Ward C. Wheeler

Broad phylogenomic sampling improves resolution of the animal tree of life.

Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.

Systematic review of the frog family Hylidae, with special reference to Hylinae: Phylogenetic analysis and taxonomic revision

Abstract Hylidae is a large family of American, Australopapuan, and temperate Eurasian treefrogs of approximately 870 known species, divided among four subfamilies. Although some groups of Hylidae have been addressed phylogenetically, a comprehensive phylogenetic analysis has never been presented. The first goal of this paper is to review the current state of hylid systematics. We focus on the very large subfamily Hylinae (590 species), evaluate the monophyly of named taxa, and examine the evidential basis of the existing taxonomy. The second objective is to perform a phylogenetic analysis using mostly DNA sequence data in order to (1) test the monophyly of the Hylidae; (2) determine its constituent taxa, with special attention to the genera and species groups which form the subfamily Hylinae, and c) propose a new, monophyletic taxonomy consistent with the hypothesized relationships. We present a phylogenetic analysis of hylid frogs based on 276 terminals, including 228 hylids and 48 outgroup taxa. Included are exemplars of all but 1 of the 41 genera of Hylidae (of all four nominal subfamilies) and 39 of the 41 currently recognized species groups of the species-rich genus Hyla. The included taxa allowed us to test the monophyly of 24 of the 35 nonmonotypic genera and 25 species groups of Hyla. The phylogenetic analysis includes approximately 5100 base pairs from four mitochondrial (12S, tRNA valine, 16S, and cytochrome b) and five nuclear genes (rhodopsin, tyrosinase, RAG-1, seventh in absentia, and 28S), and a small data set from foot musculature. Concurring with previous studies, the present analysis indicates that Hemiphractinae are not related to the other three hylid subfamilies. It is therefore removed from the family and tentatively considered a subfamily of the paraphyletic Leptodactylidae. Hylidae is now restricted to Hylinae, Pelodryadinae, and Phyllomedusinae. Our results support a sister-group relationship between Pelodryadinae and Phyllomedusinae, which together form the sister taxon of Hylinae. Agalychnis, Phyllomedusa, Litoria, Hyla, Osteocephalus, Phrynohyas, Ptychohyla, Scinax, Smilisca, and Trachycephalus are not monophyletic. Within Hyla, the H. albomarginata, H. albopunctata, H. arborea, H. boans, H. cinerea, H. eximia, H. geographica, H. granosa, H. microcephala, H. miotympanum, H. tuberculosa, and H. versicolor groups are also demonstrably nonmonophyletic. Hylinae is composed of four major clades. The first of these includes the Andean stream-breeding Hyla, Aplastodiscus, all Gladiator Frogs, and a Tepuian clade. The second clade is composed of the 30-chromosome Hyla, Lysapsus, Pseudis, Scarthyla, Scinax (including the H. uruguaya group), Sphaenorhynchus, and Xenohyla. The third major clade is composed of Nyctimantis, Phrynohyas, Phyllodytes, and all South American/ West Indian casque-headed frogs: Aparasphenodon, Argenteohyla, Corythomantis, Osteocephalus, Osteopilus, Tepuihyla, and Trachycephalus. The fourth major clade is composed of most of the Middle American/Holarctic species groups of Hyla and the genera Acris, Anotheca, Duellmanohyla, Plectrohyla, Pseudacris, Ptychohyla, Pternohyla, Smilisca, and Triprion. A new monophyletic taxonomy mirroring these results is presented where Hylinae is divided into four tribes. Of the species currently in “Hyla”, 297 of the 353 species are placed in 15 genera; of these, 4 are currently recognized, 4 are resurrected names, and 7 are new. Hyla is restricted to H. femoralis and the H. arborea, H. cinerea, H. eximia, and H. versicolor groups, whose contents are redefined. Phrynohyas is placed in the synonymy of Trachycephalus, and Pternohyla is placed in the synonymy of Smilisca. The genus Dendropsophus is resurrected to include all former species of Hyla known or suspected to have 30 chromosomes. Exerodonta is resurrected to include the former Hyla sumichrasti group and some members of the former H. miotympanum group. Hyloscirtus is resurrected for the former Hyla armata, H. bogotensis, and H. larinopygion groups. Hypsiboas is resurrected to include several species groups—many of them redefined here—of Gladiator Frogs. The former Hyla albofrenata and H. albosignata complexes of the H. albomarginata group are included in Aplastodiscus. New generic names are erected for (1) Agalychnis calcarifer and A. craspedopus; (2) Osteocephalus langsdorffii; the (3) Hyla aromatica, (4) H. bromeliacia, (5) H. godmani, (6) H. mixomaculata, (7) H. taeniopus, (8) and H. tuberculosa groups; (9) the clade composed of the H. pictipes and H. pseudopuma groups; and (10) a clade composed of the H. circumdata, H. claresignata, H. martinsi, and H. pseudopseudis groups.

