Phylogenetic framework for Dioryctria (Lepidoptera: Pyralidae: Phycitinae) based on combined analysis of mitochondrial DNA and morphology

2005 ◽  
Vol 137 (6) ◽  
pp. 685-711 ◽  
Author(s):  
Yanli Du ◽  
Amanda D. Roe ◽  
Felix A.H. Sperling
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Species Group ◽  
Morphological Data ◽  
Combined Analysis ◽  
Mitochondrial Coi ◽  
The North ◽  
Phylogenetic Framework ◽  
Species Groups

AbstractConeworms of the genus Dioryctria Zeller are important lepidopterous pests of conifer cones throughout the Holarctic region. Seventy-nine Dioryctria species are currently recognized and arranged into 11 species groups, but a globally unified classification of these species groups has not been attained. We surveyed 14 Dioryctria species belonging to 7 species groups recognized as being taxonomically problematic. Mitochondrial DNA sequences and morphological characters were used to resolve relationships among and within species groups and species. Sequences were obtained for 2.3 kb of the mitochondrial COI + COII genes and related to 52 morphological characters. Parsimony analyses of separate and combined data showed that (i) the five included Chinese species (D. abietella (Denis and Schiffermüller), D. rubella Hampson, D. nr. rubella, D. magnifica Munroe, and D. yiai Mutuura and Munroe) were distinct from the North American taxa, and their relationships were interspersed among Nearctic and European species; (ii) three of the four species groups represented by more than one species formed robust, well-supported clades (abietella group, sylvestrella group, and zimmermani group) for both mtDNA sequences and morphology; (iii) mtDNA and morphology gave conflicting interspecific and intergroup relationships for the auranticella, schuetzeella, ponderosae, and baumhoferi groups; (iv) all eight species for which more than one specimen was sampled were characterized by discrete clusters of mitochondrial DNA haplotypes, and mtDNA divergences among species in the same species group were generally less than those among species in different species groups; and (v) combining mtDNA data with morphological data increased support for most nodes in the phylogeny, with morphological characters providing support for species groups and mtDNA being essential for distinguishing species within species groups. This study demonstrates the value of a combined analysis of both mtDNA and morphological characters and establishes a phylogenetic framework for broader and more comprehensive studies of Dioryctria species.

scholarly journals Hypotheses from mitochondrial DNA: congruence and conflict between DNA sequences and morphology in Dolichopodinae systematics (Diptera:Dolichopodidae)

2010 ◽  
Vol 24 (1) ◽  
pp. 32 ◽  
Author(s):  
Marc Pollet ◽  
Christoph Germann ◽  
Samuel Tanner ◽  
Marco Valerio Bernasconi
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Molecular Analysis ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Species Group ◽  
Data Matrix ◽  
Cyt B ◽  
Molecular Phylogenetic ◽  
Species Groups

The molecular phylogeny of the subfamily Dolichopodinae (Diptera : Dolichopodidae) is reconstructed based on 79 species of 7 dolichopodine genera as ingroup, and 10 non-dolichopodine species from different genera as outgroup. A Bayesian analysis based on a mitochondrial DNA dataset consisting of 1702 characters (COI : 810; 12S : 366; 16S : 526) was carried out. Genital and non-genital morphological characters from a hitherto unpublished data matrix (based on 57 Dolichopodidae species) were used to explain and support the lineages hypothesised by our molecular phylogenetic analysis. The monophyly of the subfamily Dolichopodinae, and of the genera Dolichopus and Gymnopternus, was confirmed. The molecular analysis yielded nine species groups in Dolichopus that were proposed in previous studies using COI and Cyt-b. No evidence was found to support a clade including Dolichopus, Ethiromyia, and Gymnopternus. The genus Hercostomus proved polyphyletic with respect to Poecilobothrus, Sybistroma, and Gymnopternus. The following lineages were represented by strongly supported clades: Hercostomus germanus species group, H. vivax species group, H. nigrilamellatus species group, H. plagiatus species group, H. longiventris species group, H. fulvicaudis species group, and Poecilobothrus, Gymnopternus, Tachytrechus and Sybistroma (including Hercostomus nanus and H. parvilamellatus). Two clades that were previously established on the basis of morphology were confirmed in our phylogenetic analysis: (i) Poecilobothrus and the flower-feeding Hercostomus germanus species group, and (ii) the H. longiventris lineage and Sybistroma. In most cases, the groups identified in the molecular analysis could be supported and explained by morphological characters. Species of the Hercostomus germanus species group, Poecilobothrus, the Hercostomus longiventris species group, and a Sybistroma subclade have a similar microhabitat affinity.

