Molecular phylogeny of the subfamily Exoristinae (Diptera,Tachinidae), with discussions on the evolutionary history of female oviposition strategy

Abstract. Phylogenetic relationships among tribes in the tachinid subfamily Exoristinae (Diptera, Tachinidae) are inferred from four genes, namely white, 18S, 28S and 16S rDNA. For phylogenetic inferences, maximum parsimony, maximum likelihood and Bayesian Markov chain Monte Carlo analyses were performed. The resultant, very similar, trees are nearly concordant with the traditional classification based on morphological characters. Our results suggest that the Tachinidae are monophyletic and sister to the Sarcophagidae. The tribal relationships within Exoristinae are supported in part with high reliabilities and are similar to those inferred by Stireman. Based on the resultant trees, the phylogenetic relationships and possible morphological synapomorphies were investigated. In addition, we evaluated the transformation of female reproductive habits in the Exoristinae, finding support for the hypothesis that ovolarviparity evolved independently from oviparity in several clades, and obtaining different results concerning the evolutionary history of micro‐ovolarviparity depending on character optimization.     

Signal through the noise? Phylogeny of the Tachinidae (Diptera) as inferred from morphological evidence

The oestroid family Tachinidae represents one of the most diverse lineages of insect parasitoids. Despite their broad distribution, diversity and important role as biological control agents, the phylogeny of this family remains poorly known. Here, we review the history of tachinid systematics and present the first quantitative phylogenetic analysis of the family based on morphological data. Cladistic analyses were conducted using 135 morphological characters from 492 species belonging to 180 tachinid genera, including the four currently recognized subfamilies (Dexiinae, Exoristinae, Phasiinae, Tachininae) and all major tribes. We used characters of eggs, first‐instar larvae and adults of both sexes. We examined the effects of implied weighting by reanalysing the data with varying concavity factors. Our analysis generally supports the subfamily groupings Dexiinae + Phasiinae and Tachininae + Exoristinae, with only the Exoristinae and the Phasiinae reconstructed as monophyletic assemblages under a wide range of weighting schemes. Under these conditions, the Dexiinae, which were previously considered a well‐established monophyletic assemblage, are reconstructed as being paraphyletic with respect to the Phasiinae. The Tachininae are reconstructed as a paraphyletic grade from which the monophyletic Exoristinae arose. The Exoristinae are reconstructed as a monophyletic lineage, but phylogenetic relationships within the subfamily are largely unresolved. We further explored the evolution of oviposition strategy and found that the oviparous groups are nested within ovolarviparous assemblages, suggesting that ovipary may have evolved several times independently from ovolarviparous ancestors. This counterintuitive pattern is a novel hypothesis suggested by the results of this analysis. Finally, two major patterns emerge when considering host associations across our phylogeny under equal weights: (i) although more than 60% of tachinids are parasitoids of Lepidoptera larvae, none of the basal clades is unambiguously associated with Lepidoptera as a primitive condition, suggesting that tachinids were slow to colonize these hosts, but then radiated extensively on them; and (ii) there is general agreement between host use and monophyly of the major lineages.     

Relationships within the Munnopsidae (Crustacea, Isopoda, Asellota) based on three genes

The Munnopsidae are a diverse group of asellote isopods that are an important component of deep‐sea fauna. Morphologically‐based phylogenetic inference attempts have proven to be of limited use due to the ecological and morphological diversity within the clade. Monophyly of the family is well‐established but relationships within the group remain unresolved. This project is the first molecularly‐based effort focused specifically on resolving phylogenetic relationships within the Munnopsidae. Partial 28S and COI and complete 18S genes were sequenced for 28 asellotes, 15 additional taxa were included from which only one or two of the three target sequences could be obtained, and 18S sequences for five additional taxa were available from GenBank. Sequences were analysed both as individual genes and in combination using Bayesian and maximum parsimony approaches. Each gene provided a phylogenetic signal that could be identified in the combined analyses, with 18S analyses providing the most resolution of phylogenetic relationships. The available representatives of subfamilies Munnopsinae and Ilyarachninae were monophyletic, as was the genus Munneurycope. Relationships within the subfamily Munnopsinae were well‐resolved by thorough taxon sampling, several new species were placed, and the need for taxonomic revision of Munnopsis/Munnopsoides was supported. These analyses supported putative Eurycope paraphyly and emphasized the need for careful revision of this highly variable genus. Tytthocope was sister to Munnopsurus. Syneurycope was suggested as the sister group to the ilyarachnines. Combined analyses provided increased support for clades suggested in at least two individual gene analyses and for clades not strongly contradicted by individual analyses. Further work is required to fully resolve the munnopsid phylogeny and should consist of increased taxon sampling for the complete 18S sequence and possibly identification of at least one slowly evolving, nuclear protein‐coding gene to resolve the basal polytomy and enable placement of the root.     

