scholarly journals DNA Barcoding: Mixed results for big-headed flies (Diptera: Pipunculidae)

Zootaxa ◽  
2007 ◽  
Vol 1423 (1) ◽  
pp. 1-26 ◽  
Author(s):  
JEFFREY H. SKEVINGTON ◽  
CHRISTIAN KEHLMAIER ◽  
GUNILLA STÅHLS
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Base Pairs ◽  
Data Set ◽  
Taxonomic Decision ◽  
Morphological Species

Sequence data from 658 base pairs of mitochondrial cytochrome c oxidase I (cox1) were analysed for 28 described species of Pipunculidae (Diptera) in an effort to test the concept of DNA Barcoding on this family. Two recently revised but distantly related pipunculid lineages with presumed different evolutionary histories were used for the test (Clistoabdominalis Skevington, 2001 and Nephrocerus Zetterstedt, 1838). An effort was made to test the concept using sister taxa and morphologically similar sibling species swarms in these two genera. Morphological species concepts for Clistoabdominalis taxa were either supported by cox1 data or found to be too broad. Most of the discordance could be accounted for after reassessing morphological characters. In these cases, the molecular data were invaluable in assisting taxonomic decision-making. The radiation of Nearctic species of Nephrocerus could not be diagnosed using cox1. The ability of cox1 to recover phylogenetic signal was also tested on Clistoabdominalis. Morphological data for Clistoabdominalis were combined with the molecular data set. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology. Partitioned Bremer support is used to localize areas of conflict between the datasets.

scholarly journals The phylogenetic conundrum of Lutzia (Diptera: Culicidae: Culicini): a cautionary account of conflict and support

2015 ◽  
Vol 46 (3) ◽  
pp. 269-290 ◽  
Author(s):  
Ian J. Kitching ◽  
C. Lorna Culverwell ◽  
Ralph E. Harbach
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Set ◽  
Generic Status ◽  
Strong Signal ◽  
Phylogenetic Studies ◽  
Data Support

Lutzia Theobald was reduced to a subgenus of Culex in 1932 and was treated as such until it was restored to its original generic status in 2003, based mainly on modifications of the larvae for predation. Previous phylogenetic studies based on morphological and molecular data have provided conflicting support for the generic status of Lutzia: analyses of morphological data support the generic status whereas analyses based on DNA sequences do not. Our previous phylogenetic analyses of Culicini (based on 169 morphological characters and 86 species representing the four genera and 26 subgenera of Culicini, most informal group taxa of subgenus Culex and five outgroup species from other tribes) seemed to indicate a conflict between adult and larval morphological data. Hence, we conducted a series of comparative and data exclusion analyses to determine whether the alternative positions of Lutzia are due to conflicting signal or to a lack of strong signal. We found that separate and combined analyses of adult and larval data support different patterns of relationships between Lutzia and other Culicini. However, the majority of conflicting clades are poorly supported and once these are removed from consideration, most of the topological disparity disappears, along with much of the resolution, suggesting that morphology alone does not have sufficiently strong signal to resolve the position of Lutzia. We critically examine the results of other phylogenetic studies of culicinine relationships and conclude that no morphological or molecular data set analysed in any study conducted to date has adequate signal to place Lutzia unequivocally with regard to other taxa in Culicini. Phylogenetic relationships observed thus far suggest that Lutzia is placed within Culex but further data and extended taxon sampling are required to confirm its position relative to Culex.

The greenhouse thrips, Heliothrips haemorrhoidalis, and its generic relationships within the subfamily Panchaetothripinae (Thysanoptera: Thripidae)

2001 ◽  
Vol 32 (2) ◽  
pp. 205-216 ◽  
Author(s):  
John W.H. Trueman ◽  
Rita Marullo ◽  
Laurence A. Mound
Keyword(s):  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Sister Group Relationship ◽  
Pest Species ◽  
Data Set ◽  
Weak Support ◽  
Heliothrips Haemorrhoidalis ◽  
Generic Relationships

AbstractThe subfamily Panchaetothripinae, comprising 35 genera and 98 species, includes several pest species of which the most notorious is the greenhouse thrips, Heliothrips haemorrhoidalis. In an attempt to establish the sister-group of Heliothrips, the relationships of this genus to 31 of the other genera in the subfamily were examined cladistically, using 35 parsimony-informative morphological characters. The analysis indicated that there was no support for two of the three tribes into which this subfamily is customarily arranged, the Monilothripini and the Panchaetothripini, but weak support for the tribe Tryphactothripini. No clear sister-group relationship could be identified for the New World genus Heliothrips, although it grouped with three old world genera Australothrips, Retithrips and Rhipiphorothrips. It is concluded that a morphological data set is not capable of producing a robust phylogeny of the Panchaetothripinae, and that the subject requires re-examination using molecular data.

