A molecular phylogeny of Callianassidae and related families (Crustacea : Decapoda : Axiidea) with morphological support

2020 ◽  
Vol 34 (2) ◽  
pp. 113 ◽  
Author(s):  
Rafael Robles ◽  
Peter C. Dworschak ◽  
Darryl L. Felder ◽  
Gary C. B. Poore ◽  
Fernando L. Mantelatto
Keyword(s):  
Bayesian Analysis ◽  
Molecular Analysis ◽  
Single Species ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
12S Rrna ◽  
New Genera ◽  
Key Species ◽  
The Family

The axiidean families Callianassidae and Ctenochelidae, sometimes treated together as Callianassoidea, are shown to represent a monophyletic taxon. It comprises 265 accepted species in 74 genera, twice this number of species if fossil taxa are included. The higher taxonomy of the group has proved difficult and fluid. In a molecular phylogenetic approach, we inferred evolutionary relationships from a maximum-likelihood (ML) and Bayesian analysis of four genes, mitochondrial 16S rRNA and 12S rRNA along with nuclear histone H3 and 18S rRNA. Our sample consisted of 298 specimens representing 123 species plus two species each of Axiidae and Callianideidae serving as outgroups. This number represented about half of all known species, but included 26 species undescribed or not confidently identified, 9% of all known. In a parallel morphological approach, the published descriptions of all species were examined and detailed observations made on about two-thirds of the known fauna in museum collections. A DELTA (Description Language for Taxonomy), database of 135 characters was made for 195 putative species, 18 of which were undescribed. A PAUP analysis found small clades coincident with the terminal clades found in the molecular treatment. Bayesian analysis of a total-evidence dataset combined elements of both molecular and morphological analyses. Clades were interpreted as seven families and 53 genera. Seventeen new genera are required to reflect the molecular and morphological phylograms. Relationships between the families and genera inferred from the two analyses differed between the two strategies in spite of retrospective searches for morphological features supporting intermediate clades. The family Ctenochelidae was recovered in both analyses but the monophyly of Paragourretia was not supported by molecular data. The hitherto well recognised family Eucalliacidae was found to be polyphyletic in the molecular analysis, but the family and its genera were well defined by morphological synapomorphies. The phylogram for Callianassidae suggested the isolation of several species from the genera to which they had traditionally been assigned and necessitated 12 new generic names. The same was true for Callichiridae, with stronger ML than Bayesian support, and five new genera are proposed. Morphological data did not reliably reflect generic relationships inferred from the molecular analysis though they did diagnose terminal taxa treated as genera. We conclude that discrepancies between molecular and morphological analyses are due at least in part to missing sequences for key species, but no less to our inability to recognise unambiguously informative morphological synapomorphies. The ML analysis revealed the presence of at least 10 complexes wherein 2–4 cryptic species masquerade under single species names.

scholarly journals Reclassification of the Angraecum-alliance (Orchidaceae, Vandoideae) based on molecular and morphological data

2013 ◽  
Vol 29 (1) ◽  
pp. 1-23 ◽  
Author(s):  
Dariusz L. Szlachetko ◽  
Piotr Tukałło ◽  
Joanna Mytnik-Ejsmont ◽  
Elżbieta Grochocka
Keyword(s):  
Bayesian Analysis ◽  
Molecular Analysis ◽  
Nuclear Genome ◽  
Intergenic Spacer ◽  
Its Region ◽  
The Other ◽  
Morphological Data ◽  
New Genera ◽  
New Classification ◽  
Morphological Studies

