Polyclad phylogeny persists to be problematic

Abstract Two conflicting morphological approaches to polyclad systematics highlight the relevance of molecular data for resolving the interrelationships of Polycladida. In the present study, phylogenetic trees were reconstructed based on a short alignment of the 28S rDNA marker gene with 118 polyclad terminals (24 new) including 100 different polyclad species from 44 genera and 22 families, as well as on a combined dataset using 18S and 28S rDNA genes with 27 polyclad terminals (19 new) covering 26 different polyclad species. In both approaches, Theamatidae and Cestoplanidae were included, two families that have previously been shown to switch from Acotylea to Cotylea. Three different alignment methods were used, both with and without alignment curation by Gblocks, and all alignments were subjected to Bayesian inference and maximum likelihood tree calculations. Over all trees of the combined dataset, an extended majority-rule consensus tree had weak support for Theamatidae and Cestoplanidae as acotyleans, and also the cotylean genera Boninia, Chromyella and Pericelis appeared as acotyleans. With the most inclusive short 28S dataset, on the other hand, there is good support for the aforementioned taxa as cotyleans. Especially with the short 28S matrix, taxon sampling, outgroup selection, alignment method and curation, as well as model choice were all decisive for tree topology. Well-supported parts of the phylogeny over all trees include Pseudocerotoidea, Prosthiostomoidea, Stylochoidea, Leptoplanoidea and Cryptoceloidea, the latter three with new definitions. Unstable positions in the tree were found not only for Theamatidae, Cestoplanidae, Boninia, Chromyella and Pericelis, but also for Anonymus, Chromoplana and Cycloporus.

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Origin of the European avian-like swine influenza viruses

Journal of General Virology ◽

10.1099/vir.0.068569-0 ◽

2014 ◽

Vol 95 (11) ◽

pp. 2372-2376 ◽

Cited By ~ 10

Author(s):

Andi Krumbholz ◽

Jeannette Lange ◽

Andreas Sauerbrei ◽

Marco Groth ◽

Matthias Platzer ◽

...

Keyword(s):

Avian Influenza ◽

Phylogenetic Trees ◽

Sequence Data ◽

Swine Influenza ◽

H1n1 Influenza ◽

Molecular Data ◽

Influenza Viruses ◽

Time Resolved ◽

Genotype Constellation ◽

Tree Inference

The avian-like swine influenza viruses emerged in 1979 in Belgium and Germany. Thereafter, they spread through many European swine-producing countries, replaced the circulating classical swine H1N1 influenza viruses, and became endemic. Serological and subsequent molecular data indicated an avian source, but details remained obscure due to a lack of relevant avian influenza virus sequence data. Here, the origin of the European avian-like swine influenza viruses was analysed using a collection of 16 European swine H1N1 influenza viruses sampled in 1979–1981 in Germany, the Netherlands, Belgium, Italy and France, as well as several contemporaneous avian influenza viruses of various serotypes. The phylogenetic trees suggested a triple reassortant with a unique genotype constellation. Time-resolved maximum clade credibility trees indicated times to the most recent common ancestors of 34–46 years (before 2008) depending on the RNA segment and the method of tree inference.

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Accuracy of estimated phylogenetic trees from molecular data

Journal of Molecular Evolution ◽

10.1007/bf02300753 ◽

1983 ◽

Vol 19 (2) ◽

pp. 153-170 ◽

Cited By ~ 1520

Author(s):

Masatoshi Nei ◽

Fumio Tajima ◽

Yoshio Tateno

Keyword(s):

Phylogenetic Trees ◽

Molecular Data

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New species and findings of Pagastia Oliver (Diptera: Chironomidae: Diamesinae) from Central Asia, with DNA barcoding of known species of the genus

Zootaxa ◽

10.11646/zootaxa.4951.3.8 ◽

2021 ◽

Vol 4951 (3) ◽

pp. 559-570

Author(s):

EUGENYI A. MAKARCHENKO ◽

ALEXANDER A. SEMENCHENKO ◽

DMITRY M. PALATOV

Keyword(s):