scholarly journals Synonymization of the male-based ant genus Phaulomyrma (Hymenoptera, Formicidae) with Leptanilla based upon Bayesian total-evidence phylogenetic inference

2020 ◽  
Author(s):  
Zachary H. Griebenow
Keyword(s):  
Sequence Data ◽  
Phylogenetic Inference ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Systematic Revision ◽  
Dna Sequence Data ◽  
Evidence Framework ◽  
Nuclear Loci

Abstract.Although molecular data have proven indispensable in confidently resolving the phylogeny of many clades across the tree of life, these data may be inaccessible for certain taxa. The resolution of taxonomy in the ant subfamily Leptanillinae is made problematic by the absence of DNA sequence data for leptanilline taxa that are known only from male specimens, including the monotypic genus Phaulomyrma Wheeler & Wheeler. Focusing upon the considerable diversity of undescribed male leptanilline morphospecies, the phylogeny of 35 putative morphospecies sampled from across the Leptanillinae, plus an outgroup, is inferred from 11 nuclear loci and 41 discrete male morphological characters using a Bayesian total-evidence framework, with Phaulomyrma represented by morphological data only. Based upon the results of this analysis Phaulomyrma is synonymized with Leptanilla Emery, and male-based diagnoses for Leptanilla that are grounded in phylogeny are provided, under both broad and narrow circumscriptions of that genus. This demonstrates the potential utility of a total-evidence approach in inferring the phylogeny of rare extant taxa for which molecular data are unavailable and begins a long-overdue systematic revision of the Leptanillinae that is focused on male material.

Molecular phylogeny and systematic evaluation of the Caragana opulens species complex (Fabaceae, Papilionoideae) based on the molecular and morphological data

Phytotaxa ◽  
2021 ◽  
Vol 478 (2) ◽  
pp. 179-200
Author(s):  
SHABIR A. RATHER ◽  
WANG SHU ◽  
MAYANK DHAR DWIVEDI ◽  
CHANG ZHAOYANG
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Systematic Evaluation ◽  
Morphological Variations ◽  
Dna Sequence Data ◽  
Different Populations ◽  
Morphological And Molecular Data

In this study, we explored the evolutionary history and taxonomic treatment of the Caragana opulens complex taking information from morphological and molecular data. The complex consists of three species, C. opulens, C. licentiana and C. kansuensis. Moreover, the morphological characters currently used to differentiate the species present in the complex have been found insignificant and inconsistent and do not help diagnose the species. For the present study, we investigated its range and sampled 139 accessions from the different populations of the genus Caragana and 17 accessions of the complex. DNA sequence data from one nrDNA ITS and one cpDNA trnH-psbA loci were sequenced and analyzed using Maximum Likelihood and Bayesian methods. The resulting phylogenies were congruent in topologies. Based on morphological and molecular data, it is concluded that all three species of the complex are one of the same with significant morphological variations. Hence C. opulens is accepted as the correct name along with C. licentiana and C. kansuensis as synonyms.

scholarly journals Corrigendum to: Phylogeny and biogeography of the ant subfamily Myrmeciinae (Hymenoptera : Formicidae)

2003 ◽  
Vol 17 (4) ◽  
pp. 605 ◽  
Author(s):  
Philip S. Ward ◽  
Seán G. Brady
Keyword(s):  
Sequence Data ◽  
Strong Support ◽  
Sister Group ◽  
Molecular Data ◽  
Morphological Data ◽  
Recent Common Ancestor ◽  
Bootstrap Support ◽  
Data Set ◽  
Molecular Sequence Data ◽  
Most Recent Common Ancestor

