Evolution of ecological traits and wing morphology in Hemileuca (Saturniidae) based on a two-gene phylogeny

We present a molecular phylogeny for the genus Hemileuca (Saturniidae), based on 624 bp of mitochondrial cytochrome oxidase I (COI) and 932 bp of the nuclear gene elongation factor 1 alpha (EF1alpha). Combined analysis of both gene sequences increased resolution and supported most of the phylogenetic relationships suggested by separate analysis of each gene. However, a maximum parsimony (MP) model for just COI sequence from one sample of most taxa produced a phylogeny incongruent with EF1alpha and combined dataset analyses under either MP or ML models. Time of year and time of day during which adult moths fly corresponded strongly with the phylogeny. Although most Hemileuca are diurnal, ancestral Hemileuca probably were nocturnal, fall-flying insects. The two-gene molecular phylogeny suggests that wing morphology is frequently homoplastic. There was no correlation between the primary larval hostplants and phylogenetic placement of taxa. No phylogenetic pattern of specialization was evident for single hostplant families across the genus. Our results suggest that phenological behavioral characters may be more conserved than the wing morphology characters that are more commonly used to infer phylogenetic relationships in Lepidoptera. Inclusion of a molecular component in the re-evaluation of systematic data is likely to alter prior assumptions of phylogenetic relationships in groups where such potentially homoplastic characters have been used.     

Phylogenetic analyses of the rhipicephaline ticks indicate that the genus Rhipicephalus is paraphyletic

We inferred the phylogeny of 21 species and subspecies of ticks from the subfamilies Rhipicephalinae and Hyalomminae using cytochrome c oxidase subunit I (COI) and 12S rRNA mitochondrial gene sequences. Two members of the subfamily Haemaphysalinae were used for outgroup reference. The largest rhipicephaline genus, Rhipicephalus, was represented by ticks from six of the species groups, the second largest genus, Dermacentor, by species from two of three of its subgenera, and the genus Boophilus by 3 of its 5 species. We analyzed the 12S and COI sequences separately and together; statistically significant incongruence between the 12S rDNA and the COI sequences was not detected in the combined dataset using the incongruence length difference test. The combined dataset provided greater phylogenetic resolution than the individual datasets, and although the 12S rDNA data had only 25% of the parsimony-informative characters, it provided half of the total partitioned Bremer support for the combined dataset. We present the first hypothesis of phylogenetic relationships among some species groups of Rhipicephalus but our most controversial result was that the genus Rhipicephalus is apparently paraphyletic, unless species of Boophilus are included in it. The species of Rhipicephalus most closely related to Boophilus spp. were from the R. pravus and R. evertsi species groups, which may implicate an African origin for this important group of ticks.     

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.     

A molecular phylogeny of the marine mussel genus Perna (Bivalvia: Mytilidae) based on nuclear (ITS1&2) and mitochondrial (COI) DNA sequences

A molecular phylogeny is presented for marine mussels of the genus Perna, based on nuclear (ITS1,ITS2) and mitochondrial (COI) DNA sequence data. The three generally recognised species (Perna viridis, Perna perna and Perna canaliculus) and one putative species (Perna picta) were each sampled from several locations within their known geographic distributions. A range of phylogenetic analyses was used to investigate the current taxonomic assignments, evolutionary relationships and the biogeographical history of the genus. The different analyses produced similar, well supported topologies and verified the monophyly of the genus with respect to five mytilid outgroup species. P. perna (Atlantic), P. viridis (Indo-West Pacific), and P. canaliculus (New Zealand) each formed distinct clades, confirming their specific status. Putative P. picta from North Africa clustered within the P. perna clade and is not regarded as a separate species. P. perna and P. canaliculus were the most closely related of the three species. Possible biogeographic explanations for the present species distributions are evaluated.     

