Phylogenetic Reconstruction Methods Research Articles

Asymmetric Cluster-Based Measures for Comparative Phylogenetics.

Phylogenetic inference and reconstruction methods generate hypotheses on evolutionary history. Competing inference methods are frequently used, and the evaluation of the generated hypotheses is achieved using tree comparison costs. The Robinson-Foulds (RF) distance is a widely used cost to compare the topology of two trees, but this cost is sensitive to tree error and can overestimate tree differences. To overcome this limitation, a refined version of the RF distance called the Cluster Affinity (CA) distance was introduced. However, CA distances are symmetric and cannot compare different types of trees. These asymmetric comparisons occur when gene trees are compared with species trees, when disparate datasets are integrated into a supertree, or when tree comparison measures are used to infer a phylogenetic network. In this study, we introduce a relaxation of the original Affinity distance to compare heterogeneous trees called the asymmetric CA cost. We also develop a biologically interpretable cost, the Cluster Support cost that normalizes by cluster size across gene trees. The characteristics of these costs are similar to the symmetric CA cost. We describe efficient algorithms, derive the exact diameters, and use these to standardize the cost to be applicable in practice. These costs provide objective, fine-scale, and biologically interpretable values that can assess differences and similarities between phylogenetic trees.

Maximum likelihood estimation of log-concave densities on tree space

Phylogenetic trees are key data objects in biology, and the method of phylogenetic reconstruction has been highly developed. The space of phylogenetic trees is a nonpositively curved metric space. Recently, statistical methods to analyze samples of trees on this space are being developed utilizing this property. Meanwhile, in Euclidean space, the log-concave maximum likelihood method has emerged as a new nonparametric method for probability density estimation. In this paper, we derive a sufficient condition for the existence and uniqueness of the log-concave maximum likelihood estimator on tree space. We also propose an estimation algorithm for one and two dimensions. Since various factors affect the inferred trees, it is difficult to specify the distribution of a sample of trees. The class of log-concave densities is nonparametric, and yet the estimation can be conducted by the maximum likelihood method without selecting hyperparameters. We compare the estimation performance with a previously developed kernel density estimator numerically. In our examples where the true density is log-concave, we demonstrate that our estimator has a smaller integrated squared error when the sample size is large. We also conduct numerical experiments of clustering using the Expectation-Maximization algorithm and compare the results with k-means++ clustering using Fréchet mean.

Limits of mitochondrial genes in delimiting species within a Carbula species complex (Hemiptera: Pentatomidae).

Molecular data has become a powerful tool for species delimitation, particularly among those that present limited morphological differences; while the mitochondrial genome, with its moderate length, low cost of sequencing and fast lineage sorting, has emerged as a practical data set. Due to the limited morphological differences among the closely related species of Carbula Stål 1865, the species boundaries between Carbula abbreviata (Motschulsky, 1866), Carbula humerigera (Uhler, 1860), and Carbula putoni (Jakovlev, 1876) have remained particularly unclear. In this study, we applied two phylogenetic reconstruction methods to two data sets (mitogenome and COI) to assess the phylogeny of Carbula distributed in Asia, and five species delimitation methods to determine the boundaries between East Asian Carbula species. Our phylogenetic analyses showed Carbula to be paraphyletic; the seven known species distributed within East Asia to form a single monophyletic group, and within this, C. abbreviata, C. humerigera, C. putoni and middle-type to comprise a C. humerigera species complex. Our results show that mitogenome data alone, while effective in the differentiation of more distantly related Carbula species, is not sufficient to accurately delimit the species within this newly described complex.

Designing Weights for Quartet-Based Methods When Data are Heterogeneous Across Lineages