Phylogeny of the plant bug subfamily Mirinae (Hemiptera: Heteroptera: Cimicomorpha: Miridae) based on total evidence analysis

The first comprehensive phylogenetic analyses of the most diverse subfamily of plant bugs, Mirinae, is presented in this study, for 110 representative taxa based on total evidence analysis. A total of 85 morphological characters and 3898 bp of mitochondrial (16S, COI) and nuclear (18S, 28S) sequences were analysed for each partitioned and combined dataset based on parsimony, maximum likelihood and Bayesian inference. Major results obtained in this study include monophyly of the tribe Mecistoscelini. The largest tribe, Mirini, was recovered as polyphyletic, and Stenodemini was recovered as paraphyletic. The clade of Stenodemini + Mecistoscelini is the sister group of the remaining Mirinae. The monophyly of two complexes composed of superficially similar genera were tested; the Lygus complex was recovered as nonmonophyletic, and the Adelphocoris–Creontiades–Megacoelum complex was confirmed to be monophyletic. The generic relationships of the main clades within each tribe based on the phylogeny, as well as their supported morphological characters, are discussed.     

Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling

In this paper we included a very broad representation of grass family diversity (84% of tribes and 42% of genera). Phylogenetic inference was based on three plastid DNA regions rbcL, matK and trnL-F, using maximum parsimony and Bayesian methods. Our results resolved most of the subfamily relationships within the major clades (BEP and PACCMAD), which had previously been unclear, such as, among others the: (i) BEP and PACCMAD sister relationship, (ii) composition of clades and the sister-relationship of Ehrhartoideae and Bambusoideae + Pooideae, (iii) paraphyly of tribe Bambuseae, (iv) position of Gynerium as sister to Panicoideae, (v) phylogenetic position of Micrairoideae. With the presence of a relatively large amount of missing data, we were able to increase taxon sampling substantially in our analyses from 107 to 295 taxa. However, bootstrap support and to a lesser extent Bayesian inference posterior probabilities were generally lower in analyses involving missing data than those not including them. We produced a fully resolved phylogenetic summary tree for the grass family at subfamily level and indicated the most likely relationships of all included tribes in our analysis.     

Relationships within Cornales and circumscription of Cornaceae-matK and rbcL sequence data and effects of outgroups and long branches

