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.     

Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: Heterogeneity among amino acid sites

The internal branch lengths estimated by distance methods such as neighbor joining are shown to be biased to be short when the evolutionary rate differs among sites. The variable-invariable model for site heterogeneity fits the amino acid sequence data encoded by the mitochondrial DNA from Hominoidea remarkably well. By assuming the orangutan separation to be 13 or 16 Myr old, a maximum-likelihood analysis estimates a young date of 3.6 ± 0.6 or 4.4 ± 0.7 Myr (±1 SE) for the human/chimpanzee separation, and these estimates turn out to be robust against differences in the assumed model for amino acid substitutions. Although some uncertainties still exist in our estimates, this analysis suggests that humans separated from chimpanzees some 4–5 Myr ago.Correspondence to: M. Hasewaga     

Phylogeny and biogeography of Valerianaceae (Dipsacales) with special reference to the South American valerians

Species of Valerianaceae are a common component of the alpine flora throughout the Northern Hemisphere as well as the Andes of South America. Sequence data from three chloroplast markers (psbA-trnH intron, trnK-matK intron, and the trnL-F region) along with the internal transcribed spacer region (ITS) of nuclear ribosomal DNA were used to infer relationships within Valerianaceae. Both genomes, as well as a combined data set, provide support for the major clades within the group and do not support a monophyletic Valeriana. In addition, these data indicate that Plectritis is nested within South American Valeriana, as opposed to being sister to Centhranthus as previously hypothesized. Valerianaceae appear to have originated in Asia, probably in the Himalayas, and subsequently to have dispersed several times to Europe and to the New World. Our results imply that Valerianaceae colonized South America on multiple occasions from the north. In one of these cases there appears to have been a substantial and rapid radiation, primarily in the high elevation paramo habitat. A variety of methods were used to estimate divergence times to determine when Valerianaceae might have colonized South America. Regardless of the method and fossil constraints applied, our estimates suggest that Valerianaceae colonized South America prior to the formation of the Isthmus of Panama.     

Phylogenetic relationships in rhinonyssid mites (Acari: Rhinonyssidae) based on mitochondrial 16S rDNA sequences

A 390 bp region of the 16S rDNA gene was sequenced from six species ofrhinonyssid mites (Tinaminyssus columbae, T. minisetosum, Sternostomaturdi, S. sternahirundo, S. fulicae and Ptilonyssus euroturdi) andtwo subspecies (Tinaminyssus melloi melloi andTinaminyssus melloi streptopeliae) to examine the level ofsequence variation and the taxonomic levels to show utility in phylogenyestimation. Furthemore, two different geographic locations of T. m.melloi and T. m. streptopeliae were analyzed todetect variation between populations. Molecular data revealed the existence oftwo distinct groups in the genus Tinaminyssus parasitic oncolumbiform birds. These results are in agreement with those reported by someauthors using morphological characters. Sternostoma turdi parasitizing aerial birds appeared to be phylogenetically separated from otherspecies of this genus isolated from aquatic birds. Moreover, our studyaddressesthe validity of the subspecies status of T. melloistreptopeliae. This region of the mitochondrial 16S rDNA gene is auseful marker for inferring phylogenetic relationships among closely relatedrhinonyssid species, but not for more distantly related taxa.     

Phylogeny of Passerida (Aves: Passeriformes) based on nuclear and mitochondrial sequence data

Passerida is a monophyletic group of oscine passerines that includes almost 3500 species (about 36%) of all bird species in the world. The current understanding of higher-level relationships within Passerida is based on DNA-DNA hybridizations [C.G. Sibley, J.E. Ahlquist, Phylogeny and Classification of Birds, 1990, Yale University Press, New Haven, CT]. Our results are based on analyses of 3130 aligned nucleotide sequence data obtained from 48 ingroup and 13 outgroup genera. Three nuclear genes were sequenced: c-myc (498-510 bp), RAG-1 (930 bp), and myoglobin (693-722 bp), as well one mitochondrial gene; cytochrome b (879 bp). The data were analysed by parsimony, maximum-likelihood, and Bayesian inference. The African rockfowl and rockjumper are found to constitute the deepest branch within Passerida, but relationships among the other taxa are poorly resolved--only four major clades receive statistical support. One clade corresponds to Passeroidea of [C.G. Sibley, B.L. Monroe, Distribution and Taxonomy of Birds of the World, 1990, Yale University Press, New Haven, CT] and includes, e.g., flowerpeckers, sunbirds, accentors, weavers, estrilds, wagtails, finches, and sparrows. Starlings, mockingbirds, thrushes, Old World flycatchers, and dippers also group together in a clade corresponding to Muscicapoidea of Sibley and Monroe [op. cit.]. Monophyly of their Sylvioidea could not be corroborated--these taxa falls either into a clade with wrens, gnatcatchers, and nuthatches, or one with, e.g., warblers, bulbuls, babblers, and white-eyes. The tits, penduline tits, and waxwings belong to Passerida but have no close relatives among the taxa studied herein.     