Phylogeny of the scathophagidae (Diptera, calyptratae) based on mitochondrial DNA sequences

The family Scathophagidae constitutes, together with members of the families Muscidae, Fannidae, and Anthomyiidae, the Muscoidea superfamily. The species Scathophaga stercoraria has been used extensively to investigate questions in animal ecology and evolution, particularly as a model system for studies of sperm competition and life history evolution. However, no phylogenetic studies have ever been performed on the Scathophagidae and the relationships within this family remain unclear. This study represents a molecular approach aimed at uncovering the phylogenetic relationships among 61 species representing 22 genera of Scathophagidae. A fragment of the terminal region of the mitochondrial gene COI (subunit I of the cytochrome oxidase gene) was sequenced in scathophagid species covering a wide geographic area, as well as a diverse spectrum of ecological habitats. Several clades grouping different genera and species have been identified, but the resolution power of the COI was insufficient to establish the exact relationships between these clades. The molecular data confirm the existence of a group consisting of the genera Delina, Chylizosoma, and Americina, which could represent the subfamily Delinae. Concerning the controversial position of the genus Phrosia, our data clearly suggest that it should be removed from the Delinae and placed within the genus Cordilura. Monophyly of most genera was confirmed, except for the genus Scathophaga, which should be divided into several different taxa.     

Phylogenetic relationships of the genus Cheilosia and the tribe Rhingiini (Diptera, Syrphidae) based on morphological and molecular characters

The phylogenetic relationships of the tribe Rhingiini and the genus Cheilosia (Diptera, Syrphidae) were investigated using morphological and molecular characters. The genus Cheilosia is one of the most diverse lineages of hoverflies (Syrphidae). The mitochondrial protein coding gene cytochrome c oxidase subunit I (COI), and the D2‐3 region of the nuclear 28S rRNA gene were chosen for sequencing, and morphological characters were scored for both adults and immature stages. The combined dataset included 56 ingroup taxa. The datasets were analyzed separately and in conjunction, using both static and dynamic alignment under the parsimony criterion. The aim of the study was to assess the phylogenetic relationships of the tribe Rhingiini, and to explore if the subgenera of Cheilosia were supported as monophyletic clades. Results showed that the monophyly of subtribes of Rhingiini remained ambiguous, especially due to unstable phylogenetic placements of the genera Portevinia and Rhingia. We recovered most subgenera of Cheilosia as monophyletic clades. Dynamic alignment, using the optimization alignment program POY, always recovered more parsimonious topologies under all parameter weighting schemes, than did parsimony analyses using static alignment and analyzed with NONA.     

New molecular data for tardigrade phylogeny, with the erection of Paramacrobiotus gen. nov.

Up to few years ago, the phylogenies of tardigrade taxa have been investigated using morphological data, but relationships within and between many taxa are still unresolved. Our aim has been to verify those relationships adding molecular analysis to morphological analysis, using nearly complete 18S ribosomal DNA gene sequences (five new) of 19 species, as well as cytochrome oxidase subunit 1 (COI) mitochondrial DNA gene sequences (15 new) from 20 species, from a total of seven families. The 18S rDNA tree was calculated by minimum evolution, maximum parsimony (MP) and maximum likelihood (ML) analyses. DNA sequences coding for COI were translated to amino acid sequences and a tree was also calculated by neighbour-joining, MP and ML analyses. For both trees (18S rDNA and COI) posterior probabilities were calculated by MrBayes. Prominent findings are as follows: the molecular data on Echiniscidae (Heterotardigrada) are in line with the phylogenetic relationships identifiable by morphological analysis. Among Eutardigrada, orders Apochela and Parachela are confirmed as sister groups. Ramazzottius (Hypsibiidae) results more related to Macrobiotidae than to the genera here considered of Hypsibiidae. Macrobiotidae and Macrobiotus result not monophyletic and confirm morphological data on the presence of at least two large groups within Macrobiotus. Using 18S rDNA and COI mtDNA genes, a new phylogenetic line has been identified within Macrobiotus , corresponding to the ' richtersi-areolatus group'. Moreover, cryptic species have been identified within the Macrobiotus ' richtersi group' and within Richtersius . Some evolutionary lines of tardigrades are confirmed, but others suggest taxonomic revision. In particular, the new genus Paramacrobiotus gen. n. has been identified, corresponding to the phylogenetic line represented by the ' richtersi-areolatus group'.     

