Chromosomal relationships of the tortoises (family Testudinidae)

Banded chromosomes of five species of testudinid turtles (Geochelone pardalis, G. elongata, G. elephantopus, Gopherus berlandieri, and G. polyphemus) reveal little variation within either genus, although there are differences in amount and distribution of heterochromatin between Geochelone pardalis and G. elongata. The chromosomal position and size of the nucleolar-organizer region differs between species of the two genera.Comparisons of standard karyotypes of these species and Malacochersus tornieri with data in the literature on other tortoises show a diploid number of 52 characterizes the family. These data are consistent with those for other families which show turtles are karyotypically conservative. G-banded chromosomes of Geochelone are identical to those of Chinemys reevesi, a karyotypically primitive batagurine emydid, supporting a derivation of the tortoises from a batagurine ancestor.     

Comparison of complete mitochondrial DNA control regions among five Asian freshwater turtle species and their phylogenetic relationships

The complete mitochondrial DNA (mtDNA) control regions (CR), cytochrome b (Cyt b), NADH dehydrogenase subunit 4 (ND4) and cytochrome coxidase subunit I (CO I) genes of four Asian freshwater turtles, Mauremys japonica, Ocadia sinensis, M. mutica, and Annamemys annamensis, were sequenced using universal PCR and long-PCR techniques. Combined with CR sequences of Chinemys reevesii, the composition and structure of CR of the five species were compared and analyzed. Three functional domains (TAS, CD and CSB) in CR and their conserved sequences (TAS, CSB-F, CSB-1, CSB-2, and CSB-3) were identified based on sequence similarity to those of other turtles. At the 3' end of CSB, six type motifs of variable number of tandem repeats (VNTRs) of five species were recognized, in which the TTATATTA motif may be the VNTR motif of the ancestral species of these five turtles. Comparison of nucleotide divergences among Cyt b, ND4, CO I, and CR of 11 turtle species using transitions + transversions and transversions-only methods supported the conclusion that CR evolved 2.6- to 5.7-fold faster than the other mtDNA genes. After excluding VNTRs of CR, molecular phylogenetic trees were constructed with maximum parsimony, maximum likelihood and Bayesian inference methods. The results supported an expanded clade of Mauremys, which included species formerly in Ocadia, Chinemys, Mauremys, and Annamemys; this was also reflected in the results of VNTR analysis.     

Evolution of pipoid frogs:intergeneric relationships of the aquatic frog family Pipidae (Anura)

The 27 species of the aquatic frog family Pipidae are currently arranged in four genera: Xenopus (15 species), Hymenochirus (four species), and the poorly known genus Pseudhymenochirus (one species) occur in Africa; Pipa (seven species) is found in South America and lower Central America. Despite extensive work on the biology of Xenopus from various disciplines, the evolutionary relationships of Xenopus to other pipids have not been resolved. Phylogenetic analyis of morphological features of pipid frogs indicates that, contrary to earlier opinions, Hymenochirus and Pipa are closest relatives (sister-groups); these genera are placed in the subfamily Pipinae. Also, the currently recognized species of Xenopus do not form a natural group; the species tropicalis and epitropicalis are more closely related to Hymenochirus + Pipa than to the remaining species of Xenopus . The two discordant species are transferred to the genus Silurana , which is relegated to the new subfamily Siluraninae; it is the sister-group of the Pipinae. The remaining species of Xenopus constitute a monophyletic group that is placed in the subfamily Xenopodinae as the sister-group of the other genera of pipids.     

