Geography-linked phylogeny of theDamaster ground beetles inferred from mitochondrial ND5 gene sequences

We have constructed phylogenetic trees based on sequence comparisons of mitochondrial NADH dehydrogenase subunit 5 gene for 11Damaster blaptoides specimens from various localities of Japan. The specimens consist of eight subspecies.Coptolabrus fruhstorferi, Acoptolabrus gehinii, andProcrustes kolbei, which are taxonomically related toDamaster, have also been analyzed for comparison.Damaster is more related toAcoptolabrus than toCoptolabrus in the ND5 trees, in contrast to the generally accepted view thatDamaster is derived fromCoptolabrus, whereasAcoptolabrus is the sister group ofDamaster/Coptolabrus. The emergence ofProcrustes is much earlier than the rest of the genera. TheDamaster subspecies are monophyletic. Four major lineages are recognized, which are geography linked within the Japanese archipelago. The origin and diversification process have been discussed based on these findings.The nucleotide sequence data reported in this paper will appear in the GSDB, DDBJ, EMBL, and NCBI nucleotide sequence databases with the accession numbers D50422-D50429     

Extensive trans-species mitochondrial polymorphisms in the carabid beetles Carabus subgenus Ohomopterus caused by repeated introgressive hybridization

To study the potential importance of introgressive hybridization to the evolutionary diversification of a carabid beetle lineage, we studied intraspecific and trans-species polymorphisms in the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequence (1083 bp) in four species of the subgenus Ohomopterus (genus Carabus) in central and eastern Honshu, Japan. Of the four species, C. insulicola is parapatric with the other three, and can hybridize naturally with at least two. This species possesses two haplotypes of remote lineages. We classified ND5 haplotypes using polymerase chain reaction-restriction fragment length polymorphism with TaqI endonuclease for 524 specimens, and sequenced 143 samples. Analysis revealed that each species was polyphyletic in its mitochondrial DNA phylogeny, representing a marked case of trans-species polymorphism. Recent one-way introgression of mitochondria from C. arrowianus nakamurai to C. insulicola, and from C. insulicola to C. esakii, was inferred from the frequency of identical sequences between these species and from direct evidence of hybridization in their contact zones. Other intraspecific polymorphisms in the four species may be due to undetected introgressive hybridization (e.g. C. insulicola to C. maiyasanus) or from stochastic lineage sorting of ancestral polymorphisms. This beetle group has a genital lock-and-key system, with species-specific or subspecies-specific genital morphology that may act as a barrier to hybridization. However, our results demonstrate that introgressive hybridization has occurred multiple times, at least for mitochondria, despite differences among, and stability within, morphological characters that distinguish local populations. Thus, hybridization and introgression could have been key processes in the evolutionary diversification of Ohomopterus.     

AFLPs resolve phylogeny and reveal mitochondrial introgression within a species flock of African electric fish (Mormyroidea: Teleostei)

Estimating species phylogeny from a single gene tree can be especially problematic for studies of species flocks in which diversification has been rapid. Here we compare a phylogenetic hypothesis derived from cytochrome b (cyt b) sequences with another based on amplified fragment length polymorphisms (AFLP) for 60 specimens of a monophyletic riverine species flock of mormyrid electric fishes collected in Gabon, west-central Africa. We analyze the aligned cyt b sequences by Wagner parsimony and AFLP data generated from 10 primer combinations using neighbor-joining from a Nei-Li distance matrix, Wagner parsimony, and Dollo parsimony. The different analysis methods yield AFLP tree topologies with few conflicting nodes. Recovered basal relationships in the group are similar between cyt b and AFLP analyses, but differ substantially at many of the more derived nodes. More of the clades recovered with the AFLP characters are consistent with the morphological characters used to designate operational taxonomic units in this group. These results support our hypothesis that the mitochondrial gene tree differs from the overall species phylogeny due at least in part to mitochondrial introgession among lineages. Mapping the two forms of electric organ found in this group onto the AFLP tree suggests that posteriorly innervated electrocytes with nonpenetrating stalks have independently evolved from anteriorly innervated, penetrating-stalk electrocytes at least three times.     