Abstract Results of molecular analysis compared with morphological studies were used for reclassification of the Angraecumalliance (Orchidaceae). For the purpose of this study we sequenced the ITS region (ITS1-5.8S-ITS2) of nrDNA representing nuclear genome and the plastid region trnL-F (including intron of trnL gene and trnL-trnF intergenic spacer). The ITS matrix includes 97 samples representing 86 species and the trnL-F matrix includes 94 samples representing 86 species. We focus mainly on the genus Angraecum, however the other genera of Angraecinae are also included (Aeranthes, Campylocentrum, Dendrophylax, Cryptopus, Calyptrochilum, Lemurorchis, Jumellea, Neobathiea, Oeonia, Oeoniella, Sobennikoffia). Additional 43 sequences, including an outgroup (Polystachya modesta) and other representatives of the subtribes Aeridinae (Aerides) and Aerangidinae (Aerangis, Angraecopsis, Erasanthe, Solenangis), were obtained from NCBI resources. Bayesian analysis using MrBayes 3.1.2 on the combined ITS/trnL-F matrix were performed. The monophyly of Angraecinae with an inclusion of Aerangidinae is highly supported by both methods (93 BP/100 PP). The Angraecoid taxa formed two well supported clades, namely clade I (89 BP/100 PP) and clade II (84 BP/100 PP). New classification based on both molecular and classical taxonomy studies is presented including a key to the genera. The subtribe Angraecinae includes 36 genera, 18 of them, included within Angraecum by different authors so far, are treated here. Five new genera are described: Eichlerangraecum, Hermansia, Lesliegraecum, Pectianriella and Rudolfangraecum. Ten sections of Angraecum are raised to the generic status.

Analysis of the differences between Syntormon pallipes and S. pseudospicatus (Diptera: Dolichopodidae): morphological and molecular data

2019 ◽  
Vol 28 (2) ◽  
pp. 305-316
Author(s):  
M.A. Chursina ◽  
I.Ya. Grichanov
Keyword(s):  
Dna Analysis ◽  
Distinct Species ◽  
Molecular Data ◽  
Wing Shape ◽  
Morphological Data ◽  
12S Rrna ◽  
Separate Species ◽  
Geometric Morphometric ◽  
Geometric Morphometric Analysis ◽  
Morphological And Molecular Data

The recent catalogues of the family Dolichopodidae considered Syntormon pallipes (Fabricius, 1794) and S. pseudospicatus Strobl, 1899 as separate species. In this study, we used three approaches to estimate the significance of differences between the two species: molecular analysis (COI and 12S rRNA sequences), analysis of leg colour characters and geometric morphometric analysis of wing shape. The morphological data confirmed the absence of significant differences between S. pallipes and S. pseudospicatus found in the DNA analysis. Significant differences in the wing shape of two species have not been revealed. Hence, according to our data, there is no reason to consider S. pseudospicatus as a distinct species.

Phylogeny and taxonomy of the Rhinorhynchinae (Coleoptera:Nemonychidae)

2010 ◽  
Vol 24 (6) ◽  
pp. 573 ◽  
Author(s):  
Guillermo Kuschel ◽  
Richard A. B. Leschen
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
New Caledonia ◽  
Molecular Data ◽  
Host Use ◽  
New Genera ◽  
Plant Associations ◽  
The Family ◽  
Fossil Genus ◽  
Subjective Synonym

An overview of the taxa of Rhinorhynchinae (Nemonychidae) is presented. A phylogenetic analysis of the 19 extant genera of the Rhinorhynchinae and one fossil genus from the Lower Cretaceous (Cratomacer Zherikhin & Gratshev), based on 29 characters of adults, larvae and host plant associations, shows three monophyletic groups, treated as tribes (Rhinorhynchini, Mecomacerini and Rhynchitomacerini). Primitive associations are unknown for Rhinorhynchinae and early host use diversification included associations with Ranunculaceae (Nemonyx Redtenbacher), Pinaceae (Cimberis Gozis), Nothofagaceae (Rhynchitomacerini) and Podocarpaceae (Rhinorhynchini). While Mecomacerini diversified on Araucariaceae, within Rhinorhynchini there was a single reversal to Araucariaceae and a shift in Atopomacer Kuschel to Pinaceae. Placement of Cratomacer into Mecomacerini is consistent with geological and molecular data that suggest gymnosperms may have been the primitive hosts for the family. Three new genera are described in Rhinorhynchinae: Araucomacer, gen. nov. (type species A. hirticeps Kuschel) from Chile, Idiomacer, gen. nov. (type species I. basicornis, sp. nov.) from New Caledonia, and Zimmiellus, gen. nov. (type species Z. fronto, sp. nov.) from Queensland, Australia, while Stenomacer Kuschel, stat. nov. from Chile is reinstated from synonymy. Seven species are described as new: Atopomacer grandifurca, sp. nov. from Costa Rica and Panama, A. obrieni, sp. nov. from Mexico, A. panamensis, sp. nov. from Panama, A. pini, sp. nov. from Mexico, A. podocarpi, sp. nov. from Venezuela, Basiliogeus dracrycarpi, sp. nov. from western New Guinea and B. inops, sp. nov. from Queensland. Rhynchitomacer rufus Kuschel is a new junior subjective synonym of R. nigritus Kuschel, syn. nov., R. viridulus Kuschel is a new junior subjective synonym of R. flavus Voss, syn. nov. and Stenomacer fuscus Kuschel is a new junior subjective synonym of S. vernus Kuschel, syn. nov. Keys to genera of Rhinorhynchinae and to species of Atopomacer, Rhynchitomacer and Stenomacer are included. Diagnoses of the three extant subfamilies of Nemonychidae are included.

