Molecular phylogenetics and ecological diversification of the transisthmian fish genus Centropomus (Perciformes: Centropomidae).

Phylogenetic relationships among the 12 recognized fish species in the New World genus Centropomus (Pisces, Centropomidae) were analyzed using allozyme electrophoresis and 618 bp of the mitochondrial DNA 16S ribosomal RNA (rRNA) gene. Molecular phylogenetic trees were generally consistent with previously published partial hypotheses based on morphological evidence. However, previously undefined sister group relationships between major species groups were resolved using molecular data, and phylogenetic hypotheses for Centropomus based on 16S rRNA sequences were better supported than were allozyme-based hypotheses. The high level of congruence among the trees inferred from the nuclear and mitochondrial characters provided a firm phylogenetic basis for analysis of ecological diversification and molecular evolution in the genus. Compared to basal Centropomus species, members of the most nested species group were significantly larger in body size and occupied a marine niche only peripherally utilized by their congeners. We also observed substitution rate heterogeneity among 16S rRNA lineages; in contrast to expectations based on "metabolic rate" and "generation interval" models, relative substitution rates were faster than expected for the group of large-bodied snooks. Using the Pliocene rise of the Central American isthmian marine barrier to calibrate rates of 16S ribosomal gene evolution in Centropomus, we found that the rates for the genus were similar to those reported for higher vertebrates. Analysis of the three sets of transisthmian geminate taxa in Centropomus indicated that two of the pairs were probably formed during the Pliocene rise of the isthmus while the third pair diverged several million years earlier.     

Phylogeny of the shore crab family Grapsidae (Decapoda: Brachyura: Thoracotremata) based on a multilocus approach

The Grapsidae are a thoracotreme crab family with 40 species in eight genera (in their strict definition), and possess a number of morphological and molecular synapomorphies. Previous phylogenetic studies based on mitochondrial DNA markers established the monophyly of this family, but suggested possible paraphyly or polyphyly of some of the constituent genera. To test the validity of previous hypotheses, the present study reconstructed a molecular phylogeny of the grapsid crabs based on five molecular markers, including mitochondrial DNA markers and the first use of nuclear protein‐coding markers to address this issue. Monophyly of Grapsidae was confirmed, with the exception of the position of the monotypic genus Leptograpsodes. The polyphyly of the genus Pachygrapsus is consistent with previous molecular phylogenies, as members from this genus are dispersed throughout our gene tree. Grapsus and Planes were shown to be paraphyletic, with species of Pachygrapsus nested within them. Our study found incongruences between the currently adopted classification of the family, and hence taxonomic revisions will be needed. We hereby demonstrate the use of nuclear protein‐coding markers for high confidence reconstruction of decapod phylogenies, resolving most of the early splits that mitochondrial DNA markers alone are unable to tackle. © 2015 The Linnean Society of London     

Phylogenetic relationships of bufonid frogs and tests of alternate macroevolutionary hypotheses characterizing their radiation

The frog family Bufonidae is a large group distributed throughout all major land masses of die world except the polar regions. Although the monophyly of Bufonidae is strongly supported, phylogenetic relationships within the group are not well understood. Because of apparently large differences in rates of morphological and behavioral evolution, speciation, and geographical range, Bufonidae raises intriguing macroevolutionary questions. For example, one might imagine that the group's evolutionary history is congruent (1) with its morphological and behavioral character distribution, or (2) with its current geographical positioning. To examine phylogenetic relationships within Bufonidae and test these alternate hypotheses, DNA sequence data were obtained from four genes, three mitochondrial and one nuclear, from populations throughout the geographic and taxonomic breadth of the family. Phylogenetic analyses of these sequences by several methods support several hypotheses of relationships, notably: (1) contrary to the previous hypotheses of some workers, Bufo is not the basal, wildly paraphyletic genus of Bufonidae, although it is also not monophyletic, (2) the basal splits within bufonids separate South American 'atelopodid'genera from all other bufonids, although the monophyly of the 'atelopodids' is not supported, and (3) the most highly supported clades within the family generally correspond to small- to medium-sized, geographically and morphologically homogeneous groups. These trees are used to test the two alternate macroevolutionary hypotheses, and, while neither hypothesis fully explains the observed phylogenetic relationships, these relationships are broadly consistent with both character distribution and geography at particular levels.     

