Supertree Analysis Research Articles

Testing the agreement of trees with internal labels

BackgroundA semi-labeled tree is a tree where all leaves as well as, possibly, some internal nodes are labeled with taxa. Semi-labeled trees encompass ordinary phylogenetic trees and taxonomies. Suppose we are given a collection {mathcal {P}}= {{mathcal {T}}_1, {mathcal {T}}_2, ldots , {mathcal {T}}_k} of semi-labeled trees, called input trees, over partially overlapping sets of taxa. The agreement problem asks whether there exists a tree {mathcal {T}}, called an agreement tree, whose taxon set is the union of the taxon sets of the input trees such that the restriction of {mathcal {T}} to the taxon set of {mathcal {T}}_i is isomorphic to {mathcal {T}}_i, for each i in {1, 2, ldots , k}. The agreement problems is a special case of the supertree problem, the problem of synthesizing a collection of phylogenetic trees with partially overlapping taxon sets into a single supertree that represents the information in the input trees. An obstacle to building large phylogenetic supertrees is the limited amount of taxonomic overlap among the phylogenetic studies from which the input trees are obtained. Incorporating taxonomies into supertree analyses can alleviate this issue. ResultsWe give a {mathcal {O}}(n k (sum _{i in [k]} d_i + log ^2(nk))) algorithm for the agreement problem, where n is the total number of distinct taxa in {mathcal {P}}, k is the number of trees in {mathcal {P}}, and d_i is the maximum number of children of a node in {mathcal {T}}_i.ConclusionOur algorithm can aid in integrating taxonomies into supertree analyses. Our computational experience with the algorithm suggests that its performance in practice is much better than its worst-case bound indicates.

Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-2 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, yet limited progress was obtained, principally owing to the disability of these methods to reasonably integrate phylogenetic information from all genes of SARS-CoV-2. Supertree method based on multiple trees can produce the overall reasonable phylogenetic tree. However, the supertree method has been barely used for phylogenetic analysis of viruses. Here we applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2. Compared with other phylogenetic analysis methods, the supertree method showed more resolution power for phylogenetic analysis of coronaviruses. In particular, the MRP pseudo-sequence supertree analysis firmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS-CoV-2, which was implied by other phylogenetic tree analysis based on viral genome sequences. Furthermore, the discovery of evolution and mutation in SARS-CoV-2 was achieved by MRP pseudo-sequence supertree analysis. Taken together, the MRP pseudo-sequence supertree provided more information on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.

Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families.

RNA sequencing (RNA-seq) has become one of the most powerful tools to unravel the genomic basis of biological adaptation and diversity. Although challenging, RNA-seq is particularly promising for research on non-model, secretive species that cannot be observed in nature easily and therefore remain comparatively understudied. Among such animals, the caecilians (order Gymnophiona) likely constitute the least known group of vertebrates, despite being an old and remarkably distinct lineage of amphibians. Here, we characterize multi-tissue transcriptomes for five species of caecilians that represent a broad level of diversity across the order. We identified vertebrate homologous elements of caecilian functional genes of varying tissue specificity that reveal a great number of unclassified gene families, especially for the skin. We annotated several protein domains for those unknown candidate gene families to investigate their function. We also conducted supertree analyses of a phylogenomic dataset of 1,955 candidate orthologous genes among five caecilian species and other major lineages of vertebrates, with the inferred tree being in agreement with current views of vertebrate evolution and systematics. Our study provides insights into the evolution of vertebrate protein-coding genes, and a basis for future research on the molecular elements underlying the particular biology and adaptations of caecilian amphibians.

Taxonomic variation among <i>Schinus molle</i> L. plants associated with a slight change in elevation

This study examined the degree of variations in DNA fingerprints associated with slight altitudinal change of Schinus molle grown in Abha region, Saudi Arabia. Seven populations from Schinus molle plants located at 2193.0, 2246.0, 2197.7, 2441.0, 2372.0, 2250.6 and 2175.0 meters had been investigated. The degree of genetic variability was evaluated using random amplified polymorphic DNA (RAPD), mixed RAPD and intersimple sequence repeat markers (ISSR). The genetic similarity coefficients from RAPD analysis revealed the maximum similarity value (89.9%) was between population at 2250.6 m and population at 2175.0 m. The genetic similarity coefficients from mixed RAPD primers displayed the highest similarity value (87.6%) between population at 2246.0 m and population at 2197.7 m. Similarity coefficients from ISSR analysis revealed the highest similarity value (86.2%) among populations at 2193.0 m, 2246.0 m, 2441.0 m and at 2250.6 m. Super tree analysis (RAPD + mixed RAPD + ISSR) showed the highest similarity value (85.5%) between population at 2441.0 m and population at 2250.6 m. In conclusion, marker systems including RAPD, mixed RAPD and ISSR, alone or combined can be effectively used in determining the genetic relationship among Schinus molle plants even at very close populations.Bangladesh J. Plant Taxon. 24(2): 205–214.

Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes.

The oomycetes are a class of microscopic, filamentous eukaryotes within the Stramenopiles-Alveolata-Rhizaria (SAR) supergroup which includes ecologically significant animal and plant pathogens, most infamously the causative agent of potato blight Phytophthora infestans. Single-gene and concatenated phylogenetic studies both of individual oomycete genera and of members of the larger class have resulted in conflicting conclusions concerning species phylogenies within the oomycetes, particularly for the large Phytophthora genus. Genome-scale phylogenetic studies have successfully resolved many eukaryotic relationships by using supertree methods, which combine large numbers of potentially disparate trees to determine evolutionary relationships that cannot be inferred from individual phylogenies alone. With a sufficient amount of genomic data now available, we have undertaken the first whole-genome phylogenetic analysis of the oomycetes using data from 37 oomycete species and 6 SAR species. In our analysis, we used established supertree methods to generate phylogenies from 8,355 homologous oomycete and SAR gene families and have complemented those analyses with both phylogenomic network and concatenated supermatrix analyses. Our results show that a genome-scale approach to oomycete phylogeny resolves oomycete classes and individual clades within the problematic Phytophthora genus. Support for the resolution of the inferred relationships between individual Phytophthora clades varies depending on the methodology used. Our analysis represents an important first step in large-scale phylogenomic analysis of the oomycetes. IMPORTANCE The oomycetes are a class of eukaryotes and include ecologically significant animal and plant pathogens. Single-gene and multigene phylogenetic studies of individual oomycete genera and of members of the larger classes have resulted in conflicting conclusions concerning interspecies relationships among these species, particularly for the Phytophthora genus. The onset of next-generation sequencing techniques now means that a wealth of oomycete genomic data is available. For the first time, we have used genome-scale phylogenetic methods to resolve oomycete phylogenetic relationships. We used supertree methods to generate single-gene and multigene species phylogenies. Overall, our supertree analyses utilized phylogenetic data from 8,355 oomycete gene families. We have also complemented our analyses with superalignment phylogenies derived from 131 single-copy ubiquitous gene families. Our results show that a genome-scale approach to oomycete phylogeny resolves oomycete classes and clades. Our analysis represents an important first step in large-scale phylogenomic analysis of the oomycetes.

The phylogeny of stiletto flies (Diptera: Therevidae)

AbstractThe therevoid clade represents a group of four families (Apsilocephalidae, Evocoidae, Scenopinidae and Therevidae) of lower brachyceran Diptera in the superfamily Asiloidea. The largest of these families is that of the stiletto flies (Therevidae). A large‐scale (i.e. supermatrix) phylogeny of Therevidae is presented based on DNA sequence data from seven genetic loci (16S, 18S and 28S ribosomal DNA and four protein‐encoding genes: elongation factor 1‐alpha, triose phosphate isomerase, short‐wavelength rhodopsin and the CPSase region of carbamoyl‐phosphate synthase‐aspartate transcarbamoylase‐dihydroorotase). Results are presented from Bayesian phylogenetic analyses of approximately 8.7 kb of sequence data for 204 taxa representing all subfamilies and genus groups of Therevidae. Our results strongly support the sister‐group relationship between Therevidae and Scenopinidae, with Apsilocephalidae as sister to Evocoidae. Previous estimates of stiletto fly phylogeny based on morphology or DNA sequence data, or supertree analysis, have failed to find significant support for relationships among subfamilies. We report for the first time strong support for the placement of the subfamily Phycinae as sister to the remaining Therevidae, originating during the Mid Cretaceous. As in previous studies, the sister‐group relationship between the species‐rich subfamilies Agapophytinae and Therevinae is strongly supported. Agapophytinae are recovered as monophyletic, inclusive of the Taenogera group. Therevinae comprise the bulk of the species richness in the family and appear to be a relatively recent and rapid radiation originating in the southern hemisphere (Australia + Antarctica + South America) during the Late Cretaceous. Genus groups are defined for all subfamilies based on these results.