Homogeneity across lineages is a general assumption in phylogenetics according to which nucleotide substitution rates are common to all lineages. Many phylogenetic methods relax this hypothesis but keep a simple enough model to make the process of sequence evolution more tractable. On the other hand, dealing successfully with the general case (heterogeneity of rates across lineages) is one of the key features of phylogenetic reconstruction methods based on algebraic tools. The goal of this paper is twofold. First, we present a new weighting system for quartets (ASAQ) based on algebraic and semi-algebraic tools, thus especially indicated to deal with data evolving under heterogeneous rates. This method combines the weights of two previous methods by means of a test based on the positivity of the branch lengths estimated with the paralinear distance. ASAQ is statistically consistent when applied to data generated under the general Markov model, considers rate and base composition heterogeneity among lineages and does not assume stationarity nor time-reversibility. Second, we test and compare the performance of several quartet-based methods for phylogenetic tree reconstruction (namely QFM, wQFM, quartet puzzling, weight optimization and Willson’s method) in combination with several systems of weights, including ASAQ weights and other weights based on algebraic and semi-algebraic methods or on the paralinear distance. These tests are applied to both simulated and real data and support weight optimization with ASAQ weights as a reliable and successful reconstruction method that improves upon the accuracy of global methods (such as neighbor-joining or maximum likelihood) in the presence of long branches or on mixtures of distributions on trees.

Phylogenetic Relationship and Molecular Divergence Dating Using SRY Gene Polymorphism about Four Ladoum Sheep Lineages in Senegal

Animal genetic resources are playing a vital role in livestock production and are essential to food security. The present study aims to contribute to a better understanding genetic local sheep breeds and to elucidate the phylogenetic relationships through the evolution of the SRY gene in four different lineages of Ladoum sheep raised in Senegal. After a brief analysis of genetic diversity, the phylogenetic relationships and molecular dating were inferred through haplotype networks and four phylogenetic reconstruction methods. The different haplotype networks are constructed with NETWORK ver. 5.0.0.0 using the Median-Joining method. Phylogenetic trees were reconstructed using neighbor-joining, maximum parsimony, maximum likelihood and Bayesian inference. The robustness of the nodes in phylogenetic trees of the three first methods was assessed by 1000 bootstraps. For Bayesian inference, the posterior probability distribution of the trees was estimated by 4 MCMC chains. 5,000,000 generations were performed for each of the chains by sampling the different parameters every 1000 generations. Results show a low polymorphism. Haplotypic diversity is much higher than the average nucleotide divergence between all pairs of haplotypes. The majority and central haplotype indicates a close relationship between “Batling” and “Tyson” individuals. “Birahim” lineage is very distinct from the rest. Phylogenetic trees confirm two genetically separate clades between “Birahim” and the other lineages. The period of divergence between “Birahim” lineage versus the common ancestor of the other three lineages was 2504 years ago. The polyphyly revealed in “Birahim” lindicates that this lineage does not contain the common ancestor of all individuals who compose it. It could therefore be derived from two or more sheep breeds with a common ancestor, Ovis aries. The monophyletic clade appears to be a group including a common ancestor and all of its genetic descendants. This group, bringing together the other three lineages, is in the process of being structured into sub-lineages. This study is the first to show that there are only two genetic lines within ladoum sheep in Senegal.

Molecular delimitation methods validate morphologically similar species of red snappers (Perciformes: Lutjanidae).

In this study, we tested the taxonomic validation of red snappers species (Southern red snapper Lutjanus purpureus; Silk snapper L. vivanus; Blackfin snapper L. buccanella; and Pacific red snapper L. peru) based on comparative analysis, using four methods for species delimitation. These methods were based on either genetic similarity or phylogenetic trees inferred from two mitochondrial (Cytochrome b and D-loop) and two nuclear (Myostatin and S7 introns) markers. On one hand, the genetic results corroborated the presence of four red snapper species, confirming their taxonomic validation despite their remarkable morphological similarity. On the other hand, few incongruencies in the species delimitation methods were observed according to the phylogenetic reconstruction method (maximum likelihood or Bayesian inference) when using. Based on the phylogenetic results, L. buccanella should represent a more ancient lineage in relation to the clade that encompasses L. purpureus, L. peru and L. vivanus. The single-locus phylogenetic analysis based on Cytb recovered each the red snapper species as a well-supported clade. Overall, this study provided a DNA-based validation of the traditional morphological taxonomy of red snappers.