Phylogenetic relationships among microgastrine braconid wasp genera based on data from the 16S, COI and 28S genes and morphology

Abstract Phylogenetic relationships among the genera of the large braconid wasp subfamily Microgastrinae were explored using DNA sequence data from the mitochondrial large ribosomal subunit (16S), nuclear large ribosomal subunit (28S) and mitochondrial cytochrome oxidase (COI) genes, along with morphological characters, both new and from previous studies. The taxonomic history of this group of wasps is reviewed, along with a critique of previous phylogenetic studies on the group. Molecular data were sampled from forty-six species representing twenty-six genera of microgastrines, plus three species representing the close outgroup taxa Cardiochilinae and Miracinae. Some 2300 base pairs of aligned sequence were obtained per taxon from the three genes. In addition, fifty-three morphological characters were coded for all known genera, including two undescribed genera, except Semionis Nixon (known from only a single male type specimen). Relationships among several groups of genera are clarified and challenge some major assumptions made in earlier classifications. In particular, it is clear that dependence on one or a few major morphological character systems oversimplifies relationships, and can lead to misleading results. Despite the large amount of data analysed, basal divergences within the subfamily remain poorly resolved and essentially unsupported in any rigorous statistical sense.     

Molecular evaluation of phylogenetic significances in the highly divergent karyotypes of the genus Gonocephalus (Reptilia: Agamidae) from tropical Asia

The Oriental large-bodied crested dragons of the genus Gonocephalus are known to include two distinct karyomorphs. To evaluate their phylogenetic significances, we conducted phylogenetic analyses of the genus together with other agamid genera on the basis of 862 base positions of mitochondrial 12S and 16S rRNA genes. Results suggested the presence of two distinct lineages within Gonocephalus, of which one, represented by G. robinsonii that has a 2n = 32 karyotype, was closer to other Oriental agamid genera than to the other congeneric lineage. Monophyly of the latter, characterized by unique chromosomal arrangement among agamid genera (2n = 42 karyotype), was confirmed. It is thus likely that states of morphological characters shared between the two lineages are derived through convergence, or represent symplesiomorphy. Our results also suggest that the karyological similarity between G. robinsonii and several Australian agamids, pointed out in a previous study, is actually attributable to homoplasy rather than their recent common ancestry.     

A phylogenetic analysis of relationships among genera of Conopidae (Diptera) based on molecular and morphological data

Members of the family Conopidae (Diptera) have been the focus of little targeted phylogenetic research. The most comprehensive test of phylogenetic support for the present subfamily classification of Conopidae is presented here using 66 specimens, including 59 species of Conopidae and seven outgroup taxa. Relationships among subfamily clades are also explored. A total of 6824 bp of DNA sequence data from five gene regions (12S ribosomal DNA, cytochrome c oxidase subunit I, cytochrome b, 28S ribosomal DNA and alanyl‐tRNA synthetase) are combined with 111 morphological characters in a combined analysis using both parsimony and Bayesian methods. Parsimony analysis recovers three shortest trees. Bayesian analysis recovers a nearly identical tree. Five monophyletic subfamilies of Conopidae are recovered. The rarely acknowledged Zodioninae is restored, including the genera Zodion and Parazodion. The genus Sicus is removed from Myopinae. Morphological synapomorphies are discussed for each subfamily and inter‐subfamily clade, including a comprehensive review of the character interpretaions of previous authors. Included are detailed comparative illustrations of male and female genitalia of representatives of all five subfamilies with new morphological interpretation.     

Phylogeny and classification of the Culicidae (Diptera)

The generic relationships and higher classification of the family Culicidae are examined on the basis of a phylogenetic analysis. New and traditional morphological characters studied and compared throughout the Culicidae resulted in the acquisition of character data relative to the majority of species within each genus. Polymorphisms and morphological observations are discussed and additional information and illustrations are provided for the majority of characters and their character states. The analysis of seventy-three adult, pupal and fourth-instar larval characters coded for the thirty-eight currently recognized genera of mosquitoes resulted in relationships and groupings which differ significantly from traditional hypotheses. The analysis supports the monophyly of the subfamily Anophelinae and the tribes Culicini and Sabethini. The Anophelinae form the most basal clade of the family. The results indicate that Aedini is a paraphyletic assemblage with respect to the Mansoniini, each of which is monophyletic in itself. The Aedini + Mansoniini form a sister group to the Culicini + Sabethini, with the Aedini and the Culicini placed in ancestral relationships to the Mansoniini and the Sabethini, respectively. Based on the topography of generic relationships among more 'generalized' mosquitoes, the boundaries and relationships of the tribes Aedeomyiini, Uranotaeniini, Ficalbiini, Hodgesiini, Orthopodomyiini and Culisetini appear to be problematic. Relationships between genera of the tribe Aedini are generally poorly resolved due to a significant amount of polymorphism, especially within the genus Aedes as currently defined. There is no support for separate subfamily recognition for the genus Toxorhynchites , which is downgraded to tribal status as a result of the analysis. The results are discussed in relation to previous hypotheses based on subjective inference and cladistic analyses.     

