Molecular phylogeny of the western South Atlantic Sciaenidae based on mitochondrial and nuclear data

Fragments of mitochondrial (COI and rRNA 16S) and nuclear (Tmo-4C4) genes were sequenced to evaluate the phylogenetic relationships among 15 genera of the western South Atlantic Sciaenidae, two freshwater genera and the northwest Pacific Larimichthys crocea.Our results suggest a great diversification for the western Atlantic assemblage; the monophyly of Macrodon, Menticirrhus and Plagioscion genera; the distinctiveness of Bardiella, Stellifer and Ophioscion as belonging to the same clade; the possible existence of two distinct groups in Stellifer; the closer relationship between Lonchurus and Paralonchurus; the non-monophyly of Cynoscion; and the remarkable diversification of Larimus breviceps populations in the Brazilian coast. This is the most comprehensive study evaluating the phylogenetic relationships of the western Atlantic sciaenid and provides a guide for future studies within this family.     

Molecular phylogenetics of the bee-eaters (Aves: Meropidae) based on nuclear and mitochondrial DNA sequence data

The bee-eaters (family Meropidae) comprise a group of brightly colored, but morphologically homogeneous, birds with a wide variety of life history characteristics. A phylogeny of bee-eaters was reconstructed using nuclear and mitochondrial DNA sequence data from 23 of the 25 named bee-eater species. Analysis of the combined data set provided a well-supported phylogenetic hypothesis for the family. Nyctiornis is the sister taxon to all other bee-eaters. Within the genus Merops, we recovered two well-supported clades that can be broadly separated into two groups along geographic and ecological lines, one clade with mostly African resident species and the other clade containing a mixture of African and Asian taxa that are mostly migratory species. The clade containing resident African species can be further split into two groups along ecological lines by habitat preference into lowland forest specialists and montane forest and forest edge species. Intraspecific sampling in several of the taxa revealed moderate to high (3.7-6.5%, ND2) levels of divergence in the resident taxa, whereas the lone migratory taxon showed negligible levels of intraspecific divergence. This robust molecular phylogeny provides the phylogenetic framework for future comparative tests of hypotheses about the evolution of plumage patterns, sociality, migration, and delayed breeding strategies.     

Molecular phylogeny of Macaranga, Mallotus, and related genera (Euphorbiaceae s.s.): insights from plastid and nuclear DNA sequence data

Macaranga and Mallotus (Euphorbiaceae s.s.) are two closely related, large paleo(sub)tropical genera. To investigate the phylogenetic relationships between and within them and to determine the position of related genera belonging to the subtribe Rottlerinae, we sequenced one plastid (trnL-F) and three nuclear (ITS, ncpGS, phyC) markers for species representative of these genera. The analyses demonstrated the monophyly of Macaranga and the paraphyly of Mallotus and revealed three highly supported main clades. The genera Cordemoya and Deuteromallotus and the Mallotus sections Hancea and Oliganthae form a basal Cordemoya s.l. clade. The two other clades, the Macaranga clade and the Mallotus s.s. clade (the latter with Coccoceras, Neotrewia, Octospermum, and Trewia), are sister groups. In the Macaranga clade, two basal lineages (comprising mostly sect. Pseudorottlera) and a crown group with three geographically homogenous main clades were identified. The phylogeny of the Mallotus s.s. clade is less clear because of internal conflict in all four data sets. Many of the sections and informal infrageneric groups of Macaranga and Mallotus do not appear to be monophyletic. In both the Macaranga and Mallotus s.s. clades, the African and/or Madagascan taxa are nested in Asian clades, suggesting migrations or dispersals from Asia to Africa and Madagascar.     

Molecular phylogeny and habitat diversification of the genus Farfugium (Asteraceae) based on nuclear rDNA and plastid DNA

Background and Aims

Farfugium (Asteraceae) is a small genus that contains the two species F. japonicum and F. hiberniflorum and is distributed along a long archipelago in east Asia. The common taxon, F. japonicum, includes three varieties associated with a wide range of habitats, including forest understorey (sciophytes), coastal crag (heliophytes) and riverbed (rheophytes). Leaf shape is an important taxonomic character within this genus and is associated with the habitat.

Methods

Twenty populations that included all Farfugium taxa were collected throughout its range. Leaf morphology was measured to determine differences amongst the taxa. Phylogenetic analyses based on sequences of the internal transcribed spacer of nuclear rDNA and four plastid DNA regions (matK, trnL-trnF, trnH-psbA and rpl20-rps12) were conducted separately.