Stochastic Safety Radius on UPGMA

Unweighted Pair Group Method with Arithmetic Mean (UPGMA) is one of the most popular distance-based methods to reconstruct an equidistant phylogenetic tree from a distance matrix computed from an alignment of sequences. Since we use equidistant trees as gene trees for phylogenomic analyses under the multi-species coalescent model and since an input distance matrix computed from an alignment of each gene in a genome is estimated via the maximum likelihood estimators, it is important to conduct a robust analysis on UPGMA. Stochastic safety radius, introduced by Steel and Gascuel, provides a lower bound for the probability that a phylogenetic tree reconstruction method returns the true tree topology from a given distance matrix. In this article, we compute the stochastic safety radius of UPGMA for a phylogenetic tree with n leaves. Computational experiments show an improved gap between empirical probabilities estimated from random samples and the true tree topology from UPGMA, increasing confidence in phylogenic results.

Revised molecular phylogeny, global biogeography, and diversification of palms subfamily Coryphoideae (Arecaceae) based on low copy nuclear and plastid regions.

Coryphoideae are palmate-leaved palms from the family Arecaceae consisting of 46 genera representing 421 species. Although several phylogenetic analyses based on different genomic regions have been carried out on Coryphoideae, a fully resolved molecular phylogenetic tree has not been reported yet. To achieve this, we applied two phylogenetic reconstruction methods: Maximum Likelihood and Bayesian Inference, using amplified sampling by retrieving chloroplast and nuclear DNA sequences from NCBI and adding newly produced sequences from Indian accession into the dataset. The same dataset (chloroplast + nuclear DNA sequences) was used to estimate divergence times and the evolutionary history of Coryphoideae with a Bayesian uncorrelated, lognormal relaxed-clock approach and a Statistical Divergence-Vicariance Analysis method,respectively. The phylogenetic analyses based on a combined chloroplast and nuclear DNA sequence dataset showed well-resolved relationships within the subfamily. Both phylogenetic trees divide Coryphoideae into two main groups: CSPT (Crysophileae, Sabaleae, Phoeniceae, and Trachycarpeae) and the Syncarpous group. These main groups are segregated into eight tribes (Trachycarpeae, Phoeniceae, Sabaleae, Crysophileae, Borasseae, Corypheae, Caryoteae, and Chuniophoeniceae) and four subtribes (Rhapidine, Livistoninae, Hyphaeninae, and Lataniinae) with strong support-values. Most previously unresolved and doubtful relationships within tribes Trachycarpeae and Crysophilieae are now resolved and well-supported. The reconstructed phylogenetic trees support all previous systematic revisions of the subfamily. All Indian sampled species of Arenga, Bentinckia, Hyphaene, and Trachycarpus show close relation with their respective congeneric species. Molecular dating results and integration of biogeography suggest that Coryphoideae originated in Laurasia at ~95.12Ma and then diverged into the tropical and subtropical regions of the whole world. This study offers the correct combination of nuclear and plastid regions to test the current and future systematic revisions.

A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods.

Affinity maturation (AM) of B cells through somatic hypermutations (SHMs) enables the immune system to evolve to recognize diverse pathogens. The accumulation of SHMs leads to the formation of clonal lineages of antibody-secreting b cells that have evolved from a common naïve B cell. Advances in high-throughput sequencing have enabled deep scans of B cell receptor repertoires, paving the way for reconstructing clonal trees. However, it is not clear if clonal trees, which capture microevolutionary time scales, can be reconstructed using traditional phylogenetic reconstruction methods with adequate accuracy. In fact, several clonal tree reconstruction methods have been developed to fix supposed shortcomings of phylogenetic methods. Nevertheless, no consensus has been reached regarding the relative accuracy of these methods, partially because evaluation is challenging. Benchmarking the performance of existing methods and developing better methods would both benefit from realistic models of clonal lineage evolution specifically designed for emulating B cell evolution. In this paper, we propose a model for modeling B cell clonal lineage evolution and use this model to benchmark several existing clonal tree reconstruction methods. Our model, designed to be extensible, has several features: by evolving the clonal tree and sequences simultaneously, it allows modeling selective pressure due to changes in affinity binding; it enables scalable simulations of large numbers of cells; it enables several rounds of infection by an evolving pathogen; and, it models building of memory. In addition, we also suggest a set of metrics for comparing clonal trees and measuring their properties. Our results show that while maximum likelihood phylogenetic reconstruction methods can fail to capture key features of clonal tree expansion if applied naively, a simple post-processing of their results, where short branches are contracted, leads to inferences that are better than alternative methods.

