Molecular phylogeny of parasitic Platyhelminthes based on sequences of partial 28S rDNA D1 and mitochondrial cytochrome c oxidase subunit I

The phylogenic relationships existing among 14 parasitic Platyhelminthes in the Republic of Korea were investigated via the use of the partial 28S ribosomal DNA (rDNA) D1 region and the partial mitochondrial cytochrome c oxidase subunit 1 (mCOI) DNA sequences. The nucleotide sequences were analyzed by length, G + C %, nucleotide differences and gaps in order to determine the analyzed phylogenic relationships. The phylogenic patterns of the 28S rDNA D1 and mCOI regions were closely related within the same class and order as analyzed by the PAUP 4.0 program, with the exception of a few species. These findings indicate that the 28S rDNA gene sequence is more highly conserved than are the mCOI gene sequences. The 28S rDNA gene may prove useful in studies of the systematics and population genetic structures of parasitic Platyhelminthes.     

Molecular phylogenic location of the Plagiorchis muris (Digenea, Plagiorchiidae) based on sequences of partial 28S D1 rDNA and mitochondrial cytochrome C oxidase subunit I

To determine the molecular phylogenic location of Plagiorchis muris, 28S D1 ribosomal DNA (rDNA) and mitochondrial cytochrome C oxidase subunit I (mtCOI) were sequenced and compared with other trematodes in the family Plagiorchiidae. The 28S D1 tree of P. muris was found to be closely related to those of P. elegans and other Plagiorchis species. And, the mtCOI tree also showed that P. muris is in a separate clade with genus Glypthelmins. These results support a phylogenic relationship between members of the Plagiorchiidae, as suggested by morphologic features.     

Molecular phylogenetic study on the origin and evolution of Mustelidae

The family Mustelidae, which consists of Mustelinae, Lutrinae, Melinae, and Taxidiinae, is the largest family among Carnivora and is a highly diverse group. Recent molecular phylogenetic studies have clarified the phylogenetic relations among Mustelidae, but there remain several unresolved problems, particularly concerning the deep branchings. Whereas many studies support the monophyly of Mustelidae+Procyonidae among Musteloidea, the relations between Mustelidae+Procyonidae, Ailuridae, and Miphitidae are still unclear. To address these problems, we inferred a tree on the basis of the sequences of mitochondrial genomes and of multiple nuclear genes using the maximum likelihood method. Our results strongly support the hypothesis that the Taxidiinae branched at first, followed by the branching of the Melinae. After that, Mustelinae diversified, and Lutrinae evolved within Mustelinae. With respect to the deep branchings in Musteloidea, the Ailuridae/Mephitidae monophyly tree and the Mephitidae-basal tree are indistinguishable in log-likelihood score, and this problem remains unresolved.     

Molecular biogeography: using the Corsica-Sardinia microplate disjunction to calibrate mitochondrial rDNA evolutionary rates in mountain newts (Euproctus)

Mitochondrial DNA (mtDNA) sequence variation was examined in the three species belonging to the newt genus Euproctus: E. asper, E. montanus, and E. platycephalus, and in three other species belonging to the same family: Triturus carnifex, T. vulgaris and Pleurodeles waltl. The Euproctus species inhabit mountain streams in the Pyrenean region, Corsica, and Sardinia, respectively. This vicariant distribution is believed to be a result of the disjunction and rotation of the Sardinia-Corsica microplate from the Pyrenean region and suggested dates for each cladogenetic event are available. A total of 915 bp from 12S and 16S ribosomal rRNA genes were compared for each taxon. These are the first mt-rDNA sequence data for salamanders. Sequences were used to reconstruct phylogenetic trees, investigate evolutionary rates for these genes, calibrate them with absolute time since divergence, and compare rates with published ones. Using P. waltl as the outgroup, all phylogenetic methods used (parsimony, maximum likelihood, and Neighbor Joining) produced trees with identical topologies and similar bootstrap values associated with each node. These sequence data cannot unambiguously resolve the splitting events leading to the main radiation of the genus Triturus and the origin of the genus Euproctus. These events may well have occurred very close in time, consistent with other sorts of data. Although it is unlikely strict linearity holds for all kinds of substitutions, relative rate tests of the molecular clock hypothesis could not reject clock-like behavior of sequence changes along Euproctus lineages. Estimates of absolute rates of base changes are 0.35% per Myr since divergence for all substitutions and 0.14% per Myr for transversions; these estimates are similar to other vertebrate estimates. A comparison with distance measures from allozyme studies agrees quite well with regard to relative divergences of the three Euproctus species.     