Back to the Future? Molecules Take Us Back to the 1925 Classification of the Lembophyllaceae (Bryopsida)

2009 ◽  
Vol 34 (3) ◽  
pp. 443-454 ◽  
Author(s):  
Dietmar Quandt ◽  
Sanna Huttunen ◽  
Ray Tangney ◽  
Michael Stech
Keyword(s):  
Single Species ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
New Family ◽  
Morphological Studies ◽  
The Family ◽  
Family Level ◽  
Plastid Markers ◽  
Pleurocarpous Moss

Although the Lembophyllaceae has undergone considerable revision during the last century, the generic and familial level relationships of this pleurocarpous moss family are still poorly understood. To address this problem, a generic revision of the Lembophyllaceae based on molecular data was undertaken. We analyzed two plastid markers, the trnL-trnF and the psbT-psbH region in combination with the ITS2 of nuclear ribosomal DNA. The molecular data reveal that the current circumscription of the family is too narrow and that several genera previously placed in the Lembophyllaceae should be reincluded. The family includes: Bestia, Camptochaete, Dolichomitra, Dolichomitriopsis, Fallaciella, Fifea, Isothecium, Lembophyllum, Looseria stat. nov., Pilotrichella, Rigodium, Tripterocladium, and Weymouthia. Looseria contains a single species: Looseria orbiculata comb. nov. Acrocladium is excluded and provisionally accommodated in the Lepyrodontaceae. Generic limits supported by the molecular data support a return to the early twentieth century family concept of Brotherus. The analyses indicate that the segregate genus Orthostichella is distinct from its parent genus Pilotrichella, probably at the family level. Whereas Pilotrichella is resolved within the Lembophyllaceae, Orthostichella clusters with Porotrichum and Porothamnium forming a clade (OPP-clade) sister to the remaining Neckeraceae and Lembophyllaceae. Hence, the Neckeraceae is paraphyletic. Recognition of the OPP-clade as a new family is desirable but awaits the results of detailed ongoing morphological studies.

Global classification and evolution of brushlegged mayflies (Insecta: Ephemeroptera: Oligoneuriidae): phylogenetic analyses of morphological and molecular data and dated historical biogeography

2019 ◽  
Vol 187 (2) ◽  
pp. 378-412 ◽  
Author(s):  
Fabiana Criste Massariol ◽  
Daniela Maeda Takiya ◽  
Frederico Falcão Salles
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Time Estimation ◽  
Single Species ◽  
Molecular Data ◽  
Neotropical Region ◽  
Fossil Species ◽  
Divergence Time Estimation ◽  
The Family ◽  
Family Based

