A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians

A time-calibrated salamander phylogeny including 765 species and 503 genes.

The growing use of comparative methods to address evolutionary questions has generated an increased need for robust hypotheses of evolutionary relationships for a wide range of organisms. Where a phylogeny exists for a group, often more than one phylogeny will exist for that group, and it is uncommon that the same taxa are in each of the existing trees. The types of data used to generate evolutionary trees can also vary greatly, and thus combining data sets is often difficult or impossible. To address comparative questions for groups where multiple phylogenetic hypotheses already exist, we need to combine different hypotheses in a way that provides the best estimate of the phylogeny for that group. Here, we combine seven seabird phylogenies (based on behavioral, DNA–DNA hybridization, isozyme, life history, morphological, and sequence data) to generate a comprehensive supertree for the Procellariiformes using matrix representation with parsimony. This phylogeny contains 122 taxa and represents a conservative estimate of combined relationships presented in the original seven source trees. We compared the supertree with results of a combined sequence data supermatrix for 103 seabird taxa. Results of the two approaches are broadly concordant, but matrix representation with parsimony provides a more comprehensive and more conservative estimate of the phylogeny of the group because it is less influenced by the largest of the source studies (which uses a single, relatively quickly evolving gene). Genetic data sets that can be combined in a supermatrix approach are currently less likely to be available than phylogenies that can be combined using some form of supertree approach. Although there are limitations to both of those approaches, both would be simpler if all phylogenetic studies made both their data sets and trees they generate available through databases such as TREEBASE.

BackgroundThe extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata.ResultsThe estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy.ConclusionsWe present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes.

Ineffective protein feature representation poses problems in protein classification in hierarchical structures. Discrete wavelet transform (DWT) is a feature representation method which generates global and local features based on different wavelet families and decomposition levels. To represent protein sequences, the proper wavelet family and decomposition level must be selected. This paper proposed a hybrid optimization method using particle swarm optimization and the firefly algorithm (FAPSO) to choose the suitable wavelet family and decomposition level of wavelet transformation for protein feature representation. The suggested approach improved on the work of earlier researchers who, in most cases, manually selected the wavelet family and level of decomposition based solely on experience and not on data. The paper also applied the virtual class methods to overcome the error propagation problems in hierarchical classification. The effectiveness of the proposed method was tested on a G-Protein Coupled Receptor (GPCR) protein data set consisting of 5 classes at the family level, 38 classes at the subfamily level, and 87 classes at the sub-subfamily level. Based on the result obtained, the most selected wavelet family and decomposition level chosen to represent GPCR classes by FAPSO are Biorthogonal wavelets and decomposition level 1, respectively. The experimental results show that the representation of GPCR protein using the FAPSO algorithm with virtual classes can yield 97.9%, 86.9%, and 81.3% classification accuracy at the family, subfamily, and sub-subfamily levels, respectively. In conclusion, the result shows that the selection of optimized wavelet family and decomposition level by the FAPSO algorithm, and the virtual class method can be potentially used as the feature representation method and a hierarchical classification method for GPCR protein.

The Platygastroidea are a diverse group of mostly small to tiny wasps, the common biology for which is endoparasitism of insect and spider eggs. No analytically-based phylogeny exists for the superfamily, and the current suprageneric classification is flawed in part because of its reliance on homoplasious and pleisiomorphic morphological characters. To determine platygastroid relationships as a basis for investigating host and ovipositor evolution, phylogenies of > 70 in-group species (representing 55 genera) were reconstructed by parsimony and Bayesian methods using three molecular markers; the mitochondrial cytochrome oxidase I and the nuclear genes 28S and 18S rRNA. The results strongly support the monophyly of the superfamily and one of the two families, Platygastridae, but the Scelionidae are most likely polyphyletic. However, within the Scelionidae, there is a well supported ‘main scelionid clade’ that contains the majority of genera assigned to the family. At the subfamilial level, both putative subfamilies of Platygastridae, the Platygastrinae, and Sceliotrachelinae, are likely to be polyphyletic. Within the Scelionidae, both the Teleasinae and Telenominae are monophyletic, but the Scelioninae is clearly not so. The current tribal classification for the Scelionidae is in need of major reassessment because no tribes, with the exception of the Scelionini s.s., were found to be monophyletic. Further illustrating the problems associated with the current classification is the nonmonophyly of a number of genera, namely Opisthacantha Caloteleia, Telenomus, Trimorus, Teleas and Idris. Analysis of ovipositor evolution in the superfamily revealed that the Ceratobaeus-type ovipositor system is ancestral; however, this trait was lost prior to the evolution of the main scelionid clade, for which the Scelio-type ovipositor system is ancestral and defines a mostly paraphyletic assemblage. Ancestral state analysis indicates that the Ceratobaeus-type ovipositor was subsequently re-evolved in the main scelionid clade, representing a possible contradiction of Dollo's law. Previously, the tribal placement has been used to predict the host associations of genera for which host data were unavailable. However, the fact that most tribes are not monophyletic throws into doubt any such speculation based on the current classification.