Phylogeny of the Bovidae (Artiodactyla, Mammalia), based on mitochondrial ribosomal DNA sequences.

Portions of the 12S and 16S mitochondrial ribosomal genes for 16 species representing nine tribes in the mammal family Bovidae were compared with six previously published orthologous sequences. Phylogenetic analysis of variable nucleotide positions under different constraints and weighting schemes revealed no robust groupings among tribes. Consensus trees support previous hypotheses of monophyly for four clades, including the traditional subfamily Bovinae. However, the basal diversification of bovid tribes, which was largely unresolved by morphological, immunodiffusion, allozyme, and protein sequence data, remains unresolved with the addition of DNA sequence data. The intractability of this systematic problem is consistent with a rapid radiation of the major bovid groups. Several analyses of our data show that monophyly of the Bovidae, which was weakly supported by previous morphological and molecular work, is questionable.     

Evaluation of relationships within the endemic Hawaiian Platynini (Coleoptera: Carabidae) based on molecular and morphological evidence

Relationships among 69 species of Hawaiian Platynini, a monophyletic beetle radiation, was investigated based on evidence from five data partitions, comprising mitochondrial and nuclear DNA sequences (cytochrome oxidase II, 624 bp; cytochrome b, 783 bp; 28S rDNA, 668 bp; wingless; 441 bp) and morphology (206 features of external and internal anatomy). Results from individual and combined data analyses generally support the monophyly of three putative divisions within Platynini in Hawaii: Division 0 (Colpocaccus species group), Division 1 (Blackburnia species group), and Division 2 (Metromenus species group). However, relationships within and among these three divisions differ from previous morphological hypotheses. An extensive series of sensitivity analyses was performed to assess robustness of recovered clades under a variety of weighted parsimony conditions. Sensitivity analyses support the monophyly of Divisions 0 and 1, but were equivocal for the monophyly of Division 2. A phylogeny based on combined data suggests at least four independent losses/reductions of platynine flight wings. The combined analysis provides corroboration for biogeographic hypotheses, including (1) colonization of Kauai by Hawaiian Platynini with subsequent dispersal and colonization along the island chain from Oahu to Maui Nui to Hawaii Island and (2) incongruent area relationships among Eastern Molokai, West Maui, and Haleakala for two species triplets.     

Molecular phylogeny of the stromateoid fishes (Teleostei: Perciformes) inferred from mitochondrial DNA sequences and compared with morphology-based hypotheses

The phylogenetic relationships among 21 species of stromateoid fishes, representing five families and 13 genera, were reconstructed using 3263bp of mitochondrial DNA sequences, including the posterior half of the 16S rRNA and entire COI and Cytb genes. The resultant molecular phylogenies were compared with previous phylogenetic hypotheses inferred from morphological characters. Molecular phylogenetic trees were constructed using the maximum parsimony, maximum likelihood, and Bayesian methods. All three methods resulted in well-resolved trees with most nodes being supported by moderate to high support values. In contrast to previous morphological analyses, which resulted in non-monophyly of Centrolophidae, all three methods utilized for the present molecular analyses supported the monophyly of Centrolophidae, as well as the reciprocal monophyly of the other stromateoid families, previous morphological hypotheses being rejected by the Templeton and Shimodaira-Hasegawa tests. In addition, the three methods indicated a sister-group relationship between Ariommatidae and Nomeidae. The position of Tetragonuridae was, however, incongruent between the MP method and the ML and Bayesian methods, being placed in the most basal position of Stromateoidei in the former, but occupying a sister relationship to Stromateidae in the latter. Comparison of the molecular phylogenies to previous morphological hypotheses suggested that evolutionary changes in morphological characters have not occurred equally among the stromateoid lineages, the evolution of the centrolophids not having been accompanied by appreciable morphological changes, whereas other stromateoids have undergone considerable morphological changes during their evolutionary history. The molecular phylogenies also shed some light on the evolutionary pattern of the pharyngeal sac, two of the four types of sac corresponding to two main lineages of Stromateoidei. Some taxonomic implications were also discussed.     