Phylogenetic relationships in Cornales were assessed using sequences rbcL and matK. Various combinations of outgroups were assessed for their suitability and the effects of long branches and outgroups on tree topology were examined using RASA 2.4 prior to conducting phylogenetic analyses. RASA identified several potentially problematic taxa having long branches in individual data sets that may have obscured phylogenetic signal, but when data sets were combined RASA no longer detected long branch problems. t(RASA) provides a more conservative measurement for phylogenetic signal than the PTP and skewness tests. The separate matK and rbcL sequence data sets were measured as not containing phylogenetic signal by RASA, but PTP and skewness tests suggested the reverse [corrected]. Nonetheless, the matK and rbcL sequence data sets suggested relationships within Cornales largely congruent with those suggested by the combined matK-rbcL sequence data set that contains significant phylogenetic signal as measured by t(RASA), PTP, and skewness tests. Our analyses also showed that a taxon having a long branch on the tree may not be identified as a "long-branched" taxon by RASA. The long branches identified by RASA had little effect on the arrangement of other taxa in the tree, but the placements of the long-branched taxa themselves were often problematic. Removing the long-branched taxa from analyses generally increased bootstrap support, often substantially. Use of non-optimal outgroups (as identified by RASA) decreased phylogenetic resolution in parsimony analyses and suggested different relationships in maximum likelihood analyses, although usually weakly supported clades (less than 50% support) were impacted. Our results do not recommend using t(RASA) as a sole criterion to discard data or taxa in phylogenetic analyses, but t(RASA) and the taxon variance ratio obtained from RASA may be useful as a guide for improved phylogenetic analyses. Results of parsimony and ML analyses of the sequence data using optimal outgroups suggested by RASA revealed four major clades within Cornales: (1) Curtisia-Grubbia, (2) Cornus-Alangium, (3) Nyssa-Camptotheca-Davidia-Mastixia-Diplopanax, and (4) Hydrangeaceae-Loasaceae, with clades (2) and (3) forming a monophyletic group sister to clade (4) and clade (1) sister to the remainder of Cornales. However, there was not strong bootstrap support for relationships among the major clades. The placement of Hydrostachys could not be reliably determined, although most analyses place the genus within Hydrangeaceae; ML analyses, for example, placed the genus as the sister of Hydrangeeae. Our results supported a Cornales including the systematically problematic Hydrostachys, a Cornaceae consisting of Cornus and Alangium, a Nyssaceae consisting of Nyssa and Camptotheca, a monogeneric Davidiaceae, a Mastixiaceae consisting of Mastixia and Diplopanax, and an expanded Grubbiaceae consisting of Grubbia and Curtisia, and two larger families, Hydrangeaceae and Loasaceae.     

The major opsin in bees (Insecta: Hymenoptera): A promising nuclear gene for higher level phylogenetics.

We report the phylogenetic utility of the nuclear gene encoding the long-wavelength opsin (LW Rh) for tribes of bees. Aligned nucleotide sequences were examined in multiple taxa from the four tribes comprising the corbiculate bees within the subfamily Apinae. Phylogenetic analyses of sequence variation in a 502-bp fragment (approx 40% of the coding region) strongly supported the monophyly of each of the four tribes, which are well established from previous studies of morphology and DNA. Trees estimated from parsimony and maximum likelihood analyses of LW Rh sequences show a strongly supported relationship between the tribes Meliponini and Bombini, a relationship that has been found uniformly in studies of other genes (28S, 16S, and cytochrome b). All of the tribal clades as well as relationships among the tribes are supported by high bootstrap values, suggesting the utility of LW Rh in estimating tribal and subfamily rank for these bees. The sequences exhibit minimal base composition bias. Both 1st + 2nd and 3rd position sites provide information for estimating a reliable tree topology. These results suggest that LW Rh, which has not been reported previously in studies of organismal phylogenetics, could provide important new data from the nuclear genome for phylogeny reconstruction.     

Phylogeny of West AfricanCaryedon(Coleoptera: Bruchidae): Congruence between Molecular and Morphological Data

Seed beetles belonging to the Old World genusCaryedonfeed in the seeds of various Caesalpinioideae, Mimosoideae, and Combretaceae. In an attempt to resolve broad phylogenetic relationships within the genus, we obtained 332 base pair sequences of mitochondrial 12S ribosomal DNA and morphological data for the 16 West AfricanCaryedonspecies. Morphological characters were analyzed under maximum parsimony and sequences were compared under maximum parsimony, maximum likelihood, and neighbor joining. Using a partition homogeneity test, we determined that morphological and molecular data sets were combinable. Combined data were analyzed under maximum parsimony. Morphological and molecular trees were congruent at the species group level and total evidence analyses yielded the same topologies as molecular data with each of the three outgroups used. Four main terminal clades are recognized, each corresponding with a group of species generally feeding on the same host plant family, subfamily, genus, or species. The monophyly of legume feedingCaryedonis supported by both data sets, and Combretaceae feeders split in two monophyletic assemblages.     