10种帘蛤科贝类COI基因序列分析及系统发育研究

应用通用引物扩增了凸加夫蛤(Gafrarium tumidum)、锯齿巴非蛤(Paphiagallus)、细纹卵蛤(Pitar striatum)、钝缀锦蛤(Tapes dorsatus)、裂纹格特蛤(Marcia hiantina)5种帘蛤科贝类COI基因片段,并与GenBank数据库收录的加夫蛤(Gafrarium pectinatum)、沟纹巴非蛤(Paphia exarata)、日本卵蛤(Pitar japonicum)、日本格特蛤(Marcia japonica)、四射缀锦蛤(Tapes belcheri)5种帘蛤科贝类的同源序列进行比对分析.结果表明:所有物种扩增片段长度均为616 bp,序列A+T平均含量(62.9％)明显高于G+C含量.在616个位点中,保守位点数为282个,变异位点数为334个,其中简约信息位点数为283个.以COI基因片段序列为标记,以海螂科砂海螂(Mya arenaria)作外群,构建了帘蛤科贝类的系统进化树,其拓扑结构显示:细纹卵蛤和日本卵蛤聚为一枝,凸加夫蛤和加夫蛤聚为一枝,锯齿巴非蛤和沟纹巴非蛤聚为一枝,四射缀锦蛤单独聚为一枝,钝缀锦蛤、裂纹格特蛤和日本格特蛤聚为一枝,最后所有帘蛤科物种聚为一枝,与外群相区别,其结果与传统形态分类基本一致.研究表明,线粒体COI基因作为帘蛤科贝类DNA条形码在物种鉴定方面具有可靠性,可以作为物种分类的重要辅助手段.     

Nuclear introgression without mitochondrial introgression in two turtle species exhibiting sex‐specific trophic differentiation

Despite the presence of reproductive barriers between species, interspecific gene introgression has been documented in a range of natural systems. Comparing patterns of genetic introgression in biparental versus matrilineal markers can potentially reveal sex‐specific barriers to interspecific gene flow. Hybridization has been documented in the freshwater turtles Graptemys geographica and G. pseudogeographica, whose ranges are largely sympatric. Morphological differentiation between the species is restricted to females, with female G. geographica possessing large heads and jaws compared to the narrow heads of G. pseudogeographica females. If hybrid females are morphologically intermediate, they may be less successful at exploiting parental feeding niches, thereby limiting the introgression of maternally inherited, but not biparental, molecular markers. We paired sequence data with stable isotope analysis and examined sex‐specific genetic introgression and trophic differentiation in sympatric populations of G. geographica and G. pseudogeographica. We observed introgression from G. pseudogeographica into G. geographica at three nuclear loci, but not at the mitochondrial locus. Analysis of ?¹⁵N and ?¹³C was consistent with species differences in trophic positioning in females, but not males. These results suggest that ecological divergence in females may reduce the opportunity for gene flow in this system.     

10种帘蛤科贝类COI基因序列分析及系统发育研究

应用通用引物扩增了凸加夫蛤（Gafrarium tumidum）、锯齿巴非蛤（Paphia gallus）、细纹卵蛤（Pitar striatum）、钝缀锦蛤（Tapes dorsatus）、裂纹格特蛤（Marcia hiantina） 5种帘蛤科贝类COI基因片段,并与GenBank数据库收录的加夫蛤（Gafrarium pectinatum）、沟纹巴非蛤（Paphia exarata）、日本卵蛤（Pitar japonicum）、日本格特蛤（Marcia japonica）、四射缀锦蛤（Tapes belcheri ）5种帘蛤科贝类的同源序列进行比对分析。结果表明：所有物种扩增片段长度均为616 bp,序列A+T平均含量（62.9%）明显高于G+C含量。在 616个位点中,保守位点数为282个,变异位点数为334个,其中简约信息位点数为283个。以COI基因片段序列为标记,以海螂科砂海螂（Mya arenaria）作外群,构建了帘蛤科贝类的系统进化树,其拓扑结构显示：细纹卵蛤和日本卵蛤聚为一枝,凸加夫蛤和加夫蛤聚为一枝,锯齿巴非蛤和沟纹巴非蛤聚为一枝,四射缀锦蛤单独聚为一枝,钝缀锦蛤、裂纹格特蛤和日本格特蛤聚为一枝,最后所有帘蛤科物种聚为一枝,与外群相区别,其结果与传统形态分类基本一致。研究表明,线粒体COI基因作为帘蛤科贝类DNA条形码在物种鉴定方面具有可靠性,可以作为物种分类的重要辅助手段。     

