Phylogenetic relationships of the New World Troidini swallowtails (Lepidoptera: Papilionidae) based on COI, COII, and EF-1alpha genes

A phylogeny of the Neotropical members of the Tribe Troidini (Lepidoptera: Papilionidae) was obtained with sequences of three protein-coding genes: two mitochondrial (COI and COII), and one nuclear (EF-1alpha). Parsimony and Bayesian analyses of 33 taxa resulted in very similar trees regardless of method used with the 27 troidines always forming a monophyletic clade. Within Troidini, the genus Battus is sister group to the remaining troidines, followed by a clade formed by the Paleotropical taxa (here represented by three exemplars). The genus Euryades is the next branch, and sister group of Parides. The genus Parides is monophyletic, and is divided into four main groups by Maximum Parsimony analysis, with the most basal group composed of tailed species restricted to SE Brazil. Character optimization of ecological and morphological traits over the phylogeny proposed for troidines indicated that the use of several species of Aristolochia is ancestral over the use of few or a single host-plant. For the other three characters, the ancestral states were the absence of long tails, forest as the primary habitat and oviposition solitary or in loose group of several eggs.     

Molecular phylogeny of Pemphiginae (Hemiptera: Aphididae) inferred from nuclear gene EF-1alpha sequences

Three traditional tribes of Fordini, Pemphigini and Eriosomatini comprise Pemphiginae, and there are two subtribes in Fordini and Pemphigini, respectively. Most of the species in this subfamily live heteroecious holocyclic lives with distinct primary host specificity. The three tribes of Pemphigini (except Prociphilina), Eriosomatini and Fordini use three families of plants, Salicaceae (Populus), Ulmaceae (Ulums) and Anacardiaceae (Pistacia and Rhus), as primary hosts, respectively, and form galls on them. Therefore, the Pemphigids are well known as gall makers, and their galls can be divided into true galls and pseudo-galls in type. We performed the first molecular phylogenetic study of Pemphiginae based on molecular data (EF-1alpha sequences). Results show that Pemphiginae is probably not a monophylum, but the monophyly of Fordini is supported robustly. The monophyly of Pemphigini is not supported, and two subtribes in it, Pemphigina and Prociphilina, are suggested to be raised to tribal level, equal with Fordini and Eriosomatini. The molecular phylogenetic analysis does not show definite relationships among the four tribes of Pemphiginae, as in the previous phylogenetic study based on morphology. It seems that the four tribes radiated at nearly the same time and then evolved independently. Based on this, we can speculate that galls originated independently four times in the four tribes, and there is no evidence to support that true galls are preceded by pseudo-galls, as in the case of thrips and willow sawflies.     

Molecular phylogeny of Fordini (Hemiptera: Aphididae: Pemphiginae) inferred from nuclear gene EF-1 alpha and mitochondrial gene COI

The tribe Fordini is a fascinating group because of its complicated life history, primary host specificity and gall-forming characteristic. Different species produce galls with different morphology on different parts of the host plants. The EF-1alpha-based, COI-based and combined sequences-based phylogenetic trees with three algorithms MP, ML and Bayes all strongly suggest that Fordini is a monophyletic group with two clades corresponding to two subtribes, Fordina and Melaphidina, each also monophyletic. Some important morphological characters and primary host plants of aphids were mapped onto the phylogenetic tree to analyse the division of subtribes and to uncover at which level the aphids correspond to their primary hosts, Pistacia and Rhus. Results suggest that the division of subtribes in Fordini is closely related to host selection of aphids. The evolution of gall morphology and the probable driving force behind it in this tribe were also discussed. The Fordini aphids seem to have evolved towards a better ability to manipulate their host plant, induce strong sinks and gain high reproductive success. Galls in this tribe evolved mainly along two directions to attain this goal: (i) by enlarging the gall from small bag to spherical, even big cauliflower-like, and changing the galls' location or forming two galls in their life cycle (Fordina); (ii) by moving the gall position from midrib, petiole of the leaflet, and eventually to the common petiole of the compound leaf (Melaphidina).     