scholarly journals Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers

2005 ◽  
Vol 272 (1572) ◽  
pp. 1577-1586 ◽  
Author(s):  
Niklas Wahlberg ◽  
Michael F Braby ◽  
Andrew V.Z Brower ◽  
Rienk de Jong ◽  
Ming-Min Lee ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Synergistic Effects ◽  
Strong Support ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Data Matrix ◽  
Morphological Data ◽  
Combined Analysis

Phylogenetic relationships among major clades of butterflies and skippers have long been controversial, with no general consensus even today. Such lack of resolution is a substantial impediment to using the otherwise well studied butterflies as a model group in biology. Here we report the results of a combined analysis of DNA sequences from three genes and a morphological data matrix for 57 taxa (3258 characters, 1290 parsimony informative) representing all major lineages from the three putative butterfly super-families (Hedyloidea, Hesperioidea and Papilionoidea), plus out-groups representing other ditrysian Lepidoptera families. Recently, the utility of morphological data as a source of phylogenetic evidence has been debated. We present the first well supported phylogenetic hypothesis for the butterflies and skippers based on a total-evidence analysis of both traditional morphological characters and new molecular characters from three gene regions ( COI , EF-1α and wingless ). All four data partitions show substantial hidden support for the deeper nodes, which emerges only in a combined analysis in which the addition of morphological data plays a crucial role. With the exception of Nymphalidae, the traditionally recognized families are found to be strongly supported monophyletic clades with the following relationships: (Hesperiidae+(Papilionidae+(Pieridae+(Nymphalidae+(Lycaenidae+Riodinidae))))). Nymphalidae is recovered as a monophyletic clade but this clade does not have strong support. Lycaenidae and Riodinidae are sister groups with strong support and we suggest that the latter be given family rank. The position of Pieridae as the sister taxon to nymphalids, lycaenids and riodinids is supported by morphology and the EF-1α data but conflicted by the COI and wingless data. Hedylidae are more likely to be related to butterflies and skippers than geometrid moths and appear to be the sister group to Papilionoidea+Hesperioidea.

scholarly journals Revision of the genus Dichaetophora Duda (Diptera: Drosophilidae), part I: DNA bar-coding and molecular phylogenetic reconstruction

2021 ◽  
Author(s):  
Takehiro K Katoh ◽  
Ji-Min Chen ◽  
Jin-Hua Yang ◽  
Guang Zhang ◽  
Lu Wang ◽  
...  
Keyword(s):  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Morphological Data ◽  
Sister Relationship ◽  
Mitochondrial Coi ◽  
Adaptive Diversification ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Cladistic Analyses ◽  
Species Groups