Molecular phylogenetics of the genus Ceratitis (Diptera: Tephritidae)

The Afrotropical fruit fly genus Ceratitis MacLeay is an economically important group that comprises over 89 species, subdivided into six subgenera. Cladistic analyses of morphological and host use characters have produced several phylogenetic hypotheses for the genus. Only monophyly of the subgenera Pardalaspis and Ceratitis (sensu stricto) and polyphyly of the subgenus Ceratalaspis are common to all of these phylogenies. In this study, the hypotheses developed from morphological and host use characters are tested using gene trees produced from DNA sequence data of two mitochondrial genes (cytochrome oxidase I and NADH-dehydrogenase subunit 6) and a nuclear gene (period). Comparison of gene trees indicates the following relationships: the subgenus Pardalaspis is monophyletic, subsection A of the subgenus Pterandrus is monophyletic, the subgenus Pterandrus may be either paraphyletic or polyphyletic, the subgenus Ceratalaspis is polyphyletic, and the subgenus Ceratitis s. s. might not be monophyletic. In addition, the genera Ceratitis and Trirhithrum do not form reciprocally monophyletic clades in the gene trees. Although the data statistically reject monophyly for Trirhithrum under the Shimodaira-Hasegawa test, they do not reject monophyly of Ceratitis.     

Cytochrome b and Bayesian inference of whale phylogeny

In the mid 1990s cytochrome b and other mitochondrial DNA data reinvigorated cetacean phylogenetics by proposing many novel and provocative hypotheses of cetacean relationships. These results sparked a revision and reanalysis of morphological datasets, and the collection of new nuclear DNA data from numerous loci. Some of the most controversial mitochondrial hypotheses have now become benchmark clades, corroborated with nuclear DNA and morphological data; others have been resolved in favor of more traditional views. That major conflicts in cetacean phylogeny are disappearing is encouraging. However, most recent papers aim specifically to resolve higher-level conflicts by adding characters, at the cost of densely sampling taxa to resolve lower-level relationships. No molecular study to date has included more than 33 cetaceans. More detailed molecular phylogenies will provide better tools for evolutionary studies. Until more genes are available for a high number of taxa, can we rely on readily available single gene mitochondrial data? Here, we estimate the phylogeny of 66 cetacean taxa and 24 outgroups based on Cytb sequences. We judge the reliability of our phylogeny based on the recovery of several deep-level benchmark clades. A Bayesian phylogenetic analysis recovered all benchmark clades and for the first time supported Odontoceti monophyly based exclusively on analysis of a single mitochondrial gene. The results recover the monophyly of all but one family level taxa within Cetacea, and most recently proposed super- and subfamilies. In contrast, parsimony never recovered all benchmark clades and was sensitive to a priori weighting decisions. These results provide the most detailed phylogeny of Cetacea to date and highlight the utility of both Bayesian methodology in general, and of Cytb in cetacean phylogenetics. They furthermore suggest that dense taxon sampling, like dense character sampling, can overcome problems in phylogenetic reconstruction.     

Utility of nuclear DNA intron markers at lower taxonomic levels: phylogenetic resolution among nine Tragelaphus spp

Phylogenetic relationships among the nine spiral-horn antelope species of the African bovid tribe Tragelaphini are controversial. In particular, mitochondrial DNA sequencing studies are not congruent with previous morphological investigations. To test the utility of nuclear DNA intron markers at lower taxonomic levels and to provide additional data pertinent to tragelaphid evolution, we sequenced four nuclear DNA segments (MGF, PRKCI, SPTBN, and THY) and combined these data with mitochondrial DNA sequences from three genes (cytochrome b, 12S rRNA, and 16S rRNA). Our molecular supermatrix comprised 4682 characters which were analyzed independently and in combination. Parsimony and model based phylogenetic analyses of the combined nuclear DNA data are congruent with those derived from the analysis of mitochondrial gene sequences. The corroboration between nuclear and mtDNA gene trees reject the possibility that genetic processes such as lineage sorting, gene duplication/deletion and hybrid speciation account for the conflict evident in the previously published phylogenies. It suggests rather that the morphological characters used to delimit the Tragelaphid species are subject to convergent evolution. Divergence times among species, calculated using a relaxed Bayesian molecular clock, are consistent with hypotheses proposing that climatic oscillations and their impact on habitats were the major forces driving speciation in the tribe Tragelaphini.     

