Phylogeny and taxonomic revision of all genera of Conopidae (Diptera) based on morphological data

All global genera of the fly family Conopidae are revised here. A cladistic analysis of 117 morphological characters recorded from 154 species, including representatives of 59 genera and subgenera, recovers a phylogenetic hypothesis for the family. This hypothesis is used as the basis of a new classification for the family. Both Sicini and Zodionini are removed from Myopinae and elevated to subfamilial status. A new tribe, Thecophorini, is proposed within Myopinae to accommodate Thecophora, Scatoccemyia, and Pseudoconops. Two genera, Pseudomyopa and Parazodion, are removed from Dalmanniinae and placed in Myopinae and Zodioninae, respectively. Conopinae is divided into 11 tribes, seven of which are newly described (Asiconopini, Caenoconopini, Gyroconopini, Microconopini, Neoconopini, and Siniconopini). Some examined species are transferred to different or new genera and subgenera. A new genus, Schedophysoconops gen. nov. , and subgenus Asiconops (Aegloconops) subgen. nov. within Conopinae are described. A review of character evolution and phylogeography is included in light of the new classification. A catalogue of all genus‐group names is included with new emendations noted.     

The phylogenetic relationships of the physaloid genera (Solanaceae) based on morphological data

A group of genera, e.g., Chamaesaracha, Leucophysalis, Physaliastrum, Margaranthus, and Withania, in the subfamily Solanoideae (Solanaceae) is centered around the genus Physalis and has been named the physaloid group. It comprises a number of small and often poorly known genera, sometimes seen as united with Physalis and/or each other. A hypothesis of the phylogenetic relationships within this group, based on parsimony analyses of morphological data, is here presented for the first time. The result is discussed in relation to prevailing generic circumsciptions and taxonomic consequences. It is also compared with hypotheses of relationships based on cpDNA data.     

A phylogenetic analysis of Coelopidae (Diptera) based on morphological and DNA sequence data

The phylogenetic relationships of 22 species of Coelopidae are reconstructed based on a data matrix consisting of morphological and DNA sequence characters (16S rDNA, EF-1alpha). Optimal gap and transversion costs are determined via a sensitivity analysis and both equal weighting and a transversion cost of 2 are found to perform best based on taxonomic congruence, character incongruence, and tree support. The preferred phylogenetic hypothesis is fully resolved and well-supported by jackknife, bootstrap, and Bremer support values, but it is in conflict with the cladogram based on morphological characters alone. Most notably, the Coelopidae and the genus Coelopa are not monophyletic. However, partitioned Bremer Support and an analysis of node stability under different gap and transversion costs reveal that the critical clades rendering these taxa non-monophyletic are poorly supported. Furthermore, the monophyly of Coelopidae and Coelopa is not rejected in analyses using 16S rDNA that was manually aligned. The resolution of the tree based on this reduced data sets is, however, lower than for the tree based on the full data sets. Partitioned Bremer support values reveal that 16S rDNA characters provide the largest amount of tree support, but the support values are heavily dependent on analysis conditions. Problems with direct comparison of branch support values for trees derived using fixed alignments with those obtained under optimization alignment are discussed. Biogeographic history and available behavioral and genetic data are also discussed in light of this first cladogram for Coelopidae based on a quantitative phylogenetic analysis.     

The phylogenetic relationships among infraorders and superfamilies of Diptera based on morphological evidence

