A phylogeny of the megapodes (Aves: Megapodiidae) based on nuclear and mitochondrial DNA sequences

DNA sequences from the first intron of the nuclear gene rhodopsin (RDP1) and from the mitochondrial gene ND2 were used to construct a phylogeny of the avian family Megapodiidae. RDP1 sequences evolved about six times more slowly than ND2 and showed less homoplasy, substitution bias, and rate heterogeneity across sites. Analysis of RDP1 produced a phylogeny that was well resolved at the genus level, but RDP1 did not evolve rapidly enough for intrageneric comparisons. The ND2 phylogeny resolved intrageneric relationships and was congruent with the RDP1 phylogeny except for a single node: this node was the only aspect of tree topology sensitive to weighting in parsimony analyses. Despite differences in sequence evolution, RDP1 and ND2 contained congruent phylogenetic signal and were combined to produce a phylogeny that reflects the resolving power of both genes. This phylogeny shows an early split within the megapodes, leading to two major clades: (1) Macrocephalon and the mound-building genera Talegalla, Leipoa, Aepypodius, and Alectura, and (2) Eulipoa and Megapodius. It differs significantly from previous hypotheses based on morphology but is consistent with affiliations suggested by a recent study of parasitic chewing lice.     

A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML, and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species.     

Molecular phylogeny of the genus Buteo (Aves: Accipitridae) based on mitochondrial marker sequences

DNA sequences of the mitochondrial nd6 gene and the non-repetitive part of the pseudo-control region (PsiCR) were isolated from 101 individuals to analyze the phylogenetic relationships among all buzzards of the genus Buteo and other buteonine genera. Comparisons of the two marker sequences indicate that the PsiCR evolved two times faster than the nd6 gene. The PsiCR proved to be an efficient, neutral genetic marker sequence for phylogenetic analyses at the intrageneric level, especially suitable for analyses based on old tissues, where only short fragments can be obtained. The molecular data set implies a neotropical origin of the genus Buteo. Monophyly of the genus Buteo as currently defined is contradicted due to the positions of Asturina nitida, Geranoaetus melanoleucus, Buteo magnirostris, and Buteo leucorrhous. These findings suggest several taxonomic consequences. A. nitida and G. melanoleucus should be included into the genus Buteo. Moreover, B. leucorrhous should be transferred into the genus Percnohierax (which clusters with Parabuteo), and B. magnirostris into the genus Rupornis. According to this classification of the genus Buteo, the basal lineage of the genus is formed by a clade containing Buteo polyosoma, Buteo poecilochrous, and Buteo melanoleucus. The "woodland buteos" form a paraphyletic assemblage with B. magnirostris as a clearly separated lineage basal to the genus Buteo.     

Phylogeny of the owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence

The avian family Aegothelidae (Owlet-nightjars) comprises nine extant species and one extinct species, all of which are currently classified in a single genus, Aegotheles. Owlet-nightjars are secretive nocturnal birds of the South Pacific. They are relatively poorly studied and some species are known from only a few specimens. Furthermore, their confusing morphological variation has made it difficult to cluster existing specimens unambiguously into hierarchical taxonomic units. Here we sample all extant owlet-nightjar species and all but three currently recognized subspecies. We use DNA extracted primarily from museum specimens to obtain mitochondrial gene sequences and construct a molecular phylogeny. Our phylogeny suggests that most species are reciprocally monophyletic, however A. albertisi appears paraphyletic. Our data also suggest splitting A. bennettii into two species and splitting A. insignis and A. tatei as suggested in another recent paper.     

Molecular phylogeny of gibbons inferred from mitochondrial DNA sequences: Preliminary report

We analyzed the 896 base-pair (bp) mitochondrial DNA (mtDNA) sequences for seven gibbons, representative of three out of four subgenera. The result from our molecular analysis is consistent with previous studies as to the monophyly of subgenus Hylobates species, yet the relationship among subgenera remains slightly ambiguous. A striking result of the analysis is the phylogenetic location of Kloss's gibbon (H. klossii). Kloss's gibbon has been considered to be an initial off-shoot of the subgenus Hylobates because of its morphological primitiveness. However, our molecular data strongly suggest that Kloss's gibbon speciated most recently within the subgenus Hylobates. Correspondence to: S. Horai     