Pattern of morphological diversification in the Leptocarabus ground beetles (Coleoptera: Carabidae) as deduced from mitochondrial ND5 gene and nuclear 28S rDNA sequences

Most of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene and a part of nuclear 28S ribosomal RNA gene were sequenced for 14 species of ground beetles belonging to the genus Leptocarabus. In both the ND5 and the 28S rDNA phylogenetic trees of Leptocarabus, three major lineages were recognized: (1) L. marcilhaci/L. yokoael/Leptocarabus sp. from China, (2) L. koreanus/L. truncaticollis/L. seishinensis/L. semiopacus/L. canaliculatus/L. kurilensis from the northern Eurasian continent including Korea and Hokkaido, Japan, and (3) all of the Japanese species except L. kurilensis. Clustering of the species in the trees is largely linked to their geographic distribution and does not correlate with morphological characters. The species belonging to different species groups are clustered in the same lineages, and those in the same species group are scattered among the different lineages. One of the possible interpretations of the present results would be that morphological transformations independently took place in the different lineages, sometimes with accompanying parallel morphological evolution, resulting in the occurrence of the morphological species belonging to the same species group (= type) in the different lineages.     

A salmon id phylogeny inferred from mitochondrial cytochrome b gene sequences

Partial mitochondrial cytochrome b gene sequences of eight salmonid species were used in a PAUP analysis to generate a phylogeny of the group. The four genera represented are Salmo, Salvelinus, Oncorhynchus and Thymallus . The inferred phylogenetic tree coincides well with the classically derived one for these genera. The recent reclassification of the rainbow trout as a member of the genus Oncorhynchus is supported. The assignment of grayling as the outgroup is vindicated. The utility of gene sequence data to infer the phylogenetic relationships of the Salmonidae is discussed.     

Molecular phylogeny and phylogeography of flightless beetles Parechthistatus gibber and Hayashiechthistatus inexpectus (Coleoptera: Cerambycidae) inferred from mitochondrial COI gene sequences

To elucidate the speciation patterns of two endemic flightless cerambycid beetles, Parechthistatus gibber and Hayashiechthistatus inexpectus, molecular phylogenetic analysis was carried out. A 1144 bp region of the cytochrome oxidase subunit I gene was sequenced for individuals from 51 local populations of these species. There were nine haplotype lineages of P. gibber, and H. inexpectus was included within a P. gibber lineage. These lineages were highly divergent and occurred in different regions. Based on previously published molecular change rates for the COI gene (1.5–2.3% per million years), the time of divergence of P. gibber COI haplotypes was inferred to be 3.0–4.6 million years ago, in the Pliocene.     

Resolving phylogeny at the family level by mitochondrial cytochrome oxidase sequences: phylogeny of carrion beetles (Coleoptera, Silphidae)

We investigated the phylogenetic relationships of carrion beetles (Coleoptera, Silphidae) using 2094 bp of their mitochondrial cytochrome oxidase subunit I and II and tRNA leucine gene sequences. Shorter fragments of this gene region previously have been used to establish generic relationships in insects. In this study, they provided more than sufficient resolution, although the third positions of the protein-coding sequences reached saturation for the deeper divergences. This first published phylogeny for the Silphidae comprises 23 species from 13 genera sampled across the geographic range of the family. In addition, we included species from three related families as outgroups. One of these families, the Agyrtidae, was, until recently, included in the Silphidae, but its resolution here justifies its current position as a separate family. The silphid subfamilies Nicrophorinae and Silphinae are monophyletic in all analyses. All genera for which several species were sampled are supported as monophyletic groups, with the exception of the genus Silpha. European and North American representatives of two Nicrophorus species described from both continents are supported as each others' closest relatives. The lineage that colonized Gondwanaland and that most likely originated in the Palearctic is the most basal within the Silphinae.     