基于COI基因序列的九种真蝽属昆虫的分子系统学研究(半翅目:蝽科)

通过对真蝽属Pentatoma 9种昆虫线粒体COI基因约798bp的序列进行分子进化分析,并以同蝽科宽铗同蝽Acanthosoma labiduroides为外群,采用最大简约法、最大似然法和邻接法构建了分子系统树,来探讨真蝽属的系统发育关系.研究结果支持褐真蝽群P. semiannulata-group的划分,绿角真蝽Pentatoma viridicornuta应划归到褐真蝽群P. Semiannulata-group;红足真蝽群中的角肩真蝽P. angulata与红足真蝽P. rufipes遗传距离较小,它们是否为1个物种值得关注;真蝽属各群之间的系统发育关系以及是否可分为3个属值得进一步研究.     

Phylogenetic relationships of Hamadryas (Nymphalidae: Biblidinae) based on the combined analysis of morphological and molecular data

A new phylogenetic hypothesis for the Neotropical butterfly genus Hamadryas, based on the combination of a morphological matrix, one mitochondrial (COI) and four nuclear markers (CAD, RpS5, EF1a, and Wingless), is presented. Results from analyses of the molecular evidence are compared with a previously published morphological phylogeny. Molecular data and the analysis of the complete dataset support the monophyly of Hamadryas and most sister groups suggested by morphological data alone. The addition of DNA sequences to the morphological matrix helped define species groups for which no morphological synapomorphies were found. Partitioned Bremer support indicates that COI, CAD, and morphology were consistently in agreement with the combined evidence tree. In contrast, signal from the nuclear markers Rps5, EF1a, and Wingless showed indifference at most levels of the tree, and minor conflict at nodes solving the relationships between species groups. Though resolved, the combined evidence tree shows low resample values, particularly among species groups whose relationships were characterized by short internodes. A reassessment about the pattern of character change for sound production is presented and discussed.     

Molecular phylogeny and systematic in the genus Brachycaudus (Homoptera: Aphididae): insights from a combined analysis of nuclear and mitochondrial genes

Phylogenetic relationships among members of the Aphid genus Brachycaudus (Homoptera: Aphididae) were inferred from partial sequences of mitochondrial cytochrome B oxidase (CytB), two partial fragments of mitochondrial cytochrome C oxidase subunit I (COI) and the internal transcribed spacer II (ITS2) of ribosomal DNA. Twenty-nine species, with several specimens per species, were included, representing all the historically recognized species-groups and subgenera used in the genus except the monospecific subgenus Mordvilkomemor. Results indicate that the genus Brachycaudus is a well-supported monophyletic group. While our results validate the monophyly of subgenera Thuleaphis , Appelia and Brachycaudus s. str. , they reveal two discrepancies in the classical taxonomy. First, the monotypic subgenus Nevskyaphis does not appear valid. Second, the traditionally defined Acaudus subgenus is not monophyletic. On the other hand, our phylogenetic trees corroborate Andreev's recent definition of Acaudus and Brachycaudina. However, they clearly show that the subgenera Prunaphis , Nevskyaphis and Scrophulaphis as defined by this author do not form monophyletic groups. Our results also highlight a highly supported clade that has not been discussed by previous authors; this clade could form a new subgenus, the subgenus Nevskyaphis . Finally, our study shows that molecular data and morphology meet the same limits in delimiting species groups and species themselves. Species groups in which taxonomic treatment is difficult are polytomous. Furthermore, except for one node clustering Brachycaudus s. str . and Appelia, intersubgeneric relationships remain poorly resolved even when several genes are added to the phylogenetic analysis. These results, together with previous studies in other aphid groups suggest that diversification might have been a rapid process in aphids.     