As the most abundant and diverse biological entities, prokaryotic viruses play pivotal roles in ecological systems. Their taxonomic classification has been instrumental in elucidating their diversity and ecological functions. However, determination of viral taxonomy remains a considerable challenge. Recently developed approaches succeed in assignment of viral taxonomy at higher ranks, such as at the family level and above, but struggle at the subfamily level and below to the genus and species resolutions. We describe a phylogeny-informed methodology to provide species-level taxonomic assignments of viruses. We used single-copy marker genes relevant to specific taxa and reference phylogenetic trees for these groups which facilitates direct comparisons with the taxonomic framework of the International Committee on Taxonomy of Viruses (ICTV). Our method demonstrated significant congruence with the ICTV taxonomy, showing 84%-91% alignment at the subfamily and genus levels. For species-level classification, our strategy was integrated with average nucleotide identity, yielding a high congruence rate of over 92% with the taxonomic data from the NCBI Virus database. This framework is implemented in vClassifier, a high-accuracy toolkit developed for standardized viral taxonomic assignment. Benchmarking comparisons revealed that vClassifier matches or surpasses other available tools regarding assignment rates. By achieving objectivity and high levels of consistency, vClassifier streamlines the taxonomic categorization of prokaryotic viral genomes. Accurate assignments at the subfamily, genus, and species levels will significantly refine the taxonomic resolution of viruses, fostering a deeper understanding of viral diversity in microbiomes and ecosystems. vClassifier is publicly accessible via https://github.com/AnantharamanLab/vClassifier.

Dogs, cats, and kin: A molecular species-level phylogeny of Carnivora

Stasis and convergence characterize morphological evolution in eupolypod II ferns.

The land snail genus Bothriembryon Pilsbry, 1894, endemic to southern Australia, contains seven fossil and 39 extant species, and forms part of the Gondwanan family Bothriembryontidae. Little published data on the geographical distribution of fossil Bothriembryon exists. In this study, fossil and modern data of Bothriembryon from nine Australian museums and institutes were mapped for the first time. The fossil Bothriembryon collection in the Western Australian Museum was curated to current taxonomy. Using this data set, the geological age of fossil and extant species was documented. Twenty two extant Bothriembryon species were identified in the fossil collection, with 15 of these species having a published fossil record for the first time. Several fossil and extant species had range extensions. The geological age span of Bothriembryon was determined as a minimum of Late Oligocene to recent, with extant endemic Western Australian Bothriembryon species determined as younger, traced to Pleistocene age. Extant Bothriembryon species from the Nullarbor region were older, dated Late Pliocene to Early Pleistocene. Cave environments proved an excellent source of fossil Bothriembryon material, where shells often showed signs of predation. The dataset from this study provided insights into the origin and radiation of Bothriembryon, and will enable future phylogenetic dating.

Conserved residues at the family and subfamily levels determine enzyme activity and substrate binding in glycoside hydrolase family 13