Conservation of repeated DNA base sequences in theCrustacea: A molecular approach to decapod phylogeny

Summary Analysis of data obtained from molecular hybridization of³H-labeled repetitious DNA has been utilized to reconstruct the broad outlines of phylogenetic relationships among decapod Crustacea. This molecular reconstruction agrees reasonably well with the paleontological record, and with other schemes obtained by comparative morphological and serological approaches. Preliminary evidence is in line with the hypothesis that continuous addition of new repeated sequence families to the genome over long periods of time may in part account for the correlation observed between percent repetitious DNA hybridized and divergence time. It is tentatively concluded that a core of DNA base sequence homology has been highly conserved throughout the evolution of theCrustacea. Demonstration of inter-species sequence homology has important implications to models which relegate a genetic regulatory function to repeated DNAs.     

Molecular systematics and diversification of the Asian scimitar babblers (Timaliidae, Aves) based on mitochondrial and nuclear DNA sequences

The Asian scimitar babblers, including the genus Pomatorhinus and Xiphirhynchus, are a small group of babblers characterized by long down-curved bills and a distribution throughout East and Southeast Asia. To infer the molecular phylogeny of this group and their divergence time, we examined sequences of multiple fragments including two entire mitochondrial genes and four nuclear introns (4352 bp in total) from multiple samples of eight of the nine recognized species of Asian scimitar babblers. The phylogeny resulting from the concatenated multi-locus dataset suggests that Pomatorhinus is paraphyletic. Due to its paraphyly, we propose dividing the traditional genus Pomatorhinus into two morphologically and genetically diagnosable genera: Pomatorhinus and Erythrogenys. Results of the molecular dating based on the conventional mitochondrial DNA divergence rate indicates that the diversification of these babblers is likely congruent with the historical climatic events. Our findings shed light on the diversification of avian species in southern Asia, a poorly studied biodiversity hotspot.     

A new phylogeny of swiftlets (Aves: Apodidae) based on cytochrome-b DNA

Due to a lack of distinctive morphological characters, swift taxonomy and phylogeny has always been an area of disagreement. To shed more light on this subject, we reconstructed swift(let) phylogeny based on 1143 bp of mitochondrial cytochrome-b DNA sequence. Although this is not the first attempt to reconstruct swift phylogeny using molecular data, our results show higher support for many of the branches due to our much longer sequences. However, placement of Hydrochous is still unexpected. Implementation of more conservative genetic regions and sampling of more taxa could solve this problem. Most importantly, the Collocaliini resolve as a monophyletic group. The internal structure of the group shows that non-echolocating Collocalia and echolocating Aerodramus form two distinct clades. This is in congruence with earlier classifications based on morphological characters, but in contrast with more recent classifications.     

A molecular phylogeny of anseriformes based on mitochondrial DNA analysis

To study the phylogenetic relationships among Anseriformes, sequences for the complete mitochondrial control region (CR) were determined from 45 waterfowl representing 24 genera, i.e., half of the existing genera. To confirm the results based on CR analysis we also analyzed representative species based on two mitochondrial protein-coding genes, cytochrome b (cytb) and NADH dehydrogenase subunit 2 (ND2). These data allowed us to construct a robust phylogeny of the Anseriformes and to compare it with existing phylogenies based on morphological or molecular data. Chauna and Dendrocygna were identified as early offshoots of the Anseriformes. All the remaining taxa fell into two clades that correspond to the two subfamilies Anatinae and Anserinae. Within Anserinae Branta and Anser cluster together, whereas Coscoroba, Cygnus, and Cereopsis form a relatively weak clade with Cygnus diverging first. Five clades are clearly recognizable among Anatinae: (i) the Anatini with Anas and Lophonetta; (ii) the Aythyini with Aythya and Netta; (iii) the Cairinini with Cairina and Aix; (iv) the Mergini with Mergus, Bucephala, Melanitta, Callonetta, Somateria, and Clangula, and (v) the Tadornini with Tadorna, Chloephaga, and Alopochen. The Tadornini diverged early on from the Anatinae; then the Mergini and a large group that comprises the Anatini, Aythyini, Cairinini, and two isolated genera, Chenonetta and Marmaronetta, diverged. The phylogeny obtained with the control region appears more robust than the one obtained with mitochondrial protein-coding genes such as ND2 and cytb. This suggests that the CR is a powerful tool for bird phylogeny, not only at a small scale (i.e., relationships between species) but also at the family level. Whereas morphological analysis effectively resolved the split between Anatinae and Anserinae and the existence of some of the clades, the precise composition of the clades are different when morphological and molecular data are compared.     