Phylogenetic implications of karyotypic variation in the Batagurinae (Testudines: Emydidae)

The present study examined karyotypes of 16 genera and, along with previous reports, chromosomal data are now available for 18 of the 23 recognized batagurine genera. There are no karyotypic data available for the members of McDowell's (1964) Hardella complex. The Batagur, Heosemys and Geoemyda complexes retain the hypothesized primitive karyotype for the subfamily (2n=52). All the genera in these three complexes have been examined except Batagur and Annamemys. The Orlitia complex is karyotypically distinct with 2n=50 and the NOR located terminally on a large microchromosome. The genus Malayemys inclusion in the Batagur complex is not supported. Malayemys is characterized by a 2n=50 karyotype, with the NOR located interstitially on a large microchromosome. The Malayemys complex is erected to contain this genus at a point intermediate between the Orlitia complex and the subfamily Emydinae. Malayemys and the emydines are karyotypically indistinguishable. The Neotropical genus Rhinoclemmys (Geoemyda complex) differs only slightly from the primitive batagurine karyotype in the position of the NOR. The species R. funerea and R. punctularia further differ in possessing one less metacentric macrochomosome. An interesting situation involves two subspecies of R. punctularia. The nominate subspecies is characterized by a 2n=56 karyotype, while R. p. melanosterna reportedly has a 2n=52 karyotype. Such a difference is interpreted as indicative of genetic differentiation between the two forms of a magnitude inconsistent with considering them as conspecific. Taken together with zoogeographic considerations, the karyotypic difference between the forms R. p. punctularia and R. p. melanosterna seem sufficient to warrant species distinction for R. melanosterna as previously suggested by Pritchard (1979b).     

Phylogeny of the Archiborborinae (Diptera: Sphaeroceridae) Based on Combined Morphological and Molecular Analysis

The Archiborborinae is a diverse Neotropical subfamily of Sphaeroceridae, with many undescribed species. The existing generic classification includes three genera consisting of brachypterous species, with all other species placed in the genus Archiborborus. We present the first phylogenetic hypothesis for the subfamily based on morphological, molecular, and combined datasets. Morphological data include 53 characters and cover all valid described taxa (33 species in 4 genera) in the subfamily, as well as 83 undescribed species. Molecular data for five genes (mitochondrial 12S rDNA, cytochrome c oxidase subunit I, and cytochrome B, and nuclear alanyl-tRNA synthetase and 28S rDNA) were obtained for 21 ingroup taxa. Data support the separation of the Archiborborinae from the Copromyzinae, with which they were formerly combined. Analyses support consistent groups within the subfamily, but relationships between groups are poorly resolved. The validity of the brachypterous genera Penola Richards and Frutillaria Richards is supported. The former genus Archiborborus Duda is paraphyletic, and will be divided into monophyletic genera on the basis of this work. Aptery and brachyptery have evolved multiple times in the subfamily. Antrops Enderlein, previously including a single brachypterous species, is a senior synonym of Archiborborus.     

Phylogeny of Triatomine Vectors of Trypanosoma cruzi Suggested by Mitochondrial DNA Sequences