The genus Dichaetophora Duda is of 69 formally described, Old World species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita. Most of these species were delimitated morphologically, with the within-genus relationship established largely via cladistic analyses of morphological characters. In the present study, we first conducted species-delimitation with aids of morphological data as well DNA barcodes (nucleotide sequences of the mitochondrial COI, i.e., cytochrome c oxidase subunit I, gene), for a huge sample of Dichaetophora and allied taxa (genus Mulgravea and subgenus Dudaica of Drosophila) collected from a wide geographical range. Then, multiple-locus phylogenetic reconstruction was conducted based on elaborate taxon sampling from the known and newly recognized species in the above taxa, with the maximum likelihood (ML) and Bayesian inference (BI) methods. As a result, 189 species (186 of Dichaetophora, 2 of Mulgravea, and 1 for Dudaica) were newly recognized. In our ML and BI trees, several well-supported species clusters equivalent to the species groups agbo (excluding of neocirricauda), tenuicauda, sinensis (inclusive of neocirricauda) and trilobita of Dichaetophora, were recovered, with the sister-relationship between the third and fourth proved. Other well-supported clusters include 1) a clade comprising of Di. acutissima group and Dudaica, with the former proved to be paraphyletic to the latter; 2) genus Mulgravea; 3) a clade comprising exclusively of newly recognized Dichaetophora species, and was placed as sister to Mulgravea. Three of the remaining five representatives of Dichaetophora species form a solid cluster, leaving the positions of the last two unresolved. The present study greatly renewed out knowledge about the species diversity in a pan-Dichaetophora clade, providing us with an unprecedented historical framework for further taxonomy revision of this clade, and valuable baseline knowledge for future reconstruction of the history of its adaptive diversification in the particular microhabitats.

Cryptic species diversity and character congruence: review of the tribe Anthracini (Diptera : Bombyliidae) in Australia

1998 ◽  
Vol 12 (6) ◽  
pp. 977 ◽  
Author(s):  
David K. Yeates ◽  
Christine L. Lambkin
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Species Group ◽  
Morphological Data ◽  
Distribution Maps ◽  
Eastern Australia ◽  
Wing Patterns ◽  
Species Groups

The Australian Anthracini are revised. In all, 28 new species are described, bringing the total fauna to 34 species. The previously described species of Anthrax Scopoli – A. maculatus Macquart, A. incomptus Walker, A. confluensisRoberts, A. lepidiotus Roberts and A. proconcisus Hardy – are diagnosed and the following eight new species of Anthrax are described: A. argentia, A. asciculus, A. clinatus, A. crenatus, A. dolabratus, A. funestus, A. opacus and A. torulus. This taxonomic study reveals a group of at least 20 cryptic species previously included in collections under the name Anthrax angularis Thomson. A new genus, Thraxan, is erected to contain this cryptic group of species and the following 20 new species are described: T. acutus, T. abditus, T. caligneus, T. cinctus, T. cornuatus, T. depressus, T. echinatus, T. ebenus, T. emicatus, T. hamulus, T. luteus, T. misatulus, T. nodus, T. norrisi, T. obstipus, T. patielus, T. planus, T. prolatus, T. simulatusand T. spiculus. Many of these cryptic species have been collected sympatrically, hill topping together in eastern Australia. A key is provided to the species of Anthrax and Thraxan, genitalia drawings are presented for most species and distribution maps of all species are presented. A cladistic analysis of the species of Anthrax and Thraxan is also presented. A total of 26 of the species is compared for 125 synapomorphies in 39 adult morphological characters. Three species-groups were found: Thraxan, and two species-groups within Anthrax, the A. proconcisus species-group and the A. maculatusspecies-group. Previous authors divided Anthrax into species-groups on the basis of wing patterns, but found that these species-groups were not confirmed when other characters were taken into consideration. We studied the congruence of seven different character sets within the clade comprising Anthrax and Thraxan – antennae, venation, wing patterns, vestiture, genitalia, male genitalia and female genitalia – using several incongruence indices. Significance of incongruence was measured using a randomisation procedure. Results of these studies indicate that the wing-pattern character set is significantly incongruent with the other morphological data. These quantitative cladistic results explain the difficulty previous authors experienced in finding suites of characters to support species-groups in Anthrax on the basis of wing patterns. A relationship is found between the level of incongruence and the distance over which mate-recognition signals operate.