A molecular phylogeny of the cotingas (Aves: Cotingidae)

The phylogenetic relationships of members of Cotingidae were investigated using >2100 bp of sequence data from two nuclear introns (myoglobin intron 2 and G3PDH intron 11) and one protein-coding mitochondrial gene (cytochrome b). Strong support was found for a monophyletic clade including 23 traditional cotingid genera, corresponding to the Cotingidae sensu [Remsen, J.V. Jr., Jaramillo, A., Nores, M., Pacheco, J.F., Robbins, M.B., Schulenberg, T.S., Stiles, F.G., da Silva, J.M.C., Stotz, D.F., Zimmer, K.J., 2005. Version 2005-11-15. A classification of the bird species of South America. American Ornithologists' Union. ]. Neither Oxyruncus nor any of the genera in Tityrinae sensu [Prum, R.O, Lanyon, W.E., 1989. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 91, 444-461.] are members of Cotingidae. Within Cotingidae a polytomy of four well-supported clades was recovered: (1) the fruiteaters Pipreola and Ampelioides; (2) the Ampelion group, including Phytotoma; (3) Rupicola and Phoenicircus; and (4) the 'core cotingas' consisting of the remainder of the Cotingas (e.g. fruitcrows, Cotinga, Procnias, Lipaugus, and Carpodectes), with Snowornis in a basal position. The separation of Snowornis from Lipaugus [Prum, R.O, Lanyon, W.E., 1989. Monophyly and phylogeny of the Schiffornis group (Tyrannoidea). Condor 91, 444-461.] was strongly supported, as were the close relationships between Gymnoderus and Conioptilon, and between Tijuca and Lipaugus. However, basal relationships among 'core cotinga' clades were not resolved.     

The phylogeny of echinoderm classes based on mitochondrial gene arrangements

Summary Previous analyses have demonstrated that, among the echinoderms, the sea star (class: Asteroidea) mitochondrial genome contains a large inversion in comparison to the mitochondrial DNA of sea urchins (class: Echinoidea). Polymerase chain reaction amplification, DNA cloning, and sequencing have been used to examine the relationships of the brittle stars (class: Ophiuroidea) and sea cucumbers (class: Holothuroidea) to the sea stars and sea urchins. The DNA sequence of the regions spanning potential inversion junctions in both brittle stars and sea cucumbers has been determined. This study has also revealed a highly modified tRNA cluster in the ophiuroid mitochondrial genome. Our data indicate mitochondrial gene arrangement patterns that group the sea cucumbers with sea urchins and sea stars with brittle stars. This use of molecular characters clarifies the relationships among these classes.     

A molecular phylogeny of the genus Gammarus (Crustacea: Amphipoda) based on mitochondrial and nuclear gene sequences

A phylogeny of the genus Gammarus Fabricius, 1775 was constructed using DNA sequence data from the mitochondrial genes COI and 16S, and the nuclear genes 18S and 28S. Both parsimony and Bayesian analyses were conducted on separate and combined data partitions. The Bayesian phylogeny from the combined analysis was selected as the preferred phylogenetic hypothesis. The hypothesis supports monophyly of the genus Gammarus, paraphyly of the European-North American Gammarus, and monophyly of the Asian Gammarus. The Asian clade was further split into a southeastern group and a northwestern group. The dramatic climate change following the uplift of the Tibetan Plateau was probably the most important factor in triggering the diversification of southeastern and northwestern groups. The genus Sinogammarus is invalid and should be part of the genus Gammarus.     

