Systematic revision of the genus Aglyptodactylus Boulenger, 1919 (Amphibia: Ranidae), and analysis of its phylogenetic relationships to other Madagascan ranid genera (Tomopterna, Boophis, Mantidactylus, and Mantella)

Recent field studies revealed two new species of the genus Aglyptodactylus (Amphibia: Anura: Ranidae), which was hitherto considered as monotypic and confined to humid eastern Madagascar. Both new species, Aglyptodactylus laticeps sp. n. and Aglyptodactylus securifer sp. n. , occur syntopically in the deciduous dry forest of Kirindy in western Madagascar. In comparison to Aglyptodactylus madagascariensis from eastern rainforests, the new species A. laticeps shows a remarkable morphological divergence, which may be partly due to adaptations to burrowing habits in dry environments. Despite of the morphological differentiation, advertisement calls and osteology indicate that all three species of Aglyptodactylus are closely related. A phylogenetic analysis of the Madagascan ranid genera Aglyptodactylus, Mantella, Mantidactylus, Boophis , and Tomopterna (the latter including species from Madagascar, Africa, and Asia) strongly supports a sister group relationship of Aglyptodactylus with the ranine genus Tomopterna . We therefore transfer Aglyptodactylus from the Rhacophorinae to the Raninae and discuss implications of this rearrangement for ranoid systematics. The existence of the endemic genus Aglyptodactylus in Madagascar as well as its close phylogenetic relationships to Tomopterna confirm that the Raninae were already present on the Madagascan plate before its separation from Africa. The Madagascan Tomopterna labrosa shows several important differences both to Asian and to African species of the genus, and is therefore transferred from the subgenus Sphaerotheca (now restricted to Asia) to a new subgenus Laliostoma subgen. n .     

Opalinidae in African Anura. III. Genus Cepedea

During 1988 and 1989, 409 specimens of southern African Anura comprising 50 species in 9 families were checked for opalinids in the cloaca. Cepedea acuta n. sp. was found in six of 19 Tomopterna cryptotis and four of seven T. krugerensis (Ranidae); C. affinis (Nazaretskaja, 1992) in two of four Afrixalus aureus, two of four Hyperolius horstocki, 23 of 42 H. marmoratus, one of seven H. pusillus, two of six H. semidiscus, and eight of 12 H. tuberilinguis (Hyperoliidae); C. magna Metcalf, 1923 in one of 20 Bufo garmani, eight of 33 B. gutturalis and two of nine B. rangeri (all Bufonidae), one of two Heleophryne natalensis (juveniles) (Heleophrynidae), four of six Kassina maculata, three of seven K. senegalensis and two of six Semnodactylus wealii (all Hyperoliidae), three of five Phrynomerus bifasciatus (Microhylidae), three of 12 Phrynobatrachus natalensis, 11 of 19 Tomopterna cryptotis, 13 of 14 T. delalandii, one of seven T. krugerensis and one of six T. natalensis (all Ranidae), and four of five Chiromantis xerampelina (Rhacophoridae); Cepedea vanniekerkae n. sp. in one of 19 Tomopterna cryptotis. It is suggested that the Ranidae (in particular the genus Tomopterna) and the Hyperoliidae (in particular the genus Hyperolius) are among the major carriers of Cepedea in the Afrotropical Region.     

Advertisement calls of two anuran amphibians,Rana tigrina andTomopterna breviceps

Rana tigrina andTomopterna breviceps occur as sympatric species at Dharwad, India. Sexually mature males produce advertisement calls. The advertisement call of both the species consist of a number of calls produced in series forming a call group. Each call group ofRana tigrina comprises 10–40 calls, whereas that ofTomopterna breviceps consists 13–141 calls. Each call consists of a pulse group with variable number of pulses which lack pulse interval. Calls of both the species exhibit similarities in (i) call consisting of series of calls with a pulse group in each call, (ii) absence of pulse interval within the pulse group, (iii) the amplitude of the first pulse being always small, and (iv) the frequency spectrum beginning from 200 Hz. Based on the similarities in the spectral features of the calls, it is suggested that the two species may be closely related to each other.     