Members of the megadiverse insect order Diptera (flies) have successfully colonized all continents and nearly all habitats. There are more than 154 000 described fly species, representing 10–12% of animal species. Elucidating the phylogenetic relationships of such a large component of global biodiversity is challenging, but significant advances have been made in the last few decades. Since Hennig first discussed the monophyly of major groupings, Diptera has attracted much study, but most researchers have used non‐numerical qualitative methods to assess morphological data. More recently, quantitative phylogenetic methods have been used on both morphological and molecular data. All previous quantitative morphological studies addressed narrower phylogenetic problems, often below the suborder or infraorder level. Here we present the first numerical analysis of phylogenetic relationships of the entire order using a comprehensive morphological character matrix. We scored 371 external and internal morphological characters from larvae, pupae and adults for 42 species, representing all infraorders selected from 42 families. Almost all characters were obtained from previous studies but required revision for this ordinal‐level study, with homology assessed beyond their original formulation and across all infraorders. We found significant support for many major clades (including the Diptera, Culicomorpha, Bibionomorpha, Brachycera, Eremoneura, Cyclorrhapha, Schizophora, Calyptratae and Oestroidea) and we summarize the character evidence for these groups. We found low levels of support for relationships between the infraorders of lower Diptera, lower Brachycera and major lineages of lower Cyclorrhapha, and this is consistent with findings from molecular studies. These poorly supported areas of the tree may be due to periods of rapid radiation that left few synapomorphies in surviving lineages.     

Molecular dating and phylogenetic relationships among Teiidae (Squamata) inferred by molecular and morphological data

We present a phylogenetic analysis of teiid lizards based on partitioned and combined analyses of 12S and 16S mitochondrial DNA sequences, and morphological and ultrastructural characters. There were some divergences between 12S and 16S cladograms, but phylogenetic analyses of the combined molecular data corroborated the monophyly of Tupinambinae, Teiinae, and "cnemidophorines", with high support values. The total combined analysis (molecules+morphology) produced similar results, with well-supported Teiinae and "cnemidophorines". We present an evolutionary scenario for the evolution of Teiidae, based on molecular dating of evolutionary events using Bayesian methods, ancestral areas analysis, the fossil record, the geographic distribution of genera, and environmental and geologic changes during the Tertiary. According to this scenario, (1) all current teiid genera, except Aspidoscelis, originated in isolation in South America; (2) most teiid genera originated during the Eocene, a period characterized by savanna expansion in South America; and (3) Cnemidophorus originated in South America, after which some populations dispersed to Central America during the Late Miocene.     

A phylogenetic analysis ofDuguetia (Annonaceae) based on morphological data

In this paper we present a phylogeny based on a study of the general morphology of 61 of the ca. 80 species ofDuguetia. Analyses were performed with PAUP. The resulting phylogeny is compared with the classification ofDuguetia as suggested byFries (1934, 1937, 1939, 1959). The results are partly corresponding withFries's classification. SectionAlcmene includingD. rionegrensis, and sects.Geanthemum, Synsepalantha, andCalothrix withoutD. uniflora, are upheld by this analysis. It is concluded that sect.Xylopipetalum should be united with sect.Duguetia. Before other taxonomic decisions at the section level can be made, more solid data must be available. Most dissimilarities found are considered to be not strong enough to propose alterations.Studies inAnnonaceae XXIII. For 22nd part seeZuilen & Maas (1994).     

Determination of phylogenetic position ofPipizini (Diptera: Syrphidae): based on molecular biological and morphological data

Based on the sequence analysis of 5.8S subunit and internal transcribed spacers (ITS) of ribosomal RNA gene (rDNA), the molecular phylogenetic tree of representative species of Pipizini and three groups of Syrphidae with different feeding habits (seven species belong to six genera) was constructed. Meanwhile, the phylogenetic tree of tribes (including Pipizini and other 17 tribes of Syrphidae) was constructed using morphological characteristics of adults and larvae and the number of chromosomes. Both the results show that the relationship between Pipizini and predatory groups is closer than that between Pipizini and saprophagous groups. So it is suggested that Pipizini be transferred from Milesiinae to Syrphinae.     