The subfamily Triatominae (Hemiptera: Reduviidae) comprises hematophagous insects, most of which are actual or potential vectors of Trypanosoma cruzi, the protozoan agent of Chagas' disease (American trypanosomiasis). DNA sequence comparisons of mitochondrial DNA (mtDNA) genes were used to infer phylogenetic relationships among 32 species of the subfamily Triatominae, 26 belonging to the genus Triatoma and six species of different genera. We analyzed mtDNA fragments of the 12S and 16S ribosomal RNA genes (totaling 848-851 bp) from each of the 32 species, as well as of the cytochrome oxidase I (COI, 1447 bp) gene from nine. The phylogenetic analyses unambiguously supported several clusters within the genus Triatoma. In the morphological classification, T. costalimai was placed tentatively within the infestans complex while T. guazu was not included in any Triatoma complex. The placement of these species in the molecular phylogeny indicated that both belong to the infestans complex. We confirmed with a strong support the inclusion of T. circummaculata, a member of a different complex based on morphology, within the infestans complex. On the other hand, the present phylogenetics analysis did not support the monophyly of the infestans complex species as it was suggested in our previous studies. While no strong inference of polyphyly of the genus Triatoma was provided by the bootstrap analyses, the other species belonging to Triatomini analyzed could not be distinguished from the species of Triatoma.     

Systematics of the genera of Bodotriidae (Crustacea: Cumacea)

The cumacean family Bodotriidae includes 382 species in 31 genera grouped in three subfamilies: Bodotriinae, Mancocumatinae and Vaunthompsoniinae. Generic diagnoses are based on few characters that often have overlapping states among genera, complicating the understanding of the relationships within the group. The goals of this study are to illuminate the phylogenetic relationships among the genera of the Bodotriidae using morphological characters and to review the systematics of the family. For this purpose, all species within each genus were studied from the literature to code all the variability of genera for 109 variable morphological characters. Phylogenetic analyses show that there is independent reduction of the pleopods in two clades from a plesiomorphic state of five pairs, while the number of exopods of peraeopods has been reduced gradually in more derived groups of bodotriids. The subfamily Bodotriinae is the most derived and the Vaunthompsoniinae the most basal, and is paraphyletic with the Mancocumatinae embedded within it. No discriminatory characters were found between the subfamilies Mancocumatinae and Vaunthompsoniinae and they are not clearly separated in the phylogeny. Mancocumatinae is synonymized with Vaunthompsoniinae and all the genera of the former Mancocumatinae should be included within Vaunthompsoniinae. Analyses of character evolution justify a few other taxonomic changes. All genera were redescribed based on all the coded characters and a complete list of all valid species for each genus is included. Finally, dichotomous keys for identification to genus level are provided.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 151 , 1–58.     

16S rDNA sequence analysis of bacterial isolates from biodeteriorated mural paintings in the Servilia tomb (Necropolis of carmona, Seville, Spain)

Bacteria were isolated from damaged mural paintings of the Servilia tomb (necropolis of Carmona, Seville, Spain). Selected strains, representative for different clusters of isolates with similar fatty acid profiles, were analysed by 16S rDNA sequence analysis. Bacillus is the dominant genus among the isolates: members of the rRNA species complexes of B. megaterium, B. pumilus and B. firmus were found as well as several other Bacillus species. One group of halotolerant isolates falls in the Bacillus sensu lato group, with closest relatedness to the genera Salibacillus and Virgibacillus. Other genera found are Artbrobacter, Micrococcus, Streptomyces, Sphingomonas, Paenibacillus, and a genus closely related to Paracraurococcus. Many isolates showed low 16S rDNA sequence similarities with the closest related database entries, a strong indication for the presence of several new species among the isolates.     

Phylogenetic relationships of the pipid frogs Xenopus and Silurana: an integration of ribosomal DNA and morphology

Relationships of the pipid frog genus Silurana (= Xenopus tropicalis group of some authors) are of particular interest to developmental and molecular biologists because of the purported ancestral (i.e., unduplicated) karyotype of S. tropicalis relative to the genus Xenopus. Although most previous studies have assumed that Silurana is the sister group of Xenopus, recent morphological work suggests that Silurana is more closely related both to the South American genus Pipa and to the African genera Hymenochirus and Pseudhymenochirus than it is to Xenopus. We examined 1,486 bp of relatively variable regions of the ribosomal DNA array (including portions of the 18S and 28S genes, as well as part of an internal transcribed spacer) in Hymenochirus, Silurana, and Xenopus, as well as the outgroup genus Spea, in order to test the alternative hypotheses of relationships for Silurana. Maximum-parsimony analysis using bootstrapping and an analysis using Lake's method of invariants both significantly support the sister-group relationship between Xenopus and Silurana rather than the relationship suggested by morphology. Analysis of the combined morphological/molecular data matrix also significantly supports the Xenopus-Silurana relationship. Although our results are not inconsistent with the recognition of the genus Silurana to accommodate the species formerly called X. tropicalis and X. epitropicalis, the proposed relationships do not require the recognition of this genus in order to render Xenopus monophyletic.     