Key Results

Leaf morphology was significantly different amongst taxa, but morphological variations were partly explained by adaptation to certain environmental conditions that each population inhabited. Molecular phylogenies for the nDNA internal transcribed spacer and cpDNA were consistent in classifying F. hiberniflorum and the Taiwanese var. formosanum, whilst suggesting polyphyletic origins for the rheophyte, sciophyte and heliophyte taxa. All samples from the southern Ryukyus (Japan) and Taiwan clustered into a monophyletic group, which corroborates the land configuration theory involving Quaternary land-bridge formation and subsequent fragmentation into islands. The incongruence between the two DNA datasets may imply traces of introgressive hybridization and/or incomplete lineage sorting.

Conclusions

The occurrence of rheophyte, sciophyte and heliophyte plants within Farfugium may be attributable to their isolation on islands and subsequent adaptation to the riparian, coastal crag and forest understorey environments, following their migration over the Quaternary land-bridge formation along their distribution range. Nearly identical DNA sequences coupled with highly divergent morphologies amongst these taxa suggest that diversification was rapid.     

Molecular phylogeny of Old WorldTrifolium (Fabaceae), based on plastid and nuclear markers

Phylogenies of Old WorldTrifolium species were constructed using nucleotide sequence data of the internal transcribed spacers (ITS) of nuclear ribosomal DNA and chloroplast DNA restriction site data from PCR-amplified genes and genic regions (rbcL,trnK, andrpoC1–C2). Biogeography, morphological evolution, and the existing classification forTrifolium were examined. The genusTrifolium is strongly supported as monophyletic, however, only one small section (Chronosemium) is monophyletic, although the data are in conflict regarding its placement. The two largest sections of the genus, Sects.Lotoidea andTrifolium, are not supported as monophyletic, as currently circumscribed. Many members of Sect.Lotoidea are basal within the genus, supporting previously-proposed hypotheses concerning plesiomorphic morphological characters and a Mediterranean-Mideast biogeographic origin of the genus.     

Molecular phylogeny of Oryzeae (Poaceae) based on DNA sequences from chloroplast, mitochondrial, and nuclear genomes

The phylogeny and evolutionary history of the rice tribe (Oryzeae) were explored using sequences of five DNA fragments (matK, trnL, nad1, Adh2, and GPA1) from chloroplast, mitochondrial, and nuclear genomes. Results indicate that (1) Oryzeae is monophyletic and falls into two main clades corresponding to the traditionally recognized subtribes; (2) previous recognition of three monotypic genera (Hydrochloa, Porteresia, and Prosphytochloa) is not justified; and (3) close affinities of the monoecious genera are not supported, suggesting the possibility of multiple origins of unisexual florets. Based on the magnitude of matK and GPA1 sequence divergence, we suggest that Oryza and Leersia branched off from the remaining genera of Oryzeae ～20 million years ago (mya), and separated from each other ～14 mya. A divergence time of ～9 mya is obtained for the most basal split within Oryza. These estimates suggest that Oryzeae diverged during the Miocene, and thus imply that long-distance dispersal appears to be one of the important factors in the diversification of the tribe.     

Molecular phylogeny of Phalaenopsis Blume (Orchidaceae) on the basis of plastid and nuclear DNA

Representatives of the genus Ancistrocladus, woody lianas of tropical Africa and Asia, contain pharmaceutically interesting alkaloids and have been the subjects of intensive phytochemical investigations. In Southeast Asia, Ancistrocladus tectorius, previously regarded as the only species of the genus from this region, is extremely polymorphic with respect to naphthylisoquinoline alkaloids, indicating that this taxon might be comprised of several morphologically similar species. We performed a comparative study of the ITS region of nuclear rDNA and of the trnK intron of cpDNA as well as an ISSR fingerprint analysis. Using 75 samples of A. tectorius from 21 locations in comparison to samples of other Ancistrocladus species from Asia and from West and Central Africa, we investigated patterns of species differentiation within this taxon. We found the high variability of chemical compounds described for A. tectorius to be paralleled by a high genetic variability of the units that have been assigned to this taxon. Samples assigned to A. tectorius were paraphyletic with respect to species from the Indian subcontinent, and intraspecific variability was comparable to interspecific variability among the African taxa. In addition, groups of individuals occurring in sympatry were found to be more similar to those from other locations, suggesting low levels of gene flow between those sympatric groups. This indicates either a considerable number of hybridization events during the evolution of A. tectorius or the existence of several distinguishable species not yet recognized. Our results are a first step in the development of species or population-specific markers for the prediction of the alkaloid spectrum of samples. This will help to improve the reproducibility of phytochemical research on Ancistrocladus.     