PHYLOGENETIC RELATIONSHIPS AMONG EXTANT BRACHIOPODS

Abstract— The monophyletic status of the Brachiopoda and phylogenetic relationships within the phylum have long been contentious issues for brachiopod systematists. The relationship of brachiopods to other lophophore-bearing taxa is also uncertain; results from recent morphological and molecular studies are in conflict. To test current hypotheses of relationship, a phylogenetic analysis was completed (using PAUP 3.1.1) with 112 morphological and embryological characters that vary among extant representatives of seven brachiopod superfamilies, using bryozoans, phoronids, pterobranchs and sipunculids as outgroups. In the range of analyses performed, brachiopod monophyly is well supported, particularly by characters of soft anatomy. Arguments concerning single or multiple origins of a bivalved shell are not relevant to recognizing brachiopods as a clade. Articulate monophyly is very strongly supported, but inarticulate monophyly receives relatively weak support. Unlike previous studies, the nature of uncertainties about the clade status of Inarticulata are detailed explicitly here, making them easier to test in the future. Calcareous inarticulates appear to share derived characters with the other inarticulates, while sharing many primitive characters with other calcareous brachiopods (the articulates). Experimental manipulation of the data matrix reveals potential sources of bias in previous hypotheses of brachiopod phylogeny. Although not tested explicitly, lophophorate monophyly is very tentatively supported. Molecular systematic studies of a diverse group of brachiopods and other lophophorates will be particularly welcome in providing a test of the conclusions presented here.     

Evolutionary relationships among scyphozoan jellyfish families based on complete taxon sampling and phylogenetic analyses of 18S and 28S ribosomal DNA

A stable phylogenetic hypothesis for families within jellyfish class Scyphozoa has been elusive. Reasons for the lack of resolution of scyphozoan familial relationships include a dearth of morphological characters that reliably distinguish taxa and incomplete taxonomic sampling in molecular studies. Here, we address the latter issue by using maximum likelihood and Bayesian methods to reconstruct the phylogenetic relationships among all 19 currently valid scyphozoan families, using sequence data from two nuclear genes: 18S and 28S rDNA. Consistent with prior morphological hypotheses, we find strong evidence for monophyly of subclass Discomedusae, order Coronatae, rhizostome suborder Kolpophorae and superfamilies Actinomyariae, Kampylomyariae, Krikomyariae, and Scapulatae. Eleven of the 19 currently recognized scyphozoan families are robustly monophyletic, and we suggest recognition of two new families pending further analyses. In contrast to long-standing morphological hypotheses, the phylogeny shows coronate family Nausithoidae, semaeostome family Cyaneidae, and rhizostome suborder Daktyliophorae to be nonmonophyletic. Our analyses neither strongly support nor strongly refute monophyly of order Rhizostomeae, superfamily Inscapulatae, and families Ulmaridae, Catostylidae, Lychnorhizidae, and Rhizostomatidae. These taxa, as well as familial relationships within Coronatae and within rhizostome superfamily Inscapulatae, remain unclear and may be resolved by additional genomic and taxonomic sampling. In addition to clarifying some historically difficult taxonomic questions and highlighting nodes in particular need of further attention, the molecular phylogeny presented here will facilitate more robust study of phenotypic evolution in the Scyphozoa, including the evolution characters associated with mass occurrences of jellyfish.     

On the monophyly of Dactylorhiza Necker ex Nevski (Orchidaceae): is Coeloglossum viride (L.) Hartman a Dactylorhiza?