中国绿水螅分子系统发生地位的初步探讨

目的:初步探讨中国绿水螅(Hydra sinensis)分子系统发生地位以及水螅属内部各类群系统发生关系。方法:采用酚-氯仿法提取中国绿水螅总DNA,扩增线粒体COI和16S r RNA基因片段并进行DNA序列测定,再利用Clustal及MEGA等生物信息学分析软件进行系统发生分析。结果:在本研究重建的所有系统发生树中,中国绿水螅始终与绿水螅Hydra viridissima的不同种群一起构成绿水螅单系群。同时,棕色水螅群的单系性被基于COI基因的NJ树以及基于16S r RNA基因的NJ树和ML树支持,唯独基于COI基因的ML树不支持棕色水螅群的单系发生。在基于COI基因的ML树中纤弱水螅族在系统树的基部独立为一支系,而绿水螅群和其他棕色水螅群水螅一起组成另一支系,提示纤弱水螅族水螅的系统发生地位值得进一步探讨。值得注意的是,根据本文的结果,棕色水螅群内3族的划分仍然有一定疑问。基于COI基因的NJ树和ML树支持普通水螅族、寡水螅族和纤弱水螅族各自族内的单系发生,但16S r RNA基因的NJ树和ML树中仅普通水螅族水螅聚为单系群,而寡水螅族和纤弱水螅族水螅各自并非单系发生。结论:把水螅属划分为绿水螅群及棕色水螅群有一定的合理性,但棕色水螅群内寡水螅族、普通水螅族和纤弱水螅族3族的划分还有待商榷。     

速足目主要类群系统发育的分子证据

文章基于速足目现生主要类群18S rDNA、28S rDNA和COI基因序列,采用贝叶斯法、邻接法和最大简约法,尝试构建速足目的分子系统树;结合形态特征和化石记录,主要对速足目各超科级分类阶元的系统发育关系进行探讨。结果表明,速足目现生超科Bairdiacea、Darwinulacea、Cypridacea和Cytheracea均为单系群,支持形态学上关于上述4个超科的的界定;3种基因均支持形态学上Darwinulacea和Cypridacea具有较近的亲缘关系的观点。18S rDNA序列分析在较显著水平上支持Darwinulacea和Bairdiacea为姐妹群,Darwinulacea可能从Bairdia-cea中的一支演化而来;Bairdiacea和Darwinulacea组成的分支是Cypridacea的姐妹群,支持将三者合并为Bairdio-copina亚目的观点;Cytheracea是Cypridacea(Darwinulacea Bairdiacea)的姐妹群,可提升为Cytheracopina亚目。     

Molecular characterization of closely related species in the parasitic genus Encarsia (Hymenoptera: Aphelinidae) based on the mitochondrial cytochrome oxidase subunit I gene

The genus Encarsia F?rster includes parasitoid species that are effective natural enemies of whitefly and armoured scale insect agricultural pests. Within this genus, several species groups have been recognized on the basis of morphological similarity, although their monophyly appears uncertain. It is often difficult to separate morphologically similar species, and there is evidence that some species could in fact be complexes of cryptic species. Their correct identification is fundamental for biological control purposes. Recently, due to unreliability of morphological characters, molecular techniques have been investigated to identify markers that differentiate closely related species. In this study, DNA variation in an approximately 900 bp segment of the mitochondrial cytochrome oxidase subunit I (COI) gene was examined by both sequencing and PCR-RFLP. Two pairs of species that are difficult to distinguish morphologically were analysed: Encarsia formosa Gahan and Encarsialuteola Howard, belonging to the luteola group, and two populations of Encarsiasophia (Girault & Dodd) from Pakistan and Spain, belonging to the strenua group, recently characterized as cryptic species. High sequence divergence and species-specific restriction patterns clearly differentiate both species pairs. Parsimony analysis of the nucleotide sequences was also performed, including Encarsiahispida De Santis (luteola group) and Encarsia protransvena Viggiani (strenua group). Two monophyletic clades supporting the two groups of species considered were resolved. The results of this study support the use of the COI gene as a useful marker in separating species of Encarsia, for which morphological differences are subtle. Moreover, the COI gene appears potentially useful for understanding phylogenetic relationships in this genus.     