Inter-generic relationships of the crows, jays, magpies and allied groups (Aves: Corvidae) based on nucleotide sequence data

Phylogenetic relationships were studied based on DNA sequences obtained from all recognized genera of the family Corvidae sensu stricto . The aligned data set consists 2589 bp obtained from one mitochondrial and two nuclear genes. Maximum parsimony, maximum-likelihood, and Bayesian inference analyses were used to estimate phylogenetic relationships. The analyses were done for each gene separately, as well as for all genes combined. An analysis of a taxonomically expanded data set of cytochrome b sequences was performed in order to infer the phylogenetic positions of six genera for which nuclear genes could not be obtained. Monophyly of the Corvidae is supported by all analyses, as well as by the occurrence of a deletion of 16 bp in the β-fibrinogen intron in all ingroup taxa. Temnurus and Pyrrhocorax are placed as the sister group to all other corvids, while Cissa and Urocissa appear as the next clade inside them. Further up in the tree, two larger and well-supported clades of genera were recovered by the analyses. One has an entirely New World distribution (the New World jays), while the other includes mostly Eurasian (and one African) taxa. Outside these two major clades are Cyanopica and Perisoreus whose phylogenetic positions could not be determined by the present data. A biogeographic analysis of our data suggests that the Corvidae underwent an initial radiation in Southeast Asia. This is consistent with the observation that almost all basal clades in the phylogenetic tree consist of species adapted to tropical and subtropical forest habitats.     

Phylogenetic relationships,subdivision, and biogeography of the cyprinid tribe Labeonini (sensu ) (Teleostei: Cypriniformes), with comments on the implications of lips and associated structures in the labeonin classification

The Labeonini (sensu Rainboth, 1991) is a tribe of the subfamily Cyprininae, the largest subfamily of Cypriniformes. With around 400 species in 34 genera, this tribe is widely distributed in the freshwaters of tropical Africa and Asia. Most species are adapted to fast-flowing streams and rivers, and exhibit unique morphological modifications associated with their lips and other structures around the mouth. The monophyly of this tribe has been tested and generally accepted in previous morphological and molecular studies. The major objectives of this study were to reconstruct the phylogenetic relationships within the tribe Labeonini, test its monophyly and explore the taxonomic subdivisions, intrarelationships and biogeography of the group. The value of the morphological characters associated with the lips and other associated structures in the taxonomic classification of labeonins was also discussed. Nucleotide sequences (3867 bp) of four unlinked nuclear loci were obtained from 51 species in 18 Labeonini genera from throughout the range of the tribe. Maximum parsimony, partitioned maximum likelihood and partitioned Bayesian analyses were used for phylogenetic inference from combined and separate gene data sets. Based on our results, the monophyly of Labeonini was well supported. Two major clades could be recovered within the tribe. Three subclades could further be recognized from the first clade. These clades/subclades are not consistent with groupings of any of previous workers using either morphological or molecular characters for phylogenetic inference. Only five currently recognized genera in this analysis are monophyletic. The similarity between some lips and associated structures (e.g. suctorial discs) of labeonins may due to convergence or parallelism instead of common ancestry. Labeonins of Southeast Asia, India and China are closely related to each other; the multiple clades of African taxa do not form a single monophyletic group, indicating multiple, independent dispersal events of labeonins into Africa from Asia.     

Polemoniaceae phylogeny and classification: implications of sequence data from the chloroplast gene ndhF

The chloroplast gene ndhF was used to study phylogenetic relationships of the Polemoniaceae at two levels: among members of the Ericales and among genera of the family. Sequence data for interfamilial analyses consisted of 2266 bp for 14 members of the Ericales, including four species of the Polemoniaceae, plus three outgroup taxa. The Polemoniaceae were found to be related to Diospyros, Fouquieria, the Primulales, Rhododendron, and Impatiens, but relationships among taxa were generally not well supported. The precise position of the Polemoniaceae within the Ericales remains obscure. Data for intrafamilial analyses consisted of 1031 bp for 27 species of the Polemoniaceae, including at least one species from most genera of the family, plus five outgroup taxa. A single most parsimonious tree was identified. The analyses suggested that subfamily Cobaeoideae, excluding Loeselia, is monophyletic and that Huthia is sister to Cantua. Acanthogilia was sister to the remainder of subfamily Cobaeoideae. Subfamily Polemonioideae plus Loeselia formed four subclades that were strongly supported as monophyletic and represent the major lineages of the subfamily.     