scholarly journals Empria longicornis species group: taxonomic revision with notes on phylogeny and ecology (Hymenoptera, Tenthredinidae)

Zootaxa ◽  
2011 ◽  
Vol 2756 (1) ◽  
pp. 1 ◽  
Author(s):  
MARKO PROUS ◽  
MIKK HEIDEMAA ◽  
VILLU SOON
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Host Plants ◽  
Taxonomic Revision ◽  
Species Group ◽  
Valid Species ◽  
Mitochondrial Coi ◽  
Species Phylogeny ◽  
Species Circumscription ◽  
Its1 And Its2

The Empria longicornis species group (Hymenoptera, Tenthredinidae) is revised. Empria japonica Heidemaa & Prous, sp. nov. is described from Japan. The lectotypes of Empria gussakovskii Dovnar-Zapolskij, 1929, E. konowi Dovnar-Zapolskij, 1929, Poecilosoma longicornis Thomson, 1871, P. mongolica Konow, 1895, and P. tridens Konow, 1896 are designated. Empria konowi Dovnar-Zapolskij, 1929 (syn. nov.) and E. gussakovskii Dovnar-Zapolskij, 1929 (syn. nov.) are synonymized with E. tridens (Konow, 1896), and Empria waldstaetterense Liston, 1980 (syn. nov.) with E. alector Benson, 1938. Empria alpina Benson, 1938 and E. minuta Lindqvist, 1968, earlier misidentified as E. gussakovskii, are treated as valid species. Nine species are confirmed to belong in the longicornis-group: E. alector, E. alpina, E. basalis, E. japonica, E. loktini, E. longicornis, E. minuta, E. mongolica, and E. tridens. Distributional data of the species and a key to the imagines are provided. Ex ovo rearings of the four most common and often misidentified species in the group (E. alector, E. basalis, E. longicornis, and E. tridens) were carried out to verify their host plants and male conspecifics. External morphology, morphometrics (geometric and traditional), and DNA sequences (mitochondrial COI and nuclear ITS1 and ITS2) are used to delimit species within the group and to assess their phylogenetic relationships. Mitochondrial DNA sequences analyzed are mostly regarded as unsuitable for species circumscription, DNA barcoding and for reconstructing species phylogeny within the group. In this regard, analyses of the ITS sequences yielded more concordant results.

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.

The endemic New Guinean genus Murexia (Dasyuromorphia : Dasyuridae). How many species? An analysis based on morphological, distributional and molecular data

2019 ◽  
Vol 67 (3) ◽  
pp. 134
Author(s):  
Patricia A. Woolley ◽  
Carey Krajewski ◽  
Michael Westerman
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Molecular Data ◽  
Morphological Data ◽  
Species Boundaries ◽  
Individual Species ◽  
External Appearance ◽  
Multiple Exemplars ◽  
Species Groups

Five species are currently recognised in the dasyurid genus Murexia, i.e. longicaudata, naso, habbema, melanurus and rothschildi. Morphological data, including spacing of premolar teeth, the footpads and aspects of external appearance, together with nuclear and mitochondrial DNA sequences from multiple exemplars from across the range of each species, suggest that at least three of these represent species groups rather than individual species. Some of the taxa currently synonymised in the five species may warrant reinstatement, including M. murex, M. aspera, M. maxima in the ‘M. longicaudata’ group, M. tafa in the ‘M. naso’ group and M. wilhelmina in the ‘M. melanurus’ group. Our data also suggest the presence of other, synonymised or undescribed taxa within the ‘longicaudata’, ‘naso’, ‘melanurus’ and ‘habbema’ species groups whose species boundaries require clarification by further collections and study.

scholarly journals Partial revision of the neustonic genus Scapholeberis Schoedler, 1858 (Crustacea: Cladocera): decoding of the barcoding results