Phylogeny of Australian Coptotermes (Isoptera: Rhinotermitidae) species inferred from mitochondrial COII sequences

Six Australian species of Coptotermes are traditionally recognized, but recent cuticular hydrocarbon studies suggest that some of these may represent more than one species. An understanding of the phylogenetic diversity of Australian Coptotermes, particularly the pest species, is likely to be important for the improvement of termite management strategies. A study of phylogenetic relationships among species of this genus was performed, based on the mitochondrial cytochrome oxidase (COII) gene, comparing the data with recent data from Asian species. Representatives of the species C. lacteus (Froggatt), C. frenchi Hill and C. michaelseni Silvestri were each found to form closely related monophyletic groups, however representatives of C. acinaciformis (Froggatt) were not. For C. acinaciformis, representatives from northern mound-building populations were found to form a distinct group to southern, tree-nesting forms. Among southern C. acinaciformis, two Western Australian representatives were found to be divergent from other populations. The results suggest that C. acinaciformis probably represents a complex of species rather than one, as has been suggested previously. One unidentified Coptotermes sp. taxon from Melbourne was found to be divergent from other taxa. Notably, some Australian species were more closely related to Asian species than other Australian species.     

Phylogenetic relationships among the Nymphalidae (Lepidoptera) inferred from partial sequences of the wingless gene

A cladistic analysis was performed on a 378 bp region of the wingless gene from 103 nymphalid species and three pierid outgroups in order to infer higher level patterns of relationship among nymphalid subfamilies and tribes. Although the data are highly homoplastic, in many instances the most parsimonious cladograms corroborate traditionally recognized groups. The results suggest that this short gene region provides a useful source of data for phylogenetic inference, provided that adequate effort is made to sample a diversity of taxa.     

Phylogeny of the Nymphalidae (Lepidoptera)

A generic-level phylogeny for the butterfly family Nymphalidae was produced by cladistic analysis of 234 characters from all life stages. The 95 species in the matrix (selected from the 213 studied) represent all important recognized lineages within this family. The analysis showed the taxa grouping into six main lineages. The basal branch is the Libytheinae, with the Danainae and Ithomiinae on the next branch. The remaining lineages are grouped into two main branches: the Heliconiinae-Nymphalinae, primarily flower-visitors (but including the fruit-attracted Coeini); and the Limenitidinae (sensu strictu), Biblidinae, and the satyroid lineage (Apaturinae, Charaxinae, Biinae, Calinaginae, Morphinae, Brassolinae, and Satyrinae), primarily fruit-attracted. Data partitions showed that the two data sets (immatures and adults) are very different, and a partitioned Bremer support analysis showed that the adult characters are the main source of conflict in the nodes of the combined analysis tree. This phylogeny includes the widest taxon coverage of any morphological study on Nymphalid butterflies to date, and supports the monophyly and relationships of most presently recognized subgroups, providing strong evidence for the presently accepted phylogenetic scheme.     

利用线粒体COII基因序列对中国尾蛱蝶属系统分化的研究(鳞翅目:蛱蝶科)

利用线粒体C0II基因序列分析法,研究了我国尾蛱蝶属5种蝴蝶的系统分化.结果表明,在尾蛱蝶属5个种的12个样品中,405 bp长的COII片段有11.4%的位点为多态性位点,大部分的碱基改变是转换.各物种内不同个体间的差异明显小于不同物种间的差异,种内个体间的差异一般为0.5%～1.5%,各物种间的差异绝大多数在4%以上.利用最大似然性法构建的尾蛱蝶属聚类关系图显示,尾蛱蝶属蝴蝶分为两大分支,一支包括大二尾蛱蝶、二尾蛱蝶和忘忧尾蛱蝶,另外一个分支包括窄斑凤尾蛱蝶和黑凤尾蛱蝶聚在一起.在大二尾蛱蝶、二尾蛱蝶和忘忧尾蛱蝶这一分支中,大二尾蛱蝶和忘忧尾蛱蝶的亲缘关系较近,而二尾蛱蝶较远.这些分子系统学的结果均与形态学的结果相一致,是对形态分类的有力支持.     