Arthropod phylogeny based on eight molecular loci and morphology.

The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean–hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal ‘total evidence’ cladogram supports the crustacean–hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

PHYLOGENETIC SYSTEMATICS OF DART-POISON FROGS AND THEIR RELATIVES (AMPHIBIA: ATHESPHATANURA: DENDROBATIDAE)

Abstract The known diversity of dart-poison frog species has grown from 70 in the 1960s to 247 at present, with no sign that the discovery of new species will wane in the foreseeable future. Although this growth in knowledge of the diversity of this group has been accompanied by detailed investigations of many aspects of the biology of dendrobatids, their phylogenetic relationships remain poorly understood. This study was designed to test hypotheses of dendrobatid diversification by combining new and prior genotypic and phenotypic evidence in a total evidence analysis. DNA sequences were sampled for five mitochondrial and six nuclear loci (approximately 6,100 base pairs [bp]; x¯ = 3,740 bp per terminal; total dataset composed of approximately 1.55 million bp), and 174 phenotypic characters were scored from adult and larval morphology, alkaloid profiles, and behavior. These data were combined with relevant published DNA sequences. Ingroup sampling targeted several previously unsampled species, including Aromobates nocturnus, which was hypothesized previously to be the sister of all other dendrobatids. Undescribed and problematic species were sampled from multiple localities when possible. The final dataset consisted of 414 terminals: 367 ingroup terminals of 156 species and 47 outgroup terminals of 46 species. Direct optimization parsimony analysis of the equally weighted evidence resulted in 25,872 optimal trees. Forty nodes collapse in the strict consensus, with all conflict restricted to conspecific terminals. Dendrobatids were recovered as monophyletic, and their sister group consisted of Crossodactylus, Hylodes, and Megaelosia, recognized herein as Hylodidae. Among outgroup taxa, Centrolenidae was found to be the sister group of all athesphatanurans except Hylidae, Leptodactyidae was polyphyletic, Thoropa was nested within Cycloramphidae, and Ceratophryinae was paraphyletic with respect to Telmatobiinae. Among dendrobatids, the monophyly and content of Mannophryne and Phyllobates were corroborated. Aromobates nocturnus and Colostethus saltuensis were found to be nested within Nephelobates, and Minyobates was paraphyletic and nested within Dendrobates. Colostethus was shown to be rampantly nonmonophyletic, with most species falling into two unrelated cis- and trans-Andean clades. A morphologically and behaviorally diverse clade of median lingual process-possessing species was discovered. In light of these findings and the growth in knowledge of the diversity of this large clade over the past 40 years, we propose a new, monophyletic taxonomy for dendrobatids, recognizing the inclusive clade as a superfamily (Dendrobatoidea) composed of two families (one of which is new), six subfamilies (three new), and 16 genera (four new). Although poisonous frogs did not form a monophyletic group, the three poisonous lineages are all confined to the revised family Dendrobatidae, in keeping with the traditional application of this name. We also propose changes to achieve a monophyletic higher-level taxonomy for the athesphatanuran outgroup taxa. Analysis of character evolution revealed multiple origins of phytotelm-breeding, parental provisioning of nutritive oocytes for larval consumption (larval oophagy), and endotrophy. Available evidence indicates that transport of tadpoles on the dorsum of parent nurse frogs—a dendrobatid synapomorphy—is carried out primitively by male nurse frogs, with three independent origins of female transport and five independent origins of biparental transport. Reproductive amplexus is optimally explained as having been lost in the most recent common ancestor of Dendrobatoidea, with cephalic amplexus arising independently three times.

The Phylogeny of the Extant Chelicerate Orders

The phylogeny of the extant chelicerate orders is examined in the light of morphological and molecular evidence. Representatives from each of the chelicerate ‘orders’ and mandibulate and onychophoran outgroups are examined. Molecular (small and large ribosomal subunit DNA) and morphological information is combined in a total evidence regime to determine the most consistent picture of extant chelicerate relationships for these data. Multiple phylogenetic analyses are performed with variable analysis parameters yielding largely consistent results. A normalized incongruence length metric is used to assay the relative merit of the multiple analyses. The combined analysis with lowest character incongruence yields the scheme of relationships (Pycnogonida+ (Xiphosura+((Opiliones+((Solifugae+Pseudoscorpiones)+Scorpiones))+((Ricinulei+Acari)+(Palpigradi+ ((Thelyphonida+Schizomida=Uropygi)+(Amblypygi+ Araneae))))))). This result is fairly robust to variation in analysis parameters, with the placement of solifugids and the status of the pedipalps responsible for most disagreement.

Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data.

The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high‐level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the “Cyphopalpatores” or “Palpatores.” The topology obtained is congruent with the previous hypothesis of “Palpatores” paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones.

NUCLEIC ACID SEQUENCE PHYLOGENY AND RANDOM OUTGROUPS

Abstract— When divergent taxa are used to root networks, it is assumed that the character stales in the outgroup have historical similarity to those in the ingroup. Yet, if the data are nucleic acid sequences, the character stales shared by a divergent outgroup may be based not on history but on random similarity. A simple procedure is proposed to test this possibility. In the absence of an appropriate outgroup, root position can be estimated with the use of an asymmetrical character transformation matrix. If the matrix is sufficiently biased, it can supply the polarity information usually derived from an outgroup. This outgroup test and rooting procedure are demonstrated with ADH sequences from the genus Drosophila.

POY version 4: phylogenetic analysis using dynamic homologies

We present POY version 4, an open source program for the phylogenetic analysis of morphological, prealigned sequence, unaligned sequence, and genomic data. POY allows phylogenetic inference when not only substitutions, but insertions, deletions, and rearrangement events are allowed (computed using the breakpoint or inversion distance). Compared with previous versions, POY 4 provides greater flexibility, a larger number of supported parameter sets, numerous execution time improvements, a vastly improved user interface, greater quality control, and extensive documentation. We introduce POY’s basic features, and present a simple example illustrating the performance improvements over previous versions of the application.

Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search.

A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple‐alignment step, thereby creating topology‐specific, dynamic homology statements. Hence, no multiple‐alignment is required to generate cladograms. Unlike general and globally optimal multiple‐alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These “lines of correspondence” link ancestor–descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion–deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed.

Scorpion higher phylogeny and classification, taxonomic anarchy, and standards for peer review in online publishing

Soleglad and Fets (2003a) attempt to reconstruct the phylogeny of Recent (including extant) scorpions, the revised classification derived from it, and recent emendations, mostly published in their self‐edited online journal, Euscorpius, are deficient. Separate analyses of three independent matrices (morphology, 16S rDNA, 18S rDNA) were presented. In the morphological matrix, 52 binary and 10 tristate trichobothrial characters were replaced with one character comprising six ordered states representing trichobothrial “types”. The remaining matrix of 105 characters was further reduced to 33 “fundamental” characters (20% of the morphological dataset), the analysis of which appears to be the basis for the revised classification presented. The taxon sample for the morphological analysis included 14 supraspecific terminal taxa representing genera, the monophyly of only 7 (12.5%) of which has been confirmed. A composite terminal, assembled from the fragments of fossils that may not be confamilial let alone monophyletic, was created for the Palaeopisthacanthidae, employed as the primary outgroup for the analysis. Other important outgroup taxa, notably eurypterids, xiphosurans and other arachnids, were omitted entirely. The morphological characters presented contained numerous unjustifiable assumptions of character polarity and phylogenetic relationship. An approach to character coding, deliberately adopted to reduce “homoplasy”, biased the analysis towards a preconceived result. Structurally and topographically similar features in different taxa were explicitly assigned separate (often autapomorphic) states according to presumed phylogenetic relationships among the taxa in which they were observed. Putative “reversals” were coded as separate characters or states. Character transformation was forced by ordering, additive coding or Sankoff optimization through allegedly intermediate states for which there is no empirical evidence. Many characters were defined in a manner that demonstrates either a lack of understanding of, or disregard for, established methods and standards of morphological character coding. Some states display overlapping variation whereas others subsume variation that is not structurally or topographically similar. Polymorphic “states” were created for terminals with interspecific variation and unknown “states” for terminals that should have been scored unknown. Many characters were not evaluated for particular terminal taxa, but merely scored inapplicable although the structures and, consequently, the characters in question are present and therefore applicable to them. In view of the significant theoretical and empirical problems with the approach to cladistics taken by Soleglad and Fet, we find no justification for accepting either the results of their analyses or the revised classification derived from them. Pending the outcome of a rigorous phylogenetic analysis, published according to acceptable standards of scholarship in a peer‐reviewed journal, we revert to the suprageneric classification of Scorpiones reflected by the most recent peer‐reviewed, published treatments and reject all changes to the classification proposed by Soleglad, Fet and colleagues since 2001. We argue that an analysis and revised classification of the kind presented in various papers by these authors could not survive the peer‐review process of a mainstream scientific journal. The poor scholarship exemplified by these and other papers published in Euscorpius emphasize the importance of quality control associated with the emergent infrastructure of online publishing. A centralized register of taxa may be the only solution for ensuring quality control in the taxonomy of the future.