How many species are in the genus Batrachuperus? A phylogeographical analysis of the stream salamanders (family Hynobiidae) from southwestern China

Phylogeographical analysis of DNA sequence data has been routinely used to test species boundaries using the monophyly criterion; however, a complementary criterion, reproductive isolation, is often ignored. We used a combination of phylogenetic and population genetic approaches to determine species boundaries among stream salamanders in the genus Batrachuperus . First, cytochrome b sequence data from 174 Batrachuperus individuals, sampled from 78 populations, were used to reconstruct historical relationships within the genus. Second, allozyme data for 14 presumptive nuclear loci, from 463 individuals sampled from 60 populations, were collected and analysed to assess population similarity or disparity, as well as potential reproductive isolation. The DNA sequence data grouped all populations into seven major monophyletic groups, and the allozyme data provided evidence for reproductive isolation among four of the seven groups, thereby supporting the species status of these groups. The allozyme data suggested that two of the other groups share the same gene pool, and therefore belong to a single species. Finally, the allozyme data revealed two reproductively isolated units within the seventh group, which we suggest represents a case of 'budding speciation' based on the DNA gene tree. In total, seven species of the genus Batrachuperus were defined, two of which were previously unknown. The phylogeographical analysis also revealed that vicariance events might have dominated the evolutionary history of this group, but the speciation events might precede the formation of the existing mountain topology. This study demonstrates the importance of including frequency data from multiple nuclear gene loci in determining species boundaries.     

Phylogenetic relationships in the Ranidae. Independent origin of direct development in the genera Philautus and Taylorana

Phylogenetic relationships within a group of Ranidae were studied, particularly between the genera Philautus and Taylorana, to determine whether their original reproductive mode (direct development) appeared independently. To study these relationships, we used the DNA sequences of the 5' end of the gene coding for mitochondrial ribosome small subunit in 28 species. Parsimony analysis resulted in two equiparsimonious trees, 867 steps long (CI = 0.382; RI = 0.429). Data saturation was studied and we applied weighting (weight of 5 for transversions and 1 for transitions) to enhance the phylogenetic information. The tree we obtained (2,212 steps long, CI = 0.408; RI = 0.482) is best supported and allows us to determine clearly that direct development has appeared independently in Philautus and Taylorana. In addition, it is confirmed that the genus Rana sensu lato is heterogeneous. The genera Occidozyga and Phrynoglossus form a clade basal to all the group but this position is not supported. The inclusion of the Rhacophorinae in the Ranidae is confirmed. Finally, this study confirms that the relationships within the group Tomopterna sensu Boulenger, 1918 should be re-evaluated.     

DNA base alignment and taxonomic study of genus Malassezia based upon partial sequences of mitochondrial large subunit ribosomal RNA gene

The sequences of the large subunit of mitochondrial ribosomal RNA (LsmtrRNA) gene of Malassezia species were analysed. The sequences of the seven species of Malassezia are well separated in each species. Therefore the LsmtrRNA gene is thought to be one of the gene targets for species identification in the genus Malassezia. The dendrogram obtained from this gene supports the previous study of Malassezia species based upon the chromosomal genes. This is the first report of taxonomic analysis of Malassezia species based upon the mitochondrial gene.     

Molecular phylogenetic relationships of the deep-sea fish genus Coryphaenoides (Gadiformes: Macrouridae) based on mitochondrial DNA

In order to characterize the phylogenetic relationship and deep-sea adaptation process of the deep-sea fish genus Coryphaenoides, the nucleotide sequences of the mitochondrial (mt) 12 S rRNA and COI gene sequences for seven Coryphaenoides species were analyzed. Our molecular phylogenetic tree shows a new arrangement of seven Coryphaenoides species, which form two distinct groups, abyssal and nonabyssal species, and differs from the results of previous taxonomic studies. Using the mutation rate of mitochondrial genes, the divergence time between abyssal and nonabyssal Coryphaenoides was found to be 3.2-7.6 million years ago. Our study suggests that hydraulic pressure plays an important role in the speciation process in the marine environment.     

Phylogenomic analyses reveal intractable evolutionary history of a temperate bamboo genus (Poaceae: Bambusoideae)

Shibataea is a genus of temperate bamboos(Poaceae:Bambusoideae)endemic to China,but little is known about its phylogenetic position and interspecific relationships.To elucidate the phylogenetic relationship of the bamboo genus Shibataea,we performed genome-scale phylogenetic analysis of all seven species and one variety of the genus using double digest restriction-site associated DNA sequencing(dd RAD-seq)and whole plastid genomes generated using genome skimming.Our phylogenomic analyses based on dd RAD-seq and plastome data congruently recovered Shibataea as monophyletic.The nuclear data resolved S.hispida as the earliest diverged species,followed by S.chinensis,while the rest of Shibataea can be further divided into two clades.However,the plastid and nuclear topologies conflict significantly.By comparing the results of network analysis and topologies reconstructed from different datasets,we identify S.kumasasa as the most admixed species,which may be caused by incomplete lineage sorting(ILS)or interspecific gene flow with four sympatric species.This study highlights the power of dd RAD and plastome data in resolving complex relationships in the intractable bamboo genus.     