A phylogenetic analysis of Sciomyzidae (Diptera) and some related genera

Sciomyzidae is a family of acalyptrate flies with 546 species in 61 genera that is among the most extensively studied groups of higher Diptera. Most of the known larvae are obligate enemies of Gastropoda. Hundreds of studies published over the past 50 years have resulted in detailed information concerning morphology of adults and immature stages, biology, development, behaviour, phenology and distribution. However, studies of phylogenetic relationships are based almost exclusively on morphological characters of adults, and no comprehensive molecular analysis across the family has been published. Here we fill this void by generating and analysing molecular data for 54 species of Sciomyzidae (22 genera), including Phaeomyiidae (one genus), and seven representative species of five other families of Sciomyzoidea (Coelopidae, Dryomyzidae, Helcomyzidae, Heteromyzidae and Huttoninidae) as outgroups. The reconstruction is based on morphological characters as well as nucleotide sequences for genes from the mitochondrial (12S, 16S, COI, COII, Cytb) and nuclear genome (28S, EF1α). The results are compared with recent morphological analyses. Our analyses support the monophyly of Sciomyzidae + Phaeomyiidae, and place Phaeomyiinae as a unique lineage within Sciomyzidae. A modified classification comprising three subfamilies is proposed. The major subfamily, Sciomyzinae, consists of two monophyletic and well separated groups, the tribes Sciomyzini and Tetanocerini.     

Determination of phylogenetic position of Pipizini (Diptera: Syrphidae): based on molecular biological and morphological data

Based on the sequence analysis of 5.8S subunit and internal transcribed spacers (ITS ) of ribosomal RNA gene (rDNA), the molecular phylogenetic tree of representative species of Pipizini and three groups of Syrphidae with different feeding habits (seven species belong to six genera) was constructed. Meanwhile, the phylogenetic tree of tribes (including Pipizini and other 17 tribes of Syrphidae) was constructed using morphological characteristics of adults and larvae and the number of chromosomes. Both the results show that the relationship between Pipizini and predatory groups is closer than that between Pipizini and saprophagous groups. So it is suggested that Pipizini be transferred from Milesiinae to Syrphinae.     

Determination of phylogenetic position of Pipizini (Diptera: Syrphidae): based on molecular biological and morphological data

Based on the sequence analysis of 5.8S subunit and internal transcribed spacers (ITS ) of ribosomal RNA gene (rDNA), the molecular phylogenetic tree of representative species of Pipizini and three groups of Syrphidae with different feeding habits (seven species belong to six genera) was constructed. Meanwhile, the phylogenetic tree of tribes (including Pipizini and other 17 tribes of Syrphidae) was constructed using morphological characteristics of adults and larvae and the number of chromosomes. Both the results show that the relationship between Pipizini and predatory groups is closer than that between Pipizini and saprophagous groups. So it is suggested that Pipizini be transferred from Milesiinae to Syrphinae.     

Phylogenetic relationships of Microdontinae (Diptera: Syrphidae) based on molecular and morphological characters

The intrasubfamilial classification of Microdontinae Rondani (Diptera: Syrphidae) has been a challenge: until recently more than 300 out of more than 400 valid species names were classified in Microdon Meigen. We present phylogenetic analyses of molecular and morphological characters (both separate and combined) of Microdontinae. The morphological dataset contains 174 characters, scored for 189 taxa (9 outgroup), representing all 43 presently recognized genera and several subgenera and species groups. The molecular dataset, representing 90 ingroup species of 28 genera, comprises sequences of five partitions in total from the mitochondrial gene COI and the nuclear ribosomal genes 18S and 28S. We test the sister‐group relationship of Spheginobaccha with the other Microdontinae, attempt to elucidate phylogenetic relationships within the Microdontinae and discuss uncertainties in the classification of Microdontinae. Trees based on molecular characters alone are poorly resolved, but combined data are better resolved. Support for many deeper nodes is low, and placement of such nodes differs between parsimony and Bayesian analyses. However, Spheginobaccha is recovered as highly supported sister group in both. Both analyses agree on the early branching of Mixogaster, Schizoceratomyia, Afromicrodon and Paramicrodon. The taxonomical rank in relation to the other Syrphidae is discussed briefly. An additional analysis based on morphological characters only, including all 189 taxa, used implied weighting. A range of weighting strengths (k‐values) is applied, chosen such that values of character fit of the resulting trees are divided into regular intervals. Results of this analysis are used for discussing the phylogenetic relationships of genera unrepresented in the molecular dataset.     