AbstractOligoneuriidae is a Pantropical family of Ephemeroptera, with 68 species described in 12 genera. Three subfamilies are recognized: Chromarcyinae, with a single species from East Asia; Colocrurinae, with two fossil species from Brazil; and Oligoneuriinae, with the remaining species distributed in the Neotropical, Nearctic, Afrotropical and Palaearctic regions. Phylogenetic and biogeographical analyses were performed for the family based on 2762 characters [73 morphological and 2689 molecular (COI, 16S, 18S and 28S)]. Four major groups were recovered in all analyses (parsimony, maximum likelihood and Bayesian inference), and they were assigned to tribal level, namely Oligoneuriini, Homoeoneuriini trib. nov., Oligoneuriellini trib. nov. and Elassoneuriini trib. nov. In addition, Yawari and Madeconeuria were elevated to genus level. According to Statistical Dispersal-Vicariance (S-DIVA), Dispersal Extinction Cladogenesis (DEC) and divergence time estimation analyses, Oligoneuriidae originated ~150 Mya in the Gondwanan supercontinent, but was probably restricted to the currently delimited Neotropical region. The initial divergence of Oligoneuriidae involved a range expansion to Oriental and Afrotropical areas, sometime between 150 and 118 Mya. At ~118 Mya, the family started its diversification, reaching the Nearctic through dispersal from the Neotropical region and the Palaearctic and Madagascar from the Afrotropical region.

scholarly journals Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

2016 ◽  
Vol 12 (5) ◽  
pp. 20151003 ◽  
Author(s):  
Thomas Guillerme ◽  
Natalie Cooper
Keyword(s):  
Data Collection ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Living Species ◽  
Anatomical Characters ◽  
The Impact

Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies.

scholarly journals Synonymization of the male-based ant genus Phaulomyrma (Hymenoptera, Formicidae) with Leptanilla based upon Bayesian total-evidence phylogenetic inference

2020 ◽  
Author(s):  
Zachary H. Griebenow
Keyword(s):  
Sequence Data ◽  
Phylogenetic Inference ◽  
Morphological Characters ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Systematic Revision ◽  
Dna Sequence Data ◽  
Evidence Framework ◽  
Nuclear Loci

Abstract.Although molecular data have proven indispensable in confidently resolving the phylogeny of many clades across the tree of life, these data may be inaccessible for certain taxa. The resolution of taxonomy in the ant subfamily Leptanillinae is made problematic by the absence of DNA sequence data for leptanilline taxa that are known only from male specimens, including the monotypic genus Phaulomyrma Wheeler & Wheeler. Focusing upon the considerable diversity of undescribed male leptanilline morphospecies, the phylogeny of 35 putative morphospecies sampled from across the Leptanillinae, plus an outgroup, is inferred from 11 nuclear loci and 41 discrete male morphological characters using a Bayesian total-evidence framework, with Phaulomyrma represented by morphological data only. Based upon the results of this analysis Phaulomyrma is synonymized with Leptanilla Emery, and male-based diagnoses for Leptanilla that are grounded in phylogeny are provided, under both broad and narrow circumscriptions of that genus. This demonstrates the potential utility of a total-evidence approach in inferring the phylogeny of rare extant taxa for which molecular data are unavailable and begins a long-overdue systematic revision of the Leptanillinae that is focused on male material.

Contributions to Molecular Phylogeny of Lichen-Forming Fungi, 1. The Family Candelariaceae

2020 ◽  
Vol 62 (3-4) ◽  
pp. 293-307
Author(s):  
S. Y. Kondratyuk ◽  
L. Lőkös ◽  
M.-H. Jeong ◽  
S.-O. Oh ◽  
A. S. Kondratiuk ◽  
...  
Keyword(s):  
South America ◽  
Molecular Phylogeny ◽  
South Korea ◽  
Phylogenetic Tree ◽  
Single Species ◽  
Molecular Data ◽  
New Combinations ◽  
New Synonym ◽  
The Family ◽  
First Time