Phylogeny and a new tribal classification of the Panicoideae s.l. (Poaceae) based on plastid and nuclear sequence data and structural data

? Premise of the study: The subfamily Panicoideae (Poaceae) encompasses nearly one-third of the diversity of grass species, including important crops such as maize and sugarcane. Previous analyses recovered strong support for a Panicoideae+Centothecoideae lineage within the diverse Panicoideae+Arundinoideae+Chloridoideae+Micrairoideae+Aristidoideae+Danthonioideae (PACMAD) clade, although support for internal relationships was inconsistent. The objectives of this research were to (1) further test the monophyly of each subfamily and previously recovered clades within the Panicoideae+Centothecoideae lineage, (2) establish phylogenetic relationships among these groups, and (3) propose a new tribal classification for this lineage based explicitly on the phylogeny. ? Methods: Maximum parsimony and Bayesian inference analyses of 37 taxa were based on previously published sequences (ndhF and rpl16 intron) and on new plastid and nuclear (rbcL and granule-bound starch synthase I) sequence data as well as structural data. ? Key results. The Panicoideae+Centothecoideae lineage and a majority of the clades identified in previous analyses continue to be robustly supported, but resolution along the backbone of the topology remains elusive. Support for the monophyly of both subfamilies was lacking although support values for some clades increased. The tribes Centotheceae and Arundinelleae were confirmed as polyphyletic. ? Conclusions: Subfamily Centothecoideae is formally submerged into the Panicoideae, and a new tribal classification for the expanded Panicoideae is proposed based explicitly on the phylogeny. This classification includes 12 tribes of which Chasmanthieae and Zeugiteae are segretated from the Centotheceae; Tristachyideae is segregated from Arundinelleae, and a new tribe, Cyperochloeae, is validated to accommodate two isolated genera. A key to the tribes is provided.     

Phylogenetic relationships in the grass family (Poaceae) based on the nuclear single copy locus topoisomerase 6 compared with chloroplast DNA

Phylogenetic relationships within the grass family were studied using a newly obtained locus of the nuclear single copy gene topoisomerase 6 (Topo6) spanning the four exons 8–11 and the chloroplast matK gene. Data were evaluated using maximum parsimony, maximum likelihood and Bayesian methods. All analyses showed genera Streptochaeta and Anomochloa as early diverging, followed by Pharus as sister to the rest of the Poaceae, and monophyly of the subfamily Anomochlooideae was supported by the nuclear dataset. The remaining grasses formed a strongly supported and monophyletic group, which split into the major clades BEP and PACMAD in the Topo6 analyses. Monophyly of the BEP clade was strongly supported by the Topo6 data. The results showed clearly incongruity between the two sets of data, such as the different subfamilial relationships of Bambusoideae, Ehrhartoideae and Pooideae. Most of the analysed species are representatives of subfamily Pooideae, which was analysed in more detail by PCR fragment length differences of another Topo6 region spanning the exons 17–19. Monophyly of Pooideae was strongly supported by the matK data, whereas the nuclear data placed Brachyelytrum outside of the remaining Pooideae. Relationships within the early evolutionary lineages remained largely unresolved in the phylogenetic trees, but the ‘core’ Pooideae (Aveneae/Poeae tribe complex and Hordeeae) were highly supported in all analyses. The differences in amplification lengths illustrate the tribe and subtribe classification of Pooideae. The comparatively conserved structure of the newly studied Topo6 region makes it a promising marker from the nuclear genome that could be successfully PCR-amplified to study higher-level phylogenetic relationships within grasses and perhaps between families within the order Poales.     