The complete nucleotide sequence of the mitochondrial DNA of the fin whale,Balaenoptera physalus

Summary The composition of the mitochondrial DNA (mtDNA) of the fin whale,Balaenoptera physalus, was determined. The length of the molecule is 16,398 bp, and its organization conforms with that of other mammals. The general similarity between the mtDNA of the fin whale and the cow is greater than the similarity between the fin whale and other species (human, mouse, rat) in which the composition of the entire molecule has been described. The D-loop region of the mtDNA of the fin whale is 81% identical to the D-loop of dolphin DNA, and the central portion of the D-loop is similar to the bovine D-loop. The accumulation of transversions and gaps in the 12S and 16S rRNA genes was assessed by comparing the fin whale, cow, and human. The sequence difference between human and the whale and human and the cow was at the same level, indicating that the rate of evolution of the mtDNA rRNA genes is about the same in artiodactyls and cetaceans. In the 12S rRNA gene an accumulation rate of 0.05% per million years places the separation of cetaceans and artiodactyls at about 55 million years ago. The corresponding figure for human and either the whale or the cow is about 80 million years. In the 16S rRNA gene a 0.08% accumulation rate of transversions and gaps per million years yields concurring figures. A comparison between the cytochromeb gene of the fin whale and cytochromeb sequences in the literature, including dolphin (Stenella) sequences, identified the cetaceans as monophyletic and the artiodactyls as their closest relatives. The comparison between the cytochromeb sequences of the fin whale andStenella showed that differences in codon positions one or two were frequently associated with a change in another codon position.     

A phylogenetic analysis of the major groups of catfishes (Teleostei: Siluriformes) using rag1 and rag2 nuclear gene sequences

Higher-level relationships among catfishes were investigated by parsimony, maximum likelihood and Bayesian analyses of two nuclear genes across 110 catfish species representing 36 of 37 families and Conorhynchos (family incertae sedis). Analysis of 3660 aligned base pairs from the rag1 and rag2 genes confirms monophyly of Siluriformes, of most siluriform families and of a number of multifamily groups, some recognized, some novel. South American Loricarioidei are recovered as the sistergroup to other catfishes which are divided into Diplomystidae and Siluroidei. This result contrasts with the prevailing hypothesis that Diplomystidae is the sister to all other catfishes. Monophyly of Siluroidei is supported by rag data including a unique three-codon deletion from rag1. Deep within Siluroidei are 12 large, strongly supported groups with poorly resolved interrelationships. Five are single families: Cetopsidae, Plotosidae, Chacidae, Siluridae and Pangasiidae. Four others are monophyletic taxa ranked here as superfamilies: Clarioidea (Clariidae, Heteropneustidae), Arioidea (Ariidae, Anchariidae), Pimelodoidea (Pimelodidae, Pseudopimelodidae, Heptapteridae, Conorhynchos), Ictaluroidea (Ictaluridae, Cranoglanididae). South American Doradoidea (Doradidae, Auchenipteridae) and Aspredinidae are a sistergroup pair. Sisoroidea (without Aspredinidae), Ailia+Laides, Horabagridae, and Bagridae (without Rita) form a large, predominantly Asian clade, "Big Asia." Mochokidae, Malapteruridae, Amphiliidae, Claroteidae, and African schilbids are united as a species-rich African clade, "Big Africa." The three large continental clades, "Big Asia," "Big Africa" and Neotropical Loricarioidei suggest a prevalence of intracontinental diversification of catfishes. South America is the home of the Gymnotiformes, putative sistergroup of catfishes, plus two of the deepest siluriform clades, Loricarioidei and Diplomystidae, thus suggesting an ancient siluriform presence if not origin there. The rag phylogeny does not identify any African-South American catfish clade. The well-known African-Asian relationships within families Clariidae and Bagridae are confirmed, as is the recently found North American-Asian relationship between Ictaluridae and Cranoglanididae.     