ASSESSING REPRODUCTIVE ISOLATION IN HIGHLY DIVERSE COMMUNITIES OF THE LICHEN-FORMING FUNGAL GENUS PELTIGERA

The lichen-forming fungal genus Peltigera includes a number of species that are extremely widespread, both geographically and ecologically. However, morphological variability has lead to doubts about the distinctness of some species, and it has been suggested that hybridization is common in nature. We examined species boundaries by looking for evidence of hybridization and gene flow among seven described species collected at five sites in British Columbia, Canada. We found no evidence of gene flow or hybridization between described species, with fixed differences between species for two or more of the three loci examined. Reproductive isolation did not reflect a solely clonal mode of reproduction as there was evidence of ongoing gene flow within species. In addition, we found five undescribed species that were reproductively isolated, although there was evidence of ongoing or historical gene flow between two of the new species. These results indicate that the genus Peltigera is more diverse in western North America than originally perceived, and that morphological variability is due largely to the presence of undescribed species rather than hybridization or intraspecific variation.     

EST data suggest that poplar is an ancient polyploid

We analysed the publicly available expressed sequence tag (EST) collections for the genus Populus to examine whether evidence can be found for large-scale gene-duplication events in the evolutionary past of this genus. The ESTs were clustered into unigenes for each poplar species examined. Gene families were constructed for all proteins deduced from these unigenes, and K(S) dating was performed on all paralogs within a gene family. The fraction of paralogs was then plotted against the K(S) values, which resulted in a distribution reflecting the age of duplicated genes in poplar. Sufficient EST data were available for seven different poplar species spanning four of the six sections of the genus Populus. For all these species, there was evidence that a large-scale gene-duplication event had occurred. From our analysis it is clear that all poplar species have shared the same large-scale gene-duplication event, suggesting that this event must have occurred in the ancestor of poplar, or at least very early in the evolution of the Populus genus.     

Patterns of Historical Balancing Selection on the Salmonid Major Histocompatibility Complex Class II β Gene

Allelic variation in the major histocompatibility class (MHC) IIB gene of salmonids is analyzed for patterns indicative of natural selection acting at the molecular level. Sequence data for the second exon of this MHC gene were generated for 11 species in three salmonid genera: Oncorhynchus, Salmo, and Salvelinus. Phylogenetic analysis of nucleotide sequences revealed: (1) monophyletic grouping of alleles from each genus, (2) transspecies evolution of alleles within Salmo and Salvelinus, and (3) differential patterns of transspecies evolution within the genus Oncorhynchus. Within Oncorhynchus, five of seven species had alleles that were species-specific or nearly so, while the remaining two, O. mykiss and O. clarkii, retained ancestral polymorphisms. The different patterns in Oncorhynchus and the other two genera could be due to historical demographic effects or functional differences in MHC molecules in the three genera, but the two hypotheses could not be distinguished with the current dataset. An analysis of recombination/gene conversion identified numerous recombinant alleles, which is consistent with what has been found in other vertebrate taxa. However, these gene conversion events could not account for the species-specific allelic lineages observed in five of the Oncorhynchus species. Analyses of the relative rates of nonsynonymous and synonymous substitutions revealed the signature of selection on the class IIB gene in all 11 of the salmonid species for both the ABS and the non-ABS codons. Codon-based analyses of selection identified seven codons that have experienced selection in the majority of the species. More than half of these sites were mammalian ABS codons, but several were not, suggesting subtle functional differences in the mammalian and teleost fish MHC molecules.     

Systematic relationships among Lutzomyia sand flies (Diptera: Psychodidae) of Peru and Colombia based on the analysis of 12S and 28S ribosomal DNA sequences

Lutzomyia spp. are New World phlebotomine sand flies, many of which are involved in the transmission of human diseases, such as leishmaniases and bartonellosis. The systematic classification of the approximately 400 species in the genus has been based on morphological characters, but the relationships within the genus are still very much in question. We have inferred phylogenies of 32 species of phlebotomine sand flies belonging to seven sub-genera and two species groups, by using fragments of the mitochondrial small subunit (12SrRNA) and of the nuclear large subunit (28SrRNA) ribosomal gene sequences. The subgenus Helcocyrtomyia and the Verrucarum species group, prominent representatives of the Peruvian sand fly fauna, were represented by 11 and 7 species, respectively. Although based on a limited number of taxa, the resulting phylogenies, based on 837 characters, provide an initial phylogenetic backbone for the progressive reconstruction of infrageneric relationships within Lutzomyia.     

