scholarly journals A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7386 ◽  
Author(s):  
Leidys Murillo-Ramos ◽  
Gunnar Brehm ◽  
Pasi Sihvonen ◽  
Axel Hausmann ◽  
Sille Holm ◽  
...  
Keyword(s):  
Nuclear Gene ◽  
Molecular Data ◽  
Data Set ◽  
Protein Coding ◽  
Mitochondrial Coi ◽  
The Family ◽  
Taxonomic Changes ◽  
Biogeographical Regions ◽  
Molecular Dataset ◽  
Close Relatives

Our study aims to investigate the relationships of the major lineages within the moth family Geometridae, with a focus on the poorly studied Oenochrominae-Desmobathrinae complex, and to translate some of the results into a coherent subfamilial and tribal level classification for the family. We analyzed a molecular dataset of 1,206 Geometroidea terminal taxa from all biogeographical regions comprising up to 11 molecular markers that includes one mitochondrial (COI) and 10 protein-coding nuclear gene regions (wingless, ArgK, MDH, RpS5, GAPDH, IDH, Ca-ATPase, Nex9, EF-1alpha, CAD). The molecular data set was analyzed using maximum likelihood as implemented in IQ-TREE and RAxML. We found high support for the subfamilies Larentiinae, Geometrinae and Ennominae in their traditional scopes. Sterrhinae becomes monophyletic only if Ergavia Walker, Ametris Hübner and Macrotes Westwood, which are currently placed in Oenochrominae, are formally transferred to Sterrhinae. Desmobathrinae and Oenochrominae are found to be polyphyletic. The concepts of Oenochrominae and Desmobathrinae required major revision and, after appropriate rearrangements, these groups also form monophyletic subfamily-level entities. Oenochrominae s.str. as originally conceived by Guenée is phylogenetically distant from Epidesmia and its close relatives. The latter is hereby described as the subfamily Epidesmiinae Murillo-Ramos, Sihvonen & Brehm, subfam. nov. Epidesmiinae are a lineage of “slender-bodied Oenochrominae” that include the genera Ecphyas Turner, Systatica Turner, Adeixis Warren, Dichromodes Guenée, Phrixocomes Turner, Abraxaphantes Warren, Epidesmia Duncan & Westwood and Phrataria Walker. Archiearinae are monophyletic when Dirce and Acalyphes are formally transferred to Ennominae. We also found that many tribes were para- or polyphyletic and therefore propose tens of taxonomic changes at the tribe and subfamily levels. Archaeobalbini stat. rev. Viidalepp (Geometrinae) is raised from synonymy with Pseudoterpnini Warren to tribal rank. Chlorodontoperini Murillo-Ramos, Sihvonen & Brehm, trib. nov. and Drepanogynini Murillo-Ramos, Sihvonen & Brehm, trib. nov. are described as new tribes in Geometrinae and Ennominae, respectively.

The molecular systematics of blowflies and screwworm flies (Diptera: Calliphoridae) using 28S rRNA, COX1 and EF-1α: insights into the evolution of dipteran parasitism

Parasitology ◽  
2011 ◽  
Vol 138 (13) ◽  
pp. 1760-1777 ◽  
Author(s):  
LAURA M. McDONAGH ◽  
JAMIE R. STEVENS
Keyword(s):  
Sequence Data ◽  
Single Gene ◽  
Nuclear Gene ◽  
Evolutionary Status ◽  
28S Rrna ◽  
Gene Trees ◽  
Data Set ◽  
Protein Coding ◽  
Nucleotide Sequence Data ◽  
The Family

SUMMARYThe Calliphoridae include some of the most economically significant myiasis-causing flies in the world – blowflies and screwworm flies – with many being notorious for their parasitism of livestock. However, despite more than 50 years of research, key taxonomic relationships within the family remain unresolved. This study utilizes nucleotide sequence data from the protein-coding genes COX1 (mitochondrial) and EF1α (nuclear), and the 28S rRNA (nuclear) gene, from 57 blowfly taxa to improve resolution of key evolutionary relationships within the family Calliphoridae. Bayesian phylogenetic inference was carried out for each single-gene data set, demonstrating significant topological difference between the three gene trees. Nevertheless, all gene trees supported a Calliphorinae-Luciliinae subfamily sister-lineage, with respect to Chrysomyinae. In addition, this study also elucidates the taxonomic and evolutionary status of several less well-studied groups, including the genus Bengalia (either within Calliphoridae or as a separate sister-family), genus Onesia (as a sister-genera to, or sub-genera within, Calliphora), genus Dyscritomyia and Lucilia bufonivora, a specialised parasite of frogs and toads. The occurrence of cross-species hybridisation within Calliphoridae is also further explored, focusing on the two economically significant species Lucilia cuprina and Lucilia sericata. In summary, this study represents the most comprehensive molecular phylogenetic analysis of family Calliphoridae undertaken to date.