Towards a phylogeny of the flesh flies (Diptera: Sarcophagidae): morphology and phylogenetic implications of the acrophallus in the subfamily Sarcophaginae

The morphology of the acrophallus, the distal portion of the male phallus carrying the phallotreme, was studied in 72 exemplar species representing 56 genera and subgenera of the flesh fly subfamily Sarcophaginae. For 42 of those species, scanning electron microscopy was used to clarify the phallic morphology. Terms used to describe the male genitalia were updated based on new interpretations of homology. Male genitalic characters, combined with other morphological characters of adult males and females and of larvae, were used to construct a phylogeny. The monophyly of the subfamily was supported, and some generic‐level sister‐group relationships proposed in the literature, but without previous cladistic analyses, were also supported. The genus Blaesoxipha Loew, as currently recognized, was not monophyletic in our analysis. The genus Helicobia Coquillett is synonymized with Sarcophaga Meigen syn. nov. and treated as a subgenus of the latter. The Sarcophaga subgenera Neobellieria Blanchard and Mehria Enderlein were not monophyletic. Many of the clades in the analysis were supported primarily or exclusively by male genitalic character states, highlighting the importance of the male genitalia as a source of morphological characters for sarcophagine phylogeny. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 740–778.     

Molecular phylogeny of the ranid frogs from Southwest India based on the mitochondrial ribosomal RNA gene sequences

The Western Ghats of Southwestern India are known as one of the world's "hotspots" of biodiversity. We collected frog specimens from the family Ranidae and investigated the phylogenetic relationships among ranid species, particularly among the Fejervarya, a genus whose morphological diagnostic characteristics and phylogenetic features remain little known. We analyzed partial sequences of the mitochondrial 12S (428 bp) and 16S rDNAs (549 bp). Results showed that the members of Fejervarya form a monophyletic group with the genera Hoplobatrachus and Euphlyctis among ranid genera. This confirms the recent allocation of Fejervarya, including it within the subfamily Dicroglossinae. The mitochondrial rDNA data in our study also appeared to be useful as a marker to distinguish Fejervarya species without morphological differences. The phylogenetic tree based on the 16S rDNA sequence showed a correlation between Fejervarya phylogenies and their geographic distributions. Lastly, our results suggested the recent occurrence of a radiation event of Fejervarya species in the Indian-Sri Lankan region.     

A new cestode (Tetraphyllidea: Phyllobothriidae) in elasmobranchs from the Taiwan Strait

In total, 20 fanrays, Platyrhina sinensis (Rajiformes: Rhinobatidae), collected from the Taiwan Strait, were examined. A new phyllobothriid genus and species (Tetraphyllidea: Phyllobothriidae) was found and described. Biotobothrium platyrhina n. gen., n. sp. is assigned to the Rhinebothriinae Euzet, 1953, because it possesses 4 stalked bothridia that are each divided by septa into numerous small facial loculi but that lack apical suckers. The new genus and species is clearly different from any other in Rhinebothriinae in that each bothridium bears 2 sets of 5 small facial loculi, with 1 set located at each of the distal ends of the bothridium, rather than facial loculi throughout the entire distal surface of the bothridium, as is seen in all other genera in the subfamily. This character has not been previously reported for members of Rhinebothriinae. In addition, the testicular arrangement in the anterior quarter of the proglottid is unique. The posterior range of the vas deferens almost reaches the ovarian bridge, and the morphology of the cirrus sac and several other morphological characters are at variance with presently described species in the subfamily.     

