Phylogenetic relationships of Hemidactylus geckos from the Gulf of Guinea islands: patterns of natural colonizations and anthropogenic introductions estimated from mitochondrial and nuclear DNA sequences

Mitochondrial DNA (12S rRNA, 16S rRNA, and cytochrome b) sequences and nuclear sequences (C-mos and alpha-Enolase) were analyzed within all known Hemidactylus species from all three volcanic islands in the Gulf of Guinea that have never been connected to the continent. These comprise both endemic and widespread species. Our aim was to determine if the widespread species was introduced anthropogenically, to determine the number of distinct genetic lineages within the islands, and to determine if the endemic forms constituted a monophyletic group. Our results suggest that a previously undescribed species on S?o Tomé is the sister taxon to Hemidactylus newtoni, endemic to Annobon. Genetic variation between populations of Hemidactylus greefii from S?o Tomé and Principe is very high based on mtDNA sequences, but the forms cannot be distinguished using the nuclear DNA sequences. Hemidactylus mabouia appears to have been anthropogenically introduced to all three islands. The island endemics do not form a monophyletic group, suggesting multiple independent colonizations of the islands.     

Evolution and biogeography of the genus Tarentola (Sauria: Gekkonidae) in the Canary Islands,inferred from mitochondrial DNA sequences

Sequences from fragments of the 12S ribosomal RNA and cytochrome b mitochondrial genes were used to analyze phylogenetic relationships among geckos of genus Tarentola from the Canary Islands. A surprisingly high level of within island differentiation was found in T. delalandii in Tenerife and T. boettgeri in Gran Canaria. Molecular differentiation between populations of T. angustimentalis on Lanzarote and Fuerteventura, and between Moroccan and Iberian Peninsula T. mauritanica, also indicate that at least two subspecies should be recognized within each of them. Phylogenetic relationships among these species reveals a higher level of differentiation and a more complex colonization pattern than those found for the endemic genus Gallotia. Lack of evidence for the presence of T. boettgeri bischoffi on the island of Madeira does not seem to support the origin of T. delalandii, T. gomerensis and the canarian subspecies of T. boettgeri from this island, whereas molecular data confirms that T. angustimentalis is a sister species of the continental T. mauritanica. Several independent colonization events from the continent and the extinction of some species are probably responsible for the current distribution of Tarentola in the Canary Islands.     

Phylogenetic relationships among Pneumocystis from Asian macaques inferred from mitochondrial rRNA sequences

The presence of Pneumocystis organisms was detected by nested-PCR at mitochondrial large subunit (mtLSU) rRNA gene in 23 respiratory samples from Asian macaques representing two species: Macaca mulatta and M. fascicularis. A very high level of sequence heterogeneity was detected with 18 original sequence types. Two genetic groups of Pneumocystis could be distinguished from the samples. Within each group, the extent of genetic divergence was low (2.5+/-1.4% in group 1 and 2.3+/-1.7% in group 2). Genetic divergences were systematically higher when macaque-derived sequence types were compared with Pneumocystis mtLSU sequences from other primate species (from 5.3+/-2.7% to 19.3+/-3.0%). The two macaque-derived groups may be considered as distinct Pneumocystis species. Surprisingly, these Pneumocystis species were recovered from both M. mulatta and M. fascicularis suggesting that host-species restriction may not systematically occur in the genus Pneumocystis. Alternatively, these observations question about the species concept in macaques.     

Phylogeny and divergence times of some racerunner lizards (Lacertidae: Eremias) inferred from mitochondrial 16S rRNA gene segments