基于核基因c-mos的鸫亚科部分鸟类系统发生关系

采用分子系统学方法对鸫亚科Turdinae 11属21种鸟类的核基因c-mos进行了系统发生分析.所测序列经对位排列后共572个位点,其中核苷酸变异位点111个,简约信息位点71个.以太平鸟Bombycilla garrulus作外群,采用邻接法、最大简约法和最大似然法分别构建其系统发生树.重建的系统发生树显示:所研究鸫亚科21种鸟类分成2个支系,第1个支系包括鸫属Turdus和地鸫属Zoothera.第2个支系包括红尾鸲属Phoenicurus、矶鸫属Monticola、水鸲属Rhyacornis、鸲属Tarsiger、溪鸲属Chainarrornis、石即鸟属Saxicola、燕尾属Enivurus、歌鸲属Luscinia和鹊鸲属Copsychus.红尾鸲属为并系类群,水鸲属和溪鸲属聚到这一支系;歌鸲属与燕尾属互为姐妹群,再与鸲属聚合构成另一支系;宝兴歌鸫Turdus mupinensis独立于鸫属及地鸫属之外,形成单独一个分支.     

Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences

The family Cyprinidae is one of the largest families of fishes in the world and a well-known component of the East Asian freshwater fish fauna. However, the phylogenetic relationships among cyprinids are still poorly understood despite much effort paid on the cyprinid molecular phylogenetics. Original nucleotide sequence data of the nuclear recombination activating gene 2 were collected from 109 cyprinid species and four non-cyprinid cypriniform outgroup taxa and used to infer the cyprinid phylogenetic relationships and to estimate node divergence times. Phylogenetic reconstructions using maximum parsimony, maximum likelihood, and Bayesian analysis retrieved the same clades, only branching order within these clades varied slightly between trees. Although the morphological diversity is remarkable, the endemic cyprinid taxa in East Asia emerged as a monophyletic clade referred to as Xenocypridini. The monophyly for the subfamilies including Cyprininae and Leuciscinae, as well as the tribes including Labeonini, Gobionini, Acheilognathini, and Leuciscini, was also well resolved with high nodal support. Analysis of the RAG2 gene supported the following cyprinid molecular phylogeny: the Danioninae is the most basal subfamily within the family Cyprinidae and the Cyprininae is the sister group of the Leuciscinae. The divergence times were estimated for the nodes corresponding to the principal clades within the Cyprinidae. The family Cyprinidae appears to have originated in the mid-Eocene in Asia, with the cladogenic event of the key basal group Danioninae occurring in the early Oligocene (about 31-30 MYA), and the origins of the two subfamilies, Cyprininae and Leuciscinae, occurring in the mid-Oligocene (around 26 MYA).     

Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes

Veneridae is one of the most diverse families of bivalve molluscs. However, their phylogenetic relationships among subfamilies have been debated for years. To explore phylogenetic relationships of Veneridae, we sequenced 13 complete mitochondrial genome sequences from eight subfamilies and compared with available complete mitochondrial genome of other Veneridae taxa (18 previously reported sequences). Phylogenetic analyses using probabilistic methods recovered two highly supported clades. In addition, the protein‐coding gene order revealed a highly conserved pattern among the same subclade lineages. According to our molecular analyses, Tapetinae should be recognized as a valid subfamily, but the genera formed para‐polyphyletic clades. Chioninae was recovered not monophyletic that differs from a previously molecular phylogeny. Furthermore, the reconstructed chronogram calibrated with fossils recovered the Veneridae have originated during the early Permian (about 290 million years ago). Noticeably, programmed frameshift was found in the nad4 gene of Leukoma jedoensis, Anomalodiscus squamosus and Antigona lamellaris and cob gene of L. jedoensis. This is the first time that the presence of the programmed frameshift has been found in the protein‐coding genes of Heterodonta species. Our results improved the phylogenetic resolution within Veneridae, and a more taxonomic sampling analysis of the subfamily Chioninae is supposed to construct.     

