Discordance between morphological species identification and mtDNA phylogeny in the flesh fly genus Ravinia (Diptera : Sarcophagidae)

2015 ◽  
Vol 29 (1) ◽  
pp. 1 ◽  
Author(s):  
Evan S. Wong ◽  
Gregory A. Dahlem ◽  
Trevor I. Stamper ◽  
Ronald W. DeBry
Keyword(s):  
Cytochrome Oxidase ◽  
Phylogenetic Relationships ◽  
Mitochondrial Gene ◽  
Bootstrap Support ◽  
Likelihood Methods ◽  
Mtdna Phylogeny ◽  
Maximum Likelihood Methods ◽  
Morphological Species ◽  
Cytochrome Oxidase Ii ◽  
Species Definitions

In order to better understand the phylogenetic relationships among species in the genus Ravinia Robineau-Desvoidy, 1863, we analysed data from two mitochondrial gene fragments: cytochrome oxidase I (COI) and cytochrome oxidase II (COII). We used Bayesian inference and maximum likelihood methods to infer phylogenetic relationships. Our results indicate that the genera Ravinia and Chaetoravinia, previously synonymised into the genus Ravinia (sensu lato) are each likely to be monophyletic (posterior probability 1; bootstrap support 85%). We found highly supported paraphyletic relationships among species of Ravinia, with relatively deep splits in the phylogeny. This conflict between the morphological species definitions and the mtDNA phylogeny could be indicative of the presence of cryptic species in Ravinia anxia (Walker, 1849), Ravinia floridensis (Aldrich, 1916), Ravinia lherminieri (Robineau-Desvoidy, 1830), and Ravinia querula (Walker, 1849).

scholarly journals Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae)

2019 ◽  
Vol 69 (1) ◽  
pp. 91-109 ◽  
Author(s):  
Marie K Brandrud ◽  
Juliane Baar ◽  
Maria T Lorenzo ◽  
Alexander Athanasiadis ◽  
Richard M Bateman ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Diploid Species ◽  
Climatic Conditions ◽  
Likelihood Methods ◽  
Allopolyploid Speciation ◽  
Naturally Occurring ◽  
Maximum Likelihood Methods ◽  
History Of ◽  
Challenging Situation ◽  
Age Estimates

Abstract Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.

The mitochondrial genome of Leuctra sp. (Plecoptera: Leuctridae) and its performance in phylogenetic analyses

Zootaxa ◽  
2019 ◽  
Vol 4671 (4) ◽  
pp. 571-580 ◽  
Author(s):  
YUE SHEN ◽  
YU-ZHOU DU
Keyword(s):  
Mitochondrial Genome ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Likelihood Methods ◽  
Protein Coding ◽  
Maximum Likelihood Methods ◽  
Rna Genes ◽  
Drosophila Yakuba

The nearly complete mitochondrial genome (mitogenome) of Leuctra sp. (Plecoptera: Leuctridae) was sequenced. The 14,585-bp long mitogenome of L. sp. contained 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). The mitochondrial gene arrangement of L. sp. was identical with other stoneflies and the putative ancestral mitogenome of Drosophila yakuba Burla. Most PCGs used standard ATN start codons and TAN termination codons. Twenty-one of the 22 tRNAs in each mitogenome exhibited the cloverleaf secondary structures, while the dihydrouridine (DHU) arm of trnSer (AGN) was reduced. Phylogenetic analyses using our new Leuctra sp. genome and all other publicly available genomes for Plecoptera and Bayesian inference (BI) and maximum likelihood methods (ML) generated identical topologies, both supporting the monophyly of all stonefly families for which tests were possible and the infraorder Systellognatha. Scopuridae and Gripopterygidae were grouped with the infraorder Euholognatha. The final relationships within Plecoptera were recovered as (((((Perlodidae + Chloroperlidae) + Perlidae) + Pteronarcyidae) + Peltoperlidae) + Styloperlidae) + (((((Capniidae + Taeniopterygidae) + Nemouridae) + Scopuridae) + Leuctridae) + Gripopterygidae). 

Phylogenetic relationships among Unionicola (Acari: Unionicolidae) mussel-mites of North America based on mitochondrial cytochrome oxidase I sequences

Zootaxa ◽  
2010 ◽  
Vol 2537 (1) ◽  
pp. 47 ◽  
Author(s):  
DALE D. EDWARDS ◽  
MALCOLM F. VIDRINE ◽  
BRIAN R. ERNSTING
Keyword(s):  
North America ◽  
Cytochrome Oxidase ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Bootstrap Support ◽  
Cox1 Gene ◽  
Symbiotic Association ◽  
Gene Trees ◽  
Molecular Sequence Data ◽  
Molecular Sequence

Water mites of the genus Unionicola Haldeman, 1842 are common symbionts of molluscs, living on the gills or mantle and foot of their hosts and using these tissues as sites of oviposition. Phylogenetic relationships among species that comprise the genus are poorly understood and what is known has been based on a limited number of morphological and life history characters or molecular sequence data using closely-related taxa. The present study uses sequence data from the cytochrome oxidase subunit I (cox1) gene (664 bp) to reconstruct evolutionary relationships among representative species of North American Unionicola from eight subgenera that occur in symbiotic association with freshwater mussels. Maximum parsimony and maximum likelihood analysis yielded trees with similar topologies, and most of the branches have moderate to high bootstrap support. The topologies of these gene trees are mostly congruent with a previously published morphologically-derived tree. Specifically, the gene trees support monophyly among mites from subgenera that occur in association with the gill tissues of host mussels. The molecular trees of Unionicola mites generated by this study must, however, be interpreted with caution, given that the analysis is based exclusively on Unionicola subgenera from North America. A more robust phylogeny of Unionicola mussel-mites will require the addition of molecular sequence data from taxa outside of North America.

Towards a monophyletic classification of Lejeuneaceae I: subtribe Leptolejeuneinae subtr. nov.

Phytotaxa ◽  
2014 ◽  
Vol 156 (3) ◽  
pp. 165 ◽  
Author(s):  
JOCHEN HEINRICHS ◽  
ALFONS SCHÄFER-VERWIMP ◽  
ALEKSANDRA CZUMAY ◽  
SHANSHAN DONG ◽  
ARMIN SCHEBEN ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Maximum Parsimony ◽  
Its Region ◽  
Bootstrap Support ◽  
Phylogenetic Position ◽  
Likelihood Methods ◽  
Monophyletic Lineage ◽  
Current Classification ◽  
Maximum Likelihood Methods

We employed sequences of two chloroplast regions (trnL-trnF, rbcL) and the nuclear ribosomal ITS region of seven accessions of Leptolejeunea to explore its phylogenetic position. Maximum parsimony and maximum likelihood analyses led to similar topologies but deeper nodes received good bootstrap support only with maximum likelihood methods. Leptolejeunea formed an early diverging, robust monophyletic lineage within Lejeuneaceae tribe Lejeuneeae. Contrary to earlier belief, it is not closely related to Drepanolejeunea. To amend the current classification of Lejeuneeae into subtribes, we propose Leptolejeuneinae, subtr. nov.

scholarly journals Molecular Phylogeny of the Ant-Decapitating Flies, Genus Apocephalus Coquillett (Diptera: Phoridae)

2018 ◽  
Vol 2 (4) ◽  
Author(s):  
Brian V Brown ◽  
Christine Hayes ◽  
John M Hash ◽  
Paul T Smith
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Likelihood Methods ◽  
Taxonomic Relationships ◽  
Methods Of Analysis ◽  
Maximum Likelihood Methods ◽  
New Synonymy

Abstract The phylogenetic relationships of the large, diverse genus Apocephalus Coquillett are studied using seven loci (16S, COI, NDI, 28S, AK, CAD, and TPI). Both Bayesian and Maximum Likelihood methods were used to analyze the sequences. Pre-existing taxonomic relationships, based on morphology, were largely upheld, with the notable exception of the subgenus Mesophora Borgmeier being placed deep inside the genus. Therefore, Mesophora was synonymized with Apocephalus (new synonymy) and its species referred to as belonging to the Apocephalus wheeleri group. Both methods of analysis recovered similar results, providing what we consider reasonable explanations of the data, based on morphological information.

New contributions towards the understanding of the phylogenetic relationships among economically important fruit flies (Diptera: Tephritidae)

2006 ◽  
Vol 96 (3) ◽  
pp. 279-288 ◽  
Author(s):  
M.D. Segura ◽  
C. Callejas ◽  
M.P. Fernández ◽  
M.D. Ochando
Keyword(s):  
Phylogenetic Relationships ◽  
Fruit Flies ◽  
Bactrocera Cucurbitae ◽  
Likelihood Methods ◽  
Morphological Classification ◽  
Important Group ◽  
Tephritid Species ◽  
The Family ◽  
Maximum Likelihood Methods ◽  
The Many

AbstractFruit flies (Diptera: Tephritidae) are a species-rich and economically important group. The phylogenetic relationships among the many taxa are still to be fully resolved and the monophyly of several groups is still to be confirmed. This paper reports a study of the phylogenetic relationships among 23 economically important tephritid species (representing several major lineages of the family) which examines the sequence of a region of mitochondrial DNA encompassing the cytb, tRNASer and ND1 genes. Substitutions characteristic of particular taxa were found that could help classify members of the family at any developmental stage. The trees obtained by the maximum parsimony, neighbour joining and maximum likelihood methods were generally compatible with present morphological classification patterns. However, the data reveal some characteristics of the phylogenetic relationships of this family that do not agree with present classifications. The results support the probable non-monophyletic nature of the subfamily Trypetinae and suggest that Bactrocera cucurbitae (Coquillet) is more closely related to the genus Dacus than to other species of Bactrocera.

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