Eremias, or racerunners, is a widespread lacertid genus occurring in China, Mongolia, Korea, Central Asia, Southwest Asia and Southeast Europe. It has been through a series of taxonomic revisions, but the phylogenetic relationships among the species and subgenera remain unclear. In this study, a frequently studied region of the mitochondrial 16S rRNA was used to (i) reassess the phylogenetic relationships of some Eremias species, (ii) test if the viviparous species form a monophyletic group, and (iii) estimate divergence time among lineages using a Bayesian relaxed molecular-clock approach. The resulting phylogeny supports monophyly of Eremias sensu Szczerbak and a clade comprising Eremias, Acanthodactylus and Latastia. An earlier finding demonstrating monophyly of the subgenus Pareremias is corroborated, with Eremias argus being the sister taxon to Eremias brenchleyi. We present the first evidence that viviparous species form a monophyletic group. In addition, Eremias przewalskii is nested within Eremias multiocellata, suggesting that the latter is likely a paraphyletic species or a species complex. Eremias acutirostris and Eremias persica form a clade that is closely related to the subgenus Pareremias. However, the subgenera Aspidorhinus, Scapteira, and Rhabderemias seem not to be monophyletic, respectively. The Bayesian divergence-time estimation suggests that Eremias originated at about 9.9 million years ago (with the 95% confidence interval ranging from 7.6 to 12 Ma), and diversified from Late Miocene to Pleistocene. Specifically, the divergence time of the subgenus Pareremias was dated to about 6.3 million years ago (with the 95% confidence interval ranging from 5.3 to 8.5 Ma), which suggests that the diversification of this subgenus might be correlated with the evolution of an East Asian monsoon climate triggered by the rapid uplift of the Tibetan Plateau approximately 8 Ma.     

Phylogeography and genetic relationships of North African <Emphasis Type="Italic">Bufo mauritanicus</Emphasis> Schlegel, 1841 estimated from mitochondrial DNA sequences

Genetic variation within the North African toad Bufo mauritanicus was estimated by sequencing partial 12S rRNA and 16S rRNA mitochondrial regions from widespread populations in Morocco, Algeria and Tunisia. Unlike many other wide ranging species from this area, B. mauritanicus demonstrated very low levels of intraspecific variation. The minimal intraspecific genetic variation may be due to a relatively recent, possibly post-glacial, expansion into its current range. Further phylogeographic studies of other North African species are needed to assess if this is a common biogeographical phenomenon. Phylogenetic analyses support immunological data that B. mauritanicus is part of a clade of predominantly sub-Saharan Bufo, recently assigned to a new genus Amietophrynus. Two different lineages within this clade, B. mauritanicus and the B. pardalis group, appear to have reverted from 20 chromosomes to the more typical 22 chromosomes found in most other Bufonids. However, the alternative hypothesis that the Bufo species with 20 chromosomes form a monophyletic lineage cannot be rejected.     

Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences

To explore phylogenetic relationships among glyptosternoid fishes, we determined nucleotide sequences of the complete mitochondrial cytochrome b gene region (1138 base pair). Thirteen species of glyptosternoid fishes and six species of non-glyptosternoids represent 10 sisorid genera were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, minimum evolution, maximum likelihood, and Bayesian methods. Bayesian and maximum likelihood analyses support the monophyly of glyptosternoids, but our hypothesis of internal relationships differs from previous hypothesis. Results indicated that glyptosternoid is a monophyletic group and genera Glyptosternum and Exostoma are two basal species having a primitive position among it. Genera Euchiloglanis and Pareuchiloglanis form a sister-group. Then they form a sister-group with Pseudexostoma plus Oreoglanis. Our result also found that Pareuchiloglanis anteanalis might be considered as the synonyms of Parechiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.     

A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML, and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species.     

Phylogenetic relationships of Nembrothinae (Mollusca: Doridacea: Polyceridae) inferred from morphology and mitochondrial DNA

Within the Polyceridae, Nembrothinae includes some of the most striking and conspicuous sea slugs known, although several features of their biology and phylogenetic relationships remain unknown. This paper reports a phylogenetic analysis based on partial sequences of two mitochondrial genes (cytochrome c oxidase subunit I and 16S rRNA) and morphology for most species included in Nembrothinae. Our phylogenetic reconstructions using both molecular and combined morphological and molecular data support the taxonomic splitting of Nembrothinae into several taxa. Excluding one species (Tambja tentaculata), the monophyly of Roboastra was supported by all the phylogenetic analyses of the combined molecular data. Nembrotha was monophyletic both in the morphological and molecular analyses, always with high support. However, Tambja was recovered as para- or polyphyletic, depending on the analysis performed. Our study also rejects the monophyly of "phanerobranch" dorids based on molecular data.     

