scholarly journals Hidden in Plain Sight: Comprehensive Molecular Phylogeny of Keroplatidae and Lygistorrhinidae (Diptera) Reveals Parallel Evolution and Leads to a Revised Family Classification

Insects ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 348
Author(s):  
Michal Mantič ◽  
Tomáš Sikora ◽  
Nikola Burdíková ◽  
Vladimir Blagoderov ◽  
Jostein Kjærandsen ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Mitochondrial Gene ◽  
Parallel Evolution ◽  
Base Pairs ◽  
Gene Markers ◽  
Fungus Gnats ◽  
Sister Clade ◽  
The Family ◽  
Family Classification ◽  
High Support

We provide the first molecular phylogeny of Keroplatidae and Lygistorrhinidae, families of fungus gnats (Diptera: Bibionomorpha: Sciaroidea). Phylogenies reconstructed by Maximum Likelihood and Bayesian methods, based on four nuclear and four mitochondrial gene markers (5106 base pairs) sequenced for 75 genera and 105 species, show Keroplatidae as monophyletic only with the family Lygistorrhinidae included, herewith treated as the subfamily Lygistorrhininae stat. nov. The subfamily Arachnocampinae is retained in the family, although lowering its overall support. An early branching clade, comprising species of Platyura Meigen, 1803 and Paleoplatyura melanderi Fisher, 1941, forms subfamily Platyurinae Loew, 1850 stat. nov. The subfamilies Sciarokeroplatinae and Macrocerinae grouped together with three genera considered here as Keroplatidae incertae sedis. Subfamily Lygistorrhininae forms a sister clade to subfamily Keroplatinae, both retained monophyletic with high support. The traditional division of the subfamily Keroplatinae into the tribes Orfeliini and Keroplatini appears as outdated, resting largely on adaptive characters prone to parallel evolution. We find support for an alternative tribe corresponding to the Cloeophoromyia–Asindulum genus group, but a tribal reclassification of the Keroplatinae is left for future studies. The genus Heteropterna Skuse, 1888 is considered as identical with Ctenoceridion Matile, 1972 syn. nov.

scholarly journals On ‘various contrivances’: pollination, phylogeny and flower form in the Solanaceae

2010 ◽  
Vol 365 (1539) ◽  
pp. 449-460 ◽  
Author(s):  
Sandra Knapp
Keyword(s):  
Molecular Phylogeny ◽  
Adaptive Radiation ◽  
Parallel Evolution ◽  
Flower Morphology ◽  
Relative Contribution ◽  
Flower Symmetry ◽  
The Family ◽  
Flower Form ◽  
Floral Characters

Members of the euasterid angiosperm family Solanaceae have been characterized as remarkably diverse in terms of flower morphology and pollinator type. In order to test the relative contribution of phylogeny to the pattern of distribution of floral characters related to pollination, flower form and pollinators have been mapped onto a molecular phylogeny of the family. Bilateral flower symmetry (zygomorphy) is prevalent in the basal grades of the family, and more derived clades have flowers that are largely radially symmetric, with some parallel evolution of floral bilateralism. Pollinator types (‘syndromes’) are extremely homoplastic in the family, but members of subfamily Solanoideae are exceptional in being largely bee pollinated. Pollinator relationships in those genera where they have been investigated more fully are not as specific as flower morphology and the classical pollinator syndrome models might suggest, and more detailed studies in some particularly variable genera, such as Iochroma and Nicotiana , are key to understanding the role of pollinators in floral evolution and adaptive radiation in the family. More studies of pollinators in the field are a priority.

scholarly journals A molecular and morphological investigation of species boundaries and phylogenetic relationships in Australian free-tailed bats Mormopterus (Chiroptera : Molossidae)

2014 ◽  
Vol 62 (2) ◽  
pp. 109 ◽  
Author(s):  
T. B. Reardon ◽  
N. L. McKenzie ◽  
S. J. B. Cooper ◽  
B. Appleton ◽  
S. Carthew ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Phylogeographic Structure ◽  
Species Boundaries ◽  
Base Pairs ◽  
Nadh Dehydrogenase Subunit 2 ◽  
The Family ◽  
Taxonomic Uncertainty ◽  
History Of ◽  
Phylogenetic Affinities