scholarly journals Systematic Position of the Enigmatic Psocid Family Lesneiidae (Insecta: Psocodea: Psocomorpha), With Description of Two New Species

2020 ◽  
Vol 4 (6) ◽  
Author(s):  
Kazunori Yoshizawa ◽  
Yuri M Marusik ◽  
Izumi Yao ◽  
Charles Lienhard
Keyword(s):  
Molecular Data ◽  
Systematic Position ◽  
Data Set ◽  
Bayesian Analyses ◽  
The Family ◽  
The Status ◽  
Morphological Specialization ◽  
Tight Association ◽  
Close Relatives ◽  
Gene Data

Abstract The systematic placement of an enigmatic psocid family restricted to Africa, Lesneiidae, was estimated by using a multiple gene data set. The candidates for its close relatives are now classified under two different infraorders, the family Archipsocidae of the infraorder Archipsocetae or the families Elipsocidae/Mesopsocidae of the infraorder Homilopsocidea. The maximum likelihood and Bayesian analyses of the molecular data set strongly suggested that the Lesneiidae belongs to Homilopsocidea and forms a clade with Elipsocidae/Mesopsocidae/Eolachesillinae (Lachesillidae). However, the relationships among these (sub)families and Lesneiidae, including the monophyly of Elipsocidae and Mesopsocidae, were ambiguous or questionable, showing the necessity of further investigations for elucidating their relationships and validating the status of these families. Two species, L. johnsoni Yoshizawa & Lienhard, n. sp. and L. testudinata Yoshizawa & Lienhard, n. sp. (Psocodea: Lesneiidae), were described from South Africa. There appears to be a tight association between the reproductive biology and morphological specialization of this group.

Two new freshwater planarian species (Platyhelminthes: Tricladida: Dugesiidae) partially sympatric in Argentinean Patagonia

2021 ◽  
pp. 269-278
Author(s):  
M. Lenguas Francavilla ◽  
L. Negrete ◽  
A. Martínez-Aquino ◽  
C. Damborenea ◽  
F. Brusa
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Data ◽  
Neotropical Region ◽  
Free Living ◽  
Mitochondrial Coi ◽  
Argentinean Patagonia ◽  
The Family ◽  
Taxonomic Approach ◽  
Morphological And Molecular Data ◽  
Endemic Flora

Girardia Ball, 1974 is the most diverse and widely distributed genus of the family Dugesiidae (Platyhelminthes: Continenticola) in the Neotropical region. Seven out of the 52 species of the genus are known for Argentina. The Somuncurá Plateau is a region in northern Patagonia with several endemic flora and fauna, but little is known about the free-living Platyhelminthes. We describe two new species of Girardia partially inhabiting in sympatry in the Somuncurá Plateau: Girardia somuncura sp. nov. and Girardia tomasi sp. nov. The identification criteria that we followed was an integrative taxonomic approach based on morphological and molecular data. Thus, we used anatomical features focused on the reproductive system, together with a phylogenetic analysis, using a mitochondrial (COI barcode region) genetic marker. This study is the first phylogenetic analysis of the genus Girardia in which we include the southernmost representatives of America here described, thus making it possible to incorporate them in global phylogenies.

Anchialine adjustments: an updated phylogeny and classification for the family Barbouriidae Christoffersen, 1987 (Decapoda: Caridea)

2020 ◽  
Vol 40 (4) ◽  
pp. 401-411 ◽  
Author(s):  
Robert E Ditter ◽  
Luis M Mejía-Ortíz ◽  
Heather D Bracken-Grissom
Keyword(s):  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Morphological Characters ◽  
Molecular Data ◽  
Genetic Distances ◽  
Evolutionary Relationships ◽  
The Bahamas ◽  
16S Gene ◽  
Dichotomous Key ◽  
The Family