Phylogenetic relationships of the New World Troidini swallowtails (Lepidoptera: Papilionidae) based on COI, COII, and EF-1α genes

A phylogeny of the Neotropical members of the Tribe Troidini (Lepidoptera: Papilionidae) was obtained with sequences of three protein-coding genes: two mitochondrial (COI and COII), and one nuclear (EF-1α). Parsimony and Bayesian analyses of 33 taxa resulted in very similar trees regardless of method used with the 27 troidines always forming a monophyletic clade. Within Troidini, the genus Battus is sister group to the remaining troidines, followed by a clade formed by the Paleotropical taxa (here represented by three exemplars). The genus Euryades is the next branch, and sister group of Parides. The genus Parides is monophyletic, and is divided into four main groups by Maximum Parsimony analysis, with the most basal group composed of tailed species restricted to SE Brazil. Character optimization of ecological and morphological traits over the phylogeny proposed for troidines indicated that the use of several species of Aristolochia is ancestral over the use of few or a single host-plant. For the other three characters, the ancestral states were the absence of long tails, forest as the primary habitat and oviposition solitary or in loose group of several eggs.     

Phylogeny of subfamily Epidendroideae (Orchidaceae) inferred from ndhF chloroplast gene sequences

This project undertakes the first molecular-based phylogenetic study of subfamily Epidendroideae (Orchidaceae). Approximately 1200 nucleotides (from the 3' half of the chloroplast gene ndhF for 34 orchid taxa and a lilioid monocot, Clivia miniata (Amaryllidaceae), were subjected to phylogenetic analysis using parsimony and maximum likelihood methods. Oryza sativa (Poaceae), a nonlilioid monocot, was designated as outgroup. Trees from both parsimony and maximum likelihood methods suggest that subfamily Epidendroideae is monophyletic, with Listera (Neottieae) as sister. Although subtribal relationships are typically well resolved and have strong branch support, intertribal relationships are generally poorly resolved. Perhaps this general lack of resolution among tribes reflects a rapid species radiation that coincided with anatomical, physiological, and anatomical adaptations that initiated large-scale epiphytism in the ancestral Epidendroideae. Six taxa in this study exhibit deletions that are not evenly divisible by three and result in extensive sequence frameshifts. For example, one deletion is 227 bp in length and is flanked by the short direct repeat sequence; TCAATAGGAATTTCTTTT. Multiple deletions and frameshifts suggest that ndhF may be a pseudogene, in at least some orchid taxa.     

Phylogeny, biogeography, and host-plant association in the subfamily Apaturinae (Insecta: Lepidoptera: Nymphalidae) inferred from eight nuclear and seven mitochondrial genes

The subfamily Apaturinae consists of 20 genera and shows disjunct distributions and unique host-plant associations. Most genera of this subfamily are distributed in Eurasia South-East Asia and Africa, whereas the genera Doxocopa and Asterocampa are distributed mainly in South America and North America, respectively. Although the Apaturinae larvae mainly feed on the Cannabaceae, those of the genus Apatura are associated with Salix and Populus (Salicaceae), which are distantly related to the Cannabaceae. Here, we infer the phylogeny of Apaturinae and reconstruct the history of host shifting and of colonization in the New World. We analyzed 9761 bp of nuclear and mitochondrial DNA sequence data, including the genes encoding EF1a, Wg, ArgK, CAD, GAPDH, IDH, MDH, RpS5, COI, COII, ATPase8, ATPase6, COIII, ND3, and ND5 for 12 apaturine genera. We also inferred the phylogeny with six additional genera using mitochondrial sequence data alone. Within the Apaturinae, two major clades are recovered in all the datasets. These clades separate the New World genera, Doxocopa and Asterocampa, indicating that dispersal to the New World occurred at least twice. According to our divergence time estimates, these genera originated during the Early Oligocene to the Early Miocene, implying that they migrated across the Bering Land Bridge rather than the Atlantic Land Bridge. The temporal estimates also show that host shifting to Salix or Populus in Apatura occurred more than 15 million years after the divergence of their host plants. Our phylogenetic results are inconsistent with the previously accepted apaturine genus groups and indicate that their higher classification should be reconsidered.     