Molecular phylogeny of the Chinese ranids inferred from nuclear and mitochondrial DNA sequences

The phylogeny of representative species of Chinese ranids was reconstructed using two nuclear (tyrosinase and rhodopsin) and two mitochondrial (12S rRNA, 16S rRNA) DNA fragments. Maximum parsimony, Bayesian, and maximum likelihood analyses were employed. In comparison with the results from nuclear and mitochondrial data, we used nuclear gene data as our preferred phylogenetic hypothesis. We proposed two families (Ranidae, Dicroglossidae) for Chinese ranids, with the exception of genus Ingerana. Within Dicroglossidae, four tribes were supported including Dicroglossini, Paini, Limnonectini, and Occidozygini. A broader sampling strategy and evidence from additional molecular markers are required to decisively evaluate the evolutionary history of Chinese ranids.     

A single nuclear locus phylogeny of soybean based on DNA sequence

Soybean [Glycine max (L.) Merr.] evolution was examined by sequencing portions of the restriction fragment length polymorphism (RFLP) locus A-199a of 21 taxa from the Glycininae and 1 from the Phaseoleae. Four hundred nucleotides were determined in each, aligned, and then compared for these taxa. Within the annual soybean subgenus (Soja), the four accessions differed at as many as 2.2% of the nucleotides. Among 13 perennial soybean species (subgenus Glycine), nucleotide variation ranged from 1.7% to 8.4%. The nucleotide difference between the two soybean subgenera was 3.0–7.0%. Nucleotide variation between the genus Glycine and the related genera of Neonotonia, Amphicarpa, Teramnus, and Phaseolus ranged from 8.2% to 16.4%. In addition to nucleotide substitutions, insertions/deletions (indels) differences were also observed and were consistent with nucleotide-based analysis. Cladistic analysis of the A-199a sequences was performed using Wagner parsimony to construct a soybean phylogeny. Sixteen equally parsimonious trees were produced from these data. The trees were 246 steps in length with a consistency index of 0.78. Indels distribution upon the consensus topology revealed a pattern congruent with the nucleotide-based phylogeny. The current taxonomic status of the soybean subgenera and the related genera of Neonotonia, Amphicarpa, and Teramnus were well-supported and appear monophyletic in this analysis. Homoplasy within the subgenus Glycine led to a lack of resolved topology for many of these 13 taxa. However, the Glycine clade topology was consistent with phylogenies proposed using crossing experiments and cpDNA RFLPs. These genera were arranged from ancestral to derived as: Teramnus, Amphicarpa, Neonotonia, and Glycine when Phaseolus vulgaris was used as an outgroup.     

Molecular phylogeny of Philippine freshwater sardines based on mitochondrial DNA analysis

The commercially important Sardinella species (family Clupeidae or herrings) usually thrive in marine environments. An exception is Sardinella tawilis of Taal Lake, Batangas, Philippines, the only known freshwater sardine. This species is believed to have immigrated from Balayan Bay to the lake when it was formed in the course of volcanic eruptions some 240 years ago. To determine the relationship of S. tawilis to the marine species S. albella, S. fimbriata, and S. longiceps from the Balayan Bay we sequenced 358 bp of the cytochrome b gene and the mitochondrial control region. The cytochrome b gene was highly conserved and contained little phylogenetic information. The control region sequences, however, demonstrated two highly diversified main haplotypes grouping S. tawilis with S. albella, as shown by maximum parsimony and neighbor-joining analysis. The haplotypes are characterized by the presence of an 81 bp indel and up to eight 35 bp tandem repeat elements. The repeat copy number varied within individuals of S. tawilis and S. albella, thus showing heteroplasmy in these two species only. The analysis of two subpopulations of S. tawilis revealed restricted substitutions that may indicate the beginning of genetic differentiation of the two subpopulations.     