A molecular phylogenetic investigation of zoothamnium (ciliophora, peritrichia, sessilida)

The gene coding for 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in seven free-living, marine species of the sessiline peritrich genus Zoothamnium. These were Zoothamnium niveum, Zoothamnium alternans, Zoothamnium pelagicum, and four unidentified species. The ssu rRNA gene also was sequenced in Vorticella convallaria, Vorticella microstoma, and in an unidentified, freshwater species of Vorticella. Phylogenetic trees were constructed using these new sequences to test a previously published phylogenetic association between Zoothamnium arbuscula, currently in the family Zoothamniidae, and peritrichs in the family Vorticellidae. Trees constructed by means of neighbor-joining, maximum parsimony, maximum likelihood, and Bayesian inference methods all had similar topologies. The seven new sequences of Zoothamnium species grouped into three well-supported clades, each of which contained a diversity of morphological types. The three clades formed a poorly supported, larger clade that was deeply divergent from Z. arbuscula, which remained more closely associated with vorticellid peritrichs. It is apparent that Zoothamnium is a richly diverse genus and that a much more intensive investigation, involving both morphological and molecular data and a wider selection of species, will be necessary to resolve its phylogeny. A greater amount of molecular diversity than is predicted by morphological data exists within all major clades of sessiline peritrichs that have been included in molecular phylogenies, indicating that characteristics of stalk and peristomial structure traditionally used to differentiate taxa at the generic level and above may not be uniformly reliable.     

迷蛱蝶属及相关物种细胞色素b基因序列及其分子系统学研究

迷蛱蝶属Mimathyma隶属于蛱蝶科Nymphalidae闪蛱蝶亚科Apaturinae,该属所包含的种类复杂,其分类学地位存在争议.本文对迷蛱蝶属、闪蛱蝶属Apatura和带蛱蝶属Athyma7个种共19个个体的线粒体DNA细胞色素b基因部分序列进行测定分析,并以花斑螯蛱蝶Charaxes kahruba (Moore)作为外群用PAUP软件构建MP和NJ分子系统树.结果显示迷蛱蝶Mimathyma chevana(Moore)、夜迷蛱蝶Mimathyma nycteis(Ménétriès)、白斑迷蛱蝶Mimathyma schrenckii (Ménétriès)和环带迷蛱蝶Mimathyma ambica Kollar形成1个聚类簇,支持Moore将这4个种由闪蛱蝶属移出并建立迷蛱蝶属的观点.同时,尽管迷蛱蝶在形态上与该属其余3种相似,但研究发现聚类簇Ⅰ中夜迷蛱蝶、白斑迷蛱蝶和环带迷蛱蝶首先相聚,然后再与迷蛱蝶聚在一起,表明迷蛱蝶与这3种亲缘关系较远.此外,本文的研究结果还显示迷蛱蝶属与闪蛱蝶属关系密切,而与带蛱蝶属的关系较远.     

Multilocus sequence analysis of the actinobacterial genus Kribbella

Multilocus sequence analysis (MLSA) was used to refine the phylogenetic analysis of the genus Kribbella, which currently contains 17 species with validly-published names. Sequences were obtained for the 16S rRNA, gyrB, rpoB, recA, relA and atpD genes for 16 of the 17 type strains of the genus plus seven non-type strains. A five-gene concatenated sequence of 4099 nt was used to examine the phylogenetic relationships between the species of the genus Kribbella. Using the concatenated sequence of the gyrB-rpoB-recA-relA and atpD genes, most Kribbella type strains can be distinguished by a genetic distance of >0.04. Each single-gene tree had an overall topology similar to that of the concatenated sequence tree. The single-gene relA tree, used here for the first time in MLSA of actinobacteria, had good bootstrap support, comparable to the rpoB and atpD gene trees, which had topologies closest to that of the concatenated sequence tree. This illustrates that relA is a useful addition in MLSA studies of the genus Kribbella. We propose that concatenated gyrB-rpoB-recA-relA-atpD gene sequences be used for examining the phylogenetic relationships within the genus Kribbella and for determining the closest phylogenetic relatives to be used for taxonomic comparisons.     