We investigated phylogenetic relationships among the 'primitive' Australian ant genera Myrmecia and Nothomyrmecia (stat. rev.) and the Baltic amber fossil genus Prionomyrmex, using a combination of morphological and molecular data. Outgroups for the analysis included representatives from a variety of potential sister-groups, including five extant subfamilies of ants and one extinct group (Sphecomyrminae). Parsimony analysis of the morphological data provides strong support (~95% bootstrap proportions) for the monophyly of (1) genus Myrmecia, (2) genus Prionomyrmex, and (3) a clade containing those two genera plus Nothomyrmecia. A group comprising Nothomyrmecia and Prionomyrmex is also upheld (85% bootstrap support). Molecular sequence data (~2200 base pairs from the 18S and 28S ribosomal RNA genes) corroborate these findings for extant taxa, with Myrmecia and Nothomyrmecia appearing as sister-groups with ~100% bootstrap support under parsimony, neighbour-joining and maximum-likelihood analyses. Neither the molecular nor the morphological data set allows us to identify unambiguously the sister-group of (Myrmecia + (Nothomyrmecia + Prionomyrmex)). Rather, Myrmecia and relatives are part of an unresolved polytomy that encompasses most of the ant subfamilies. Taken as a whole, our results support the contention that many of the major lineages of ants – including a clade that later came to contain Myrmecia, Nothomyrmecia and Prionomyrmex – arose at around the same time during a bout of diversification in the middle or late Cretaceous. On the basis of Bayesian dating analysis, the estimated age of the most recent common ancestor of Myrmecia and Nothomyrmecia is 74 million years (95% confidence limits, 53–101�million years), a result consistent with the origin of the myrmeciine stem lineage in the Cretaceous. The ant subfamily Myrmeciinae is redefined to contain two tribes, Myrmeciini (genus Myrmecia) and Prionomyrmecini (Nothomyrmecia and Prionomyrmex). Phylogenetic analysis of the enigmatic Argentine fossils Ameghinoia and Polanskiella demonstrates that they are also members of the Myrmeciinae, probably more closely related to Prionomyrmecini than to Myrmeciini. Thus, the myrmeciine ants appear to be a formerly widespread group that retained many ancestral formicid characteristics and that became extinct everywhere except in the Australian region.

Synonymisation of the male-based ant genus Phaulomyrma (Hymenoptera:Formicidae) with Leptanilla based upon Bayesian total-evidence phylogenetic inference

2021 ◽  
Author(s):  
Zachary H. Griebenow
Keyword(s):  
Sequence Data ◽  
Phylogenetic Inference ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Systematic Revision ◽  
Dna Sequence Data ◽  
Evidence Framework ◽  
Nuclear Loci

Although molecular data have proven indispensable in confidently resolving the phylogeny of many clades across the tree of life, these data may be inaccessible for certain taxa. The resolution of taxonomy in the ant subfamily Leptanillinae is made problematic by the absence of DNA sequence data for leptanilline taxa that are known only from male specimens, including the monotypic genus Phaulomyrma Wheeler & Wheeler. Focusing upon the considerable diversity of undescribed male leptanilline morphospecies, the phylogeny of 35 putative morphospecies sampled from across the Leptanillinae, plus an outgroup, is inferred from 11 nuclear loci and 41 discrete male morphological characters using a Bayesian total-evidence framework, with Phaulomyrma represented by morphological data only. Based upon the results of this analysis Phaulomyrma is synonymised with Leptanilla Emery, and male-based diagnoses for Leptanilla that are grounded in phylogeny are provided, under both broad and narrow circumscriptions of that genus. This demonstrates the potential utility of a total-evidence approach in inferring the phylogeny of rare extant taxa for which molecular data are unavailable and begins a long-overdue systematic revision of the Leptanillinae that is focused on male material.

Affinities of four freshwater putative “Chantransia” stages (Rhodophyta) in Southern China from molecular and morphological data

Phytotaxa ◽  
2020 ◽  
Vol 441 (1) ◽  
pp. 47-59
Author(s):  
JIN-FEN HAN ◽  
FANG-RU NAN ◽  
JIA FENG ◽  
JUN-PING LV ◽  
QI LIU ◽  
...  
Keyword(s):  
Yunnan Province ◽  
Sequence Data ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Morphological Description

Four putative “Chantransia” isolates were collected from four locations in Hubei and Yunnan Provinces, China. Morphological analyses were conducted on all isolates. Two specimens (HB26 and YN2) fit the morphological description of A. pygmaea, while the other two isolates (YN1 and YN3) varied in morphology, but were within the circumscription of Audouinella hermannii. Due to the fact that the morphological characters of the “Chantransia” stages of order Batrachospermales and the species of genus Audouinella are too similar to be distinguished, a molecular analysis was performed to clarify the phylogenetic position of these four isolates based on rbcL and psbA sequences. Two “pygmaea” specimens collected from Jiugong Mountain, Hubei Province (HB26) and Shimen Gorge, Yunnan Province (YN2), such as S. jiugongshanensis and S. shimenxiaensis, are proposed primarily based on the DNA sequence data generated in this study. The description of these two new species provides more molecular data for phylogenetic analysis of the genus Sheathia. In addition to these newly described species, the results strongly support that those “hermannii” isolates (YN1 and YN3) collected from Yunnan Province were the “Chantransia” of S. arcuata. However, their gametophyte stages have not been found, meaning that critical diagnostic morphological features were unavailable and molecular methods were the only means for ascertaining their phylogenetic position. Considering the extensive application of the rbcL and psbA genes in phylogenetic analyses of freshwater red algae, we recommend using these two genes to identify species when no morphological characteristics are available.