A phylogeny for the Cisticolidae (Aves: Passeriformes) based on nuclear and mitochondrial DNA sequence data, and a re-interpretation of an unique nest-building specialization

Based on some general similarities in feeding adaptations, a large number of Old World passerine birds were in the past lumped in one broad family, the Sylviidae. Recent molecular studies, starting with the DNA-DNA hybridization work by Sibley et al. [Sibley, C.G., Ahlquist, J.E., 1990. Phylogeny and Classification of Birds: A Study in Molecular Evolution, Yale University Press, New Haven, CT], have revealed that this group is in fact a paraphyletic assemblage, mainly in the superfamily Sylvioidea, and within this assemblage a distinct group (the Cisticolidae) can be identified around the genus Cisticola. In this study we try to define natural lineages within it, based on DNA sequence data from 35 ingroup taxa representing 12 putative genera. Both nuclear myoglobin intron II (630 bp in our study) and mitochondrial ND2 (1041 bp) genes were sequenced, and 1671 bp were aligned and subjected to parsimony, maximum likelihood and Bayesian analyses. The results strongly support the monophyly of a cisticolid clade, with the Malagasy warblers Neomixis constituting the deepest branch within the clade. Three major clades receive statistical support, but not all relationships between and within these are well resolved. All species of the genus Bathmocercus belong to the Cisticolidae but in two different clades. The tailorbirds appear also polyphyletic with most species of the genus Orthotomus (but O. cucullatus falling in the outgroup) and the African metopias being in two different clades. Also the genus Apalis is polyphyletic, but all other included genera seem to be confirmed as natural units. Based on these findings we resurrect the genera Scepomycter and Artisornis. Calamonastes is confirmed to be in the Cisticolidae and grouped with Camaroptera. Main basic nest types do not follow the phylogenetic branching, and notably the peculiar "tailorbird" technique of stitching leaves together around the nest is found in different parts of the phylogeny. The basic types of nests seem to be found in particular environments, and the sewing may therefore have evolved in some ancestor of the Cisticolidae and was later lost or modified in some genera or species following the spread of drier habitats from the mid-Miocene.     

Phylogenetic relationships of the Dactyloa clade of Anolis lizards based on nuclear and mitochondrial DNA sequence data

The Dactyloa clade, one of two major subgroups of mainland Anolis lizards, is distributed from Costa Rica to Peru, including the Amazon region and the southern Lesser Antilles. We estimated the phylogenetic relationships within Dactyloa based on mitochondrial (ND2, five transfer-RNAs, COI) and nuclear (RAG1) gene regions using likelihood and Bayesian methods under different partition strategies. In addition, we tested the monophyly of five previously recognized groups within Dactyloa. The data strongly support the monophyly of Dactyloa and five major clades: eastern, latifrons, Phenacosaurus, roquet and western, each of which exhibits a coherent geographic range. Relationships among the five major clades are less clear: support for basal nodes within Dactyloa is weak and some contradictory relationships are supported by different datasets and/or phylogenetic methods. Of the previously recognized subgroups within Dactyloa, only the roquet series consistently passed the topology tests applied. The monophyly of the aequatorialis, latifrons (as traditionally circumscribed) and punctatus series was strongly rejected, and the monophyly of Phenacosaurus (as traditionally circumscribed) yielded mixed results. The results of the phylogenetic analyses suggest the need for a revised taxonomy and have implications for the biogeography and tempo of the Dactyloa radiation.     

Molecular phylogeny of the Drosophila auraria species complex and allied species of Japan based on nuclear and mitochondrial DNA sequences

We studied the phylogenetic relationships among the six species of the Drosophila auraria species complex and three species of the montium species subgroup endemic to Japan. To do this, we examined the DNA sequences of the nuclear ITS1 and the mitochondrial COII of these species. Intraspecific variation in ITS1 was observed for most of the species studied. However, interspecific variation was small and of the same magnitude as intraspecific variation among D. auraria, D. triauraria, and D. quadraria. In addition, the amount of intraspecific variation between COII sequences from D. auraria and D. triauraria was almost the same as that of the interspecific variation between these species. Phylogenetic trees based on ITS1 or COII data reveal that, with the exception of D. pectinifera, these species can be separated into two taxonomic groups. D. rufa formed a taxonomic lineage with two Japanese endemic species, D. asahinai and D. lacteicornis. Physiological and behavioral differences between D. auraria and D. triauraria have been reported, but our results differed from those previously reported. Such differences may be better explained by hybridization between D. auraria and D. triauraria than by similarity due to recent common ancestry. Both the ITS1- and COII-based phylogenetic trees placed D. pectinifera outside the auraria complex. However, D. pectinifera sequences were more similar to those of the auraria complex than those of D. punjabiensis, another species thought to be closely related to members of the auraria complex.     