双尾虫系统进化的初步探讨

双尾虫系统发生问题目前血受学者的关注。作为六足总纲中内,外颚亚纲的过渡类群,双尾虫是否单系性及其系统地位的确定是争论的焦点,也是解决六足总纲高级阶元系统关系的一个关键。文中综述了多年来双尾虫形态学和解剖学方面研究所引发的争议和达成的共识,并对近几年该方面分子系统学的工作进行了总结和初步探讨。     

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     

The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout,Oncorhynchus mykiss

The complete nucleotide sequence of the mitochondrial DNA of the rainbow trout, Onchorynchus mykiss, has been determined. The total length of the molecule is 16,660 bp. The rainbow trout mitochondrial DNA has the same organization described in eutherian mammals, the clawed frog (Xenopus laevis), and the two fish species, Oriental stream loach (Crossotoma lacustre) and carp (Cyprinus carpio). Alignment and comparison of the deduced amino acid sequences of the 13 proteins encoded by rainbow trout and other vertebrate mitochondrial genomes allowed us to estimate that COI is the most conserved mitochondrial subunit (amino acid identity ranging from 85.6% to 94.8%) whereas ATPase 8 is the most variable one (amino acid identity ranging from 30.8% to 70.4%). Putative secondary structures for the 22 tRNAs found in the molecule are given along with an extensive comparison of tRNA sequences among representative species of each major group of vertebrates. In this sense, an unusual cloverleaf structure for the tRNA^Ser(AGY) is proposed. A stem-loop structure inferred for the origin of the L-strand replication (O_L) and the presence of a large polycytidine tract in the O_L loop is described. The existence of this stretch instead of the usual T-rich sequence reported so far in mammal mtDNAs is explained in terms of a less-strict template dependence of the RNA primase involved in the initiation of L-strand replication. Correspondence to: J.M. Bautista     

The evolutionary history of cockatoos (Aves: Psittaciformes: Cacatuidae)

Cockatoos are the distinctive family Cacatuidae, a major lineage of the order of parrots (Psittaciformes) and distributed throughout the Australasian region of the world. However, the evolutionary history of cockatoos is not well understood. We investigated the phylogeny of cockatoos based on three mitochondrial and three nuclear DNA genes obtained from 16 of 21 species of Cacatuidae. In addition, five novel mitochondrial genomes were used to estimate time of divergence and our estimates indicate Cacatuidae diverged from Psittacidae approximately 40.7 million years ago (95% CI 51.6-30.3 Ma) during the Eocene. Our data shows Cacatuidae began to diversify approximately 27.9 Ma (95% CI 38.1-18.3 Ma) during the Oligocene. The early to middle Miocene (20-10 Ma) was a significant period in the evolution of modern Australian environments and vegetation, in which a transformation from mainly mesic to xeric habitats (e.g., fire-adapted sclerophyll vegetation and grasslands) occurred. We hypothesize that this environmental transformation was a driving force behind the diversification of cockatoos. A detailed multi-locus molecular phylogeny enabled us to resolve the phylogenetic placements of the Palm Cockatoo (Probosciger aterrimus), Galah (Eolophus roseicapillus), Gang-gang Cockatoo (Callocephalon fimbriatum) and Cockatiel (Nymphicus hollandicus), which have historically been difficult to place within Cacatuidae. When the molecular evidence is analysed in concert with morphology, it is clear that many of the cockatoo species' diagnostic phenotypic traits such as plumage colour, body size, wing shape and bill morphology have evolved in parallel or convergently across lineages.     

Molecular phylogeny and systematics of the Barbinae (Teleostei: Cyprinidae) in China inferred from mitochondrial DNA sequences

The taxonomy and phylogeny of the Chinese species of the Barbinae (Cypriniformes) has a confusing history. In this study, partial sequences of four mitochondrial genes (cyt b, COI, ND4 and 16S rRNA) from 75 Barbinae species and 38 outgroup species were used to investigate the taxonomy and phylogeny within the Barbinae in China. The monophyly of Neolissochilus, Sikukia and Tor are not supported. Neolissochilus benasi might represent a new genus, and Tor hemispinus and Tor qiaojiensis should be moved into Neolissochilus. Sikukia flavicaudata is not Sikukia species. Puntius paucimaculatus might be a synonym of Puntius semifasciolatus. Puntius semifasciolatus does not belong to Puntius. Onychostoma barbatum might consist of more than one species. Our molecular results corroborate that Acrossocheilus stenotaeniatus is a synonym of Acrossocheilus longipinnis. Finally, Barbonymus gonionotus from Menglun, Yunnan should be Poropuntius huangchuchieni.     