Insertions and deletions as phylogenetic signal in an alignment-free context.

Most methods for phylogenetic tree reconstruction are based on sequence alignments; they infer phylogenies from substitutions that may have occurred at the aligned sequence positions. Gaps in alignments are usually not employed as phylogenetic signal. In this paper, we explore an alignment-free approach that uses insertions and deletions (indels) as an additional source of information for phylogeny inference. For a set of four or more input sequences, we generate so-called quartet blocks of four putative homologous segments each. For pairs of such quartet blocks involving the same four sequences, we compare the distances between the two blocks in these sequences, to obtain hints about indels that may have happened between the blocks since the respective four sequences have evolved from their last common ancestor. A prototype implementation that we call Gap-SpaM is presented to infer phylogenetic trees from these data, using a quartet-tree approach or, alternatively, under the maximum-parsimony paradigm. This approach should not be regarded as an alternative to established methods, but rather as a complementary source of phylogenetic information. Interestingly, however, our software is able to produce phylogenetic trees from putative indels alone that are comparable to trees obtained with existing alignment-free methods.

Salmoniformes: marine or freshwater origin?

A long discussion about either marine or freshwater genesis of salmonids is still relevant today. So far, no convincing evidence of any point of view has been found. The arguments to freshwater origin of Salmoniformes are analyzed using the «probabilistic» method of phylogenetic reconstruction and genetic approach. The analysis shows that proposed arguments cannot be considered as evidences for freshwater genesis of this taxon. Real facts and theoretical substantiations of early freshwater Salmoniformes are absent, so there is no need to prove that they acquired freshwater dwell in the Cretaceous-Paleocene in order to become anadromous fish again in the Eocene.

Four in One: Cryptic Diversity in Geoffroy’s Side-Necked Turtle Phrynops geoffroanus (Schweigger 1812) (Testudines: Pleurodira: Chelidae) in Brazil

Turtles are one of the most threatened groups of vertebrates, with about 60% of species classified at some level of extinction risk. Compounding this extinction crisis are cryptic species and species complexes that are evaluated under a single species epithet but harbor multiple species, each of which needs to be evaluated independently. The Phrynops geoffroanus species group is a classic example. Described first in 1812, it is currently thought to harbor multiple species. To test this hypothesis, we collected mitochondrial and nuclear genomic data, morphometric data, and distribution and associated biome information. We applied statistically rigorous species delimitation analyses, taxonomic hypotheses tests, and fully coalescent phylogenetic reconstruction methods, concluding that the Phrynops geoffroanus species complex comprises four geographically structured species/lineages that diverged during the Pleistocene and are currently geographically structured along the main South American river basins and biomes. These species/lineages show subtle and largely non-significant differences in shape but are characterized by differences in coloration and patterns of marks on the head and plastron. Our results contribute to the understanding of species diversity and diversification of biodiversity in South America and provide an important basis for the conservation of freshwater turtles.

Phylogenetic reconstruction of the cultural evolution of electronic music via dynamic community detection (1975–1999)

Phylogenetic trees or networks representing cultural evolution are typically built using methods from biology that use similarities and differences in cultural traits to infer the historical relationships between the populations that produced them. While these methods have yielded important insights, researchers continue to debate the extent to which cultural phylogenies are tree-like or reticulated due to high levels of horizontal transmission. In this study, we propose a novel method for phylogenetic reconstruction using dynamic community detection that focuses not on the cultural traits themselves (e.g., musical features), but the people creating them (musicians). We used data from 1,498,483 collaborative relationships between electronic music artists to construct a cultural phylogeny based on observed population structure. The results suggest that, although vertical transmission appears to be dominant, the potential for horizontal transmission (indexed by between-population linkage) is relatively high and populations never become fully isolated from one another. In addition, we found evidence that electronic music diversity has increased between 1975 and 1999. The method used in this study is available as a new R package called DynCommPhylo. Future studies should apply this method to other cultural systems such as academic publishing and film, as well as biological systems where high resolution reproductive data is available, and develop formal inferential models to assess how levels of reticulation in evolution vary across domains.

SAQ: Semi-Algebraic Quartet Reconstruction.