Molecular phylogeny of Solms-laubachia (Brassicaceae) s.l., based on multiple nuclear and plastid DNA sequences, and its biogeographic implications

The Hengduan Mountains region of south-west China is a noted biodiversity,hotspot, but the geographic origins and historical assembly of its rich endemic flora, including the sky-island species of Solms-laubachia Muschl. (Brassicaceae), have been little studied. Previous molecular studies on the phylogeny of Solms-laubachia showed it to be paraphyletic, leading to considerable expansion not only of its taxonomic limits, but also its geographic range, with the inclusion of taxa from outside the Hengduan region. However, these studies provided little resolution of interspecific relationships, preventing inferences about historical biogeography within the clade. In the present study, new sequence data from two nuclear genes (LEAFY and G3pdh) and two chloroplast intergenic spacers (petN-psbM and psbM-trnD) were combined with existing markers to increase phylogenetic signals. Phaeonychium villosum (Maxim.) Al-Shehbaz was found to be nested within Solms-laubachia s.l. In general, phylogenetic relationships appear to be a good predictor of geography, with the Hengduan Mountain endemics embedded in a paraphyletic grade of species from the western Himalayas and central Asia, but they also imply morphological homoplasy. Incongruence was detected between the nuclear and chloroplast gene trees, perhaps resulting from incomplete lineage sorting of ancestral polymorphisms. The crown age of Solms-laubachia s.l. was estimated to be approximately 1.42-3.68 mya, using Bayesian relaxed molecular clock analysis. Historical biogeographic analysis using a parametric dispersal-extinction-cladogenesis model inferred central Asia and the western Himalayas as most probable ancestral range of Solms-laubachia s.l., and estimated higher rates of eastward expansion than westward during the diversification of descendant lineages. In summary, our results suggest that Solms-laubachia s.l. originated during the Pliocene in central Asia, and subsequently migrated eastward into the Hengduan Mountains, colonizing sky-island, alpine scree-slope habitats that may have provided novel ecological opportunity and accelerated speciation, ultimately establishing this region as the present center of diversity of the genus.     

Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data

The complete nucleotide sequences of the mitochondrial (mt) genomes of three species of squamate lizards: Blanus cinereus (Amphisbaenidae), Anguis fragilis (Anguidae), and Tarentola mauritanica (Geckkonidae) were determined anew. The deduced amino acid sequences of all 13 mt protein-coding genes were combined into a single data set and phylogenetic relationships among main squamate lineages were analyzed under maximum likelihood (ML) and Bayesian Inference (BI). Within Squamata, the monophyly of Iguanidae, Anguimorpha, Amphisbaenia, Gekkota, Serpentes, and Acrodonta received high statistical support with both methods. It is particularly striking that this is the first molecular analysis that recovers the monophyly of Scincomorpha (including Scincidae, Xantusiidae, Cordylidae, and Lacertidae), although it is only supported in the Bayesian analysis, and it is sensitive to changes in the outgroup (see below). Phylogenetic relationships among the main squamate lineages could not be resolved with ML but received strong support with BI (above 95%). The newly reconstructed phylogeny of squamates does not support the Iguania-Scleroglossa split. Acrodonta and Serpentes form a clade, which is the sister group of the remaining squamate lineages. Within these, Gekkota were the first branching out, followed by Amphisbaenia, and a clade including Anguimorpha as sister group of Scincomorpha + Iguanidae. The recovered topology differed substantially from previously reported hypotheses on squamate relationships, and the relative effect of using different outgroups, genes, and taxon samplings were explored. The sister group relationship of Serpentes + Acrodonta, and their relative basal position within Squamata could be due to a long-branch attraction artifact. Phylogenetic relationships among Scincomorpha, Amphisbaenia, and Anguimorpha were found to be rather unresolved. Future improving of squamate phylogenetic relationships would rely on finding snake and acrodont species with slower mt evolutionary rates, ensuring thorough taxon coverage of squamate diversity, and incorporating more nuclear genes with appropriate evolutionary rates.     