Evolutionary relationships among the Scarabaeini (Coleoptera: Scarabaeidae) based on combined molecular and morphological data

The Scarabaeini is an old world tribe of ball-rolling dung beetles that have origins dating back to at least the mid-upper Miocene (19-8 million years ago). The tribe has received little to no attention in morphological or molecular phylogenetics. We obtained sequence data from the mitochondrial cytochrome oxidase subunit I (1,197 bp) and 16S ribosomal RNA (461 bp) genes for 25 species of the Scarabaeini in an attempt to further resolve broad phylogenetic relationships within this tribe. Sequence data from both markers along with 216 morphological and 3 biological characters were analysed separately and combined. Independent analyses showed poorly resolved trees with many of the intermediate and basal nodes collapsed by low bootstrap values. Many sites in both genes exhibited strong A+T nucleotide bias and high interlineage divergences. The combined analysis revealed a number of well supported relationships such as the monophyly of the nocturnal species Scarabaeus satyrus, S. [Neateuchus] proboscideus, and S. zambesianus. Furthermore, the total evidence tree suggested to elevate S. (Pachysoma) to the status of an independent genus, Pachysoma, as a sister taxon to a clade containing Pachylomerus femoralis and Scarabaeus sensu lato. Within the latter, the following subgenera were maintained by the combination of data sets: S. (Scarabaeolus), S. (Sceliages), and S. (Kheper). Both, feeding specialisation and food relocation behaviour, were inferred to be polyphyletic in the Scarabaeini. Total evidence analysis found no support for common ancestry of Scarabaeini and Eucraniini.     

A phylogenetic analysis of 100+ genera and 50+ families of euasterids based on morphological and molecular data with notes on possible higher level morphological synapomorphies

 A data matrix of 143 morphological and chemical characters for 142 genera of euasterids according to the APG system was compiled and complemented with rbcL and ndhF sequences for most of the genera. The data were subjected to parsimony analysis and support was assessed by bootstrapping. Strict consensus trees from analyses of morphology alone and morphology + rbcL + ndhF are presented. The morphological data recover several groups supported by molecular data but at the level of orders and above relationships are only superficially in agreement with molecular studies. The analyses provide support for monophyly of Gentianales, Aquifoliales, Apiales, Asterales, and Dipsacales. All data indicate that Adoxaceae are closely related to Dipsacales and hence they should be included in that order. The trees were used to assess some possible morphological synapomorphies for euasterids I and II and for the orders of the APG system. Euasterids I are generally characterised by opposite leaves, entire leaf margins, hypogynous flowers, “early sympetaly” with a ring-shaped corolla primordium, fusion of stamen filaments with the corolla tube, and capsular fruits. Euasterids II often have alternate leaves, serrate-dentate leaf margins, epigynous flowers, “late sympetaly” with distinct petal primordia, free stamen filaments, and indehiscent fruits. It is unclear which of these characters represent synapomorphies and symplesiomorphies for the two groups, respectively, and there are numerous expections to be interpreted as reversals and parallelisms. Received August 28, 2000 Accepted August 7, 2001     

The phylogenetic relationships of lampridiform fishes (Teleostei: acanthomorpha), based on a total-evidence analysis of morphological and molecular data

We investigated the phylogenetic relationships among five species of lampridiform fishes, three basal outgroup species (two aulopiforms and one myctophiform), and two species of non-lampridiform acanthomorphs (Polymixia and Percopsis) using a combined parsimony analysis of morphological and molecular data. Morphological characters included 28 transformation series obtained from the literature. Molecular characters included 223 informative transformation series from an aligned 854-base pair fragment of 12S mtDNA and 139 informative transformation series from an aligned 561-base pair fragment of 16S mtDNA. A total-evidence analysis using the aulopiforms Synodus and Aulopus and the myctophiform Hygophum as outgroups corroborates the monophyly of Lampridiformes and unites Polymixia with Percopsis. Among the lampridiform fishes we examined, Metavelifer is basal, followed in ascending order by Lampris, Lophotus, Regalecus, and Trachipterus. This hypothesis is congruent with the most recent morphological analysis of the Lampridiformes and rejects a diphyletic origin of elongate body form within the clade. Analysis of a combined matrix of 12S and 16S mtDNA data yielded a phylogenetic hypothesis isomorphic with the total-evidence phylogeny. Analyses of partitioned DNA data sets reveals that single gene regions are poor predictors of the total-evidence phylogeny while combined analyses of both DNA data sets are good predictors of the total-evidence phylogeny.     