Conflicting character distribution within different data sets on cardueline finches: artifact or history?

Cardueline finches (Passeriformes: Fringillidae, Carduelinae) provide an example of unresolved species relationships despite decades of extensive study of the group. Existing morphological studies suffer from numerous cases of assumed parallel evolution due to a conflicting character distribution in different lineages. In this study, results of assumed parallel evolution due to a conflicting character distribution in different lineages. In this study, results of cytochrome b sequence analysis are compared with species relationships suggested by morphological and behavioral evidence. In the molecular analyses, species clusters mutually excluding each other were observed, lowering the statistical support of the internodes, i.e., the branches could not be resolved convincingly. Despite these difficulties, some phylogenetic signal was present in the molecular data as well as in the other approaches. In particular, any species or genus relationship suggested by cytochrome b sequence analysis was reflected by some other evidence. Based on this general congruence of the different data sets and on a considerable cytochrome b tree stability observed independent of species combination, choice of outgroup and tree-generating method, the short internodes are interpreted to reflect a historical reality. A model of cardueline evolution is proposed which assumes a population of cardueline ancestors with considerable polymorphism concerning the mitochondrial DNA and morphological characters alike. Retention of ancestral character states in different lineages and a subsequent rapid radiation are suggested to explain the conflicting character distributions observed in different fields of investigation.      

Phylogeny of the American silverfish Cubacubaninae (Hexapoda: Zygentoma: Nicoletiidae): a combined approach using morphology and five molecular loci

Relationships within the subfamily Cubacubaninae, the dominant subfamily of Nicoletiidae in America, are appraised based on parsimony analysis of 20 morphological characters and sequence data from five loci (nuclear 18S and 28S rRNA, mitochondrial 16S rRNA, nuclear protein coding gene histone H3, and mitochondrial protein coding gene cytochrome c oxidase subunit I). The data, analyzed under direct optimization for a range of analytical parameter sets, indicated that species may show some biogeographical structure. It also indicated that the presence of articulated submedian appendages on urosternum IV is not a valid discriminating character in taxonomy. Species within the traditional genera Anelpistina, Cubacubana and Neonicoletia were found to belong to a group in which no clear morphological or molecular distinction was present. It is proposed that members of these three genera should be united within a single taxon. On the contrary, the genus Prosthecina is well supported by the data. © The Willi Hennig Society 2006.     

Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae)

The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification.     

A phylogenetic analysis of the fungus-growing ants (Hymenoptera: Formicidae: Attini) based on morphological characters of the larvae

A phylogenetic hypothesis of the fungus-growing ants (subfamily Myrmicinae, tribe Attini) is proposed, based on a cladistic analysis utilizing forty-four morphological characters (109 states) of the prepupal worker larva. The fifty-one attine species analysed include representatives of eleven of the twelve currently recognized attine genera, excluding only the monotypic workerless parasite Pseudoatta ; the non-attines include two outgroups (species of the basal myrmicine genera Myrmica and Pogonomyrmex ), two myrmicine species presumed to be distantly related to the attines, and twelve species representing taxa that have been proposed by prior workers as possible sister groups of the Attini. There is strong character support for the monophyly of the Attini and for a sister-group relationship of the Attini and the Neotropical Blepharidatta brasiliensis. The Attini are divided into two distinct lineages, an 'apterostigmoid' clade (containing Apterostigma and Mycocepurus) and an 'attoid' clade (containing all other attine genera except Myrmicocrypta). The attine genus Myrmicocrypta appears to be paraphyletic with respect to these two groups; the species M.buenzlii in particular retains many attine plesiomorphies.
These results indicate that the fungus-growing behaviour had a single evolutionary origin in the ants. They also indicate that mycelium cultivation is plesiomorphic and that yeast cultivation is derived within the Attini, overturning the long-standing assumption that the yeast-growing Cyphomyrmex species are the most primitive Attini. Behavioural and ecological investigations into the origin and evolution of the fungus-growing behaviour might more profitably focus on species in the attine genus Myrmicocrypta , as well as those in the closely related non-attine genera Blepharidatta and Wasmannia.