Long-distance colonization and radiation in gekkonid lizards, Tarentola (Reptilia: Gekkonidae), revealed by mitochondrial DNA sequences

Morphological systematics makes it clear that many non-volant animal groups have undergone extensive transmarine dispersal with subsequent radiation in new, often island, areas. However, details of such events are often lacking. Here we use partial DNA sequences derived from the mitochondrial cytochrome b and 12S rRNA genes (up to 684 and 320 bp, respectively) to trace migration and speciation in Tarentola geckos, a primarily North African clade which has invaded many of the warmer islands in the North Atlantic Ocean. There were four main invasions of archipelagos presumably by rafting. (i) The subgenus Neotarentola reached Cuba up to 23 million years (Myr) ago, apparently via the North Equatorial current, a journey of at least 6000 km. (ii) The subgenus Tarentola invaded the eastern Canary Islands relatively recently covering a minimum of 120 km. (iii) The subgenus Makariogecko got to Gran Canaria and the western Canary Islands 7-17.5 Myr ago, either directly from the mainland or via the Selvages or the archipelago of Madeira, an excursion of 200-1200 km. (iv) A single species of Makariogecko from Gomera or Tenerife in the western Canaries made the 1400 km journey to the Cape Verde Islands tip to 7 Myr ago by way of the south-running Canary current. Many journeys have also occurred within archipelagos, a minimum of five taking place in the Canaries and perhaps 16 in the Cape Verde Islands. Occupation of the Cape Verde archipelago first involved an island in the northern group, perhaps São Nicolau, with subsequent spread to its close neighbours. The eastern and southern islands were colonized from these northern islands, at least two invasions widely separated in time being involved. While there are just three allopatric species of Makariogecko in the Canaries, the single invader of the Cape Verde Islands radiated into five, most of the islands being inhabited by two of these which differ in size. While size difference may possibly be a product of character displacement in the northern islands, taxa of different sizes reached the southern islands independently.     

基于线粒体和核基因序列的蜜蜂属系统发育分析

文章测定了中国分布的蜜蜂属(Apis)5种蜜蜂22个样本的线粒体基因ND2、CO2、16S rRNA以及核基因ITPR的序列,对序列的碱基组成和蜜蜂种间的遗传距离进行了分析。结合下载的蜜蜂属其他4个种的相关序列,采用最大简约法、邻接法和最大似然法重建了蜜蜂属系统发育关系。系统发育分析结果支持蜜蜂属划分为3个类群,即小蜜蜂类群(包括小蜜蜂和黑小蜜蜂)、大蜜蜂类群(包括大蜜蜂和黑大蜜蜂)和穴居蜜蜂类群(西方蜜蜂、东方蜜蜂、沙巴蜂、苏拉威西蜂、绿努蜂),且小蜜蜂类群较早分化。结果还显示,我国海南岛的大蜜蜂和大陆的大蜜蜂之间可能存在较大的遗传分歧。     

Pleistocene speciation of freshwater crabs (Crustacea: Potamidae: Geothelphusa) from northern Taiwan and southern Ryukyus, as revealed by phylogenetic relationships