Inference of phylogenetic relationships within Fabriciidae (Sabellida,Annelida) using molecular and morphological data

Cladistic relationships among fabriciids have to date been explored in the context of adult morphology, but resolution has been declining as more species are described. In this study, we incorporated data on the reproductive system, including features related to the male sperm and sperm storage by females, to supplement existing data on adult morphology (for a total of 50 characters). Three nuclear DNA markers (18S rDNA approximately 1800 bp, the D1 region of 28S rDNA approximately 320 bp, and histone H3 approximately 330 bp) were sequenced from 21 species of fabriciids. We assessed the phylogeny of Fabriciidae based on an integrative analysis of these morphological and molecular characters. Our results show that, in addition to three previously recovered apomorphies for Fabriciidae (absence of ventral lips, modification of abdominal uncini to an elongate manubrium, and presence of branchial hearts), six more apomorphies associated with the reproductive system can be used to support this clade—spermiogenesis only in the thorax, spermiogenesis in large clusters with a central cytophore, single dorsal sperm duct, sperm nuclear projection, thickening of the sperm nuclear membrane and the sperm extra‐axonemal sheath. The results require the erection of two new genera and two new species, which are described. © The Willi Hennig Society 2010.     

菝葜科基于形态学证据的系统发育分析

对全世界范围分布的菝葜科Smilacaceae的79个代表种(包括了全部的属和组), 以分布于南美洲的Philesia Comm. ex Juss.和Lapageria Ruiz &; Pav.属为外类群, 选取包括花粉和染色体性状在内的47个广义的形态学性状进行了分支分类系统发育分析, 同时以表征分类的方法构建了距离树(NJ)辅助分析, 首次对世界分布的菝葜科各属间及属内的系统发育关系作了探讨。(1)Ripogonum与菝葜属Smilax +肖菝葜属Heterosmilax互为姐妹群, 但是距离较远, 支持将类菝葜属(新拟中文名)Ripogonum独立为科的观点; (2)肖菝葜属在菝葜科内处于较为进化的分支上, 并与菝葜属土茯苓组sect. Coilanthus的部分种组成一个具较高支持率(88%)的单系分支, 分析表明肖菝葜属并非是一个好属, 应归入菝葜属; (3)菝葜属6个组的划分大都没有得到支持, 只有东亚北美间断分布的草本菝葜组sect. Nemexia的单系得到很好的支持(93%); (4)分布于南美洲巴西的种类聚为一个单系类群, 表明它们可能有共同的起源, 但由于取样局限, 南美洲种类的系统地位有待进一步研究。     

The first phylogenetic study of Mesembrinellidae (Diptera: Oestroidea) based on molecular data: clades and congruence with morphological characters

The Mesembrinellidae (Diptera: Oestroidea) comprise a small group of strictly Neotropical calyptrate flies, with 36 described species. The group has often been treated as a subfamily of Calliphoridae, but there is growing evidence that it corresponds to a distinct Oestroidea lineage. Internal relationships have so far been addressed based only on morphology, with results lacking resolution and support. This is the first molecular phylogeny for the group, which is based on the analyses of 80 terminal taxa (22 mesembrinellid and 28 outgroup species) and 5 molecular markers (ITS2, 28S, COI, COII and 16S). Maximum‐parsimony, maximum‐likelihood and Bayesian inference methods were used, the latter two with partitioning strategies considering codon position and secondary structure information. Results corroborate the Mesembrinellidae as a monophyletic lineage inside Oestroidea. Three clades were consistently recovered: (1) (Laneella + Mesembrinella patriciae); (2) (Mesembrinella (excluding M. patriciae)  + Eumesembrinella); and (3) (Huascaromusca + Giovanella). Re‐examination of the female reproductive tract of M. patriciae revealed a Laneela‐type spermatheca, which corroborates the position of the species recovered in the molecular phylogenetic analyses. Mesembrinella and Huascaromusca are in all cases paraphyletic with regards to Eumesembrinella and Giovanella, respectively. These latter two genera should, thus, be seen as subjective junior synonyms.     