Weighted quartets phylogenetics.

Despite impressive technical and theoretical developments, reconstruction of phylogenetic trees for enormous quantities of molecular data is still a challenging task. A key tool in analyses of large data sets has been the construction of separate trees for subsets (e.g., quartets) of sequences, and subsequent combination of these subtrees into a single tree for the full set (i.e., supertree analysis). Unfortunately, even amalgamating quartets into a supertree remains a computationally daunting task. Assigning weights to quartets to indicate importance or reliability was proposed more than a decade ago, but handling weighted quartets is even more challenging and has scarcely been attempted in the past. In this work, we focus on weighted quartet-based approaches. We propose a scheme to assign weights to quartets coming from weighted trees and devise a tree similarity measure for weighted trees based on weighted quartets. We also extend the quartet MaxCut (QMC algorithm) to handle weighted quartets. We evaluate these tools on simulated and real data. Our simulated data analysis highlights the additional information that is conveyed when using the new weighted tree similarity measure, and shows that extending QMC to a weighted setting improves the quality of tree reconstruction. Our analyses of a cyanobacterial data set with weighted QMC reinforce previous results achieved with other tools.

Microbial genomic taxonomy

A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, <10 in Karlin genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups.

The impact of HGT on phylogenomic reconstruction methods

Supermatrix and supertree analyses are frequently used to more accurately recover vertical evolutionary history but debate still exists over which method provides greater reliability. Traditional methods that resolve relationships among organisms from single genes are often unreliable because of the frequent lack of strong phylogenetic signal and the presence of systematic artifacts. Methods developed to reconstruct organismal history from multiple genes can be divided into supermatrix and supertree approaches. A supermatrix analysis consists of the concatenation of multiple genes into a single, possibly partitioned alignment, from which phylogenies are reconstructed using a variety of approaches. Supertrees build consensus trees from the topological information contained within individual gene trees. Both methods are now widely used and have been demonstrated to solve previously ambiguous or unresolved phylogenies with high statistical support. However, the amount of misleading signal needed to induce erroneous phylogenies for both strategies is still unknown. Using genome simulations, we test the accuracy of supertree and supermatrix approaches in recovering the true organismal phylogeny under increased amounts of horizontally transferred genes and changes in substitution rates. Our results show that overall, supermatrix approaches are preferable when a low amount of gene transfer is suspected to be present in the dataset, while supertrees have greater reliability in the presence of a moderate amount of misleading gene transfers. In the face of very high or very low substitution rates without horizontal gene transfers, supermatrix approaches outperform supertrees as individual gene trees remain unresolved and additional sequences contribute to a congruent phylogenetic signal.

Diversity and evolution of ectomycorrhizal host associations in the Sclerodermatineae (Boletales, Basidiomycota)

This study uses phylogenetic analysis of the Sclerodermatineae to reconstruct the evolution of ectomycorrhizal host associations in the group using divergence dating, ancestral range and ancestral state reconstructions. Supermatrix and supertree analysis were used to create the most inclusive phylogeny for the Sclerodermatineae. Divergence dates were estimated in BEAST. Lagrange was used to reconstruct ancestral ranges. BayesTraits was used to reconstruct ectomycorrhizal host associations using extant host associations with data derived from literature sources. The supermatrix data set was combined with internal transcribed spacer (ITS) data sets for Astraeus, Calostoma, and Pisolithus to produce a 168 operational taxonomic unit (OTU) supertree. The ensuing analysis estimated that basal Sclerodermatineae originated in the late Cretaceous while major genera diversified near the mid Cenozoic. Asia and North America are the most probable ancestral areas for all Sclerodermatineae, and angiosperms, primarily rosids, are the most probable ancestral hosts. Evolution in the Sclerodermatineae follows the biogeographic history of disjunct plant communities associated with early Cenozoic mesophytic forests and a boreotropical history. Broad geographic distributions are observed in the most promiscuous Sclerodermatineae (those with broad host ranges), while those with relatively limited distribution have fewer documented ectomycorrhizal associations. This suggests that ectomycorrhizal generalists have greater dispersal capabilities than specialists.

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates.