Abstract Barbouriidae Christoffersen, 1987 is a family comprised of 4 genera and 11 species of enigmatic shrimps restricted to anchialine or marine caves whose evolutionary history and relationships remain elusive. We investigated the evolutionary relationships among members of Barbouriidae with the inclusion of four genera and nine species, and newly collected material from Belize, the Bahamas, and the Yucatán Peninsula, Mexico. Phylogenetic analyses based on seven mitochondrial and nuclear gene regions and genetic distances calculated using partial 16S gene regions have identified a need to revisit the relationships and classification within Barbouriidae. More specifically, we find evidence to suggest Janicea Manning & Hart, 1984 as a junior synonym of Parhippolyte Borradaile, 1900, B. yanezi Mejía, Zarza & López, 2008 as a synonym of Barbouria cubensis (von Martens, 1872), and define two new subfamilies, Calliasmatinae Holthuis, 1973 and Barbouriinae Christoffersen, 1987. Included is a dichotomous key for the species of Barbouriidae that summarizes previous literature and includes new morphological characters. Our findings shed light on existing inaccuracies and gaps in molecular data from barbouriids. We also provide further clarity into evolutionary relationships among genera of Barbouriidae and their allies, suggesting phylogeographic divisions within the family. Our findings suggest an early Atlantic-Pacific divide among genera originating from a shallow-water reef ancestor.

Dissecting the major African snake radiation: a molecular phylogeny of the Lamprophiidae Fitzinger (Serpentes, Caenophidia)

Zootaxa ◽  
2008 ◽  
Vol 1945 (1) ◽  
pp. 51-66 ◽  
Author(s):  
NICOLAS VIDAL ◽  
WILLIAM R. BRANCH ◽  
OLIVIER S. G. PAUWELS ◽  
S. BLAIR HEDGES ◽  
DONALD G. BROADLEY ◽  
...  
Keyword(s):  
Mitochondrial Protein ◽  
Sister Group ◽  
Molecular Data ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Data Set ◽  
Protein Coding ◽  
Mitochondrial Rrna ◽  
Protein Coding Genes ◽  
History Of

The Elapoidea includes the Elapidae and a large (~60 genera, 280 sp.) and mostly African (including Madagascar) radiation termed Lamprophiidae by Vidal et al. (2007), that includes at least four major groups: the psammophiines, atractaspidines, lamprophiines and pseudoxyrhophiines. In this work, we reviewed the recent taxonomic history of the lamprophiids, and built a data set including two nuclear protein-coding genes (c-mos and RAG2), two mitochondrial rRNA genes (12S and 16S rRNA) and two mitochondrial protein-coding genes (cytochrome b and ND4) for 85 species belonging to 45 genera (thus representing about 75% of the generic diversity and 30% of the specific diversity of the radiation), in order to clarify the phylogenetic relationships of this large and neglected group at the subfamilial and generic levels. To this aim, 480 new sequences were produced. The vast majority of the investigated genera fall into four main monophyletic clusters, that correspond to the four subfamilies mentioned above, although the content of atractaspidines, lamprophiines and pseudoxyrhophiines is revised. We confirm the polyphyly of the genus Stenophis, and the relegation of the genus name Dromophis to the synonymy of the genus name Psammophis. Gonionotophis brussauxi is nested within Mehelya. The genus Lamprophis Fitzinger, 1843 is paraphyletic with respect to Lycodonomorphus Fitzinger, 1843. Lamprophis swazicus is the sister-group to Hormonotus modestus, and may warrant generic recognition. Molecular data do not support the traditional placement of Micrelaps within the Atractaspidinae, but its phylogenetic position, along with that of Oxyrhabdium (previously considered to belong to the Xenodermatidae), requires additional molecular data and they are both treated as Elapoidea incertae sedis. The interrelationships of Psammophiinae, Atractaspidinae, Lamprophiinae, Pseudoxyrhophiinae, Prosymna (13 sp.), Pseudaspis (1 sp.) and Pythonodipsas (1 sp.), Buhoma (2 species), and Psammodynastes (1 sp.) remain unresolved. Finally, the genus Lycognathophis, endemic to the Seychelles, does not belong to the African radiation, but to the Natricidae.

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.