Three genera new for science, i.e. Candelinella S. Y. Kondr. for the Candelariella makarevichiae group, Opeltiella S. Y. Kondr. for the Candelaria fraudans group, as well as Protocandelariella Poelt, D. Liu, J.-S. Hur et S. Y. Kondr. for the Candelariella subdeflexa group are proposed for robust monophyletic branches of the Candelariaceae on the basis of three-gene phylo- geny (i.e. concatenated nrITS, 12S mtSSU and 28S nrLSU sequences). Eight new combinations, i.e. Candelinella makarevichiae (for Candelariella makarevichiae S. Y. Kondr., L. Lokos et J.-S. Hur), Candelinella deppeanae (for Candelariella deppeanae M. Westb.), Opeltiella fraudans (for Candelaria fraudans Poelt et Oberw.), Opeltiella fibrosoides (for Candelaria fibrosoides M. Westb. et Froden), Opeltiella rubrisoli (for Candelariella rubrisoli D. Liu et J.-S. Hur), Opeltiella canadensis (for Candelariella canadensis H. Magn.), Protocandelariella subdeflexa (for Lecanora subdeflexa Nyl.), Protocandelariella blastidiata (for Candelariella blastidiata L. Yakovchenko) are provided.Molecular data provided for Candelinella makarevichiae (including holotype and iso- type), as well as additional specimens of Candelaria asiatica from South Korea for the first time. The latter species (Candelaria asiatica) from China, as well as’Candelaria’ murrayi from Argentina, South America are recorded for the first time. Voucher of Candelariella vitellina from Antarctica is also identified based on molecular phylogeny. It is for the first time shown that ’Candelaria’murrayi is positioned in the outermost position to Candelaria s. str. branch of the phylogenetic tree of the Candelariaceae, and may belong to another genus. Status of the ’Candelariella’medians group, the’Candelariella’ placodizans group, as well as single species ’Candelariella’reflexa and’Candelaria’ pacifica, forming separate branches outside the Candelariella s. str. and Candelaria s. str. clades, will be clarified when additional molecular data will be accumulated. Candelariella subsquamulosa D. Liu et Hur, recently described from South Korea (Liu et al. 2019), proved to be a new synonym of Candelinella makarevichiae.

Phylogeny and affiliation of European Anthomyzidae (Diptera) based on mitochondrial 12S and 16S rRNA

Zootaxa ◽  
2009 ◽  
Vol 2054 (1) ◽  
pp. 49-58 ◽  
Author(s):  
JINDŘICH ROHÁČEK ◽  
ANDREA TÓTHOVÁ ◽  
JAROMÍR VAŇHARA
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bayesian Analysis ◽  
Phylogenetic Relationships ◽  
Posterior Probability ◽  
Morphological Data ◽  
Rrna Gene ◽  
Gene Markers ◽  
The Family ◽  
Species Groups

The phylogenetic Bayesian analysis of combined mitochondrial 12S and 16S rRNA gene markers in European representatives of Anthomyzidae supported the monophyly of the family, confirmed the validity of the genera and provided a resolution of the generic affiliation of some aberrant species. The interrelationships of most genera have not been resolved definitively due to insufficient posterior probability values. Despite this, the clade clustering the genus Anthomyza Fallén, 1810, Fungomyza Roháček, 1999 and the Anthomyza socculata group is considered to reflect the real phylogenetic relationships of these taxa as it is also supported by morphological data. The relationships within the genus Anthomyza are resolved and monophyly of its species-groups confirmed. Within the genus Stiphrosoma Czerny, 1928, S. fissum Roháček, 1996, a species of unknown relationships, was found to be most closely allied to S. sabulosum (Haliday, 1837). Based on the above analysis a removal of the aberrant species Paranthomyza caricis Roháček, 1999 and Anthomyza socculata (Zetterstedt, 1847) from genera to which they were formerly affiliated, is suggested.

scholarly journals Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

2020 ◽  
Author(s):  
Tamara Spasojevic ◽  
Gavin R Broad ◽  
Ilari E Sääksjärvi ◽  
Martin Schwarz ◽  
Masato Ito ◽  
...  
Keyword(s):  
Evolutionary Rate ◽  
Total Evidence ◽  
Morphological Data ◽  
Phylogenetic Study ◽  
Phylogenetic Distance ◽  
Rate Heterogeneity ◽  
The Family ◽  
The Impact ◽  
Age Estimates

Abstract Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information, but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artefact that might be detrimental for total-evidence dating: “bare-branch attraction”, namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought, but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information.

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