The phylogenetic relationship among freshwater crab species of Geothelphusa from northern Taiwan and the Yaeyama Group of islands (including Iriomote and Ishigaki) in the southern Ryukyus was studied using the mitochondrial genes 16S rRNA and COI. Our results support the hypothesis that speciation of Geothelphusa among these islands was the result of cyclic glaciations and interglaciations during the Pleistocene. Two main clades, one the Taiwan Group (containing several clades, including most Taiwanese Geothelphusa species except Geothelphusa miyazakii but including Geothelphusa minei from Yaeyama), was estimated to be separated from its sister group, the southern Ryukyus-northern Taiwan (SRN) clade (including G. miyazakii, Geothelphusa shokitai, Geothelphusa fulva and G. marginata from northern Taiwan, the Pinnacle Islands [=Diaoyutai Islands or Senkaku Islands] and Yaeyama) at about 5.3 million years ago (mya). G. shokitai was separated from others within the SRN clade at 2.4 mya, but was probably derived from G. miyazakii in northern Taiwan. The ancestor of G. miyazakii is hypothesised to have dispersed from ancestors in Yaeyama and then isolated at 2.0 mya during the Pleistocene interglaciations. This is similar to the speciation of G. minei in Yaeyama at 1.5 mya, except that its ancestors originated from north-eastern Taiwan. Four clades of freshwater crabs are present in the Fushan Botanical Garden, located in the mountainous area of north-eastern Taiwan, which might be due to the historical rearrangements of the drainage and proximity of the various river origins.     

Phylogenetic relationships of rhizobia based on citrate synthase gene sequences

Partial nucleotide sequences of the citrate synthase (gltA) gene from different rhizobia genera were determined. Tree topologies based on this housekeeping gene were similar to that obtained using 16S rRNA sequences. However gltA appeared to be more reliable at determining phylogenetic relationships of closely related taxa. We propose gltA sequences as an additional tool to be used in molecular phylogenetic studies.     

Monophyly and phylogenetic relationships of the catfish genus Glyptothorax (Teleostei: Sisoridae) inferred from nuclear and mitochondrial gene sequences

GlyptothoraxBlyth (1860) is the most species-diverse and widely-distributed genus in the Sisoridae, but few studies have examined monophyly of the genus and phylogenetic relations within it. We used the nuclear RAG2 gene and mitochondrial COI and Cyt b genes from 50 of the approximately 70 species to examine monophyly of Glyptothorax and phylogenetic relationships within the genus. Molecular phylogenetic trees were constructed using maximum parsimony, maximum likelihood and Bayesian inference methods. All methods strongly supported monophyly of Glyptothorax, with Bagarius as its sister group. Both analyses of two- and three-gene datasets recovered nine major subclades of Glyptothorax, but some internal nodes remained poorly resolved. The phylogenetic relationships within the genus and existing taxonomic problems are discussed.     

Phylogenetic relationships of the Japanese minnows,Pseudorasbora (Cyprinidae), as inferred from mitochondrial 16S rRNA gene sequences

The phylogenetic relationships among threePseudorasbora fishes (Cyprinidae, Sarcocheiichthyinae) occurring in Japan (P. parva, P. pumila pumila andP. pumila subsp. sensu Nakamura [1963]) were inferred from nucleotide sequences of the mitochondrial 16S rRNA gene. The sequences. of 1240 bp, were determined and compared for 22 specimens from 2–8 populations for each taxon, with a singlePungtungia herzi specimen as an outgroup. A total of 171 sites (13.8%) were variable among the specimens, but only 0–2 sites within each population. The phylogenetic relationships estimated by neighbor-joining, maximum-parsimony and maximum-likelihood methods confirmed a sister relationship between the twoP. pumila subspecies, with a high level of confidence. However, their genetic distinction from each other (4.1±0.4SD % sequence difference on average) was at a level similar to that between them andP. parva (5.9±0.5%). The geographic distribution of the twoP. pumila subspecies, which are separated by the Fossa Magna region, suggests that the genetic divergence of the two subspecies originated from a vicariant process separating the freshwater ichthyofaunas of eastern and western Honshu.Pseudorasbora parva populations were divided into two genetic groups (1.8±0.2% sequence difference), one group comprising continental and part of the Japanese populations, and the other the remaining Japanese populations. This suggests that at least two genetically divergent lineages had been originally distributed in Japan, but a strong possibility remains that the present situation has resulted from artificial transplantation.     

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.     