Phylogeny of six oligohymenophoreans (Protozoa, Ciliophora) inferred from small subunit rRNA gene sequences

The small subunit rRNA (SSrRNA) genes of six marine oligohymenophoreans, namely Uronemella filificum , Schizocalyptra sp.-WYG07060701, Schizocalyptra aeschtae , Pleuronema sinica , P. czapikae and Paratetrahymena sp., were sequenced. Phylogenetic trees were constructed with four different methods to assess the inter- and intrageneric relationships among the scuticociliates and the phylogenetic assignment of the order Loxocephalida. The SSrRNA phylogeny indicates that: (i) Paratetrahymena is most closely related to Cardiostomatella ; (ii) the order Loxocephalida and the family Uronematidae both appear to be polyphyletic; (iii) the order Philasterida is a well-defined taxon; (iv) Cyclidium porcatum falls outside the order Pleuronematida in all analyses; (v) the validity of the genus Uronemella is confirmed; (vi) Schizocalyptra is a member of the family Pleuronematidae. Furthermore, the predicted secondary structures of the variable region 4 of the SSrRNA gene sequences show that the size of the terminal bulge in Helix E23–7 is probably different for the orders Philasterida and Pleuronematida. Also, compared to Uronema and Homalogastra , Uronemella has distinct patterns in Helices E23–1, E23–7, E23–8 and E23–9.     

Phylogeny of phagotrophic euglenids (Euglenozoa) as inferred from hsp90 gene sequences

Molecular phylogenies of euglenids are usually based on ribosomal RNA genes that do not resolve the branching order among the deeper lineages. We addressed deep euglenid phylogeny using the cytosolic form of the heat-shock protein 90 gene (hsp90), which has already been employed with some success in other groups of euglenozoans and eukaryotes in general. Hsp90 sequences were generated from three taxa of euglenids representing different degrees of ultrastructural complexity, namely Petalomonas cantuscygni and wild isolates of Entosiphon sulcatum, and Peranema trichophorum. The hsp90 gene sequence of P. trichophorum contained three short introns (ranging from 27 to 31 bp), two of which had non-canonical borders GG-GG and GG-TG and two 10-bp inverted repeats, suggesting a structure similar to that of the non-canonical introns described in Euglena gracilis. Phylogenetic analyses confirmed a closer relationship between kinetoplastids and diplonemids than to euglenids, and supported previous views regarding the branching order among primarily bacteriovorous, primarily eukaryovorous, and photosynthetic euglenids. The position of P. cantuscygni within Euglenozoa, as well as the relative support for the nodes including it were strongly dependent on outgroup selection. The results were most consistent when the jakobid Reclinomonas americana was used as the outgroup. The most robust phylogenies place P. cantuscygni as the most basal branch within the euglenid clade. However, the presence of a kinetoplast-like mitochondrial inclusion in P. cantuscygni deviates from the currently accepted apomorphy-based definition of the kinetoplastid clade and highlights the necessity of detailed studies addressing the molecular nature of the euglenid and diplonemid mitochondrial genome.     

Phylogeny of gymnosperms inferred fromrbcL gene sequences

Partial nucleotide sequences of the large subunit of ribulose-1,5-bisphosphate carboxylase (rubisco) gene (1333 base pairs: about 90% of the gene) from several seed plants were determined. Phylogenetic trees based on amino acid sequences were inferred by using the neighbor joining and maximum likelihood methods. The results indicate (1) monophyly of gnetum group (Ephedra, Gnetum, Welwitschia), (2) monophyly of extant gymnosperms containing gnetum group, which contradicts the results of morphological data.     

Phylogeny and evolution of Digitulati ground beetles (Coleoptera, Carabidae) inferred from mitochondrial ND5 gene sequences

Genealogical trees have been constructed using mitochondrial ND5 gene sequences of 87 specimens consisting of 32 species which have been believed to belong to the division Digitulati (one of the lineages of the subtribe Carabina) of the world. There have been recognized six lineages, which are well separated from each other. Each lineage contains the following genus: (1) the lineage A: Ohomopterus from Japan; (2) the lineage B: Isiocarabus from eastern Eurasian Continent; (3) the lineage C: Carabus from China which are further subdivided into three sublineages; (4) the lineage D: Carabus from USA; (5) the lineage E: Carabus from the Eurasian Continent, Japan and North America; and (6) the lineage F: Eucarabus from the Eurasian Continent. Additionally, the genus Acrocarabus which had been treated as a constituent of the division Archicarabomorphi has been recognized to be the 7th lineage of the division Digitulati from the ND5 genealogical analysis as well as morphology. These lineages are assumed to have radiated within a short period and are largely linked to their geographic distribution.     