Phylogenetic estimation of Mytilidae in the East China Sea inferred from mitochondrial genes and nuclear DNA sequence variation

We performed a phylogenetic estimation of the family Mytilidae in the East China Sea based on nuclear internal transcribed spacer (ITS) genes and two mitochondrial genes (COI and 16S RNA). Analysis of five mytilid species based on each of the three genes resulted in mostly congruent trees, although there were some discrepancies in the classification of these species. We combine the results obtained from the three separate analyses to provide a phylogenetic estimation of Mytilidae. We found that the Mytilidae was divided into two major lineages: in one clade, Mytilus galloprovincialis was grouped with Mytilus coruscus; in the second clade, Septifer bilocularis was placed at the basal position in an individual clade, and Perna viridis and Musculista senhousia were recovered as a monophyletic group. Although these finding provide important insights into the taxonomic relationships among the Mytilidae, many aspects of Mytilidae phylogeny remain unresolved. Further analysis based on more molecular information and extensive taxon sampling is necessary to elucidate the phylogenetic relationships among the major lineages within the Mytilidae.     

A comprehensive molecular phylogeny of the starlings (Aves: Sturnidae) and mockingbirds (Aves: Mimidae): congruent mtDNA and nuclear trees for a cosmopolitan avian radiation

We generated a comprehensive phylogeny for the avian families Sturnidae (starlings, mynas, Rhabdornis, oxpeckers, and allies) and Mimidae (mockingbirds, thrashers, and allies) to explore patterns of morphological and behavioral diversification. Reconstructions were based on mitochondrial DNA sequences from five coding genes (4108 bp), and nuclear intron sequences from four loci (2974 bp), for most taxa, supplemented with NDII gene sequences (1041 bp) derived from museum skin specimens from additional taxa; together the 117 sampled taxa comprise 78% of the 151 species in these families and include representatives of all currently or recently recognized genera. Phylogenetic analyses consistently identified nine major clades. The basal lineage is comprised of the two Buphagus oxpeckers, which are presently confined to Africa where they are obligately associated with large mammals. Some species in nearly all of the other major clades also feed on or around large vertebrates, and this association may be an ancestral trait that fostered the world-wide dispersal of this group. The remaining taxa divide into sister clades representing the New-World Mimidae and Old-World Sturnidae. The Mimidae are divided into two subclades, a group of Central American and West Indian catbirds and thrashers, and a pan-American clade of mockingbirds and thrashers. The Sturnidae are subdivided into six clades. The Phillipine endemic Rhabdornis are the sister lineage to a larger and substantially more recent radiation of South Asian and Pacific island starlings and mynas. A clade of largely migratory or nomadic Eurasian starlings (within which the basal lineage is the model taxon Sturnus vulgaris) is allied to three groups of largely African species. These reconstructions confirm that Buphagus should not be included in the Sturnidae, and identify many genera that are not monophyletic. They also highlight the substantial diversity among the major Sturnidae subclades in rates of species accumulation, morphological differentiation, and behavioral variation.     

Molecular analysis for mitochondrial DNA disorders

In this article, we review the current methodologies used for the molecular diagnosis of mitochondrial DNA defects. Definition of mitochondrial disorders at the molecular level has been difficult because of both clinical and genetic heterogeneity. Direct DNA analysis for common point mutations and large mtDNA deletions is readily performed and can be done routinely. However, a large number of patients who have the clinical manifestations and muscle pathology findings consistent with mitochondrial DNA disorders do not have detectable common mutations. Additional mutation screening methods are required for the detection of rare and previously undescribed mutations in the mitochondrial genome.     