Phylogenetic relationships within the Laridae (Charadriiformes: Aves) inferred from mitochondrial markers

Gulls (Aves: Laridae) constitute a recent and cosmopolite family of well-studied seabirds for which a robust phylogeny is needed to perform comparative and biogeographical analyses. The present study, the first molecular phylogeny of all Larids species (N=53), is based on a combined segment of mtDNA (partial cytochrome b and control region). We discuss our phylogenetic tree in the light of previous suggestions based on morphological, behavioral, and plumage characters. Although the phylogeny is not fully resolved, it highlights several robust species groups and confirms or identifies for the first time some sister relationships that had never been suggested before. The Dolphin Gull (Leucophaeus scoresbii) for instance, is identified as the sister species of the Grey Gull (Larus modestus) and the Ross's Gull (Rhodostethia rosea) forms a monophyletic group with the Little Gull (Larus minutus). Our results clearly demonstrate that the genus Larus as currently defined is not monophyletic, since current taxonomy of gulls is based on the use of convergent phenotypic characters. We propose a new systematic arrangement that better reflects their evolutionary history.     

DNA sequences of the mitochondrial COI gene have low levels of divergence among deep-sea octocorals (Cnidaria: Anthozoa)

We are analyzing genetic diversity in deep-seamount octocorals with the ultimate goal of studying the effect of retention and dispersal of larvae on genetic population structure. Here we report on the sequence diversity of the mitochondrial cytochrome oxidase I (COI) gene among 11 species. Uncorrected pairwise sequence divergences ranged from 0.4–10.3% for comparisons among species spanning the intrageneric to interordinal levels. Relative to other invertebrates, these divergences are very low, suggesting that COI may not be useful as a genetic marker for studying dispersal among deep-sea octocoral populations. Possible explanations for the reduced rates of divergence observed include a lower rate of evolution for octocoral mitochondrial genomes and the presence of a gene, mtMSH, which may code for a mitochondrial DNA mismatch-repair system. We report the finding of mtMSH in three deep-sea octocorals (Acanthogorgia sp., Corallium ducale, and Paramuricea sp.), which brings the total published observations of this gene to six species, all in the subclass Octocorallia.     

Phylogenetic relationships in European Ceriporiopsis species inferred from nuclear and mitochondrial ribosomal DNA sequences

The aim of this work was to clarify taxonomy and examine evolutionary relationships within European Ceriporiopsis species using a combined analysis of the large subunit (nLSU) nuclear rRNA and small subunit (mtSSU) mitochondrial rRNA gene sequences. Data from the ITS region were applied to enhance the view of the phylogenetic relationships among different species. The studied samples grouped into four complex clades, suggesting that the genus Ceriporiopsis is polyphyletic. The generic type Ceriporiopsis gilvescens formed a separate group together with Ceriporiopsis guidella and Phlebia spp. in the phlebioid clade. In this clade, the closely related species Ceriporiopsis resinascens and Ceriporiopsis pseudogilvescens grouped together with Ceriporiopsis aneirina. C. resinascens and C. pseudogilvescens have identical LSU and SSU sequences but differ in ITS. Ceriporiopsis pannocincta also fell in the phlebioid clade, but showed closer proximity to Gloeoporus dichrous than to C. gilvescens or C. aneirina–C. pseudogilvescens–C. resinascens group. Another clade was composed of a Ceriporiopsis balaenae–Ceriporiopsis consobrina group and was found to be closely related to Antrodiella and Frantisekia, with the overall clade highly reminiscent of the residual polyporoid clade. The monotypic genus Pouzaroporia, erected in the past for Ceriporiopsis subrufa due to its remarkable morphological differences, also fell within the residual polyporoid clade. Ceriporiopsis subvermispora held an isolated position from the other species of the genus. Therefore, the previously proposed name Gelatoporia subvermispora has been adopted for this species. Physisporinus rivulosus appeared unrelated to two other European Physisporinus species. Moreover, Ceriporiopsis (=Skeletocutis) jelicii grouped in a separate clade, distinct from Ceriporiopsis species. Finally, the ITS data demonstrated the proximity of some Ceriporiopsis species (Ceriporiopsis portcrosensis and Ceriporiopsis subsphaerospora) to Skeletocutis amorpha.