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10410
Author(s):  
Petr G. Garibian ◽  
Anna N. Neretina ◽  
Derek J. Taylor ◽  
Alexey A. Kotov
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Russian Far East ◽  
Far East ◽  
Species Group ◽  
The Status ◽  
Species Groups ◽  
The Republic ◽  
Partial Revision ◽  
A New Species

Water fleas (Crustacea: Cladocera) are among the most intensively studied freshwater invertebrates. However, ecologically important daphniids that live on the surface layer (neuston) remain taxonomically confused. Here we attempt to reconcile genetic and morphological information for the neustonic genus Scapholeberis Schoedler, 1858 (Cladocera: Daphniidae) and present the first revision of the Scapholeberis kingii species group. We analyzed new and existing mitochondrial DNA sequences (сytochrome C oxidase subunit I gene region) together with morphology for all but one of the known species of the neustonic daphniids. Morphological comparisons of available populations, belonging to the Scapholeberis kingii species group from several Australian, Asian and African localities, revealed, that they are almost identical according to parthenogenetic females. However, Australian populations can be reliably distinguished from Asian ones based on the morphology of gamogenetic females. Mitochondrial DNA data analyses revealed divergent lineages (>17% for the DNA barcoding COI region) for the three different species (Australia, Asia and Africa). Based on this set of data, we redescribed S. kingii Sars, 1888 from Australia, its terra typica, and described a new species, S. smirnovi sp.nov. from the Russian Far East, Korea and Japan. The status of populations from Ethiopia and the Republic of South Africa remained unclear, because in the African material and the putative type material, we found only parthenogenetic females. Our results provide an integrative revision of the S. kingii species group and improve the taxonomic scaffold used for barcoding and genomics for the remaining species groups in the daphniid genus Scapholeberis.

Discovery of New Genera Challenges the Subtribal Classification of Tok-Tok Beetles (Coleoptera: Tenebrionidae: Sepidiini)

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Olivia M Gearner ◽  
Marcin J Kamiński ◽  
Kojun Kanda ◽  
Kali Swichtenberg ◽  
Aaron D Smith
Keyword(s):  
Dna Sequences ◽  
Species Group ◽  
Phylogenetic Placement ◽  
Darkling Beetles ◽  
Species Groups ◽  
Taxonomic Groups ◽  
Inference Methods ◽  
A New Species ◽  
Coleoptera Tenebrionidae

Abstract Sepidiini is a speciose tribe of desert-inhabiting darkling beetles, which contains a number of poorly defined taxonomic groups and is in need of revision at all taxonomic levels. In this study, two previously unrecognized lineages were discovered, based on morphological traits, among the extremely speciose genera Psammodes Kirby, 1819 (164 species and subspecies) and Ocnodes Fåhraeus, 1870 (144 species and subspecies), namely the Psammodes spinosus species-group and Ocnodes humeralis species-group. In order to test their phylogenetic placement, a phylogeny of the tribe was reconstructed based on analyses of DNA sequences from six nonoverlapping genetic loci (CAD, wg, COI JP, COI BC, COII, and 28S) using Bayesian and maximum likelihood inference methods. The aforementioned, morphologically defined, species-groups were recovered as distinct and well-supported lineages within Molurina + Phanerotomeina and are interpreted as independent genera, respectively, Tibiocnodes Gearner & Kamiński gen. nov. and Tuberocnodes Gearner & Kamiński gen. nov. A new species, Tuberocnodes synhimboides Gearner & Kamiński sp. nov., is also described. Furthermore, as the recovered phylogenetic placement of Tibiocnodes and Tuberocnodes undermines the monophyly of Molurina and Phanerotomeina, an analysis of the available diagnostic characters for those subtribes is also performed. As a consequence, Phanerotomeina is considered as a synonym of the newly redefined Molurina sens. nov. Finally, spectrograms of vibrations produced by substrate tapping of two Molurina species, Toktokkus vialis (Burchell, 1822) and T. synhimboides, are presented.

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