We present the phylogenetic quartet reconstruction method SAQ (Semi-Algebraic Quartet reconstruction). SAQ is consistent with the most general Markov model of nucleotide substitution and, in particular, it allows for rate heterogeneity across lineages. Based on the algebraic and semi-algebraic description of distributions that arise from the general Markov model on a quartet, the method outputs normalized weights for the three trivalent quartets (which can be used as input of quartet-based methods). We show that SAQ is a highly competitive method that outperforms most of the well known reconstruction methods on data simulated under the general Markov model on 4-taxon trees. Moreover, it also achieves a high performance on data that violates the underlying assumptions.

An Information-Entropy Position-Weighted K-Mer Relative Measure for Whole Genome Phylogeny Reconstruction.

Alignment methods have faced disadvantages in sequence comparison and phylogeny reconstruction due to their high computational costs in handling time and space complexity. On the other hand, alignment-free methods incur low computational costs and have recently gained popularity in the field of bioinformatics. Here we propose a new alignment-free method for phylogenetic tree reconstruction based on whole genome sequences. A key component is a measure called information-entropy position-weighted k-mer relative measure (IEPWRMkmer), which combines the position-weighted measure of k-mers proposed by our group and the information entropy of frequency of k-mers. The Manhattan distance is used to calculate the pairwise distance between species. Finally, we use the Neighbor-Joining method to construct the phylogenetic tree. To evaluate the performance of this method, we perform phylogenetic analysis on two datasets used by other researchers. The results demonstrate that the IEPWRMkmer method is efficient and reliable. The source codes of our method are provided at https://github.com/ wuyaoqun37/IEPWRMkmer.

DEVOLUTION\u2014A method for phylogenetic reconstruction of aneuploid cancers based on multiregional genotyping data

Phylogenetic reconstruction of cancer cell populations remains challenging. There is a particular lack of tools that deconvolve clones based on copy number aberration analyses of multiple tumor biopsies separated in time and space from the same patient. This has hampered investigations of tumors rich in aneuploidy but few point mutations, as in many childhood cancers and high-risk adult cancer. Here, we present DEVOLUTION, an algorithm for subclonal deconvolution followed by phylogenetic reconstruction from bulk genotyping data. It integrates copy number and sequencing information across multiple tumor regions throughout the inference process, provided that the mutated clone fraction for each mutation is known. We validate DEVOLUTION on data from 56 pediatric tumors comprising 253 tumor biopsies and show a robust performance on simulations of bulk genotyping data. We also benchmark DEVOLUTION to similar bioinformatic tools using an external dataset. DEVOLUTION holds the potential to facilitate insights into the development, progression, and response to treatment, particularly in tumors with high burden of chromosomal copy number alterations.

Species Delimitation of Asteropyrum (Ranunculaceae) Based on Morphological, Molecular, and Ecological Variation.

Objectively evaluating different lines of evidence within a formalized framework is the most efficient and theoretically grounded approach for defining robust species hypotheses. Asteropyrum Drumm. et Hutch. is a small genus of perennial herb containing two species, A. cavaleriei and A. peltatum. The distinction of these two species mainly lies in the shape and size of leaf blades. However, these characters have been considered labile and could not differentiate the two species reliably. In this study, we investigated the variation of the leaf blades of 28 populations across the whole range of Asteropyrum using the landmark-based geometric morphometrics (GMM), sought genetic gaps within this genus using DNA barcoding, phylogenetic reconstruction and population genetic methods, and compared the predicted ecological niches of the two species. The results showed that the leaf form (shape and size) was overlapped between the two species; barcode gap was not detected within the genus Asteropyrum; and little ecological and geographical differentiation was found between the two taxa. Two genetic clusters detected by population genetic analysis did not match the two morphospecies. The results suggest that there are no distinct boundaries between the two species of Asteropyrum in terms of morphology, genetics and ecology and this present classification should be abandoned. We anticipate that range-wide population genomic studies would properly delineate the species boundaries and help to understand the evolution and speciation within Asteropyrum.

