Phylogenetic studies of dogs with emphasis on Japanese and Asian breeds

The first domestication of the dog occurred in East Asia, and major ancestor of the dog was a wolf subspecies, Canis lupus chanco. This finding derives from data on the nucleotide sequences of mtDNA and the frequency of genes controlling blood protein polymorphisms in various subspecies of wolves and dog breeds around the world. The results of the allele frequency distribution of genes controlling 16 blood protein polymorphisms, and the incidence of dogs possessing erythrocytes with high potassium (HK) in Japan, East Asia and Europe allowed us to posturate the following hypothesis about the origins of Japanese dogs and the history of their development. In the Jomon period the first dogs entered the Japanese archipelago from southern or northern continental Asia. These dogs eventually spread throughout Japan. Then, during the Yayoi and Kofun periods, other dogs were brought over via the Korean Peninsula, and crossbreeding occurred with the original dogs. The resulted offspring can be assumed to be the ancestors of most of the Japanese breeds that exist today. Ethological studies have revealed a significant breed difference in behavioral traits among canine breeds with Japanese dogs, showing more aggressive dispositions than most of European dogs.     

Asian origin for Polystichum （Dryopteridaceae） based on rbcL sequences

Chloroplast rbcL sequences of 60 species of Polystichum sensu lato (s.l.), including 23 new sequences from southwest China, were used to assess the phylogenetic relationships within the genus. On the basis of estimated evolution rate of rbcL gene and the genetic distance data that passed relative-rate tests, we further estimated the divergence times between some clades of the genus. The phylogenetic relationships were inferred using the neighbor-joining and maximum-parsimony methods, both methods producing trees with completely congruent topology. These trees reveal that all species of Polystichum s.l. in this study (including Cyrtomium and Cyrtomidictyum) form a monophyletic group. The basal split in Polystichum s.l. separates a clade with all Asian members from a clade containing other species from all over the world. The phylogenetic and divergence time estimation results lead us to suggest that Polystichum s.l. originated in Asia in the late Late Cretacous (≈76 Ma) and migrated into other places in the world in early Eocene(≈46 Ma).     

Molecular systematics and ultrastructural characterization of a forgotten species: Chattonidium setense (Ciliophora,Heterotrichea)

In the present paper we redescribe the ciliate Chattonidium setense Villeneuve 1937 combining morphological observations (live, stained, scanning, and transmission electron microscope) with behavioral notes and molecular data. Ultrastructural analysis revealed remarkable similarities between Chattonidium and representative members of the class Heterotrichea in cortical structure and cytoplasmic organization. The most similar genus for these aspects appears to be Condylostoma. To verify this relatedness, 18S rRNA genes from Chattonidium and from one Condylostoma species were sequenced. Phylogenetic analysis indicates Chattonidium belongs to the class Heterotrichea defined according to the modern taxonomy, and confirms its relatedness with Condylostoma already hypothesized by Villeneuve-Brachon (1940). The presence of the aboral cavity complex, a unique feature never described in other ciliates, and its peculiar organization revealed by ultrastructural analysis fully justify, in our opinion, the maintenance of Chattonidium in the separate family Chattonidiidae, established by Villeneuve-Brachon in 1940.     

A Cambrian micro-lobopodian and the evolution of arthropod locomotion and reproduction

The evolutionary success of arthropods, the most abundant and diverse animal group, is mainly based on their segmented body and jointed appendages, features that had evolved most likely already before the Cambrian. The first arthropod-like animals, the lobopodians from the Early Cambrian, were unsclerotized and worm-like, and they had unjointed tubular legs. Here we describe the first three-dimensionally preserved Cambrian lobopodian. The material presented of Orstenotubulus evamuellerae gen. et sp. nov. is the smallest and youngest of a lobopodian known. O. evamuellerae shows strikingly detailed similarities to Recent tardigrades and/or onychophorans in its cellular-structured cuticle and the telescopic spines. It also shows similarities to other, longer known lobopodians, but which are ten times as large as the new form. These similarities include the finely annulated body and legs, which is characteristic also for Recent onychophorans, and paired humps continuing into spines situated dorsally to the leg insertions, a feature lacking in the extant forms. The morphology of O. evamuellerae not only elucidates our knowledge about lobopodians, but also aids in a clearer picture of the early evolution of arthropods. An example is the single ventral gonopore between a limb pair of O. evamuellerae, which indicates that a single gonopore, as developed in onychophorans, tardigrades, pentastomids, myriapods and insects, might represent the plesiomorphic state for Arthropoda, while the paired state in chelicerates and crustaceans was convergently achieved. Concerning life habits, the lateral orientation of the limbs and their anchoring spines of the new lobopodian imply that early arthropods were crawlers rather than walkers.     

Inclusion of the Eastern Asia endemic genus Sorolepidium in Polystichum （Dryopteridaceae）： Evidence from the chloroplast rbcL gene and morphological characteristics

The taxonomic status of the Eastern Asia endemic Sorolepidium is controversial. Some authors accept it as member of the large diverse genus Polystichum, whereas others suggest that it is an independent genus separated from the later by the exindusiate sorus and the absence of aristate teeth at the pinnae margins. Here we infer phylogenetic relationship of Sorolepidium using DNA sequences of the chloro-plast rbcL gene. Phylogenies were inferred using maximum-parsimony, maximum-likelihood, and Bayesian inference methods. Molecular data establish that Sorolepidium is deeply nested within the large genus Polystichum and has a close relationship with P. duthiei and P. lachenense in the model-based analyses. The Kimura 2-parameter distances of the rbcL sequences between S. glaciale and P. duthiei and P. lachenense were 0.1 and 0.2%, respectively. Furthermore, S. glaciale differed from P. duthiei by a single nucleotide in their rbcL sequences. Close relationships between S. glaciale and P. duthiei and P. lachenense are also supported by the shared spore ornamentation with echinate fenes-trate folds.     