Phylogeny of protostome moulting animals (Ecdysozoa) inferred from 18 and 28S rRNA gene sequences

Reliability of reconstruction of phylogenetic relationships within a group of protostome moulting animals was evaluated by means of comparison of 18 and 28S rRNA gene sequences sets both taken separately and combined. Reliability of reconstructions was evaluated by values of the bootstrap support of major phylogenetic tree nodes and by degree of congruence of phylogenetic trees inferred by various methods. By both criteria, phylogenetic trees reconstructed from the combined 18 and 28S rRNA gene sequences were better than those inferred from 18 and 28S sequences taken separately. Results obtained are consistent with phylogenetic hypothesis separating protostome animals into two major clades, moulting Ecdysozoa (Priapulida + Kinorhyncha, Nematoda + Nematomorpha, Onychophora + Tardigrada, Myriapoda + Chelicerata, Crustacea + Hexapoda) and unmoulting Lophotrochozoa (Plathelminthes, Nemertini, Annelida, Mollusca, Echiura, Sipuncula). Clade Cephalorhyncha does not include nematomorphs (Nematomorpha). Conclusion was taken that it is necessary to use combined 18 and 28S data in phylogenetic studies.     

Glacial effects on sequence divergence of mitochondrial COII of Polyura eudamippus (Lepidoptera: Nymphalidae) in China

Sequence divergence of mitochondrial COII was analyzed in 50 specimens belonging to five subspecies of Polyura eudamippus (Lepidoptera: Nymphalidae) collected from southern China. There were nine haplotypes in the 405 bp of partial COII sequence. Distribution of the five subspecies was primarily consistent with the spatial distribution of haplotypes. The K (st) statistic showed genetic differentiation among these subspecies, except between the pair of P. e. kuangtungensis and P. e. formosana, which were separated by the Taiwan Strait. This is consistent with the 10,000-year history of the Taiwan Strait, not long enough for detectable differentiation. The present distribution pattern of COII haplotypes of P. eudamippus should be shaped by the alteration of Pleistocene glaciations, and Yunnan might be the refugium of P. eudamippus in the ice age, judging from the abundant haplotypes remaining. There were two routes for P. eudamippus in the postglacial expansion, one northward to Sichuan, Chongqing, and Hubei and another eastward to the southeastern coast of mainland China and Taiwan Island. Because the haplotype of butterflies on Hainan Island (P. e. whiteheadi) was completely different from that of mainland China, it was estimated that butterflies on Hainan Island might be from the Indo-China Peninsula rather than from mainland China.     

Glacial Effects on Sequence Divergence of Mitochondrial COII of Polyura eudamippus (Lepidoptera: Nymphalidae) in China

Sequence divergence of mitochondrial COII was analyzed in 50 specimens belonging to five subspecies of Polyura eudamippus (Lepidoptera: Nymphalidae) collected from southern China. There were nine haplotypes in the 405 bp of partial COII sequence. Distribution of the five subspecies was primarily consistent with the spatial distribution of haplotypes. The K _st statistic showed genetic differentiation among these subspecies, except between the pair of P. e. kuangtungensis and P. e. formosana, which were separated by the Taiwan Strait. This is consistent with the 10,000-year history of the Taiwan Strait, not long enough for detectable differentiation. The present distribution pattern of COII haplotypes of P. eudamippus should be shaped by the alteration of Pleistocene glaciations, and Yunnan might be the refugium of P. eudamippus in the ice age, judging from the abundant haplotypes remaining. There were two routes for P. eudamippus in the postglacial expansion, one northward to Sichuan, Chongqing, and Hubei and another eastward to the southeastern coast of mainland China and Taiwan Island. Because the haplotype of butterflies on Hainan Island (P. e. whiteheadi) was completely different from that of mainland China, it was estimated that butterflies on Hainan Island might be from the Indo-China Peninsula rather than from mainland China.