existing theoretical framework (Wiens 2003b). Furthermore, many contradictory studies suggesting that missing data are not generally problematic for Bayesian and likelihood analyses (given some assumptions) were not addressed by LEA. Second, the sweeping negative conclusions of LEA are not necessarily supported by their results. LEA find missing data to be problematic primarily when using sets of invariant or saturated characters and/or when obvious rate heterogeneity is ignored. Their results do not support the idea that missing data generally lead to incorrect inferences about topology when informative data are analyzed with appropriate methods. We conduct new simulations under more realistic conditions, and these results show no evidence that missing data generally lead to inaccurate Bayesian estimates of phylogeny. In fact, we show that the practice of excluding characters simply because they contain missing data cells may itself reduce accuracy. We reanalyze the “manipulated” empirical example from LEA and find that, without these artificial “manipulations” of the data, their conclusions are not supported. We also analyze eight empirical data sets, each containing many taxa with extensive missing data. We show that these incomplete taxa are consistently placed into the expected higher taxa, often with very strong support. Overall, our results confirm previous simulation and empirical studies showing that taxa with extensive missing data can be accurately placed in phylogenetic analyses and that adding characters with missing data can be beneficial (at least under some conditions). We conclude by pointing out important areas for future research on the topic of missing data and phylogenetic analysis.

The 24 000+ described species of Vespoidea include many well‐known stinging wasps, such as paper wasps and hornets (Vespidae), velvet ants (Mutillidae), spider wasps (Pompilidae) and ants (Formicidae). The compelling behaviours of vespoids have been instrumental in developing theories of stepwise evolutionary transitions, which necessarily depend on an understanding of phylogeny, yet, existing morphological phylogenies for Vespoidea conflict. We collected molecular data from four nuclear genes (elongation factor‐1α F2 copy, long‐wavelength rhodopsin, wingless and the D2–D3 regions of 28S ribosomal RNA (2700 bp in total)) to produce the first molecular phylogeny of Vespoidea. We analysed molecular data alone and in combination with published morphological data from Brothers and Carpenter. Parsimony analyses left many deeper nodes unsupported, but suggested paraphyly of three families. Total‐evidence Bayesian inference produced a more resolved tree, in which the monophyly of Vespoidea was nevertheless ambiguous. Bayesian inference of molecular data alone returned a well‐resolved consensus with posterior probabilities of over 95% for most nodes. We used this topology as the best estimate of phylogeny at the family and subfamily levels. Notable departures from previous estimates include: (i) paraphyly of Vespoidea resulting from the nesting of Apoidea within a lineage comprising Formicidae, Scoliidae and two subfamilies of Bradynobaenidae; (ii) paraphyly of Bradynobaenidae, Mutillidae and Tiphiidae; (iii) a sister relationship between Rhopalosomatidae and Vespidae; and (iv) Rhopalosomatidae + Vespidae as sister to all other vespoids/apoids. We discuss character evidence in light of the new phylogeny, and propose a new classification of Aculeata that recognizes eight superfamilies: Apoidea, Chrysidoidea, Formicoidea, Pompiloidea, Scolioidea, Tiphioidea, Thynnoidea and Vespoidea.

Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species

SuperTRI: A new approach based on branch support analyses of multiple independent data sets for assessing reliability of phylogenetic inferences


 
 
 Teeth are the most common element in the fossil record and play a critical role in taxonomic assessments. Variability in extant hominoid species is commonly used as a basis to gauge expected ranges of variability in fossil hominin species. In this study, variability in lower first molars is visualised in morphospace for four extant hominoid species and seven fossil hominin species. A size-versus-shape-based principle component analysis plot was used to recognise spatial patterns applicable to sexual dimorphism in extant species for comparison with fossil hominin species. In three African great ape species, variability occurs predominantly according to size (rather than shape), with the gorilla sample further separating into a male and a female group according to size. A different pattern is apparent for the modern human sample, in which shape variability is more evident. There is overlap between male and female modern humans and some evidence of grouping by linguistic/tribal populations. When fossil hominin species are analysed using equivalent axes of variance, the specimens group around species holotypes in quite similar patterns to those of the extant African great apes, but six individual fossil molars fall well outside of polygons circumscribing holotype clusters; at least three of these specimens are of interest for discussion in the context of sexual dimorphism, species variability and current species classifications. An implication of this study is that, especially in the case of modern humans, great caution needs to be exercised in using extant species as analogues for assessing variability considered to be a result of sexual dimorphism in fossil hominin species.
 
 
 
 
 Significance: 
 
 
 
 Caution should be exercised in using modern analogue species as proxies for fossil hominin species variability.
 Exceptionally wide ranges of molar variability between certain fossil hominin specimens currently allocated to the same species might indicate possible misclassification.
 Molar morphology in gorillas tends to reflect primarily size, rather than shape, variability between the sexes, which is a consideration in the context of assessing possible sexual dimorphism in fossil hominin species.