A molecular phylogeny of the Percidae (Teleostei, Perciformes) based on mitochondrial DNA sequence

The family Percidae is among the most speciose families of northern hemisphere fishes with > 178 178 North American species and 14 Eurasian species. Previous phylogenetic studies have been hampered by a lack of informative characters, inadequate taxonomic sampling, and conflicting data. We estimated phylogenetic relationships among 54 percid species (9 of 10 genera and all but one subgenus of darters) and four outgroup taxa using mitochondrial DNA data from the 12S rRNA and cytochrome b genes. Four primary evolutionary lineages were consistently recovered: Etheostomatinae (Ammocrypta, Crystallaria, Etheostoma, and Percina), Perca, Luciopercinae (Romanichthys, Sander, and Zingel), and Gymnocephalus. Except Etheostoma and Zingel, all polytypic genera were monophyletic. The Etheostoma subgenus Nothonotus failed to resolve with other members of the genus resulting in a paraphyletic Etheostoma. The subfamily Percinae (Gymnocephalus and Perca) was not recovered in phylogenetic analyses with Gymnocephalus sister to Luciopercinae. Etheostomatinae and Romanichthyini were never resolved as sister groups supporting convergent evolution as the cause of small, benthic, stream-inhabiting percids in North American and Eurasian waters.     

Molecular phylogeny of the lemur family cheirogaleidae (primates) based on mitochondrial DNA sequences

Cheirogaleidae currently comprises five genera whose relationships remain contentious. The taxonomic status and phylogenetic position of both Mirza coquereli and Allocebus trichotis are still unclear. The taxonomic status of the recently discovered Microcebus ravelobensis (a sympatric sibling species of Microcebus murinus) and its phylogenetic position also require further examination. A approximately 2.4-kb mitochondrial DNA sequence including part of the COIII gene, complete ND3, ND4L, and ND4 genes, and 5 tRNAs was used to clarify relationships among cheirogaleids. Mirza and Microcebus form a clade representing the sister group of Allocebus, with a clade containing Cheirogaleus major and Cheirogaleus medius diverging first. M. ravelobensis and Microcebus rufus form a subclade within Microcebus, with M. murinus as its sister group. The molecular data support the generic status of Mirza coquereli and species-level divergence of M. ravelobensis. Furthermore, "M. rufus" may well represent more than one species.     

A molecular phylogeny of Arceuthobium (Viscaceae) based on nuclear ribosomal DNA internal transcribed spacer sequences

Ribosomal DNA (rDNA) internal transcribed spacer (ITS) and 5.8S rDNA sequences were obtained from 22 species of dwarf mistletoes (Arceuthobium — Viscaceae) to test phylogenetic relationships. Interspecific distances ranged from 0 to 21.4% between New World species, values two to five times higher than those measures for the ITS region in other plants. One Old World species (A. oxycedri) and one New World species (A. abietis-religiosae) were remarkably similar to each other but exhibited up to 41% sequence divergence from the remaining species. Minimum length trees support the concept of a verticillately branched subgenus Arceuthobium; however, interspecific distances indicate this group is extremely heterogeneous. Subgenus Vaginata, Section Vaginata, is centered in Mexico and encompasses all the taxa previously placed in this group but is expanded to include several species previously classified in Section Campylopoda (e.g., A. divaricatum, A. rubrum, and A. strictum). The sister group relationship between A. divaricatum and A. douglasii, first seen following isozyme analysis, is supported by ITS sequence data. Section Campylopoda s. s. is now composed of 13 mainly U.S. species that show a high degree of morphological and genetic similarity. The eastern dwarf mistletoe, A. pusillum, is not closely related to A. douglasii but rather with A. bicarinatum from Hispaniola, which suggests that these taxa represent highly modified relicts that shared an ancestor in the early Tertiary. Two endemic species from Mexico and Central America (A. guatemalense and A. pendens) formed a sister group and have been placed in a new Section (Penda). Rapid molecular evolution in Arceuthobium may be associated with the adaptive radiation of this genus on numerous conifer hosts.     