Phylogenetic analysis using parsimony and likelihood methods

The assumptions underlying the maximum-parsimony (MP) method of phylogenetic tree reconstruction were intuitively examined by studying the way the method works. Computer simulations were performed to corroborate the intuitive examination. Parsimony appears to involve very stringent assumptions concerning the process of sequence evolution, such as constancy of substitution rates between nucleotides, constancy of rates across nucleotide sites, and equal branch lengths in the tree. For practical data analysis, the requirement of equal branch lengths means similar substitution rates among lineages (the existence of an approximate molecular clock), relatively long interior branches, and also few species in the data. However, a small amount of evolution is neither a necessary nor a sufficient requirement of the method. The difficulties involved in the application of current statistical estimation theory to tree reconstruction were discussed, and it was suggested that the approach proposed by Felsenstein (1981,J. Mol. Evol. 17: 368–376) for topology estimation, as well as its many variations and extensions, differs fundamentally from the maximum likelihood estimation of a conventional statistical parameter. Evidence was presented showing that the Felsenstein approach does not share the asymptotic efficiency of the maximum likelihood estimator of a statistical parameter. Computer simulations were performed to study the probability that MP recovers the true tree under a hierarchy of models of nucleotide substitution; its performance relative to the likelihood method was especially noted. The results appeared to support the intuitive examination of the assumptions underlying MP. When a simple model of nucleotide substitution was assumed to generate data, the probability that MP recovers the true topology could be as high as, or even higher than, that for the likelihood method. When the assumed model became more complex and realistic, e.g., when substitution rates were allowed to differ between nucleotides or across sites, the probability that MP recovers the true topology, and especially its performance relative to that of the likelihood method, generally deteriorates. As the complexity of the process of nucleotide substitution in real sequences is well recognized, the likelihood method appears preferable to parsimony. However, the development of a statistical methodology for the efficient estimation of the tree topology remains a difficult open problem.     

Phylogenetic relationships of mullets (Mugilidae) in China Seas based on partial sequences of two mitochondrial genes

Phylogenetic analyses of Mugilidae species from the China coast were carried out based on 16S and 12S rRNA mitochondrial gene sequences by maximum parsimony, maximum likelihood, Bayesian inference and neighbor joining analysis in the present study. The results suggested that Mugil cephalus is the most genetically divergent species among the Mugilidae. The four Liza species clustered together and formed a monophyletic group. The genera Osteomugil showed closer affiliation with Valamugil than with Ellochelon; these three genera then grouped together to form a monophyletic clade presenting as the sister group to Liza. Analyses of phylogenetic and genetic distance indicated that Southern and Northern lineages of Liza haematocheila may be two different species; likewise, strong genetic divergence existed between Southern and Northern M. cephalus lineages. In addition, our results supported the Southern origin of Chinese Mugilids, which is contrary to the hypothesis based on morphological characters.     

The complete mitochondrial DNA sequence of the harbor seal,Phoca vitulina

Summary The nucleotide sequence of the mitochondrial DNA (mtDNA) of the harbor seal, Phoca vitulina, was determined. The total length of the molecule was 16,826 bp. The organization of the coding regions of the molecule conforms with that of other mammals, but the control region is unusually long. A considerable portion of the control region is made up of short repeats with the motif GTACAC particularly frequent. The two rRNA genes and the 13 peptide-coding genes of the harbor seal, fin whale, cow, human, mouse, and rat were compared and the relationships between the different species assessed. At ordinal level the 12S rRNA gene and 7 out of the 13 peptide-coding genes yielded a congruent topological tree of the mtDNA relationship between the seal, cow, whale, human, and the rodents. In this tree the whale and the cow join first, and this clade is most closely related to the seal.Offprint requests to: Ú. Árnason     

Phylogenetic relationships of four endemic genera of the Phasianidae in China based on mitochondrial DNA control-region genes

The taxonomic status of some genera within the Phasianidae remains controversial. To demonstrate the phylogenetic relationships of four endemic genera (Tetraophasis, Ithaginis, Crossoptilon and Chrysolophus) and other 11 genera of Phasianidae in China, a total of 1070 nucleotides of mitochondrial DNA (mtDNA) control-region genes were sequenced. There are 376 variable sites including 345 parsimony sites. The genetic distance ranged from 0.067 (Chrysolophus and Phasianus) to 0.181 (Perdix and Bambusicola) among the 15 genera. Maximum likelihood method was used to construct a phylogenetic tree, which grouped all the genera into two deeply divergent clades. Perdix was shown to be a non-partridge genus. Alternatively, it appears ancestral to either partridges or pheasants. The sibling taxa of the four endemic genera were Lophophorus, Tragopan, Lophura and Phasianus, respectively. Calibrated rates of molecular evolution suggested that the divergence time between the four genera and related taxa was 4.00–5.00 million years ago, corresponding to the Pliocene. Considering their molecular phylogenetics, fossil and geographical distribution patterns, the four endemic genera might have originated in the southwestern mountains in China.