Parallel evolution in radiation ofOhomopterus ground beetles inferred from mitochondrial ND5 gene sequences

Molecular phylogenetic analyses using mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequences representing all 15 species and the majority of subspecies or races of theOhomopterus ground beetles from all over the Japanese archipelago have uncovered a remarkable evolutionary history. Clustering of the species in the molecular phylogenetic tree is linked to their geographic distribution and does not correlate with morphological characters. Taxonomically the same species or the members belonging to the same species-group fall out in more than two different places on the ND5 tree. Evidence has been presented against a possible participation of ancestral polymorphism and random lineage sorting or of hybrid individuals for the observed distribution of mitochondrial DNA haplotypes. The most plausible explanation of our results is that parallel evolution took place in different lineages. Most notably,O. dehaanii, O. yaconinus, andO. japonicus in a lineage reveal almost identical morphology with those of the same species (or subspecies) but belonging to the phylogenetically remote lineages.The nucleotide sequence data reported in this paper will appear in the DDBJ, EMBL, and GenBank nucleotide sequence databases with accession numbers D50711-DD-50733 and D87131-D87186.     

五种啮齿类动物mtDNA蛋白编码基因序列变化的比较

目的利用本实验室测定的中国地鼠、金黄地鼠和GenBank中田鼠、小鼠、大鼠的线粒体全基因组序列,比较分析五种啮齿类动物的mtDNA蛋白编码基因序列的变异,探讨其分子进化关系。方法将五种动物各自的13个蛋白编码基因分别连接成一个序列,用DNAstar-EditSeq分析软件计算每个序列的碱基长度和组成,计算蛋白编码基因的碱基和氨基酸的差异。以人为外群,基于连接在一起的13个蛋白编码基因的氨基酸序列,用MEGA4.0软件通过最大简约性法(MP)和非加权成对平均数法(UPGMA)构建进化树。结果在五种啮齿动物的13个蛋白基因序列中,A、T、C、G碱基的平均含量为32.4%、29.6%、26.2%和11.9%,中国地鼠mtDNA各蛋白编码序列以及其编码的氨基酸序列与其他物种相比,与金黄地鼠的相应序列差异最小,与大鼠mtDNA各蛋白编码序列以及其编码的氨基酸序列差异较大。分子进化树也显示中国地鼠和金黄地鼠的亲缘关系最近,与小鼠、大鼠存在的差异相对大。结论五种动物的碱基组成的百分比中显示G的相对缺乏,相互之间的进化关系与传统的分类地位基本吻合。     

Molecular phylogeny of cockroaches (Blattaria) based on mitochondrial COII gene sequences

Phylogenetic relationships among five cockroach families (Cryptocercidae, Polyphagidae, Blattidae, Blattellidae and Blaberidae) using seventeen species, were estimated based on the DNA sequences of the mitochondrial cytochrome oxidase subunit II (COII) gene. A cladogram inferred using the neighbour‐joining method indicated that Polyphagidae and Cryptocercidae are closely related to each other, and that these two groups are a sister group to the remaining cockroach families. The monophyly of this clade, however, was not strongly supported in terms of bootstrap percentages. Blaberidae and Blattellidae were shown to be sister groups as previously proposed, with Blattidae as a sister group to that clade. Non‐weighted and weighted parsimony analyses were also performed following analyses of nucleotide substitution patterns that indicated saturation of the COII gene among these taxa had occurred. These parsimonious cladograms suggested that Polyphagidae was the basal family, and Polyphaginae, including Cryptocercus as proposed by Grandcolas 1994a ), was not monophyletic. The inferred relationships among cockroach families (Polyphagidae, Cryptocercidae + (Blattidae + (Blattellidae + Blaberidae))) is partly in agreement with some previously published analyses. Additionally, based on molecular data, Asian and American Cryptocercus are suggested to have diverged from one another before the Oligocene (～20 mya).     