The taxonomic uncertainty surrounding several prominent genera of Australian microbat has been a long-standing impediment to research and conservation efforts on these groups. The free-tail bat genus Mormopterus is perhaps the most significant example, with a long history of acknowledged species-level confusion. This study uses a combined molecular and morphological approach to conduct a comprehensive assessment of species and subgeneric boundaries, between-species phylogenetic affinities and within-species phylogeographic structure in Australian members of Mormopterus. Phylogenetic analyses based on 759 base pairs of the NADH Dehydrogenase subunit 2 mitochondrial gene were concordant with species boundaries delineated using an expanded allozyme dataset and by phallic morphology, and also revealed strong phylogeographic structure within two species. The levels of divergence evident in the molecular and morphological analyses led us to recognise three subgenera within Australia: Micronomus, Setirostris subgen. nov. and Ozimops subgen. nov. Within Ozimops we recognise seven Australian species, three of which are new, and none are conspecific with Indo-Papuan species. The family Molossidae now comprises eleven species across three subgenera in Australia, making it the continent’s second most speciose family of bats.

scholarly journals Phylogeography and ecology of an endemic radiation of Hawaiian aquatic case-bearing moths ( Hyposmocoma : Cosmopterigidae)

2008 ◽  
Vol 363 (1508) ◽  
pp. 3459-3465 ◽  
Author(s):  
Daniel Rubinoff
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Mitochondrial Gene ◽  
Hawaiian Islands ◽  
Elongation Factor ◽  
Nuclear Gene ◽  
Base Pairs ◽  
Island Endemic ◽  
Northwestern Hawaiian Islands ◽  
Elongation Factor 1

The endemic moth genus Hyposmocoma (Lepidoptera: Cosmopterigidae) may be one of the most speciose and ecologically diverse genera in Hawaii. Among this diversity is the Hyposmocoma saccophora clade with previously unrecorded aquatic larvae. I present a molecular phylogeny based on 773 base pairs (bp) of the mitochondrial gene cytochrome c oxidase subunit I and 762 bp of the nuclear gene elongation factor 1-α. Topologies were constructed from data using maximum-parsimony, maximum-likelihood and Bayesian search criteria. Results strongly support the monophyly of the H. saccophora clade and the monophyly of the genus Hyposmocoma . The H. saccophora clade has single-island endemic species on Oahu, Molokai and West Maui. By contrast, there are three species endemic to Kauai, two being sympatric. The H. saccophora clade appears to follow the progression rule, with more basal species on older islands, including the most basal species on 11 Myr-old Necker Island, one of the Northwestern Hawaiian Islands. Aquatic behaviour either evolved recently in the species on the main Hawaiian Islands or was secondarily lost on the arid northwestern Necker Island. The phylogeny suggests that Hyposmocoma is older than any of the current main islands, which may, in part, explain Hyposmocoma 's remarkable diversity.

scholarly journals Molecular phylogeny of cave dwelling Eremogryllodes crickets (Orthoptera, Myrmecophilidae) across Zagros Mountains and Southern Iran

2021 ◽  
Vol 50 (2) ◽  
pp. 213-221
Author(s):  
Mohadeseh Sadat Tahami ◽  
Mina Hojat-Ansari ◽  
Anna Namyatova ◽  
Saber Sadeghi
Keyword(s):  
New Species ◽  
16S Rrna ◽  
Molecular Phylogeny ◽  
Mitochondrial Gene ◽  
Zagros Mountains ◽  
High Similarity ◽  
Molecular Approaches ◽  
Rrna Tree ◽  
The Family ◽  
Geographical Locations

Recently, several new species and subspecies from the genus Eremogryllodes Chopard, 1929 (Insecta: Orthoptera: Myrmecophilidae) inhabiting caves of Iran, have been described based on morphology. The high variation of genitalia structure along with high similarity of external morphology between populations hamper the precise species identification. Thus, molecular approaches are critical to determine the taxonomic positions of species/subspecies of this genus. Here we provide the molecular phylogeny, based on the 16S rRNA mitochondrial gene, of recently described species of Eremogryllodes along with some unidentified specimens from the same region. The results support the monophyly of the family Myrmecophilidae. The topology of the 16S rRNA tree did not completely support the five morpho-species. The three main recovered clades mainly grouped specimens by their geographical locations. Our study suggests the possibility of more than one species in one cave and the presence of cryptic species among cave dwelling crickets, based on the 16S rRNA marker.

scholarly journals New insights into the molecular phylogeny and taxonomy of the family Issidae (Hemiptera: Auchenorrhyncha: Fulgoroidea)

2020 ◽  
Vol 324 (1) ◽  
pp. 146-161 ◽  
Author(s):  
V.M. Gnezdilov ◽  
F.V. Konstantinov ◽  
S.Y. Bodrov
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
New World ◽  
Common Ancestor ◽  
The Family ◽  
Molecular Dataset ◽  
Western Palaearctic ◽  
High Support