A cladistic analysis of Diopsidae (Diptera) based on morphological and DNA sequence data

2002 ◽  
Vol 33 (3) ◽  
pp. 325-336 ◽  
Author(s):  
Richard Baker ◽  
Rudolf Meier
Keyword(s):  
Sensitivity Analysis ◽  
Dna Sequence ◽  
Sequence Data ◽  
Cladistic Analysis ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Set ◽  
Dna Sequence Data ◽  
Character Weighting ◽  
Character Matrix

AbstractThe results of a cladistic analysis based on a combined character matrix consisting of the morphological data set of Meier & Hilger (2000) and the molecular data set of Baker & al. (2001) is presented. The data set is subjected to an extensive sensitivity analysis and equal character weighting is found to perform best according to character incongruence and tree support. The sensitivity analysis also reveals a remarkable stability of the preferred tree with 25 of the 36 tree nodes supported under 16 different analysis conditions. Cyrtodiopsis is synonymized with Teleopsis and Shillito's (1971) synonymization of Trichodiopsis and Chaetodiopsis with Diasemopsis is confirmed. Morphological and DNA sequence data agree on all major clades and conflict is restricted to the placement of two species within their respective genera. Only in one case can the conflict be confidently resolved. Partitioned Bremer Support values reveal that 90% of the tree support is generated by the DNA sequence characters, although the average morphological character contributes twice the support of an average molecular character. The evolution of eye-stalk morphology and of a meiotic drive chromosome system in Teleopsis is briefly discussed in the light of the phylogenetic tree.

Genes, morphology and agreement: congruence in Australian anthracine bee flies (Diptera : Bombyliidae : Anthracinae)

2003 ◽  
Vol 17 (2) ◽  
pp. 161 ◽  
Author(s):  
Christine L. Lambkin ◽  
David K. Yeates
Keyword(s):  
Mitochondrial Dna ◽  
Morphological Analysis ◽  
Morphological Characters ◽  
Molecular Data ◽  
Simultaneous Analysis ◽  
Data Sources ◽  
Morphological Data ◽  
Base Pairs ◽  
The World ◽  
Species Groups

Almost half of the 4547 described bee flies (Bombyliidae : Diptera) in the world belong to the subfamily Anthracinae, with most of the world's diversity in three cosmopolitan tribes: Villini, Anthracini and Exoprosopini. Molecular data from 815 base pairs of 16S mitochondrial DNA and morphological characters from species-groups of these tribes in Australia were analysed cladistically. The results show that the relationships between the anthracine tribes reflect those found in a previous morphological analysis. The genera of the Anthracinae in Australia are monophyletic, except for Ligyra Newman, and are assigned to tribes. Although simultaneous analysis of the combined molecular and morphological data produced clades found in both separate analyses, the different data sources are significantly incongruent. We use phylogenetic measures to examine support for the relationships among the Australian Anthracinae inferred by the molecular and morphological data.

Phylogeny of the water strider genus Aquarius Schellenberg (Heteroptera: Gerridae) based on nuclear and mitochondrial DNA sequences and morphology

2000 ◽  
Vol 31 (1) ◽  
pp. 71-90 ◽  
Author(s):  
Nils Møller Andersen ◽  
Jakob Damgaard ◽  
Felix A.H. Sperling
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Morphological Data ◽  
Published Data ◽  
Data Sets ◽  
Gene Encoding ◽  
Data Set

AbstractWe examined phylogenetic relationships among gerrid water striders of the genus Aquarius Schellenberg using molecular and morphological characters. The molecular data sets included 780 bp sequence data from the mitochondrial gene encoding cytochrome oxidase subunit I (COI), and 515 bp sequence data from the nuclear gene encoding elongation factor I alpha (EF-1α). The morphological data set was a slightly modified version of a previously published data set. We included all 17 known species and one subspecies of Aquarius as well as five species from three related genera, Gigantometra gigas, Limnoporus esakii, L. rufoscutellatus, Gerris pingreensis, and G. lacustris. Unweighted parsimony analyses of the COI data set gave a single most parsimonious tree (MPT) with a topology quite similar to the morphological tree. Parsimony analyses of the EF-1α data set gave 3 MPT's and a strict consensus of these trees gave a tree with a slightly different topology. A combined analysis of the three data sets gave a single MPT with the same topology as for the morphological data set alone. The phylogeny of Aquarius presented here supports the monophyly of the A. najas, remigis, conformis and paludum species groups as well as previous hypotheses about their relationships. On the other hand, the inclusion of molecular data weakens the support for the monophyly of the genus Aquarius, and questions the specific status of the eastern North American A. nebularis (as separate from A. conformis) and members of the Nearctic A. remigis group. Finally, we discuss the implications of the reconstructed phylogeny in the biogeography and ecological phylogenetics of Aquarius.

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