Detection and analysis of six lizard adenoviruses by consensus primer PCR provides further evidence of a reptilian origin for the atadenoviruses

A consensus nested-PCR method was designed for investigation of the DNA polymerase gene of adenoviruses. Gene fragments were amplified and sequenced from six novel adenoviruses from seven lizard species, including four species from which adenoviruses had not previously been reported. Host species included Gila monster, leopard gecko, fat-tail gecko, blue-tongued skink, Tokay gecko, bearded dragon, and mountain chameleon. This is the first sequence information from lizard adenoviruses. Phylogenetic analysis indicated that these viruses belong to the genus Atadenovirus, supporting the reptilian origin of atadenoviruses. This PCR method may be useful for obtaining templates for initial sequencing of novel adenoviruses.     

Opalinidae in African Anura. II. Genera Protozelleriella n. g. and Zelleriella

During 1988 and 1989, 409 specimens of southern African Anura, comprising 50 species in 9 families, were checked for opalinids in the cloaca. Protozelleriella devilliersi n. g., n. sp. was found in three of four Capensibufo rosei (Bufonidae); Zelleriella africana Sandon, 1938 in two of three Bufo angusticeps and one of 20 B. garmani (Bufonidae) plus three of 12 Phrynobatrachus natalensis, 12 of 19 Tomopterna cryptotis, seven of 14 T. delalandii, three of seven T. krugerensis and one of six T. natalensis (all Ranidae); Z. gambieri n. sp. in one of six T. natalensis; Z. garlandi n. sp. in two of six Kassina maculata (Hyperoliidae); Z. sandoni n. sp. in two of 20 B. garmani, two of six K. maculata, one of seven K. senegalensis and one of four Leptopelis mossambicus (Hyperoliidae) plus one of five Phrynomerus bifasciatus (Microhylidae) and two of 19 T. cryptotis. It is suggested that the Ranidae (in particular the genus Tomopterna) and the Hyperoliidae are among the major carriers of Zelleriella in the Afrotropical Region.     

In situ localization of the evolutionary conserved Cpy/Cty gene in the subfamily Chironominae (Chironomidae, Diptera): establishment of chromosomal homologies

The homologous sites on the salivary gland chromosomes of 13 species from three genera: Chironomus, Glyptotendipes, Kiefferulus have been mapped by means of fluorescent in situ hybridization using the evolutionary conserved gene Cpy/Cty (clone Cla1.1). In all species of genus Chironomus and genus Kiefferulus , the Cty/Cpy gene is located on arm F of chromosome EF. The relocation of the gene among the species of genus Chironomus can be done by simple or complex homozygous inversions which occurred during the divergent evolution of the chromosome of the species. In the genus Glyptotendipes , the Cty/Cpy gene was localized in arm E of chromosome EF. Since the banding patterns of salivary gland chromosomes between genus Chironomus and genus Glyptotendipes cannot be compared directly, in situ hybridization with clone of conservative gene was performed to be established some homologous chromosomes. The results obtained indicate that the chromosome arm F of Chironomus and chromosome arm E of Glyptotendipes may be homologous.     

Molecular evolution of southern North American Cyprinidae (Actinopterygii), with the description of the new genus Tampichthys from central Mexico

Most of the recognized species of the genus Dionda inhabit drainages of the Gulf of Mexico from central Mexico to central Texas, USA, and have been considered a monophyletic group based on morphological, osteological, and allozyme investigations. Phylogenetic relationships of 15 species of Dionda and 34 species from closely related genera were inferred from one mitochondrial (cytb) and three nuclear gene sequences (S7, Rhodopsin, Rag1) totaling 4487 nucleotides. Separate analyses of all four genes yield congruent phylogenies; however the 15 putative species of Dionda evaluated were never recovered as a monophyletic group when species from nine related genera were included in the analyses. Among the ingroup taxa, one well-supported and highly divergent clade is consistently recognized and consists of six recognized and three undescribed northern species currently recognized in the genus Dionda. These nine species inhabit present or past tributaries of the Rio Grande basin of northern Mexico and southern USA, and were recovered as a basal clade in all analyses. Another large, also strongly supported clade, consisting of seven genera, include five southern recognized species currently in the genus Dionda, forming the sister group to the Codoma clade. These five species comprise the "Southern Dionda clade" and inhabit headwaters of the Pánuco-Tamesí drainage and some adjacent coastal rivers in the Tampico Embayment. The consistent and repeated identification of eight different clades recovered in most of the separate gene analyses strongly supports a division of the non-natural genus Dionda. A new genus, Tampichthys, is proposed for the clade of species endemic to east-central Mexico and formerly in Dionda. Tampichthys and the putative monotypic genus Codoma are more related to Mexican species of the genera Cyprinella and Notropis than to other species referred to Dionda sensu stricto.