A comprehensive morphological analysis of talpid moles (Mammalia) phylogenetic relationships

Some talpid moles show one of the most specialized suites of morphological characters seen among small mammals. Fossorial and more generalized shrew‐looking moles inhabit both North America and Eurasia but these land masses share none of the same genera. One of the central questions of mole evolution has been that of how many times specialized fossorial habits evolved. We investigated the origin of mole characters with a maximum parsimony analysis of 157 characters, mostly craniodental and postcranial, of representatives of all 17 living mole genera and three shrews and one hedgehog as outgroups. The result was one most‐parsimonious tree and its most novel aspect was the position of a Japanese shrew mole clade (Urotrichus, Dymecodon), which branched off after Uropsilus and was not closely related to the American shrew mole (Neurotrichus). The desmans (Galemys and Desmana) were the next clade in the tree, followed by Neurotrichus. We confirmed the monophyly of the Eurasian fossorial mole clade Talpini (Euroscaptor, Parascaptor, Mogera, Scaptochirus and Talpa). Condylura, the star‐nosed mole from North America, was sister group to a clade consisting of the Talpini plus Scaptonyx and the Scalopini (Scalopus, Scapanus, Parascalops, and Scapanulus). Based on our results and on the assumption that moles originated in Eurasia, it is most parsimonious to infer one migration from Eurasia to North America and two back‐migrations to Eurasia. It is ambiguous if Talpini and Scalopini evolved their full fossorial habits independently or not. © The Willi Hennig Society 2006.     

Phylogenetic relationships of Holarctic Teleiodini (Lepidoptera: Gelechiidae) based on analysis of morphological and molecular data

Abstract Phylogenetic relationships of 25 genera of Holarctic Teleiodini (Gelechiidae) are postulated based on morphology and molecular characters, including CO‐I, CO‐II, and 28S genes. The phylogenetic analysis of the morphology matrix yielded four equal most‐parsimonious trees (length 330 steps, CI = 0.36, RI = 0.55) and a strict consensus tree (length 335 steps, CI = 0.36, RI = 0.54) with one polytomy and one trichotomy. The phylogenetic analysis of the combined morphology and CO‐I + CO‐II + 28S matrices yielded two equally most‐parsimonious trees (length 1184 steps, CI = 0.50, RI = 0.42) and a strict consensus tree (length 1187 steps, CI = 0.50, RI = 0.42) that reinforced results from the morphological analysis and resolved the one polytomy present in the morphology consensus tree. Teleiodini are defined as a monophyletic clade with a Bremer support value greater than 5 in the consensus tree based on morphological and molecular data. Twenty‐three clades of genera are defined with Bremer support values provided. An analysis of larval host‐plant preferences based on the consensus tree for combined data indicates derivation of feeding on woody hosts from genera feeding on herbaceous hosts and a single origin of feeding on coniferous hosts. An area cladogram indicates five independent origins of Nearctic genera from Holarctic ancestors and one origin from a Palearctic genus.     

Systematic relationships of Nematomorpha based on molecular and morphological data

Abstract. We sequenced the 18S rRNA gene from 11 nematomorph species from 9 genera and derived hypotheses concerning the sister group of Nematomorpha and relationships within this taxon. The molecular and morphological data are consistent with the monophyly of Nematomorpha, a sister-group relationship between Nematomorpha and Nematoda, and a sister-group relationship between the marine genus Nectonema and all of the freshwater taxa, Gordiida. Hypotheses of relationships within Gordiida support the traditional taxa Gordiidae, Chordodidae, and Chordodinae but reject Parachordodinae and Spinochordodidae. The molecular results differ from those of previous morphological studies by suggesting a reduction of the two tail lobes at the posterior end of males in Chordodinae, monophyly of the genus Paragordionus , and paraphyly of the genus Chordodes .