Molecular relationships of the Australian Ennominae (Lepidoptera: Geometridae) and implications for the phylogeny of the Geometridae from molecular and morphological data

Zootaxa ◽  
2006 ◽  
Vol 1264 (1) ◽  
pp. 1 ◽  
Author(s):  
CATHERINE J. YOUNG
Keyword(s):  
A Priori ◽  
Nuclear Gene ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Protein Coding ◽  
Outgroup Species ◽  
Phylogenetic Framework ◽  
Molecular Relationships

Molecular data from the 28S D2 ribosomal nuclear gene fragment were utilised to construct a phylogeny for the Australian Ennominae. Sequences were obtained from 68 geometrid and 5 outgroup species. Sequences from a smaller subset of 17 species also were analysed using the nuclear protein-coding gene EF-1a. Species were sampled from all major subfamilies of the Geometridae as no a priori assumptions could be made confidently about possible sister groups to the Australian Ennominae.The major findings from these analyses were as follows:(a) Drepanidae are a sister group to Geometridae;(b) Larentiinae are derived basally within the Geometridae; the Sterrhinae are the penultimate basally derived group;(c) Oenochrominae s. str. are closely related to the Geometrinae.(d) Ennominae are not monophyletic;(e) Tasmanian Archiearinae are misplaced in the Archiearinae and have close affinities to Australian Nacophorini (Ennominae);(f) Australian Nacophorini are not monophyletic.These results are at odds with traditionally held beliefs on the origins of Geometridae but are in broad agreement with and elaborate on the findings of Abraham et al. (2001). The implications of these findings in relation to key morphological characters are discussed using the proposed phylogenetic framework.

scholarly journals Taxonomy "under construction": advances in the systematics of Apocynaceae, with emphasis on the Brazilian Asclepiadoideae

Rodriguésia ◽  
2012 ◽  
Vol 63 (1) ◽  
pp. 075-088 ◽  
Author(s):  
Alessandro Rapini
Keyword(s):  
Native Species ◽  
Morphological Evolution ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Future Research ◽  
The Family ◽  
Taxonomic Changes ◽  
Under Construction ◽  
Floristic Studies ◽  
The 19Th Century

The Apocynaceae comprise approximately 5,000 species and are widely distributed. The family belongs to the Gentianales and can be easily recognized by the presence of latex and a style-head derived from the fusion of two carpels at the apex of the styles. The largest subfamily in Apocynaceae is Asclepiadoideae. Treated as the Asclepiadaceae for almost two centuries, it comprises about 3,000 species and is defined by stamens with bisporangiate anthers and pollen transferred in specialized units called pollinaria. Since the 19th century, floristic studies and taxonomic monographs have significantly contributed to the taxonomy of Brazilian Asclepiadoideae. Nevertheless, advances in understanding the internal relationships in the subfamily were not done until this millennium, with the popularization of phylogenetic studies based on molecular data and powerful computer analyses. Advances in the systematics of Apocynaceae have provided new interpretations on the morphological evolution and biogeography of the family and have led to important changes in its classification. Nevertheless, several taxonomic rearrangements are still needed and it can be said that the taxonomy of Apocynaceae is "under construction". In this article, the major taxonomic changes in the family are reviewed, with special attention given to the systematics of Neotropical groups. A cladogram of the Apocynaceae is presented, which highlights the phylogenetic position of the Brazilian genera and their diversity in number of native species. The main studies and the diversity of Asclepiadoideae in Brazil are summarized and perspectives for future research on the subfamily are presented.

scholarly journals Taxonomy and phylogenetic relationships of the coral genera Australomussa and Parascolymia (Scleractinia, Lobophylliidae)

2014 ◽  
Vol 83 (3) ◽  
pp. 195-S7 ◽  
Author(s):  
Roberto Arrigoni ◽  
Zoe T. Richards ◽  
Chaolun Allen Chen ◽  
Andrew H. Baird ◽  
Francesca Benzoni
Keyword(s):  
Histone H3 ◽  
Taxonomic Status ◽  
Its Region ◽  
Molecular Data ◽  
Coi Gene ◽  
Phylogenetic Position ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
The Family ◽  
Micromorphological Characters

Novel micromorphological characters in combination with molecular studies have led to an extensive revision of the taxonomy and systematics of scleractinian corals. In the present work, we investigate the macro- and micromorphology and the phylogenetic position of the genera Australomussa and Parascolymia, two monotypic genera ascribed to the family Lobophylliidae. The molecular phylogeny of both genera was addressed using three markers, the partial mitochondrial COI gene and the nuclear histone H3 and the ribosomal ITS region. Based on molecular data, Australomussa and Parascolymia belong to the Lobophylliidae and they cluster together with the genera Lobophyllia and Symphyllia within the same clade. While A. rowleyensis and P. vitiensis are closely related based on the three gene regions examined, their macro and micromorphology suggest that these species are distinct, differing in several characters, such as continuity and thickness of the costosepta, the number of septa, septal tooth height, spacing, and shape, and the distribution and shape of granules. Thus, we revise the taxonomic status of the genus Australomussa as a junior synonym of Parascolymia.

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