New Species ◽

Central Asia ◽

Cytochrome Oxidase ◽

Phylogenetic Trees ◽

Morphological Characters ◽

Molecular Data ◽

Adult Males ◽

Cytochrome Oxidase Subunit ◽

Oxidase Subunit ◽

Coi Sequences

Chironomids of the genus Pagastia Oliver (Diamesinae, Diamesini) from the mountains of Central Asia are revised using both morphological characters and molecular data. Illustrated descriptions of the adult male Pagastia (P.) caelestomontana sp. nov. from Kirgizstan and Tajikistan, P. (P.) hanseni sp. nov. from Tajikistan, and record of a finding apparently a new species P. (P.) aff. lanceolata (Tokunaga) from Tajikistan as well as an updated a key to the determination of the adult males of all known species of Pagastia are provided. A phylogenetic framework is reconstructed based on two mitochondrial genes cytochrome oxidase subunit I (COI) sequences of 34 samples belonging to 7 species of the genus Pagastia and cytochrome oxidase subunit II (COII) available for most samples. Phylogenetic trees of some known species of the genus Pagastia were reconstructed using the combined dataset and Bayesian inference (BI) and Maximum Likelihood (ML) methods. The interspecific K2P distances between seven Pagastia species including P. (P.) caelestomontana sp. nov., P. (P.) hanseni sp. nov. and undescribed P. (P.) aff. lanceolata (Tokunaga) are 6.3–13.2 which corresponding to species level.

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Accuracy of estimated phylogenetic trees from molecular data

Journal of Molecular Evolution ◽

10.1007/bf01840887 ◽

1982 ◽

Vol 18 (6) ◽

pp. 387-404 ◽

Cited By ~ 123

Author(s):

Yoshio Tateno ◽

Masatoshi Nei ◽

Fumio Tajima

Keyword(s):

Phylogenetic Trees ◽

Molecular Data

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Molecular and morphometric characterisation of Xiphinema globosum Sturhan, 1978 (Nematoda: Longidoridae) from Spain

Nematology ◽

10.1163/138855410x500046 ◽

2011 ◽

Vol 13 (1) ◽

pp. 17-28 ◽

Cited By ~ 3

Author(s):

Blanca Landa ◽

Carolina Cantalapiedra-Navarrete ◽

Juan Palomares-Rius ◽

Pablo Castillo ◽

Carlos Gutiérrez-Gutiérrez

Keyword(s):

Phylogenetic Trees ◽

18S Rrna ◽

Matrix Representation ◽

Natural Environments ◽

28S Rrna ◽

Parsimony Method ◽

Rdna Genes ◽

Supertree Method ◽

The Matrix ◽

Relationship Of

AbstractDuring a recent nematode survey in natural environments of the Los Alcornocales Regional Park narrow valleys, viz., the renowned 'canutos' excavated in the mountains that maintain a humid microclimate, in southern Spain, an amphimictic population of Xiphinema globosum was identified. Morphological and morphometric studies on this population fit the original and previous descriptions and represent the first report from Spain and southern Europe. Molecular characterisation of X. globosum from Spain using D2-D3 expansion regions of 28S rRNA, 18S rRNA and ITS1-rRNA is provided and maximum likelihood and Bayesian inference analysis were used to reconstruct phylogenetic relationships within X. globosum and other Xiphinema species. A supertree solution of the different phylogenetic trees obtained in this study and in other published studies using rDNA genes are presented using the matrix representation parsimony method (MRP) and the most similar supertree method (MSSA). The results revealed a closer phylogenetic relationship of X. globosum with X. diversicaudatum, X. bakeri and with some sequences of unidentified Xiphinema spp. deposited in GenBank.

