Molecular phylogeny and systematics of Prostanthera (Lamiaceae)

2012 ◽  
Vol 25 (5) ◽  
pp. 341 ◽  
Author(s):  
Trevor C. Wilson ◽  
Barry J. Conn ◽  
Murray J. Henwood
Keyword(s):  
Bayesian Inference ◽  
Molecular Phylogeny ◽  
Morphological Variation ◽  
Maximum Parsimony ◽  
Sequence Data ◽  
Morphological Characters ◽  
Molecular Data ◽  
Sister Relationship ◽  
Definition Of ◽  
Inference Methods

Prostanthera is the largest genus of Lamiaceae in Australia and was last comprehensively revised in 1870. To test the classification, and the homology of the morphological characters on which it is based, we analysed nuclear (ETS) and chloroplast (trnT–F and ndhF–rpl32) sequence data for 71 species of Westringieae (Lamiaceae) in separate and combined datasets by using maximum-parsimony and Bayesian-inference methods. Results supported the monophyly of the Westringieae, but indicated that Prostanthera is paraphyletic with respect to Wrixonia, requiring the latter to be synonymised with the former. Although combinations of datasets provided some degree of infrageneric resolution within Prostanthera sensu lato, none of its sections or series could be recovered unambiguously. Prostanthera section Prostanthera and P. section Klanderia (regarded as entomophilous and ornithophilous, respectively) did not form a sister relationship, and neither could be unequivocally resolved as monophyletic. However, all species of P. section Klanderia nested within P. section Prostanthera raising the possibility that P. section Prostanthera is paraphyletic. Similarly, the phylogeny of Prostanthera based on molecular data could not be reconciled with the morphological definition of the traditionally recognised series. We recommend abandoning Bentham’s series as a means of organising morphological variation within the genus, but acknowledge that it is premature to discard Bentham’s sections. The evolutionary and systematic implications of the lack of congruence between our molecular phylogeny and morphologically defined subgeneric taxa are discussed.

scholarly journals Molecular phylogeny of the Taeniapterini (Diptera: Micropezidae) using nuclear and mitochondrial DNA, with a reclassification of the genus Taeniaptera Macquart

2015 ◽  
Vol 46 (5) ◽  
pp. 411-430 ◽  
Author(s):  
Morgan D. Jackson ◽  
Stephen A. Marshall ◽  
Jeffrey H. Skevington
Keyword(s):  
Mitochondrial Dna ◽  
Bayesian Inference ◽  
Molecular Phylogeny ◽  
Maximum Parsimony ◽  
New World ◽  
Molecular Data ◽  
Species Group ◽  
Mitochondrial Genes ◽  
Paraphyletic Group ◽  
Total Dna

DNA molecular data are used to generate a phylogeny for the micropezid subfamily Taeniapterinae. Thirty-two taeniapterine species were sampled, including 10 of the 20 New World genera recognized by Steyskal, as well as one genus formerly treated as a synonym of Poecilotylus Hennig (Hemichaeta Steyskal). Five species from the Micropezinae were included as outgroups. A total DNA dataset of 4705 bp, including mitochondrial genes (12S and cytochrome c oxidase I (COI)) and nuclear coding genes (wingless and CAD), was analysed using maximum parsimony and Bayesian inference. The genus Taeniaptera Macquart was found to be non-monophyletic with respect to the remainder of the Taeniapterini analysed here. Taeniaptera is restricted to the Taeniaptera trivittata Macquart species group, Mitromyia Cresson is resurrected to contain the Taeniaptera grata (Wulp) species group, and Paragrallomyia Hendel is resurrected to contain most species previously considered Taeniaptera. Poecilotylus is recognized as a paraphyletic group awaiting further research.

Gloeodontia yunnanensis sp. nov. (Russulales, Basidiomycota) from China, evidenced by morphological characters and phylogenetic analyses

Phytotaxa ◽  
2020 ◽  
Vol 432 (2) ◽  
pp. 111-118
Author(s):  
LU CHEN ◽  
ZHENG-JUN SHI ◽  
CHUN-HUA WU ◽  
CHANG-LIN ZHAO
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Morphological Characters ◽  
Fungal Species ◽  
Monophyletic Lineage ