Molecular phylogenetics of the Muscidae (Diptera:Calyptratae): new ideas in a congruence context

2007 ◽  
Vol 21 (3) ◽  
pp. 263 ◽  
Author(s):  
Guilherme Schnell e Schuehli ◽  
Claudio José Barros de Carvalho ◽  
Brian M. Wiegmann
Keyword(s):  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Mitochondrial Coi ◽  
Monophyletic Lineage ◽  
Gene Partition ◽  
New Ideas ◽  
Data Partitions ◽  
Single Set

Hypotheses about the evolution of Muscidae have long been the subject of continuous re-evaluation and reinterpretation. Current understandings of the relationships among these flies are based mainly on a single set of characters and are therefore questionable. Our understanding of muscid phylogeny thus needs greater support and further corroboration from additional suites of characters. In the current study, we analysed phylogenetic relationships among 24 species of muscid flies (18 genera and six subfamilies) using 2989 characters derived from sequences of mitochondrial (COI and COII) and nuclear genes (CAD and EF-1α). Data from each gene partition were analysed both in combined and separate phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference. Support was found for the monophyly of the Muscidae in all analyses and for a sister-group relationship between Coenosiini and Phaoniinae. The latter group was placed in a clade with sampled species of Reinwardtiini and Cyrtoneurininae. The genera Ophyra and Hydrotaea were placed in the Muscinae and a sister-group relationship for Musca and Stomoxys was supported. Sampled species of Polietina form a monophyletic lineage, while Morellia was found to be paraphyletic. Combined analysis of gene partitions improved support and resolution for resulting topologies despite significant incongruence between data partitions found through application of the Incongruence Length Difference test.

scholarly journals Phylogenetic analyses using molecular markers reveal ecological lineages in Medetera (Diptera: Dolichopodidae)

2011 ◽  
Vol 143 (6) ◽  
pp. 662-673 ◽  
Author(s):  
Marc Pollet ◽  
Christoph Germann ◽  
Marco Valerio Bernasconi
Keyword(s):  
Molecular Markers ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Species Group ◽  
Global Distribution ◽  
Sister Group Relationship ◽  
Mitochondrial Coi ◽  
Terrestrial Habitats

AbstractMedetera Fischer von Waldheim is the most speciose genus in the Medeterinae, with a nearly ubiquitous global distribution. Phylogenetic relationships within Medetera and between Medetera and four other medeterine genera were investigated using mitochondrial (COI, 16S) and nuclear (18S) markers to test morphological hypotheses. Our results confirm most of Bickel's hypotheses. Thrypticus Gerstäcker shows a sister-group relationship with Medetera + Dolichophorus Lichtwardt. The Medetera species included here split into two clades. One clade corresponds to the M. diadema L. – veles Loew species group sensu Bickel. The second clade is largely composed of the M. apicalis (Zetterstedt) species group sensu Bickel and the M. aberrans Wheeler species group sensu Bickel + Dolichophorus. Although most Medeterinae are associated with plants (mainly trees), species in at least two separate lineages demonstrate a secondary return to terrestrial habitats. The implication of this evolutionary phenomenon is briefly discussed.

scholarly journals Discovery of a new family of amphibians from northeast India with ancient links to Africa

2012 ◽  
Vol 279 (1737) ◽  
pp. 2396-2401 ◽  
Author(s):  
Rachunliu G. Kamei ◽  
Diego San Mauro ◽  
David J. Gower ◽  
Ines Van Bocxlaer ◽  
Emma Sherratt ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Northeast India ◽  
Sister Group Relationship ◽  
New Family ◽  
Ancient Lineage ◽  
Molecular Phylogenetic ◽  
Threatened Habitats

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India—an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.

A Phylogenetic Analysis and Taxonomic Revision of Bartonia (Gentianaceae: Gentianeae), Based on Molecular and Morphological Evidence

2009 ◽  
Vol 34 (1) ◽  
pp. 162-172 ◽  
Author(s):  
Katherine G. Mathews ◽  
Niall Dunne ◽  
Emily York ◽  
Lena Struwe
Keyword(s):  
Phylogenetic Analyses ◽  
Strong Support ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Species Boundaries ◽  
Morphological Evidence ◽  
Phylogenetic Study ◽  
Sister Group Relationship ◽  
Internal Transcribed Spacer Region ◽  
Test Species

A phylogenetic study and taxonomic revision of the four currently accepted species of Bartonia (Gentianaceae, subtribe Swertiinae) were conducted in order to test species boundaries and interspecific relationships. Species boundaries were examined based on measurements of key quantitative and qualitative morphological characters as given in the original descriptions. Phylogenetic analyses were performed using molecular data from the nuclear internal transcribed spacer region and chloroplast DNA (trnL intron through the trnL-F spacer), separately and combined using parsimony and Bayesian methodologies, incorporating outgroups from subtribes Swertiinae and Gentianinae. The morphological study revealed that characters of one species, B. texana, represent a subset of the morphological variation found within B. paniculata, but that B. paniculata, B. verna, and B. virginica could all be separated from one another. The molecular phylogenetic analyses all found B. texana to nest in a clade with the two recognized subspecies of B. paniculata (subsp. paniculata and subsp. iodandra), making the latter paraphyletic. Bartonia texana is here reduced to subspecific rank, as Bartonia paniculata subsp. texana. Also, the phylogenetic analyses showed strong support for a sister group relationship between B. verna and B. virginica, as opposed to between B. paniculata and B. virginica as has been previously suggested.

Preliminary use of DNA sequences for Dohrniphora (Diptera: Phoridae) phylogeny and taxonomy JOHN M. HASH, BRIAN V. BROWN & PAUL T. SMITH (USA)

Zootaxa ◽  
2011 ◽  
Vol 2991 (1) ◽  
pp. 13
Author(s):  
JOHN M. HASH ◽  
BRIAN V. BROWN ◽  
PAUL T. SMITH
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sequence Data ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Male And Female ◽  
Dna Sequence Data ◽  
16S Gene ◽  
Monophyletic Lineage ◽  
Relationship Of

Phylogenetic analysis of DNA sequence data from the nuclear CAD (rudimentary) and mitochondrial NDI, COI, and 16S gene regions (2817 bp total) recovered exemplars of the genus Dohrniphora as a monophyletic lineage. The data also supported the sister-group relationship of Dohrniphora + Diplonevra and were used to associate a morphologically dissimilar male and female of the species D. ecitophila. Further, we discuss the implications of this designation and provide support for the synonymy of D. ecitophila and D. geminata as proposed by Borgmeier (1968).

Phylogenetic position and relationships of mountain loaches (Teleostei: Balitoridae) of the Western Ghats as revealed by CO1 sequences

Zootaxa ◽  
2021 ◽  
Vol 4926 (1) ◽  
pp. 79-92 ◽  
Author(s):  
ARYA SIDHARTHAN ◽  
RAJEEV RAGHAVAN ◽  
V. K. ANOOP ◽  
ASHWINI KESKAR ◽  
NEELESH DAHANUKAR
Keyword(s):  
Western Ghats ◽  
Molecular Phylogenetics ◽  
Sister Group ◽  
Mountain Streams ◽  
Eastern Himalaya ◽  
Phylogenetic Position ◽  
Sister Group Relationship ◽  
Accurate Identification ◽  
Endemic Genera ◽  
The Western Ghats

The teleostean family Balitoridae comprises small-sized freshwater fishes adapted to swift-flowing torrential mountain streams in South and South-East Asia. Little is known about their molecular phylogenetics and evolutionary biogeography, and much of the scientific literature that references them is focused on morphological taxonomy. In this paper, we generate CO1 sequences for the endemic balitorid lineages of the Western Ghats (WG) Hotspot in India, particularly for the endemic genera, Bhavania, Ghatsa and Travancoria. Integration of these data into a phylogeny revealed that the endemic WG genera together form a well-supported monophyletic clade that shows, subject to our limited taxon sampling, a sister-group relationship to the Southeast Asian genus Pseudohomaloptera. Three WG endemic species of the genus Balitora, namely B. chipkali, B. jalpalli and B. laticauda, though morphologically distinct, have low genetic divergence and barcode gap, suggestive of recent speciation. Interestingly, a fourth WG endemic, B. mysorensis, formed a clade with two species of Balitora from Eastern-Himalaya and Indo-Burma. We also show that all available CO1 sequences assigned to WG endemic balitorid genera in GenBank are misidentifications, and provide diagnostic characters for the accurate identification of these taxa in the future. 

Ingroup relationships of Lagerpetidae (Avemetatarsalia: Dinosauromorpha): a further phylogenetic investigation on the understanding of dinosaur relatives

Zootaxa ◽  
2018 ◽  
Vol 4392 (1) ◽  
pp. 149 ◽  
Author(s):  
RODRIGO TEMP MÜLLER ◽  
MAX CARDOSO LANGER ◽  
SÉRGIO DIAS-DA-SILVA
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
The Other ◽  
Sister Taxon ◽  
Phylogenetic Study ◽  
Sister Group Relationship ◽  
Independent Data ◽  
New Findings ◽  
Alternative Topology ◽  
Western Portion

Despite representing a key-taxon in dinosauromorph phylogeny, Lagerpertidae is one of the most obscure and enigmatic branches from the stem that leads to the dinosaurs. Recent new findings have greatly increased our knowledge about lagerpetids, but no phylogenetic analysis has so far included all known members of this group. Here, we present the most inclusive phylogenetic study so far conducted for Lagerpetidae. Phylogenetic analyses were performed based on three independent data matrixes. In two of them, Lagerpeton chanarensis Romer, 1971 is the sister taxon to all other known Lagerpetidae, whereas Ixalerpeton polesinensis Cabreira et al., 2016 is in a sister group relationship with a clade that includes PVSJ 883 and Dromomeron. Conversely, the other analysis supports an alternative topology, where I. polesinensis is the sister taxon to either L. chanarensis or all other Lagerpetidae. Although coeval and geographically close, I. polesinensis and PVSJ 883 do not form a clade exclusive of other lagerpetids. As previously suggested D. gigas Martínez, Apaldetti, Correa & Abelín, 2016 is the sister taxon of D. romeri Irmis et al., 2007. The phylogenetic analyses also indicate that the earliest lagerpetids are restricted to southwestern Pangea, whereas later forms spread across the entire western portion of the supercontinent. Finally, quantification of the codified characters of our analysis reveals that Lagerpetidae is one of the poorest known among the Triassic dinosauromorph groups in terms of their anatomy, so that new discoveries of more complete specimens are awaited to establish a more robust phylogeny. 

scholarly journals Phylogeography and sister group of Lupangus, a new genus for three new flightless allopatric forest litter weevils endemic to the Eastern Arc Mountains, Tanzania (Coleoptera: Curculionidae, Molytinae)

2017 ◽  
Vol 49 (1) ◽  
pp. 37 ◽  
Author(s):  
Vasily V. Grebennikov
Keyword(s):  
Type Species ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Forest Litter ◽  
Temporal Analysis ◽  
Sister Group ◽  
Eastern Arc Mountains ◽  
Climatic Fluctuations ◽  
Mitochondrial Coi ◽  
Eastern Arc

This paper reports discovery of a new genus <em>Lupangus</em> gen. n. with three new flightless weevils endemic to the forests of the Eastern Arc Mountains in Tanzania: <em>L. asterius</em> sp. n. (East Usambara; the type species), <em>L. jason</em> sp. n. (Uluguru) and<em> L. orpheus</em> sp. n. (Udzungwa). Maximum Likelihood phylogenetic analyses using parts of mitochondrial (COI), nuclear ribosomal (28S) genes, as well as the nuclear spacer region (ITS2) from 46 terminals grouped together the reciprocally monophyletic <em>Lupangus</em> (3 terminals) and <em>Typoderus</em> (3 terminals), with all three clades strongly supported. Phylogenetic analysis of 32 COI-5’ sequences recovered <em>Lupangus</em> species as reciprocally monophyletic, with <em>L</em>. <em>orpheus</em> being the sister to the rest. Internal phylogeny within both <em>L. jason</em> and <em>L.</em> <em>orpheus</em> are geographically structured, while that of <em>L. asterius</em> is not. Temporal analysis of <em>Lupangus</em> evolution using COI-5’ data assessed under slow and fast substitution rate schemes estimated separation of mitochondrial lineages leading to three <em>Lupangus</em> species at about 7–8 Ma and about 1.9–2.1 Ma, respectively. Temporal analyses consistently failed to suggest correlation between the timing of <em>Lupangus</em> evolution and the late Pleistocene climatic fluctuations, thus rejecting the hypothesis of faunal interchanges during the wettest periods of the last million years. Applicability of flightless weevils for dispersal-vicariance analysis is reviewed, and their mostly undocumented and taxonomically entangled diversity in the Tanzanian Eastern Arc Mountains is briefly highlighted.

Phylogenetic relationships and placement of the Empidoidea (Diptera: Brachycera) based on 28S rDNA and EF-1α sequences

2002 ◽  
Vol 33 (4) ◽  
pp. 421-444 ◽  
Author(s):  
Kenneth P. Collins ◽  
Brian M. Wiegmann
Keyword(s):  
Phylogenetic Relationships ◽  
Elongation Factor ◽  
Sister Group ◽  
Morphological Data ◽  
Sister Group Relationship ◽  
Data Set ◽  
Molecular Phylogenetic ◽  
Data Partitions ◽  
28S Ribosomal Dna ◽  
Combined Data

AbstractThe phylogenetic relationships within the Eremoneura (Empidoidea + Cyclorrhapha) have been controversial. The monophyly of the Empidoidea, as well as the position and rank of higher-level empidoid clades remains unresolved despite numerous analyses using morphological data. In addition, the origin of the Cyclorrhapha and their relationship to the Empidoidea continues to be debated. We present the results of a molecular phylogenetic analysis using nucleotide sequences collected from 28S ribosomal DNA (rDNA) and elongation factor-1α (EF-1α) genes. All currently recognized empidoid families and subfamilies, many lower cyclorrhaphan families (including Opetiidae), and several asiloid outgroups are represented in this study. Unweighted and weighted parsimony, as well as maximum likelihood analyses were applied to individual data partitions and a combined data set. Our results support the monophyly of both Empidoidea and Cyclorrhapha (including Opetia), as well as their sister-group relationship. Within Empidoidea we find support for the following: 1) Chvála's (1983) proposal to divide Empidoidea into five families; 2) Atelestidae as the basal empidoid lineage; and 3) monophyly of Microphoridae + Dolichopodidae.

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