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 medaka fishes genus Oryzias (Beloniformes: Adrianichthyidae) based on nuclear and mitochondrial DNA sequences

The phylogenetic relationships among medaka fishes of 2 genera, Oryzias and Xenopoecilus, were studied using the nuclear tyrosinase and mitochondrial 12S and 16S rRNA genes. Of the 23 species currently described for these genera, 13 species of Oryzias and 2 species of Xenopoecilus were examined. The tree topologies obtained from the nuclear and mitochondrial data were consistent, indicating that Xenopoecilus is a polyphyletic genus nested within Oryzias. This result suggested the necessity for a systematic study and taxonomic revision of Xenopoecilus. The combined data analysis of all data partitions resulted in a well-resolved tree, with most internal branches supported by high statistical values. Based on our combined data phylogeny, we divided the Oryzias species into three major species groups, namely the latipes, javanicus, and celebensis groups. These three groups corresponded to the three chromosomal groups (biarmed, monoarmed, and fused chromosome groups) previously proposed from karyological analyses. The phylogeographic pattern suggests historical vicariance between Sulawesi Island and the continental shelf.     

Re-examination of the phylogeny of Rhacophoridae (Anura) based on mitochondrial and nuclear DNA

The phylogenetic relationships among rhacophorid frogs are under dispute. We use partial sequences of three mitochondrial (12S rRNA, 16S rRNA, and cytochrome b) and three nuclear protein-coding (Rag-1, rhodopsin exon 1, and tyrosinase exon 1) genes from 57 ingroup taxa and eight outgroup taxa to propose a hypothesis for phylogenetic relationships within Rhacophoridae. Our results support recognition of the genus Feihyla, and Chiromantis is the sister taxon to the clade formed by Feihyla, Polypedates and Rhacophorus. We place Aquixalus odontotarsus within Kurixalus, and the remaining species of Aquixalus and Philautus jinxiuensis into the genus Gracixalus. We give Philautus (Kirtixalus) the rank of genus and place Philautus menglaensis within it. The division of species groups among Chinese Rhacophorus needs revision, and a cryptic species is revealed within Rhacophorus nigropunctatus. Rhacophorus pingbianensis is considered a synonym of Rhacophorus omeimontis. The validity of Rhacophorus hui is confirmed by present molecular evidence.     

Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA

The Blastocladiomycota is a recently described phylum of ecologically diverse zoosporic fungi whose species have not been thoroughly sampled and placed within a molecular phylogeny. In this study, we investigated the phylogeny of the Blastocladiomycota based on ribosomal DNA sequences from strains identified by traditional morphological and ultrastructural characters. Our results support the monophyly of the Coelomomycetaceae and Physodermataceae but the Blastocladiaceae and Catenariaceae are paraphyletic or polyphyletic. The data support two clades within Allomyces with strains identified as Allomyces arbusculus in both clades, suggesting that species concepts in Allomyces are in need of revision. A clade of Catenaria species isolated from midge larvae group separately from other Catenaria species, suggesting that this genus may need revision. In the Physodermataceae, Urophlyctis species cluster with a clade of Physoderma species. The algal parasite Paraphysoderma sedebokerensis nom. prov. clusters sister to other taxa in the Physodermataceae. Catenomyces persicinus, which has been classified in the Catenariaceae, groups with the Chytridiomycota rather than Blastocladiomycota. The rDNA operon seems to be suitable for classification within the Blastocladiomycota and distinguishes among genera; however, this region alone is not suitable to determine the position of the Blastocladiomycota among other basal fungal phyla with statistical support. A focused effort to find and isolate, or directly amplify DNA from additional taxa will be necessary to evaluate diversity in this phylum. We provide this rDNA phylogeny as a preliminary framework to guide further taxon and gene sampling and to facilitate future ecological, morphological, and systematic studies.     

Phylogenetic relationships of the bulbuls (Aves: Pycnonotidae) based on mitochondrial and nuclear DNA sequence data

Bulbuls (Aves: Pycnonotidae) are a fairly speciose (ca. 130 sp.) bird family restricted to the Old World. Family limits and taxonomy have been revised substantially over the past decade, but a comprehensive molecular phylogeny for the family has not been undertaken. Using nuclear and mitochondrial DNA sequences, we reconstructed a well-supported phylogenetic hypothesis for the bulbuls. Three basal lineages were identified: a large African clade, a large Asian clade that also included African Pycnonotus species, and the monotypic African genus Calyptocichla. The African clade was sister to the other two lineages, but this placement did not have high branch support. The genus Pycnonotus was not monophyletic because three species (eutilotus, melanoleucos, and atriceps) were highly diverged from the other species and sister to all other Asian taxa. Additional taxon sampling is needed to further resolve relationships and taxonomy within the large and variable Hypsipetes complex.