylogenetic concerns within Pterista (Haptista: Centroplasthelida)

A new species of centrohelid heliozoans, Pterocystis polycristalepis sp. nov. (Pterocystidae), was examined using light and electron microscopy. The novel centrohelid is characterized by the presence of leaf-like spine-scales with a broad pedicel-like structure on the proximal part and many subparallel ribs on the lateral wing surface. The plate-scales are ovoid with medial tubular thickening and many subparallel ribs on the very extensive marginal rim. The closely related species Pterocystis striata has also been studied in detail using light and electron microscopy. Phylogenetic analysis of 18S rRNA gene sequences placed both species into a separate clade within Pterista. The closest morphologically characterized species to the new clade is Triangulopteris lacunata. The 18S rRNA sequence of Pseudoraphidiophrys veliformis was grouped within Pterista and found to be closely related to Pterocystis polycristalepis, Pterocystis striata, and Triangulopteris lacunata. Cyst-scales of various shapes, cell and cyst aggregations, syncytia, and a cell with a stalk were revealed in a clonal culture of P. veliformis. Analysis of the morphology and phylogenetic position of the studied species and other centrohelids revealed a large number of taxonomic and phylogenetic problems in Pterista.

A Phylogenetic and Taxonomic Revision of Discula theae-sinensis, the Causal Agents of Anthracnose on Camellia sinensis.

Tea (Camellia sinensis (L.) Kuntze) is one of the most important economic plants in China, and has many benefits for human health. Anthracnose is one of the most serious diseases of tea in China, and control of the fungus is important since most Chinese cultivars are susceptible to it. The agent of tea anthracnose was initially described as Gloeosporium theae-sinensis I. Miyake in Japan, which was later transferred to Discula, but this taxonomic position remains problematic. To shed light on these taxonomic and phylogenetic issues, the tea anthracnose pathogens were re-studied. Combining the morphological characteristics and a multigene phylogenetic analysis of nrITS, nrLSU, rpb2, and tef1 sequence data, a new genus Sinodiscula was proposed to accommodate the causal fungi of tea anthracnose, including a new species Sinodiscula camellicola and a new combination Sinodiscula theae-sinensis. Furthermore, the pathogenicity of the pathogens was determined according to Koch's postulates. This study thoroughly resolves the long-standing taxonomic and phylogenetic problems of the tea anthracnose pathogens.

Ordovician origin and subsequent diversification of the brown algae

Brown algae are the only group of heterokont protists exhibiting complex multicellularity. Since their origin, brown algae have adapted to various marine habitats, evolving diverse thallus morphologies and gamete types. However, the evolutionary processes behind these transitions remain unclear due to a lack of a robust phylogenetic framework and problems with time estimation. To address these issues, we employed plastid genome data from 138 species, including heterokont algae, red algae, and other red-derived algae. Based on a robust phylogeny and new interpretations of algal fossils, we estimated the geological times for brown algal origin and diversification. The results reveal that brown algae first evolved true multicellularity, with plasmodesmata and reproductive cell differentiation, during the late Ordovician Period (ca. 450 Ma), coinciding with a major diversification of marine fauna (the Great Ordovician Biodiversification Event) and a proliferation of multicellular green algae. Despite its early Paleozoic origin, the diversification of major orders within this brown algal clade accelerated only during the Mesozoic Era, coincident with both Pangea rifting and the diversification of other heterokont algae (e.g., diatoms), coccolithophores, and dinoflagellates, with their red algal-derived plastids. The transition from ancestral isogamy to oogamy was followed by three simultaneous reappearances of isogamy during the Cretaceous Period. These are concordant with a positive character correlation between parthenogenesis and isogamy. Our new brown algal timeline, combined with a knowledge of past environmental conditions, shed new light on brown algal diversification and the intertwined evolution of multicellularity and sexual reproduction.

Barkodlama Bölgesi Olarak Potentilla L. Cinsinde psbA-trnH IGS Sekanslarının Değerlendirmesi

Barkodlama Bölgesi Olarak Potentilla L. Cinsinde psbA-trnH IGS Sekanslarının Değerlendirmesi

A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins

Because of the limited effectiveness of prevailing phylogenetic methods when applied to highly divergent protein sequences, the phylogenetic analysis problem remains challenging. Here, we propose a sequence-based evolutionary distance algorithm termed sequence distance (SD), which innovatively incorporates site-to-site correlation within protein sequences into the distance estimation. In protein superfamilies, SD can effectively distinguish evolutionary relationships both within and between protein families, producing phylogenetic trees that closely align with those based on structural information, even with sequence identity less than 20%. SD is highly correlated with the similarity of the protein structure, and can calculate evolutionary distances for thousands of protein pairs within seconds using a single CPU, which is significantly faster than most protein structure prediction methods that demand high computational resources and long run times. The development of SD will significantly advance phylogenetics, providing researchers with a more accurate and reliable tool for exploring evolutionary relationships.

Computing consensus networks for collections of 1-nested phylogenetic networks

An important and well-studied problem in phylogenetics is to compute a consensus tree so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same set \(X\) of species. More recently, however, it has become of interest to find a consensus for a collection of more general, rooted directed acyclic graphs all of whose sink-sets are bijectively labeled by \(X\), so called rooted phylogenetic networks. These networks are used to analyze the evolution of species that cross with one another, such as plants and viruses. In this paper, we introduce an algorithm for computing a consensus for a collection of so-called 1-nested phylogenetic networks. Our approach builds on a previous result by Roselló et al. that describes an encoding for any 1-nested phylogenetic network in terms of a collection of ordered pairs of subsets of \(X\). More specifically, we characterize those collections of ordered pairs that arise as the encoding of some 1-nested phylogenetic network, and then use this characterization to compute a consensus network for a collection of $t \geq 1$ 1-nested networks in $O(t|X|^2+|X|^3)$ time. Applying our algorithm to a collection of phylogenetic trees yields the well-known majority rule consensus tree. Our approach leads to several new directions for future work, and we expect that it should provide a useful new tool to help understand complex evolutionary scenarios.