Phylogenetic relationships within the genus Jesogammarus (Crustacea, Amphipoda, Anisogammaridae) deduced from mitochondrial COI and 12S sequences

The genus Jesogammarus contains 16 species in two subgenera, Jesogammarus and Annanogammarus. To examine relationships among species in the genus, a molecular phylogenetic study including eight species of the former subgenus and four of the latter was conducted using partial DNA sequences of the mitochondrial COI and 12S rRNA genes. MP, NJ, and ML trees based on the combined COI and 12S data indicated monophyly of the subgenus Annanogammarus, though the monophyly of Jesogammarus was left unresolved. Consistent with few morphological differences, Jesogammarus (A.) naritai and J. (A.) suwaensis showed low genetic differentiation and did not show reciprocal monophyly, which suggests a close affinity of these taxa.     

The molecular phylogeny of the sea star Echinaster (Asteroidea: Echinasteridae) provides insights for genus taxonomy

In this study, we used sequences of two mitochondrial genes, cytochrome c oxidase I (COI) and 16S rRNA, and one nuclear gene, 28S rRNA, to test the monophyly of the sea star genus Echinaster, and understand the phylogenetic relationships among species and subgenera within this genus. Phylogenetic analyses based on Bayesian inference and maximum likelihood methods revealed three clades with high values of genetic divergence among them (K2P distances for COI over 23%). One of the clades grouped all Echinaster (Othilia) species, and the other two clades included Echinaster (non‐Othilia) species and Henricia species, respectively. Although the relationships among Henricia, Othilia, and Echinaster could not be completely clarified, the Othilia clade was a well‐supported group with shared diagnostic morphological characters. Moreover, the approximately unbiased test applied to the phylogenetic reconstruction rejected the hypothesis of the genus Echinaster as a monophyletic group. According to these results, we suggest the revalidation of Othilia as a genus instead of a subgenus within Echinaster. Our study clarifies important points about the phylogenetic relationships among species of Echinaster. Other important systematic questions about the taxonomic classification of Echinaster and Henricia still remain open, but this molecular study provides bases for future research on the topic.     

Phylogeny of Triatomine Vectors of Trypanosoma cruzi Suggested by Mitochondrial DNA Sequences

The subfamily Triatominae (Hemiptera: Reduviidae) comprises hematophagous insects, most of which are actual or potential vectors of Trypanosoma cruzi, the protozoan agent of Chagas' disease (American trypanosomiasis). DNA sequence comparisons of mitochondrial DNA (mtDNA) genes were used to infer phylogenetic relationships among 32 species of the subfamily Triatominae, 26 belonging to the genus Triatoma and six species of different genera. We analyzed mtDNA fragments of the 12S and 16S ribosomal RNA genes (totaling 848-851 bp) from each of the 32 species, as well as of the cytochrome oxidase I (COI, 1447 bp) gene from nine. The phylogenetic analyses unambiguously supported several clusters within the genus Triatoma. In the morphological classification, T. costalimai was placed tentatively within the infestans complex while T. guazu was not included in any Triatoma complex. The placement of these species in the molecular phylogeny indicated that both belong to the infestans complex. We confirmed with a strong support the inclusion of T. circummaculata, a member of a different complex based on morphology, within the infestans complex. On the other hand, the present phylogenetics analysis did not support the monophyly of the infestans complex species as it was suggested in our previous studies. While no strong inference of polyphyly of the genus Triatoma was provided by the bootstrap analyses, the other species belonging to Triatomini analyzed could not be distinguished from the species of Triatoma.     

