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     

Molecular phylogeny of Sinocyclocheilus (Cypriniformes: Cyprinidae) inferred from mitochondrial DNA sequences

More than 10 species within the freshwater fish genus Sinoncyclocheilus adapt to caves and show different degrees of degeneration of eyes and pigmentation. Therefore, this genus can be useful for studying evolutionary developmental mechanisms, role of natural selection and adaptation in cave animals. To better understand these processes, it is indispensable to have background knowledge about phylogenetic relationships of surface and cave species within this genus. To investigate phylogenetic relationships among species within this genus, we determined nucleotide sequences of complete mitochondrial cytochrome b gene (1140 bp) and partial ND4 gene (1032 bp) of 31 recognized ingroup species and one outgroup species Barbodes laticeps. Phylogenetic trees were reconstructed using maximum parsimony, Bayesian, and maximum likelihood analyses. Our phylogenetic results showed that all species except for two surface species S. jii and S. macrolepis clustered as five major monophyletic clades (I, II, III, IV, and V) with strong supports. S. jii was the most basal species in all analyses, but the position of S. macrolepis was not resolved. The cave species were polyphyletic and occurred in these five major clades. Our results indicate that adaptation to cave environments has occurred multiple times during the evolutionary history of Sinocyclocheilus. The branching orders among the clades I, II, III, and IV were not resolved, and this might be due to early rapid radiation in Sinocyclocheilus. All species distributed in Yunnan except for S. rhinocerous and S. hyalinus formed a strongly supported monophyletic group (clade V), probably reflecting their common origins. This result suggested that the diversification of Sinocyclocheilus in Yunnan may correlate with the uplifting of Yunnan Plateau.     

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.     

Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences

The taxonomy of clupeiforms has been extensively studied, yet phylogenetic relationships among component taxa remain controversial or unresolved. Here we test current and new hypotheses of relationships among clupeiforms using mitochondrial rRNA genes (12S and 16S) and nuclear RAG1 and RAG2 sequences (total of 4749bp) for 37 clupeiform taxa representing all five extant families and all subfamilies of Clupeiformes, except Pristigasterinae, plus seven outgroups. Our results, based on maximum parsimony, maximum likelihood, and Bayesian analyses of these data, show that some traditional hypotheses are supported. These include the monophyly of the families Engraulidae, consisting of two monophyletic subfamilies, Engraulinae (Engraulis and Anchoa) and Coilinae (Coilia and Setipinna), and Pristigasteridae (here represented only by Ilisha and Pellona). The basal position of Denticeps among clupeiforms is consistent with the molecular data when base compositional biases are accounted for. However, the monophyly of Clupeidae was not supported. Some clupeids were more closely related to taxa assigned to Pristigasteridae and Chirocentridae (Chirocentrus). These results suggest that a major revision in the classification of clupeiform fishes may be necessary, but should await a more complete taxonomic sampling and additional data.     

Molecular phylogeny of Mentawai macaques: taxonomic and biogeographic implications

In order to elucidate the evolutionary history and taxonomy of the Mentawai macaques, we sequenced a 567 base pairs (bp) long fragment of the mitochondrial cytochrome b gene from 39 individuals representing pigtailed macaque populations from Siberut, Sipora, South Pagai, and Sumatra. Pairwise difference analyses carried out within and among populations have shown, that: (1) variation within populations is relative low, (2) variation among populations is increased, and (3) pairwise differences within and among the populations from Sipora and South Pagai are in the same range. From phylogenetic tree reconstructions including further macaque species, we detected a paraphyletic origin of Mentawai macaques with the Siberut population more closely related to Macaca nemestrina from Sumatra, than it is to populations from the Southern islands. Based on these results, we favour a scenario in that macaques entered the Mentawai islands by two independent colonisation events. Taking together the paraphyletic origin of Mentawai macaques and the genetic differences detected among pigtailed macaque populations, which are comparable with those observed among the seven Sulawesi macaque species, we propose to separate macaques from Siberut and Sipora, North and South Pagai into two distinct species, Macaca siberu and Macaca pagensis, respectively.     