Higher-Level Phylogeny of the Therevidae (Diptera: Insecta) Based on 28S Ribosomal and Elongation Factor-1α Gene Sequences

Therevidae (stilleto flies) are a little-known family of asiloid brachyceran Diptera (Insecta). Separate and combined phylogenetic analyses of 1200 bases of the 28S ribosomal DNA and 1100 bases of elongation factor-1α were used to infer phylogenetic relationships within the family. The position of the enigmatic taxon Apsilocephala Kröber is evaluated in light of the molecular evidence. In all analyses, molecular data strongly support the monophyly of Therevidae, excluding Apsilocephala, and the division of Therevidae into two main clades corresponding to a previous classification of the family into the subfamilies Phycinae and Therevinae. Despite strong support for some relationships within these groups, relationships at the base of the two main clades are weakly supported. Short branch lengths for Australasian clades at the base of the Therevinae may represent a rapid radiation of therevids in Australia.     

Phylogenetic relationships among the microgastroid wasps (Hymenoptera: braconidae): combined analysis of 16S and 28S rDNA genes and morphological data

Relationships among the microgastroid complex of braconid wasps were investigated using sequence data from the 16S mitochondrial rDNA and 28S (D2 expansion region) nuclear rDNA genes, as well as morphological data. Parsimony analysis of these gene fragments, both separately and combined, indicated that Neoneurus (Neoneurinae) and Ichneutes (Ichneutinae) were no more closely related to the microgastroids than were a range of helconoid taxa. Combined parsimony analysis of the microgastroids indicated the relationships ((Cardiochilinae + Microgastrinae) + Miracinae) + Cheloninae, with Adeliinae falling inside the Cheloninae. Bootstrap proportions for each of these nodes were greater than 70%. Character reweighting (sensu Farris), using the rescaled consistency index, also recovered these relationships. Mapping of lifestyle traits onto this relatively well supported phylogeny indicated that solitary endoparasitism is ancestral for the microgastroids, with a single origin for egg-larval endoparasitism in the Cheloninae + Adeliinae. Mapping of the radiation of the microgastroids into lepidopteran hosts was less clear, due to the specialized biology of the most basal microgastroid clade, the Cheloninae + Adeliinae. Our data are consistent with attack of concealed lepidopteran hosts as the plesiomorphic lifestyle, at least for the Miracinae + Cardiochilinae + Microgastrinae, with radiation into more exposed hosts in the Cardiochilinae + Microgastrinae.     

Molecular Systematics of the Malagasy Babblers (Passeriformes: Timaliidae) and Warblers (Passeriformes: Sylviidae), Based on Cytochrome b and 16S rRNA Sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy “babblers” are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy “babblers” are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.     

Aphanomyces astaci mtDNA: insights into the pathogen’s differentiation and its genetic diversity from other closely related oomycetes

The causative agent of crayfish plague, Aphanomyces astaci (Saprolegniales, Oomycota), is one of the 100 world’s worst invasive alien species and represents a major threat to freshwater crayfish species worldwide. A better understanding of the biology and epidemiology of A. astaci relies on the application of efficient tools to detect the pathogen and assess its genetic diversity. In this study, we validated the specificity of two recently developed PCR-based approaches used to detect A. astaci groups. The first relies on the analysis of mitochondrial ribosomal rnnS (small) and rnnL (large) subunit sequences and the second, of sequences obtained by using genotype-specific primers designed from A. astaci whole genome sequencing. For this purpose, we tested the specificity against 76 selected isolates, including other oomycete species and the recently described species Aphanomyces fennicus, which, when used in nrITS-based specific tests for A. astaci, is known to result in a false positive. Under both approaches, we were able to efficiently and accurately identify A. astaci and its genetic groups in both pure cultures and clinical samples. We report that sequence analysis of the rnnS region alone is sufficient for the identification of A. astaci and a partial characterization of haplogroups. In contrast, the rnnL region alone is not sufficiently informative for A. astaci identification as other oomycete species present sequences identical to those of A. astaci.