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A contribution towards the systematics of Magneuptychia Forster, 1964: Caeruleuptychia francisca (Butler, 1870), n. comb. (Lepidoptera: Nymphalidae: Satyrinae)

Tijdschrift voor Entomologie ◽

10.1163/22119434-bja10004 ◽

2020 ◽

pp. 1-11

Author(s):

Shinichi Nakahara ◽

Kaylin Kleckner ◽

Gerardo Lamas ◽

Blanca Huertas ◽

Keith R. Willmott

Keyword(s):

Maximum Likelihood ◽

Molecular Data ◽

Maximum Likelihood Analysis ◽

Maximum Likelihood Tree ◽

Likelihood Analysis ◽

First Time

We here transfer an euptychiine taxon hitherto placed in the polyphyletic genus Magneuptychia Forster, 1964, to Caeruleuptychia Forster, 1964. Caeruleuptychia francisca (Butler, 1870), n. comb. is reclassified based on a morphology-based maximum likelihood analysis, which is consistent with ongoing analyses of molecular data. Two putative synapomorphic characters are identified for the “Caeruleuptychia umbrosa clade”, one of which appears to be an unusual characteristic of euptychiine butterflies and is tested by optimizing onto the maximum likelihood tree. We also discuss the systematic placement of three additional enigmatic Caeruleuptychia species. A lectotype is designated for Euptychia francisca, and the genitalia of this species are illustrated here for the first time.

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Is there a need for accepting paraphyletic taxa? A case study in the Sardinian endemic Cymbalaria muelleri (Plantaginaceae)

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boz052 ◽

2019 ◽

Vol 191 (3) ◽

pp. 325-338 ◽

Cited By ~ 3

Author(s):

Pau Carnicero ◽

Peter Schönswetter ◽

Núria Garcia-Jacas ◽

Mercè Galbany-Casals

Keyword(s):

Genome Size ◽

Phylogenetic Trees ◽

Fragment Length Polymorphism ◽

Habitat Preferences ◽

Molecular Data ◽

Disjunct Distribution ◽

Morphological Differences ◽

A New Species ◽

The Mediterranean Basin

Abstract Evolution does not always result in dichotomous phylogenetic trees. For instance, in anacladogenetic speciation, where a new species originates by budding, the ancestral taxon is often initially paraphyletic. Here we study Cymbalaria muelleri (Plantaginaceae), a chasmophytic species endemic to Sardinia, a major island in the Mediterranean Basin. Its distribution range is divided into two well-delimited geographical groups with some morphological differences. Using a combination of morphology, molecular data (amplified fragment length polymorphism fingerprinting) and relative genome size, we found that the two geographical groups should be considered two separate taxa, which split through anacladogenesis. Accordingly, we formally describe the new paraphyletic subspecies C. muelleri subsp. villosa as the ancestor, from which C. muelleri subsp. muelleri originated by budding. Morphological analyses support the differentiation of the two subspecies, and there are strong diagnostic characters to differentiate them. In addition to morphology and genetics, slightly divergent habitat preferences and the disjunct distribution of the two subspecies also support the recognition of two taxa. Genome size data obtained for the two subspecies are consistent with the previously established hexaploidy of C. muelleri.

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Molecular characterisation of, and new data on, two populations of Xiphinema ingens Luc & Dalmasso, 1964 (Nematoda: Longidoridae) from Iran

Nematology ◽

10.1163/15685411-00002858 ◽

2015 ◽

Vol 17 (2) ◽

pp. 125-138

Author(s):

Sohrab Mirzaei ◽

Ebrahim Pourjam ◽

Majid Pedram

Keyword(s):

Bayesian Inference ◽

Maximum Likelihood ◽

Morphological Variation ◽

Phylogenetic Analyses ◽

Molecular Data ◽

28S Rdna ◽

Molecular Characterisation ◽

Morphometric Data ◽

Two Populations

Two populations of Xiphinema ingens were recovered and characterised based on morphological, morphometric and molecular data. Interesting morphological variation was observed on the nature of differentiation in uterus of females between both populations, i.e. one population had only a pseudo-Z-organ in the shape of globular bodies, whilst the second population had a similar pseudo-Z-organ but also had crystalloids which varied in size and number and were located near the pseudo-Z-globules or sometimes at some distance from them towards the vagina. Variation was also observed in the shape of tail of juveniles within each population as well as between two recovered populations. Both populations had the same range of morphometric data and formed a fully supported clade in both Bayesian inference (BI) and maximum likelihood (ML) methods of phylogenetic analyses using partial sequences of 28S rDNA D2-D3 and ITS1 regions. The two populations of X. ingens formed a clade with another Xiphinema species native to Iran (X. castilloi) in 28S and two species, X. macroacanthum and X. bernardi, in ITS1 trees.