Morphometrical Identification and Phylogenetic Analysis of Rhinonyssidae (Acari: Mesostigmata) Parasitizing Avian Hosts: New Molecular Data.

Members of the family Rhinonyssidae are tiny hematophagous endoparasitic mites that inhabit the nasal cavities of birds and can cause trauma to their hosts. Traditionally, identifying species in this group has relied on observing their morphometrical characteristics. Nevertheless, determining species within this particular group has become more challenging due to the rising number of newly discovered species. Moreover, the morphometrical traits vary depending on the specific genus or group of species being studied. In this study, the complete internal transcribed spacer ITS1, 5.8S rDNA, and ITS2 regions of the ribosomal DNA from eighteen species of rhinonyssid mites belonging to four genera were sequenced to assess the utility of this genomic region in resolving taxonomic questions in this group and to estimate the phylogenetic relationships among the species. Mites were collected by dissecting the nasal cavities of birds under a stereomicroscope. Specimens used for morphometrical analyses were cleared in 85% lactic acid for 1-48 h and mounted in Hoyer's medium. Other specimens were preserved at -20 °C for molecular studies. From the data obtained in this study, it can be concluded that a thorough review and an accurate morphometrical identification and determination of the discriminatory traits are needed in this group of mites. Moreover, although the ITS1-5.8S-ITS2 fragment solves different taxonomic and phylogenetic problems at the species level, it would be necessary to test new molecular markers, or even a combination of nuclear and mitochondrial markers or different domains of the nuclear 28S rDNA, to discover a reliable taxonomic situation for rhinonyssids.

Phylogenetic analysis and temporal diversification of the tribe Alsineae (Caryophyllaceae) with the description of three new genera, Hesperostellaria, Reniostellaria and Torreyostellaria.

Alsineae are one of the most taxonomically difficult tribes in Caryophyllaceae and consist of over 500 species distributed in the northern temperate zone. Recent phylogenetic results have improved our understanding on the evolutionary relationships among Alsineae members. Nevertheless, there are still some unresolved taxonomic and phylogenetic problems at the generic level, and the evolutionary history of major clades within the tribe was unexplored to date. In this study, we carried out phylogenetic analyses and divergence time estimation of Alsineae using the nuclear ribosomal internal transcribed spacer (nrITS) and four plastid regions (matK, rbcL, rps16, trnL-F). The present analyses yielded a robustly supported phylogenetic hypothesis of the tribe. Our results showed that the monophyletic Alsineae are strongly supported to be the sister of Arenarieae, and the inter-generic relationships within Alsineae were mostly resolved with strong support. Both molecular phylogenetic and morphological evidence supported the Asian species Stellaria bistylata and the two North American species Pseudostellaria jamesiana and Stellaria americana all should be recognized as new monotypic genera respectively, and three new genera Reniostellaria, Torreyostellaria, and Hesperostellaria were thereby proposed here. Additionally, molecular and morphological evidence also supported the proposal of the new combination Schizotechium delavayi. Nineteen genera were accepted within Alsineae and a key to these genera was provided. Molecular dating analysis suggested that Alsineae splitted from its sister tribe at ca. 50.2 million-years ago (Ma) during the early Eocene and began to diverge at ca. 37.9 Ma during the late Eocene, and divergent events within Alsineae occurred mainly since the late Oligocene. Results from the present study provide insights into the historical assembly of herbaceous flora in northern temperate regions.

Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance

Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for the study of trait evolution across species while accounting for their common ancestry. These analyses typically assume a single, bifurcating phylogenetic tree describing the shared history among species. However, modern phylogenomic analyses have shown that genomes are often composed of mosaic histories that can disagree both with the species tree and with each other-so-called discordant gene trees. These gene trees describe shared histories that are not captured by the species tree, and therefore that are unaccounted for in classic comparative approaches. The application of standard comparative methods to species histories containing discordance leads to incorrect inferences about the timing, direction, and rate of evolution. Here, we develop two approaches for incorporating gene tree histories into comparative methods: one that constructs an updated phylogenetic variance-covariance matrix from gene trees, and another that applies Felsenstein's pruning algorithm over a set of gene trees to calculate trait histories and likelihoods. Using simulation, we demonstrate that our approaches generate much more accurate estimates of tree-wide rates of trait evolution than standard methods. We apply our methods to two clades of the wild tomato genus Solanum with varying rates of discordance, demonstrating the contribution of gene tree discordance to variation in a set of floral traits. Our approaches have the potential to be applied to a broad range of classic inference problems in phylogenetics, including ancestral state reconstruction and the inference of lineage-specific rate shifts.

A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings.

The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the minimum phylogenetic network problem, in which phylogenetic trees are first inferred, and then the smallest phylogenetic network that displays all the trees is computed. The approach takes advantage of the fact that the theory of phylogenetic trees is mature, and there are excellent tools available for inferring phylogenetic trees from a large number of biomolecular sequences. A tree-child network is a phylogenetic network satisfying the condition that every nonleaf node has at least one child that is of indegree one. Here, we develop a new method that infers the minimum tree-child network by aligning lineage taxon strings in the phylogenetic trees. This algorithmic innovation enables us to get around the limitations of the existing programs for phylogenetic network inference. Our new program, named ALTS, is fast enough to infer a tree-child network with a large number of reticulations for a set of up to 50 phylogenetic trees with 50 taxa that have only trivial common clusters in about a quarter of an hour on average.