BackgroundAlthough it has proven to be an important foundation for investigations of carnivoran ecology, biology and evolution, the complete species-level supertree for Carnivora of Bininda-Emonds et al. is showing its age. Additional, largely molecular sequence data are now available for many species and the advancement of computer technology means that many of the limitations of the original analysis can now be avoided. We therefore sought to provide an updated estimate of the phylogenetic relationships within all extant Carnivora, again using supertree analysis to be able to analyze as much of the global phylogenetic database for the group as possible.ResultsIn total, 188 source trees were combined, representing 114 trees from the literature together with 74 newly constructed gene trees derived from nearly 45,000 bp of sequence data from GenBank. The greater availability of sequence data means that the new supertree is almost completely resolved and also better reflects current phylogenetic opinion (for example, supporting a monophyletic Mephitidae, Eupleridae and Prionodontidae; placing Nandinia binotata as sister to the remaining Feliformia). Following an initial rapid radiation, diversification rate analyses indicate a downturn in the net speciation rate within the past three million years as well as a possible increase some 18.0 million years ago; numerous diversification rate shifts within the order were also identified.ConclusionsTogether, the two carnivore supertrees remain the only complete phylogenetic estimates for all extant species and the new supertree, like the old one, will form a key tool in helping us to further understand the biology of this charismatic group of carnivores.

Evolutionary history of tree squirrels (Rodentia, Sciurini) based on multilocus phylogeny reconstruction

Pečnerová, P. &amp; Martínková, N. (2012). Evolutionary history of tree squirrels (Rodentia, Sciurini) based on multilocus phylogeny reconstruction. —Zoologica Scripta, 41, 211–219.Tree squirrels of the tribe Sciurini represent a group with unresolved phylogenetic relationships in gene trees. We used partial sequences of mitochondrial genes for 12S rRNA, 16S rRNA, cytochrome b and d‐loop, and nuclear irbp, c‐myc exon 2 and 3 and rag1 genes to reconstruct phylogenetic relationships within the tribe, maximizing the number of analysed species. Bayesian inference analysis of the concatenated sequences revealed common trends that were similar to those retrieved with supertree reconstruction. We confirmed congruence between phylogeny and zoogeography. The first group that diverged from a common ancestor was genus Tamiasciurus, followed by Palaearctic Sciurus and Indomalayan Rheithrosciurus macrotis. Nearctic and Neotropical Sciurus species formed a monophyletic group that included Microsciurus and Syntheosciurus. Neotropical Sciurini were monophyletic with a putative exception of Syntheosciurus brochus that was included in a polychotomy with Nearctic Sciurus in supertree analyses. Our data indicate that Sciurini tree squirrels originated in the northern hemisphere and ancestors of contemporary taxa attained their current distribution through overland colonization from the nearest continent rather than through trans‐Pacific dispersal.

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

Although it has proven to be an important foundation for investigations of carnivoran ecology, biology and evolution, the complete species-level supertree for Carnivora of Bininda-Emonds et al. is showing its age. Additional, largely molecular sequence data are now available for many species and the advancement of computer technology means that many of the limitations of the original analysis can now be avoided. We therefore sought to provide an updated estimate of the phylogenetic relationships within all extant Carnivora, again using supertree analysis to be able to analyze as much of the global phylogenetic database for the group as possible. In total, 188 source trees were combined, representing 114 trees from the literature together with 74 newly constructed gene trees derived from nearly 45,000 bp of sequence data from GenBank. The greater availability of sequence data means that the new supertree is almost completely resolved and also better reflects current phylogenetic opinion (for example, supporting a monophyletic Mephitidae, Eupleridae and Prionodontidae; placing Nandinia binotata as sister to the remaining Feliformia). Following an initial rapid radiation, diversification rate analyses indicate a downturn in the net speciation rate within the past three million years as well as a possible increase some 18.0 million years ago; numerous diversification rate shifts within the order were also identified. Together, the two carnivore supertrees remain the only complete phylogenetic estimates for all extant species and the new supertree, like the old one, will form a key tool in helping us to further understand the biology of this charismatic group of carnivores.

Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data

For the predominantly southern hemisphere plant group Styphelioideae (Ericaceae) published sequence datasets of five markers are now available for all except one of the 38 recognised genera. However, several markers are highly incomplete therefore missing data is problematic for producing a genus level phylogeny. We explore the relative utility of supertree and supermatrix approaches for addressing this challenge, and examine the effects of missing data on tree topology and resolution. Although the supertree approach returned a more conservative hypothesis, overall, both supermatrix and supertree analyses concurred in the topologies they returned. Using multiple genes and a dataset of variably complete taxa we found improved support for the monophyly and position of the tribes and genus level relationships. However, there was mixed support for the Richeeae tribe appearing one node basal to the Cosmelieae tribe or vice versa. It is probable that this will only be resolved through further sequencing. Our study supports previous findings that the amount of data is more critical than the completeness of the dataset in estimating well-resolved trees. Our results suggest that a “serendipitous” scaffolding approach that includes a mixture of well and poorly sequenced taxa can lead to robust phylogenetic hypotheses.

A 10‐gene phylogeny of Solanum section Herpystichum (Solanaceae) and a comparison of phylogenetic methods

Solanum section Herpystichum is a lineage that comprises both widespread and very narrowly distributed species. This study investigates the phylogenetic relationships of sect. Herpystichum and evaluates several phylogenetic methods for analysis of multiple sequences. Sequence data from seven nuclear (ITS, GBSSI, and five COSII) and three plastid (psbA-trnH, trnT-trnF, and trnS-trnG) regions were concatenated and analyzed under maximum parsimony and Bayesian criteria. In addition, we used two analytical methods that take into account differences in topologies resulting from the analyses of the individual markers: Bayesian Estimation of Species Trees (BEST) and supertree analysis. The monophyletic Solanum sect. Herpystichum was resolved with moderate support in the concatenated maximum parsimony and Bayesian analyses and the supertree analysis, and relationships within the section were well-resolved and strongly supported. The BEST topology, however, was poorly resolved. Also, because of how BEST deals with missing sequences, >25% of our accessions, including two species, had to be excluded from the analyses. Our results indicate a progenitor-descendent relationship with two species nested within the widespread S. evolvulifolium. Analytical methods that consider individual topologies are important for studies based on multiple molecular markers. On the basis of analyses in this study, BEST had the serious shortcoming that taxa with missing sequences must be removed from the analysis or they can produce spurious topologies. Supertree analysis provided a good alternative for our data by allowing the inclusion of all 10 species of sect. Herpystichum.

Building species trees from larger parts of phylogenomic databases

Gene trees are leaf-labeled trees inferred from molecular sequences. Because of gene duplication events arising in genomes, some species host several copies of the same gene, hence individual gene trees usually have several leaves labeled with identical species names. Dealing with such multi-labeled gene trees (MUL trees) is a substantial problem in phylogenomics, e.g. current supertree methods do not handle MUL trees, which restricts studies aimed at building the Tree of Life to a very small core of mono-copy genes. We propose to tackle this problem by mainly transforming a collection of MUL trees into a collection of trees, each containing single copies of labels. To achieve that aim, we provide several fast algorithmic building stones and describe how they fit in a general framework to build a species tree. First, we propose to separately preprocess each MUL tree in order to remove its redundant parts with respect to speciation events. For this purpose, we present a tree isomorphism algorithm for MUL trees to reduce redundant parts of these trees. Second, we show how the speciation signal contained in a MUL tree can be represented by a linear set of triplets. When this set is topologically coherent (compatible), we show that it can be used to produce a single-copy gene tree to replace the MUL tree while preserving the information it contains on speciation events. As an alternative approach, we propose to extract from each MUL tree a maximum size subtree that is free of duplication events. The algorithms are finally applied in a supertree analysis of hogenom, a database of homologous genes from fully sequenced genomes.

The supertree tool kit.

BackgroundLarge phylogenies are crucial for many areas of biological research. One method of creating such large phylogenies is the supertree method, but creating supertrees containing thousands of taxa, and hence providing a comprehensive phylogeny, requires hundred or even thousands of source input trees. Managing and processing these data in a systematic and error-free manner is challenging and will become even more so as supertrees contain ever increasing numbers of taxa. Protocols for processing input source phylogenies have been proposed to ensure data quality, but no robust software implementations of these protocols as yet exist.FindingsThe aim of the Supertree Tool Kit (STK) is to aid in the collection, storage and processing of input source trees for use in supertree analysis. It is therefore invaluable when creating supertrees containing thousands of taxa and hundreds of source trees. The STK is a Perl module with executable scripts to carry out various steps in the processing protocols. In order to aid processing we have added meta-data, via XML, to each tree which contains information such as the bibliographic source information for the tree and how the data were derived, for instance the character data used to carry out the original analysis. These data are essential parts of previously proposed protocols.ConclusionsThe STK is a bioinformatics tool designed to make it easier to process source phylogenies for inclusion in supertree analysis from hundreds or thousands of input source trees, whilst reducing potential errors and enabling easy sharing of such datasets. It has been successfully used to create the largest known supertree to date containing over 5000 taxa from over 700 source phylogenies.