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Phylogenetic relationships of the monogenomic species of the wheat tribe, Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences

Genome ◽

10.1139/g95-026 ◽

1995 ◽

Vol 38 (2) ◽

pp. 211-223 ◽

Cited By ~ 147

Author(s):

C. Hsiao ◽

N. J. Chatterton ◽

K. H. Asay ◽

K. B. Jensen

Keyword(s):

Phylogenetic Relationships ◽

Internal Transcribed Spacer ◽

Phylogenetic Trees ◽

Parallel Evolution ◽

Diploid Species ◽

Its Region ◽

Molecular Data ◽

Nuclear Ribosomal Dna ◽

The Arctic ◽

Cytogenetic Evidence

Phylogenetic relationships of 30 diploid species of Triticeae (Poaceae) representing 19 genomes were estimated from the sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The ITS sequence phylogeny indicated that: (i) each genome group of species is monophyletic, concordant with cytogenetic evidence; (ii) Hordeum (I) and Critesion (H) are basal; (iii) Australopyrum (W) is closely related to Agropyron (P); (iv) Peridictyon (G), Heteranthelium (Q), and Dasypyrum (V) are closely related to Pseudoroegneria (S); (v) most of the annuals, Triticum s.l. (A, B, D), Crithopsis (K), Taeniatherum (T), Eremopyrum (F), Henrardia (O), Secale (R), and two perennials, Thinopyrum (J) and Lophopyrum (E), all of Mediterranean origin, are a monophyletic group. However, phylogenetic trees based on morphology group these Mediteranean species with various perennial lineages of the Arctic-temperate region. The molecular data and biogeography of the tribe suggest that the Mediterranean lineage is derived from the Arctic-temperate lineage and that the two lineages have evolved in parallel. Extensive morphological parallelism apparently obscures the true genealogical history of the tribe when only morphology is considered.Key words: Poaceae, Triticeae, rDNA sequence, molecular phylogeny, parallel evolution.

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Potential cryptic speciation in Mediterranean populations of Ophioderma (Echinodermata: Ophiuroidea)

Zootaxa ◽

10.11646/zootaxa.2071.1.1 ◽

2009 ◽

Vol 2071 (1) ◽

pp. 1-20 ◽

Cited By ~ 20

Author(s):

SABINE STÖHR ◽

EMILIE BOISSIN ◽

ANNE CHENUIL

Keyword(s):

Mediterranean Sea ◽

Eastern Mediterranean ◽

Molecular Data ◽

Body Colour ◽

Separate Species ◽

Mediterranean Populations ◽

Weak Support ◽

Brooding Period ◽

Eastern Atlantic Ocean ◽

Coi Sequences

Ophioderma longicauda is a large brittlestar species, common in the Mediterranean Sea and spread across the subtropical-tropical eastern Atlantic Ocean. Recently, a morphologically similar brooding form of O. longicauda was discovered in the eastern Mediterranean Sea. The brooding period is restricted to late May and early June and the largest females brood over 1,000 juveniles, all of the same ontogenetic stage. Brooders differ from non-brooding O. longicauda in body colour (dominated by green instead of red), gonad colour (in alcohol white instead of oliveto reddish-brown) and size (up to 17 mm disk diameter instead of 30 mm). These characters overlap between both forms though. Molecular data (mt-COI sequences) lend weak support to the existence of two separate species, but suggest that if a split occurred it is recent and both forms interbreed. Alternatively, the eastern Mediterranean populations could represent a poecilogonous subgroup of O. longicauda.

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