Molecular phylogeny and biogeography of the highly specialized grade schizothoracine fishes （Teleostei： Cyprinidae） inferred from cytochrome b sequences

We recovered the phylogenetic relationships among 23 species and subspecies of the highly special-ized grade schizothoracine fishes distributing at 36 geographical sites in the Tibetan Plateau and its surrounding regions by analyzing sequences of cytochrome b genes. Furthermore, we estimated the possible divergent times among lineages based on a historical geological isolation event in the Tibetan Plateau. The molecular data revealed that the highly specialized grade schizothoracine fishes were not a monophyletic group, but were the same as genera Gymnocypris and Schizogypsis. Our results indi-cated that the molecular phylogenetic relationships apparently reflected their geographical and historical associations with drainages, namely species from the same and adjacent drainages clustered together and had close relationships. The divergence times of different lineages were well consistent with the rapid uplift phases of the Tibetan Plateau in the late Cenozoic, suggesting that the origin and evolution of schizothoracine fishes were strongly influenced by environment changes resulting from the upheaval of the Tibetan Plateau.     

Phylogeny of fireflies (Coleoptera: Lampyridae) inferred from mitochondrial 16S ribosomal DNA，with references to morphological and ethological traits

We sequenced partial mitochondrial 16S ribosomal DNA (16S rDNA) of 18 firefly species from Southwest of China. Combined with homologous sequences previously reported, phylogenetic trees including Japanese, Korean and Chinese species were reconstructed by neighbor-joining, maximum parsimony and Bayesian methods. All reconstructions agree on most nodes of the trees. Monophyly of Lampyridae is not supported because Rhagophthalmus ohbai in Rhagophthalmidae is included within it. Lamprigera, a genus placed unreliably in Lampyrinae, shows a close relationship to Amydetinae. Monophyly of Luciolinae is not supported because Pristolycus sagulatus (Lampyrinae) is included within it. In the Luciolinae, monophyly of Curtos and Hotaria is well established, respectively, but both morphological and molecular data continue to indicate that Luciola is not monophyletic and its subdivision is indeed necessary. Within the Lampyrinae, both Pyrocoelia and Diaphanes are not monophyletic, but monophyly of Pyrocoelia+Diaphanes is well supported. Phylogeny of Diaphanes is discussed for the first time. Generic placement of a newly discovered species (Diaphanes pectinealis Li et Liang) sharing some characters of Pyrocoelia and Diaphanes challenges the delimitation of these two similar genera. With references to the firefly mating systems, we suggest that more emphases should be placed on those sexually selected characters such as antennal structure in taxonomy of Lampyridae.     

New invariant of DNA sequence based on 3DD-curves and its application on phylogeny

The Z_inv, a new invariant based on 3DD-curves of DNA sequence, which is simple for calculation and it approximates to the leading eigenvalues of the matrix associated with DNA sequence. The utility of our invariant is illustrated on the DNA sequence of 11 species. In this study, we use the Z_inv to analyze the phylogenetic relationships for the seven HA (H5N1) sequences of avian influenza virus.     

应用线粒体Cytb基因序列探讨果蝇科部分属间的系统发育关系

通过PCR产物直接测序的方法获得了果蝇科(Drosophilidae)果蝇属(Genus Drosophila)[包括条纹果蝇亚属(Subgenus Dorsilopha)、果蝇亚属(Subgenus Drosophila)和水果果蝇亚属(Subgenus Sophophora)]、条果蝇属(Genus Phorticella)、姬果蝇属(Genus Scaptomyza)和花果蝇属(Genus Scaptodrosophila)的5个种6个单雌系的线粒体Cytb基因的部分DNA序列,用最大似然法、邻接法和Bayesian法分别构建系统树．研究结果表明：在选取的所有属和亚属中,花果蝇属的分化是最早的,其次是条纹果蝇亚属;姬果蝇属与果蝇亚属是近源的,条果蝇属同姬果蝇属和果蝇亚属形成的并系群是近源的;水果果蝇亚属早于果蝇亚属分化,水果果蝇亚属形成的支系是果蝇亚属和其它属(花果蝇属和姬果蝇属)形成的支系的姐妹分类单位．结果还表明线粒体Cytb基因可以作为有效的分子标记探讨高阶元的果蝇系统发育关系．     

基于随机聚类方法建模的序列分析

大数据下的系统发育估计是一个组合优化问题,在有限计算时间内,现有算法很难为大量序列数据的分析提供最优解.基于前人启发式算法,提出了一种系统发育树随机聚类建树方法,可在较短时间内为系统发育过程产生的大规模序列数据提供所有具有进化意义的解及最优解,以揭示发育过程中的序列进化关系.实验结果表明,该随机聚类方法是行之有效的,对生物计算及系统发育相关领域研究具有积极意义.