Molecular evidence on Primate phylogeny from DNA sequences

Evidence from DNA sequences on the phylogenetic systematics of primates is congruent with the evidence from morphology in grouping Cercopithecoidea (Old World monkeys) and Hominoidea (apes and humans) into Catarrhini, Catarrhini and Platyrrhini (ceboids or New World monkeys) into Anthropoidea, Lemuriformes and Lorisiformes into Strepsirhini, and Anthropoidea, Tarsioidea, and Strepsirhini into Primates. With regard to the problematic relationships of Tarsioidea, DNA sequences group it with Anthropoidea into Haplorhini. In addition, the DNA evidence favors retaining Cheirogaleidae within Lemuriformes in contrast to some morphological studies that favor placing Cheirogaleids in Lorisiformes. While parsimony analysis of the present DNA sequence data provides only modest support for Haplorhini as a monophyletic taxon, it provides very strong support for Hominoidea, Catarrhini, Anthropoidea, and Strepsirhini as monophyletic taxa. The parsimony DNA evidence also rejects the hypothesis that megabats are the sister group of either Primates or Dermoptera (flying lemur) or a Primate-Dermoptera clade and instead strongly supports the monophyly of Chiroptera, with megabats grouping with microbats at considerable distance from Primates. In contrast to the confused morphological picture of sister group relationships within Hominoidea, orthologous noncoding DNA sequences (spanning alignments involving as many as 20,000 base positions) now provide by the parsimony criterion highly significant evidence for the sister group relationships defined by a cladistic classification that groups the lineages to all extant hominoids into family Hominidae, divides this ape family into subfamilies Hylobatinae (gibbons) and Homininae, divides Homininae into tribes Pongini (orangutans) and Hominini, and divides Hominini into subtribes Gorillina (gorillas) and Hominina (humans and chimpanzees). A likelihood analysis of the largest body of these noncoding orthologues and counts of putative synapomorphies using the full range of sequence data from mitochondrial and nuclear genomes also find that humans and chimpanzees share the longest common ancestry. © 1994 Wiley-Liss, Inc.     

Molecular phylogeny of JapaneseAmanita species based on nucleotide sequences of the internal transcribed spacer region of nuclear ribosomal DNA

The molecular phylogeny of 36 specimens of JapaneseAmanita species was studied based on nucleotide sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The phylogenetic tree obtained supported the traditional classification systems of Bas (1969) and Singer (1986), which are based on morphological characters, in the division of the genusAmanita is divided into subgeneraAmanita andLepidella by the amyloidity of basidiospores. However, at section-level, we suggest that subgenusAmanita should be divided into three sections (Amanita, Vaginatae, andCaesareae). Our results also showed the necessity to modify the taxonomic treatments at section-level in the subgenusLepidella. It appears that the establishment ofA. muscaria andA. pantherina from a common ancestral species might be a very recent event, or these might be lower taxa of same species. As for three subspecies ofA. hemibapha and three varieties ofA. vaginata, it is necessary to grade up their taxonomical ranks from subspecies/variety to species. A new combination,A. javanica, is proposed forA. hemibapha subsp.javanica.     

Toward the phylogeny of Caucasian rock lizards: implications from mitochondrial DNA gene sequences (Reptilia: Lacertidae)

A maximum parsimony phylogeny of 14 Caucasian species of rock lizards, genus Ijicerta , subgenus Archaeolacerta , was constructed from mitochondrial cytochrome b and ATPase 6 partial gene sequences. Congruence analyses were carried out between the two genes. A synthesis of the data sets reveals three well supported monophyletic groups: (1) the caucasica group including ( Lacerta derjugini (( Lalpina, L. clarkorum ) ( L. caucasica, L. daghestanica ))); (2) the rudis group including ( L. parvula ( L. portschinskii ( L. vakntini, L. rudis ))); and (3) the saxicola group including ( L. mixta ( L. nairensis ( L. saxicola, L. raddeijj ). Despite the diagnosis of three groups, the placement of L. praticola as a basal taxon is uncertain, as are the relationships among the three groups. The mitochondrial DNA sequence data suggested prior hybridization between L. mixta and L. alpina and possibly between L. saxicola and L. nairensis. Lacerta raddei was resolved as a paraphyletic species on the mtDNA tree; this may result from either hybridization or random gene sorting.     

Molecular phylogeny and biogeography of Kinosternon flavescens based on complete mitochondrial control region sequences

Nucleotide sequences for the complete mitochondrial control region (1158 bp) were used to determine the phylogenetic relationships among populations of the yellow mud turtle, Kinosternon flavescens (Kinosternidae). Phylogenetic analysis of the mtDNA sequences reveals a polyphyletic K. flavescens with three distinct clades: (1) K. flavescens of the Central Plains, including isolated populations of Illinois and Iowa, (2) K. arizonense in the Sonoran Desert of Arizona and Mexico, and (3) K. durangoense in the Chihuahuan Desert of Durango, Coahuila, and Chihuahua, Mexico. Sequence divergence and nucleotide diversity calculations support a hypothesis of Great Plains K. flavescens dispersal and subsequent isolation of populations in the Midwest related to climatic change during the Pleistocene.     