Evolution, biogeography, and the utility of mitochondrial 16s and COI genes in phylogenetic analysis of the crab genus Austinixa (Decapoda: Pinnotheridae)

This study used molecular data (mitochondrial 16s and COI) for the first time to explore evolutionary relationships among species of the pinnotherid crab genus Austinixa. Low levels of phylogenetic signal were detected for COI. High levels of phylogenetic signal were detected for 16s, indicating it is a more useful marker for inferring species level phylogenies in Austinixa. Phylogeographic patterns among species of Austinixa are consistent with allopatric speciation due to numerous climatic and oceanographic fluctuations during the last 5-6 my. In addition, all but two species have been derived since the closure of the Isthmus of Panama, a pattern consistent with hypotheses that the marine biota of the Caribbean and southeastern North America underwent a pulse of biotic turnover within the last 2-3 my. Austinixa aidae and Austinixa hardyi had identical 16s sequences, and differed by only 2 bp in COI, raising questions about the validity of A. hardyi as a distinct species.     

Pushing short DNA fragments to the limit: Phylogenetic relationships of ‘hydrobioid’ gastropods (Caenogastropoda: Rissooidea)

Although phylogenetic studies are increasingly utilizing multi-locus datasets, a review of GenBank data for the Gastropoda indicates a strong bias towards a few short gene fragments (most commonly COI, LSU rRNA, and SSU rRNA). This is particularly the case for the Rissooidea, one of the largest and most taxonomically difficult gastropod superfamilies. Here we analyze fragments of these three genes from 90 species to determine whether they can well resolve higher relationships within this superfamily, whether structurally aligned sequence datasets increase phylogenetic signal, and whether the inclusion of highly variable regions introduces noise. We also used the resulting phylogenetic data in combination with morphological/anatomical evidence to re-evaluate the taxonomic status of ‘hydrobioid’ family-level groups.Our results indicate that all three of the alignment strategies that were used resulted in phylogenies having similar signal levels. However, there was a slight advantage to using structural alignment for inferring family-level relationships. Moreover, the set of ‘standard’ gastropod genes supported recognition of many previously recognized families and provides new insight into the systematics of several problematic groups. However, some family-group taxa were unresolved and the relationships among families were also poorly supported, suggesting a need for more extensive sampling and inclusion of additional genes.     

Affinities among anostracan (Crustacea: Branchiopoda) families inferred from phylogenetic analyses of multiple gene sequences

To gain insights into the relationships among anostracan families, molecular phylogenetic analyses were performed on nuclear (28S D1-D3 ribosomal DNA) and mitochondrial (16S rDNA, COI) gene regions for representatives of seven families and an outgroup. Data matrices used in the analyses included 951 base pairs (bp) of aligned sequences for 28S, 465 bp for 16S, and 658 bp (219 amino acids) for COI. Maximum-parsimony and maximum-likelihood methods were used to construct phylogenetic trees, enabling the evaluation of both previous hypotheses of taxonomic relationships among families based on morphology, and of the relative merits of independent versus simultaneous analyses of multiple data sets for phylogeny construction. Data from various combinations of the gene regions produced relatively congruent patterns of phylogenetic affinity. In most analyses, two monophyletic groups were resolved: one cluster included the families Polyartemiidae, Chirocephalidae, Branchinectidae, Streptocephalidae, and Thamnocephalidae, while the other contained the Artemiidae and Branchipodidae. Comparative analyses showed that combining gene regions in a single matrix generally resulted in increased resolution and support for each cluster relative to those obtained from single-gene analyses. Statistical tests demonstrated that morphology-based hypotheses of relationships among families had poorer support than those determined from molecular data, reflecting the homoplasy in characters used to differentiate families.