On subfamily structure of the Cupedidae (Coleoptera, Archostemata): data from paleontology and an approach to solving conflicting classifications

This paper demonstrates some of main differences between the systematic constructions based mostly on paleontological research and constructions involving the other approaches. Some reasons for these differences are discussed, together with an approach to solve contradictions between the conflicting hypotheses. The multiple (multidimensional) parallelism gives a possibility to solve many problems of phylogenetic interrelations due to reconstructions based on coincidence of patterns of changes (series of interconnected facts) traced in different aspects of evolutionary processes. This principle originates in the ideas by Jean Agassiz and Ernst Haeckel defined as the principle of triple parallelism. Other aspects of the evolution can be added to the morphology, embryology, and paleontology, initially included in this method. The molecular method is one of such aspects. It is shown that the potential resolution of the morphological and molecular approaches in some cases could be rather restricted, particularly applying ancient groups with main evolutionary transformations passed far in the past. The infraorder Cupediformia and suborder Archostemata in general are examples of such cases. It is advisable in the current research period that has followed the previous interpretation of the systematic structure of the family Cupedidae recognizing three subfamilies with not quite distinct hiatus between them (Cupedinae, Ommatinae and Triadocupedinae). Some recent morphological and molecular approaches proposed to divide the Cupedidae into two separate families on the basis of incomplete information accessible after study of only modern representatives, as most events in the family evolution occurred during the Palaeozoic and Mesozoic, and these events are scarcely possible to trace without considering fossils. As the principle of multiple parallelism cannot be currently used for archostematans to the full extent of its power, it is necessary to choose the paleontological method of phylogenetic reconstruction as crucial. This approach is preferable for groups that are well-documented through very diverse fossils, and for which only few of its remnants of the past diversity reached the modern epoque.

Trends in taxonomy of Triatomini (Hemiptera, Reduviidae, Triatominae): reproductive compatibility reinforces the synonymization of Meccus St\xe5l, 1859 with Triatoma Laporte, 1832

BackgroundMeccus' taxonomy has been quite complex since the first species of this genus was described by Burmeister in 1835 as Conorhinus phyllosoma. In 1859 the species was transferred to the genus Meccus and in 1930 to Triatoma. However, in the twentieth century, the Meccus genus was revalidated (alteration corroborated by molecular studies) and, in the twenty-first century, through a comprehensive study including more sophisticated phylogenetic reconstruction methods, Meccus was again synonymous with Triatoma. Events of natural hybridization with production of fertile offspring have already been reported among sympatric species of the T. phyllosoma subcomplex, and experimental crosses demonstrated reproductive viability among practically all species of the T. phyllosoma subcomplex that were considered as belonging to the genus Meccus, as well as between these species and species of Triatoma. Based on the above, we carried out experimental crosses between T. longipennis (considered M. longipennis in some literature) and T. mopan (always considered as belonging to Triatoma) to evaluate the reproductive compatibility between species of the T. phyllosoma complex. In addition, we have grouped our results with information from the literature regarding crosses between species that were grouped in the genus Meccus with Triatoma, in order to discuss the importance of experimental crosses to confirm the generic reorganization of species.ResultsThe crosses between T. mopan female and T. longipennis male resulted in viable offspring. The hatching of hybrids, even if only in one direction and/or at low frequency, demonstrates reproductive compatibility and homeology between the genomes of the parents.ConclusionConsidering that intergeneric crosses usually do not result in viable offspring in Triatominae, the reproductive compatibility observed between the T. phyllosoma subcomplex species considered in the Meccus genus with species of the Triatoma genus shows that there is “intergeneric” genomic compatibility, which corroborates the generic reorganization of Meccus in Triatoma.Graphical

Use of partial N-gene sequences as a tool to monitor progress on rabies control and elimination efforts in Ethiopia

Ethiopia is one of the African countries most affected by rabies. A coarse catalog of rabies viruses (RABV) was created as a benchmark to assess the impact of control and elimination activities. We evaluated a 726 bp amplicon at the end of the N-gene to infer viral lineages in circulation using maximum likelihood and Bayesian methods for phylogenetic reconstruction. We sequenced 228 brain samples from wild and domestic animals collected in five Ethiopian regions during 2010–2017. Results identified co-circulating RABV lineages that are causing recurrent spillover infections into wildlife and domestic animals. We found no evidence of importation of RABVs from other African countries or vaccine-induced cases in the area studied. A divergent RABV lineage might be involved in an independent rabies cycle in jackals. This investigation provides a feasible approach to assess rabies control and elimination efforts in resource-limited countries.