Molecular phylogeny of Japanese Catocala moths based on nucleotide sequences of the mitochondrial ND5 gene

Phylogenetic relationships of 31 Japanese Catocala species were analyzed based on the partial nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene (762 bp). When several non-Catocala Noctuidae moths were designated as the outgroup, these Catocala species formed a monophyletic group. However, divergences between these Catocala species were very deep, and no close phylogenetic relationships were recognized among them except for that between the two recently separated species, C. xarippe and C. fulminea. The remote relationships implied for several pairs of species suggest that the color of the hindwings is a changeable characteristic, and does not reflect phylogenetic lineage. Continental specimens were analyzed in 20 of 31 Catocala species, and all of them showed a close relationship with their Japanese counterpart. However, the closeness of the nucleotide sequences between the Japanese and continental individuals of the same species varied from species to species, indicating that isolation between the Japanese and continental populations of these species occurred at many different times. The two analyzed species endemic to North America showed a close relationship with their morphologically inferred Japanese counterparts, indicating that the geographic separation and following speciation between these Eurasian and American species occurred much more recently compared with the speciation events among the Catocala species now found in Japan.     

Molecular phylogeny of the springhare, Pedetes capensis, based on mitochondrial DNA sequences

The phylogenetic position of the Pedetidae, represented by a single species Pedetes capensis, is controversial, reflecting in part the retention of both Hystricomorphous and Sciurognathous characteristics in this rodent. In an attempt to clarify the species evolutionary relationships, mtDNA gene sequences from 10 rodent species (representing seven families) were analyzed using phenetic, parsimony, and maximum-likelihood methods of phylogenetic inference; the rabbit, Oryctolagus cuniculus (Order Lagomorpha), and cow, Bos taurus (Order Artiodactyla), were used as outgroups. Investigation of 714 base pairs of the protein-coding cytochrome b gene indicate strong base bias at the third codon position with significant rate heterogeneity evident between the three structural domains of this gene. Similar analyses conducted on 816 base pairs of the 12S rRNA gene revealed a transversion bias in the loop sections of all taxa. The cytochrome b gene sequences proved useful in resolving associations between closely related species but failed to produce consistent tree topologies at the family level. In contrast, phylogenetic analysis of the 12S rRNA gene resulted in strong support for the clustering of Pedetidae/Heteromyidae/Geomyidae and Muridae in one clade to the exclusion of the Hystricidae/Thryonomyidae and Sciuridae, a finding which is concordant with studies of rodent fetal membranes as well as reproductive and other anatomical features.      

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.     

Molecular phylogeny and evolution of primate mitochondrial DNA

We determined nucleotide sequences of homologous 0.9-kb fragments of mitochondrial DNAs (mtDNAs) derived from four species of old-world monkeys, one species of new-world monkeys, and two species of prosimians. With these nucleotide sequences and homologous sequences for five species of hominoids, we constructed a phylogenetic tree for the four groups of primates. The phylogeny obtained is generally consistent with evolutionary trees constructed in previous studies. Our results also suggest that the rate of nucleotide substitution for mtDNAs in hominines (human, chimpanzee, and gorilla) may have slowed down compared with that for old-world monkeys. This evolutionary feature of mitochondrial genes is similar to one found in nuclear genes.      

Molecular phylogeny of the speciose vole genus Microtus (Arvicolinae, Rodentia) inferred from mitochondrial DNA sequences

Voles of the genus Microtus represent one of the most speciose mammalian genera in the Holarctic. We established a molecular phylogeny for Microtus to resolve contentious issues of systematic relationships and evolutionary history in this genus. A total of 81 specimens representing ten Microtus species endemic to Europe as well as eight Eurasian, six Asian and one Holarctic species were sequenced for the entire cytochrome b gene (1140 bp). A further 25 sequences were retrieved from GenBank, providing data on an additional 23, mainly Nearctic, Microtus species. Phylogenetic analysis of these 48 species generated four well-supported monophyletic lineages. The genus Chionomys, snow voles, formed a distinct and well-supported lineage separate from the genus Microtus. The subgenus Microtus formed the strongest supported lineage with two sublineages displaying a close relationship between the arvalis species group (common voles) and the socialis species group (social voles). Monophyly of the Palearctic pitymyid voles, subgenus Terricola, was supported, and this subgenus was also subdivided into two monophyletic species groups. Together, these groupings clarify long-standing taxonomic uncertainties in Microtus. In addition, the "Asian" and the Nearctic lineages reported previously were identified although the latter group was not supported. However, relationships among the main Microtus branches were not resolved, suggesting a rapid and potentially simultaneous radiation of a widespread ancestor early in the history of the genus. This and subsequent radiations discernible in the cytochrome b phylogeny, show the considerable potential of Microtus for analysis of historical and ecological determinants of speciation in small mammals. It is evident that speciation is an ongoing process in the genus and that the molecular data provides a vital insight into current species limits as well as cladogenic events of the past.     