The phylogenetic relationships among major lineages of the planthopper family Issidae were explored by analyzing a molecular dataset of nine fragments (COI, CytB, 12S, H3, 16S, 18SII, 18SIII, 28S D3–D5, 28S D6–D7) and 48 terminal taxa. Bayesian and Maximum likelihood analyses yielded similar and mostly well-resolved trees with moderate to high support for most branches. The obtained results suggest subdivision of the family Issidae Spinola into two subfamilies, Issinae Spinola, 1839 (= Thioniinae Melichar, 1906, = Hemisphaeriinae Melichar, 1906) and Hysteropterinae Melichar, 1906. The Issinae was clustered into the tribes Issini Spinola, 1839, with the subtribes Issina Spinola, 1839 and Thioniina Melichar, 1906, Sarimini Wang, Zhang et Bourgoin, 2016, Parahiraciini Cheng et Yang, 1991, Hemisphaeriini Melichar, 1906, and Kodaianellini Wang, Zhang et Bourgoin, 2016. The Hysteropterinae incorporates the rest of Western Palaearctic taxa except Issina. Chimetopini Gnezdilov, 2017, stat. nov. is elevated to tribe from the subtribal level. Most well-supported clades showed clear geographical pattering. Newly obtained data contradicts the scenario of an early split of American Thioniinae from other Issidae and possible origin of the family in the New World, while the combination of Palaearctic Issus Fabricius and Latissus Dlabola with Oriental and American taxa in one well supported clade may serve as an evidence for a common ancestor for extant Oriental, American, and Palaearctic issids.

scholarly journals A Molecular Phylogeny of the Dove Genera Streptopelia and Columba

The Auk ◽  
2001 ◽  
Vol 118 (4) ◽  
pp. 874-887 ◽  
Author(s):  
Kevin P. Johnson ◽  
Selvino de Kort ◽  
Karen Dinwoodey ◽  
A. C. Mateman ◽  
Carel ten Cate ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
New World ◽  
Mitochondrial Gene ◽  
Base Pairs ◽  
Old World ◽  
Phylogenetic Methods ◽  
History Of ◽  
Taxonomic Changes

Abstract Evolutionary history of the dove genus Streptopelia has not been examined with rigorous phylogenetic methods. We present a study of phylogenetic relationships of Streptopelia based on over 3,600 base pairs of nuclear and mitochondrial gene sequences. To test for monophyly of Streptopelia, we used several other columbiform taxa, including Columba (Old and New World), Macropygia, Reinwardtoena, and the enigmatic Pink Pigeon (Nesoenas mayeri). On the basis of our analyses, Streptopelia (as currently defined) is not monophyletic; Nesoenas mayeri is the sister species to S. picturata, resulting in paraphyly of Streptopelia. Three main clades of Streptopelia are identified: (1) S. chinensis plus S. senegalensis, (2) S. picturata plus Nesoenas mayeri, and (3) all other species of Streptopelia. It is unclear whether those clades form a monophyletic group to the exclusion of Old World Columba, but several analyses produce that result. Species of Old World Columba are closely related to Streptopelia, with species of New World Columba clustering outside that group. Taxonomic changes suggested by our results include merging Nesoenas with Streptopelia and changing the generic name for New World Columba species to Patagioenas. Vocal similarities between S. picturata and N. mayeri are striking, given the general diversity of vocalizations in other species.

A Survey for Predicting Enzyme Family Classes Using Machine Learning Methods

2019 ◽  
Vol 20 (5) ◽  
pp. 540-550 ◽  
Author(s):  
Jiu-Xin Tan ◽  
Hao Lv ◽  
Fang Wang ◽  
Fu-Ying Dao ◽  
Wei Chen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Catalytic Mechanism ◽  
Biological Function ◽  
Learning Methods ◽  
Biochemical Processes ◽  
Machine Learning Methods ◽  
Enzyme Family ◽  
The Family ◽  
Speed Up ◽  
Family Classification

Enzymes are proteins that act as biological catalysts to speed up cellular biochemical processes. According to their main Enzyme Commission (EC) numbers, enzymes are divided into six categories: EC-1: oxidoreductase; EC-2: transferase; EC-3: hydrolase; EC-4: lyase; EC-5: isomerase and EC-6: synthetase. Different enzymes have different biological functions and acting objects. Therefore, knowing which family an enzyme belongs to can help infer its catalytic mechanism and provide information about the relevant biological function. With the large amount of protein sequences influxing into databanks in the post-genomics age, the annotation of the family for an enzyme is very important. Since the experimental methods are cost ineffective, bioinformatics tool will be a great help for accurately classifying the family of the enzymes. In this review, we summarized the application of machine learning methods in the prediction of enzyme family from different aspects. We hope that this review will provide insights and inspirations for the researches on enzyme family classification.

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

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