Previous phylogenetic analyses of Orchidaceae subtribe Orchidinae resulted in the proposal to classify Coeloglossum viride (L.) Hartman within the genus Dactylorhiza in order to maintain its monophyly. In this paper, we report some results that contradict previous studies regarding the monophyly of the traditional Dactylorhiza and its phylogenetic relationship with Coeloglossum. Our results, which combine sequences of the internal and external transcribed spacers of the nuclear ribosomal DNA, support the monophyly of Dactylorhiza , with Coeloglossum being a sister clade. The position of C. viride in the phylogenetic tree, and the considerable morphological differences with respect to Dactylorhiza , incline us to retain both lineages as distinct genera.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 261–269.     

Probing the Monophyly of the Sphaeropleales (Chlorophyceae) Using Data From Five Genes

Molecular phylogenetic analyses have had a major impact on the classification of the green algal class Chlorophyceae, corroborating some previous evolutionary hypotheses, but primarily promoting new interpretations of morphological evolution. One set of morphological traits that feature prominently in green algal systematics is the absolute orientation of the flagellar apparatus in motile cells, which correlates strongly with taxonomic classes and orders. The order Sphaeropleales includes diverse green algae sharing the directly opposite (DO) flagellar apparatus orientation of their biflagellate motile cells. However, algae across sphaeroplealean families differ in specific components of the DO flagellar apparatus, and molecular phylogenetic studies often have failed to provide strong support for the monophyly of the order. To test the monophyly of Sphaeropleales and of taxa with the DO flagellar apparatus, we conducted a molecular phylogenetic study of 16 accessions representing all known families and diverse affiliated lineages within the order, with data from four plastid genes (psaA, psaB, psbC, rbcL) and one nuclear ribosomal gene (18S). Although single‐gene analyses varied in topology and support values, analysis of combined data strongly supported a monophyletic Sphaeropleales. Our results also corroborated previous phylogenetic hypotheses that were based on chloroplast genome data from relatively few taxa. Specifically, our data resolved Volvocales, algae possessing predominantly biflagellate motile cells with clockwise (CW) flagellar orientation, as the monophyletic sister lineage to Sphaeropleales, and an alliance of Chaetopeltidales, Chaetophorales, and Oedogoniales, orders having multiflagellate motile cells with distinct flagellar orientations involving the DO and CW forms.     

Molecular phylogenetics of subclass Peritrichia (Ciliophora: Oligohymenophorea) based on expanded analyses of 18S rRNA sequences

Phylogenetic relationships among peritrich ciliates remain unclear in spite of recent progress. To expand the analyses performed in previous studies, and to statistically test hypotheses of monophyly, we analyzed a broad sample of 18s rRNA sequences (including 15 peritrich genera), applying a conservative alignment strategy and several phylogenetic approaches. The main results are that: (i) the monophyly of Peritrichia cannot be rejected; (ii) the two main clades of Sessilida do not correspond to formally recognized taxa; (iii) the monophyly of genera Vorticella and Epistylis is significantly rejected; and (iv) morphological structures commonly used in peritrich taxonomy may be evolutionarily labile.     

Phylogeny of the cricket subfamily Eneopterinae (Orthoptera, Grylloidea, Eneopteridae) based on four molecular loci and morphology

The phylogenetic relationships of 39 species of Eneopterinae crickets are reconstructed using four molecular markers (16S rRNA, 12S rRNA, cytochrome b, 18S rRNA) and a large morphological data set. Phylogenetic analysis via direct optimisation of DNA sequence data using parsimony as optimality criterion is done for six combinations of weighting parameter sets in a sensitivity analysis. The results are discussed in a twofold purpose: first, in term of significance of the molecular markers for phylogeny reconstruction in Ensifera, as our study represents the first molecular phylogeny performed for this insect suborder at this level of diversity; second, in term of corroboration of a previous phylogeny of Eneopterinae, built on morphological data alone. The four molecular markers all convey phylogenetic signal, although variously distributed on the tree. The monophyly of the subfamily, that of three over five tribes, and of 10 over 13 genera, are recovered. Finally, previous hypotheses on the evolution of acoustic devices and signals in the Eneopterinae clade are briefly tested, and supported, by our new data set.     