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

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

Molecular phylogeny of elopomorph fishes inferred from mitochondrial 12S ribosomal RNA sequences

Wang, C. H., Kuo, C. H., Mok, H. K. & Lee, S. C. (2003). Molecular phylogeny of elopomorph fishes inferred from mitochondrial 12S ribosomal RNA sequences. — Zoologica Scripta , 32 , 231–241.
Fishes of the superorder Elopomorpha include tenpounders ( Elops ), tarpon ( Megalops ), bonefishes ( Albula ), spiny eels ( Notacanthus ), apodes, and gulper eels; despite highly diversified morphological features, all undergo a leptocephalus larval stage and are thus treated (although with some dissenting views) as monophyletic. Following analysis of 12S rRNA sequences we present results that confirm a monophyletic Elopomorpha clearly separated from Clupeomorpha. Elops and Megalops share a common ancestor and are clustered in a subclade at the bottom of Elopomorpha. Albula and Notacanthus share a common ancestor forming the sister group to Anguilliformes. Saccopharyngiformes is not a sister group of Anguilliformes, as the single species sequenced here is nested deeply within the latter. Neither the suborder Congroidei nor the superfamily Congroidea within Anguilliformes are monophyletic.     

Molecular phylogeny of the stromateoid fishes (Teleostei: Perciformes) inferred from mitochondrial DNA sequences and compared with morphology-based hypotheses

The phylogenetic relationships among 21 species of stromateoid fishes, representing five families and 13 genera, were reconstructed using 3263bp of mitochondrial DNA sequences, including the posterior half of the 16S rRNA and entire COI and Cytb genes. The resultant molecular phylogenies were compared with previous phylogenetic hypotheses inferred from morphological characters. Molecular phylogenetic trees were constructed using the maximum parsimony, maximum likelihood, and Bayesian methods. All three methods resulted in well-resolved trees with most nodes being supported by moderate to high support values. In contrast to previous morphological analyses, which resulted in non-monophyly of Centrolophidae, all three methods utilized for the present molecular analyses supported the monophyly of Centrolophidae, as well as the reciprocal monophyly of the other stromateoid families, previous morphological hypotheses being rejected by the Templeton and Shimodaira-Hasegawa tests. In addition, the three methods indicated a sister-group relationship between Ariommatidae and Nomeidae. The position of Tetragonuridae was, however, incongruent between the MP method and the ML and Bayesian methods, being placed in the most basal position of Stromateoidei in the former, but occupying a sister relationship to Stromateidae in the latter. Comparison of the molecular phylogenies to previous morphological hypotheses suggested that evolutionary changes in morphological characters have not occurred equally among the stromateoid lineages, the evolution of the centrolophids not having been accompanied by appreciable morphological changes, whereas other stromateoids have undergone considerable morphological changes during their evolutionary history. The molecular phylogenies also shed some light on the evolutionary pattern of the pharyngeal sac, two of the four types of sac corresponding to two main lineages of Stromateoidei. Some taxonomic implications were also discussed.     

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.     

Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: implications for lophotrochozoan phylogeny

The complete nucleotide sequences of the mitochondrial (mt) genomes of the entoprocts Loxocorone allax and Loxosomella aloxiata were determined. Both species carry the typical gene set of metazoan mt genomes and have similar organizations of their mt genes. However, they show differences in the positions of two tRNA(Leu) genes. Additionally, the tRNA(Val) gene, and half of the long non-coding region, is duplicated and inverted in the Loxos. aloxiata mt genome. The initiation codon of the Loxos. aloxiata cytochrome oxidase subunit I gene is expected to be ACG rather than AUG. The mt gene organizations in these two entoproct species most closely resemble those of mollusks such as Katharina tunicata and Octopus vulgaris, which have the most evolutionarily conserved mt gene organization reported to date in mollusks. Analyses of the mt gene organization in the lophotrochozoan phyla (Annelida, Brachiopoda, Echiura, Entoprocta, Mollusca, Nemertea, and Phoronida) suggested a close phylogenetic relationship between Brachiopoda, Annelida, and Echiura. However, Phoronida was excluded from this grouping. Molecular phylogenetic analyses based on the sequences of mt protein-coding genes suggested a possible close relationship between Entoprocta and Phoronida, and a close relationship among Brachiopoda, Annelida, and Echiura.