Molecular and morphological congruence in hominoid trans-species polymorphisms

Molecular and morphological data increasingly have confirmed thatHomo sapiens is more closely related to the African apes than to the Asian orangutan. At the same time, this evolutionary relationship has been questioned persistently from the standpoint of cladistic analyses of morphological characteristics, such as the incisive foramen; some proponents of cladistic approaches to phylogeny propose instead thatHomo sapiens is closer to the orangutan. This contrast can be resolved, and various kinds of evidence brought into consistency, by (1) demonstrating that particular morphological traits, including the incisive foramen, are variable across taxa, not taxon-specific; and (2) utilizing the principle of polyclinal variation to describe the preservation of widespread, shared genetic diversity among mammalian populations, particularly those of hominoid primates.     

Ribosomal RNA gene sequences and hominoid phylogeny

Sequences totaling 3,500 bases from the 28S rRNA gene and from one of the ribosomal internal transcribed spacers (ITS1) have been determined for human, chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and orangutan (Pongo pygmaeus). Analyses of the rRNA alignments show (1) a clustering of substitutions in the "variable regions" of the 28S gene, (2) a 1.5-3-fold increase in divergence in the transcribed spacer over that in the exon, and (3) that human and chimpanzee are the most closely related pair, in agreement with the results of Miyamoto et al., Sibley and Ahlquist, and Caccone and Powell.     

Deep mitochondrial introgression and hybridization among ecologically divergent vole species

The completion of speciation is typically difficult to ascertain in rapidly diverging taxa but the amount of hybridization and gene flow in sympatry or parapatry contains important information about the level of reproductive isolation achieved. Here, we examined the progress in speciation between the Mediterranean (Microtus duodecimcostatus) and the Lusitanian pine vole (M. lusitanicus), which are part of the most rapid radiation of species known in mammals. These two Iberian pine voles are classified as separate species because of differences in morphology and ecology, but relatively many ambiguous individuals can be found in sympatric conditions. Our phylogenetic analyses of rangewide data from the mitochondrial cytochrome b gene (mtDNA) demonstrated high levels of diversity and a basal separation in two parapatric lineages. However, mtDNA affiliation was at odds with morphological classification or geographical distribution of the taxa. In contrast, statistical analyses of microsatellites (nucDNA) showed two clear genetic clusters in allopatry and sympatry generally matching morphological classification. This cytonuclear discordance over a large geographic area suggests historical introgression of mtDNA from M. duodecimcostatus to M. lusitanicus. There was statistical evidence for at least two recent hybrids in the sympatry zone but gene flow is apparently low given clear‐cut differences in nucDNA. Our results indicate a relatively advanced speciation process in these Iberian pine voles without fully established reproductive isolation. This situation enables use of combined population genomic and experimental approaches for the separation of patterns and mechanisms in the ongoing explosive diversification of these and other Arvicoline rodents in the future.     

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

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

五种色蟌Cyt b基因序列及其系统发育关系

以昆虫mtDNA的Cytb基因作为分子遗传标记,用其特异性引物进行PCR扩增及DNA测序,共获得蜻蜓目束翅亚目色蟌科4属5种及1外群的Cytb基因部分序列(576bp),该片段中碱基T,C,A,G的平均含量分别为31.6,21.6,31.4和15.4%,A+T平均含量为63%,明显高于G+C含量(37%)。密码子第3位点的A+T平均含量较高,为66.4%。碱基替换多发生在密码子的第3位点。以巨齿尾溪蟌Bayadera melanopteryx作为外群构建系统发育树,结果显示,绿色蟌属Mnais和单脉色蟌属Matrona是单系群,绿色蟌属是单脉色属、细色蟌属Vestalis及艳色蟌属Neurobasis的姐妹群,是较早分化出来的一个类群。