Systematics of the tribe Podalyrieae (Fabaceae) based on DNA, morphological and chemical data

Phylogenetic relationships among nine genera and 28 species of the southern African tribe Podalyrieae were estimated from sequences of the internal transcribed spacer (ITS) of nuclear ribosomal DNA as well as morphological and chemical data. Morphological and ITS sequence data produced cladograms with similar topologies, both supporting the monophyly of Podalyrieae (excluding Hypocalyptus ). The combined data sets indicate that subtribe Xiphothecinae are monophyletic, but embedded within Podalyriinae. The high degree of congruence between previous taxonomic hypotheses and those based on DNA data provides further evidence for the utility of ITS sequences in studying phylogeny.  © 2002 The Linnean Society of London , Botanical Journal of the Linnean Society , 2002, 139 , 159–170.     

The phylogenetic relationships of the suborder Acanthuroidei (Teleostei: Perciformes) based on molecular and morphological evidence

Fragments of 12S and 16S mitochondrial DNA genes were sequenced for 14 acanthuroid taxa (representing all six families) and seven outgroup taxa. The combined data set contained 1399 bp after removal of all ambiguously aligned positions. Examination of site saturation indicated that loop regions of both genes are saturated for transitions, which led to a weighted parsimony analysis of the data set. The resulting tree topology generally agreed with previous morphological hypotheses, most notably placing the Luvaridae within the Acanthuroidei, but it also differed in several areas. The putative sister group of Acanthuroidei, Drepane, was recovered within the suborder, and the sister group of the family Acanthuridae, Zanclus, was likewise recovered within the family. Morphological characters were included to produce a combined data set of 1585 characters for 14 acanthuroid taxa and a single outgroup taxon. An analysis of the same 15 taxa was performed with only the DNA data for comparison. The total-evidence analysis supports the monophyly of the Acanthuridae. A parametric bootstrap suggests the possibility that the paraphyly of Acanthuridae indicated by the molecular analyses is the result of long-branch attraction. The disagreement between molecular and morphological data on the relationships of the basal acanthuroids and its putative sister taxon is unresolved.     

Phylogeny of pholcid spiders (Araneae: Pholcidae): combined analysis using morphology and molecules

The spider family Pholcidae comprises a large number of mainly tropical, web-weaving spiders, and is among the most diverse and dominant spider groups in the world. The phylogeny of this family has so far been investigated exclusively using morphological data. Here, we present the first molecular data for the family analyzed in a phylogenetic context. Four different gene regions (12S rRNA, 16S rRNA, cytochrome c oxidase subunit I, 28S rRNA) and 45 morphological characters were scored for 31 pholcid and three outgroup taxa. The data were analyzed both for individual genes, combined molecular data, and molecular plus morphological data, using parsimony, maximum likelihood, and Bayesian methods. Some of the phylogenetic hypotheses obtained previously using morphology alone were also supported by our results, like the monophyly of pholcines and of the New World clade. On the other hand, some of the previous hypotheses could be discarded with some confidence (monophyly of holocnemines, the position of Priscula), and still others need further investigation (the position of holocnemines, ninetines, and Metagonia). The data obtained provide an excellent basis for future investigations of phylogenetic patterns both within the family and among spider families.     

Hidden generic diversity in Neotropical birds: molecular and anatomical data support a new genus for the "Scytalopus"indigoticus species-group (Aves: Rhinocryptidae)

The genus Scytalopus is a species-rich and taxonomically complicated component of the Neotropical avian family Rhinocryptidae. Probably because Scytalopus is a superficially uniform assemblage, its monophyly has not been seriously questioned. We investigated phylogenetic relationships of a representative set of species in the genus using nuclear and mitochondrial DNA sequences as well as anatomical data, and provided the first test of its presumed monophyly by including in the analyses its hypothesized closest relatives (the genera Myornis, Eugralla, and Merulaxis) as well as most rhinocryptid genera. We found strong support for the paraphyly of the genus Scytalopus, with the Scytalopus indigoticus species-group forming a clade with Merulaxis. A well-supported clade including the genera Eugralla, Myornis, and the remaining Scytalopus was also recovered. Because these results were recovered independently and with strong support using mitochondrial and nuclear data, and were entirely consistent with anatomical data, we erect a new genus for the S.indigoticus species-group. These findings illustrate the importance of formally testing hypotheses of monophyly even for well-accepted groups of Neotropical birds.