Genomic taxonomy of Vibrios.

BackgroundVibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios.ResultsWe have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree.ConclusionThe combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding.

Supertrees and the Tree of Life: generating a metaphylogeny for a diverse invertebrate family (Insecta:Diptera:Therevidae) using constraint trees and the parsimony ratchet to overcome low taxon overlap

The dipteran family Therevidae (stiletto flies) is cosmopolitan and has been the focus of many taxonomic and phylogenetic studies over the last 25 years. Despite this work, questions remain concerning the relationships between subfamilies, genera and generic groups and membership of those groups. We use the supertree method to produce an inclusive phylogeny for the family Therevidae from 24 phylogenetic studies using matrix representation with parsimony (MRP) analysis. The supertree method, one of the most common approaches to calculating globally inclusive phylogenies from smaller more exclusive analyses, produced the therevid metaphylogeny despite only 34% of the terminal taxa being found in more than one source tree. We describe a method for handling low taxon overlap in supertree analyses, in combination with the parsimony ratchet and constraint tree techniques. The supertree presented here is an overarching phylogenetic hypothesis of the Therevidae, incorporating extensive sampling of major lineages and summarising past phylogenetic work on the family. The inclusive metaphylogeny for 362 therevid taxa robustly retrieves the subfamilies Agapophytinae, Phycinae, Therevinae and Xestomyzinae, and the tribes Cyclotelini and Therevini. The Phycinae and Xestomyzinae form a clade, sister to the remaining Therevidae. The Australasian and South American Taenogera Kröber genus-group is monophyletic and sister to a clade of Therevinae and the Australian endemic Agapophytinae. The Therevinae consists of the Anabarhynchus Macquart genus-group of Australian, South American, New Caledonian and New Zealand taxa as sister to the non-Australasian ‘higher Therevinae’, which contains the tribes Cyclotelini and Therevini. The Therevini includes the Hoplosathe Lyneborg &amp; Zaitzev, Litolinga Irwin &amp; Lyneborg, Baryphora Loew, Pandivirilia Irwin &amp; Lyneborg and Thereva Latreille generic-groups. MRP supertree methods can be used to produce inclusive metaphylogenies in situations where source trees have poor data overlap and low taxon overlap, and are therefore valuable in species-rich groups such as arthropods. These methods may be necessary for constructing the ‘Tree of Life’, representing phylogenetic relationships among the millions of known species. However, our analyses show that in situations of source tree conflict, MRP supertree analyses present only the majority signal. We also show that conflict between source trees can be hidden in MRP supertrees, thus our results emphasise the need to evaluate the resulting clades with reference to the source trees.

Triplet supertree heuristics for the tree of life

BackgroundThere is much interest in developing fast and accurate supertree methods to infer the tree of life. Supertree methods combine smaller input trees with overlapping sets of taxa to make a comprehensive phylogenetic tree that contains all of the taxa in the input trees. The intrinsically hard triplet supertree problem takes a collection of input species trees and seeks a species tree (supertree) that maximizes the number of triplet subtrees that it shares with the input trees. However, the utility of this supertree problem has been limited by a lack of efficient and effective heuristics.ResultsWe introduce fast hill-climbing heuristics for the triplet supertree problem that perform a step-wise search of the tree space, where each step is guided by an exact solution to an instance of a local search problem. To realize time efficient heuristics we designed the first nontrivial algorithms for two standard search problems, which greatly improve on the time complexity to the best known (naïve) solutions by a factor of n and n2 (the number of taxa in the supertree). These algorithms enable large-scale supertree analyses based on the triplet supertree problem that were previously not possible. We implemented hill-climbing heuristics that are based on our new algorithms, and in analyses of two published supertree data sets, we demonstrate that our new heuristics outperform other standard supertree methods in maximizing the number of triplets shared with the input trees.ConclusionWith our new heuristics, the triplet supertree problem is now computationally more tractable for large-scale supertree analyses, and it provides a potentially more accurate alternative to existing supertree methods.