Utility of the white gene in estimating phylogenetic relationships among mosquitoes (Diptera: Culicidae)

The utility of a nuclear protein-coding gene for reconstructing phylogenetic relationships within the family Culicidae was explored. Relationships among 13 species representing three subfamilies and nine genera of Culicidae were analyzed using a 762-bp fragment of coding sequence from the eye color gene, white. Outgroups for the study were two species from the sister group Chaoboridae. Sequences were determined from clone PCR products amplified from genomic DNA, and aligned following conceptual intron splicing and amino acid translation. Third codon positions were characterized by high levels of divergence and biased nucleotide composition, the intensity and direction of which varied among taxa. Equal weighting of all characters resulted in parsimony and neighboring-joining trees at odds with the generally accepted phylogenetic hypothesis based on morphology and rDNA sequences. The application of differential weighting schemes recovered the traditional hypothesis, in which the subfamily Anophelinae formed the basal clade. The subfamily Toxorhynchitinae occupied an intermediate position, and was a sister group to the subfamily Culicinae. Within Culicinae, the genera Sabethes and Tripteroides formed an ancestral clade, while the Culex-Deinocerites and Aedes- Haemagogus clades occupied increasingly derived positions in the molecular phylogeny. An intron present in the Culicinae- Toxorhynchitinae lineage and one outgroup taxon was absent in the basal Anophelinae lineage and the second outgroup taxon, suggesting that intron insertions or deletions may not always be reliable systematic characters.      

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A>T, C>G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA.     

Phylogeny in Echinocereus (Cactaceae) based on combined morphological and molecular evidence: taxonomic implications

Echinocereus is a morphologically diverse genus that includes 64 species grouped into eight taxonomic sections based on morphological traits. In previous molecular phylogenetic analyses, the relationships amongst Echinocereus species were not entirely revealed and useful characters to recognize clades were not provided. The inclusion of several sources of evidence in a phylogenetic analysis is likely to produce more supported hypotheses. Therefore, we performed a combined phylogenetic analysis with a set of 44 morphological characters and six chloroplast DNA sequences. Topologies from parsimony and Bayesian analyses were mostly congruent. However, the relationships of E. poselgeri were not consistent between analyses. A second Bayesian analysis using a long-branch extraction test resulted in a topology with the morphological position of E. poselgeri congruent with that in parsimony analysis. Parsimony and Bayesian analyses corroborated the monophyly of Echinocereus, which included eight monophyletic groups. The combined phylogeny integrated into different clades those taxa that were not determined in previous analyses and changed the relationships of some recognized clades. The clades did not recover the recent infrageneric classification. In the present study, a new sectional classification for Echinocereus is proposed based on the eight recovered clades, which is supported by a combination of morphological and molecular characters. An identification key for sections in the genus is included.     

Phylogenetic relationships among families of the Scaphopoda (Mollusca)

Phylogenetic relationships among families in the molluscan class Scaphopoda were analysed using morphological characters and cladistic parsimony methods. A maximum parsimony analysis of 34 discrete characters, treated as unordered and equally weighted, from nine ingroup terminal taxa produced a single most parsimonious tree; supplementary analyses of tree length frequency distribution and Bremer support indices indicate a strong phylogenetic signal from the data and moderate to minimally supported clades. The traditional major division of the class, the orders Dentaliida and Gadilida, is supported as both taxa are confirmed as monophyletic clades. Within the Dentaliida, two clades are recognized, the first comprised of the families Dentaliidae and Fustiariidae, the second of the Rhabdidae and Calliodentaliidae; together, these groups comprise a third clade, which has the Gadilinidae as sister. Within the Gadilida, a nested series of relationships is found among [Entalinidae, [Pulsellidae, [Wemersoniellidae, Gadilidae]]]. These results lend cladistic support to earlier hypotheses of shared common ancestry for some families, but are at variance with other previous hypotheses of evolution in the Scaphopoda. Furthermore, analysis of constituent Gadilinidae representatives provide evidence for paraphyly of this family. The relationships supported here provide a working hypothesis that the development of new characters and greater breadth of taxonomic sampling can test, with a suggested primary goal of establishing monophyly at the family level.