Comprehensive molecular phylogeny of the sub-family Dipterocarpoideae (Dipterocarpaceae) based on chloroplast DNA sequences

Dipterocarpoideae, the largest sub-family of well-known plant family Dipterocarpaceae, dominates in South Asian rain forests. Although several previous studies addressed the phylogeny of the Dipterocarpaceae family, relationships among many of its genera from the Dipterocarpoideae sub-family are still not well understood. In particular, little is known about the relationships of the genera Vateriopsis, Stemonoporus, Vateria and inconsistence remains between phylogenetic results and taxonomic classifications of Shorea and Hopea species. We studied molecular phylogeny of the sub-family Dipterocarpoideae using the trnL-trnF spacer, trnL intron and the matK gene sequences of chloroplast DNA (cpDNA). This study is the first comprehensive phylogeny reconstruction for the sub-family Dipterocarpoideae based on cpDNA, as it includes most genera (14) and a large number of species (79) with most species endemic to Sri Lanka, as well as one species from Seychelles and one species from the genus Monotes from Madagascar. Phylogenetic trees were constructed using the Neighbor Joining (NJ) and Maximum Likelihood (ML) methods using combined set of sequences including all three cpDNA regions. The topologies of the NJ and ML trees were to a certain extent, consistent with the current taxonomy of Dipterocarpoideae based on morphology and with previous molecular phylogenies based on cpDNA. Furthermore, our results provided new evidence regarding the relationships of the following genera: Vateriopsis and Stemonoporus and about the validity of the previous morphology based classifications of Shorea species. In addition, the topology of our trees was consistent with the classification of Shorea species proposed by Maury (1978), Maury-Lechon (1979) and Symington (1943). Finally, our results provided evidence for the affinity of the genus Monotes to Asian Dipterocarpoideae rather than to Tiliaceae and indicated that it is a good candidate for outgroup species for future studies of the former sub-family.     

A molecular phylogeny of the marine mussel genus Perna (Bivalvia: Mytilidae) based on nuclear (ITS1&2) and mitochondrial (COI) DNA sequences

A molecular phylogeny is presented for marine mussels of the genus Perna, based on nuclear (ITS1,ITS2) and mitochondrial (COI) DNA sequence data. The three generally recognised species (Perna viridis, Perna perna and Perna canaliculus) and one putative species (Perna picta) were each sampled from several locations within their known geographic distributions. A range of phylogenetic analyses was used to investigate the current taxonomic assignments, evolutionary relationships and the biogeographical history of the genus. The different analyses produced similar, well supported topologies and verified the monophyly of the genus with respect to five mytilid outgroup species. P. perna (Atlantic), P. viridis (Indo-West Pacific), and P. canaliculus (New Zealand) each formed distinct clades, confirming their specific status. Putative P. picta from North Africa clustered within the P. perna clade and is not regarded as a separate species. P. perna and P. canaliculus were the most closely related of the three species. Possible biogeographic explanations for the present species distributions are evaluated.     

Phylogeny of swallows (Aves: Hirundinidae) estimated from nuclear and mitochondrial DNA sequences

The phylogeny of swallows was reconstructed by comparing segments of three genes, nuclear beta-fibrinogen intron 7 (betafib7), mitochondrial cytochrome b (cytb), and mitochondrial ND2, in a variety of combinations using maximum likelihood and Bayesian methods. betafib7 was sequenced for 47 species, cytb for 74 species, and ND2 for 61 species to yield comparisons among 75 of the 84 currently recognized swallow species. The family Hirundinidae was confirmed to consist of two clades, Pseudochelidoninae (river martins) and Hirundininae (typical swallows). The Hirundininae is further divided into mud nesters (Hirundo sensu lato), core martins (Phedina, Riparia, and New World endemic genera), and basal relicts (Psalidoprocne, Cheramoeca, and Pseudhirundo). We did not resolve the hierarchy among these three hirundinine groups, but discovered many relationships within them. Mud-nesting genera have the following relationships: (Hirundo sensu stricto, Ptyonoprogne), (Delichon, (Petrochelidon, Cecropis)). Core martins have the following topology: (Phedina, Riparia cincta), (Riparia sensu stricto, Tachycineta, ((Stelgidopteryx, Progne), (Neotropical endemic genera))). Interspecific relationships among the Neotropical endemics were resolved completely; Atticora and Notiochelidon are paraphyletic, and all Neotropical endemics probably should be lumped into one or two genera. The final group of hirundinines, the basal relicts, consists of a sister pair, the Australian Cheramoeca and African Pseudhirundo. The African saw-wings (Psalidoprocne) are their likely sister group.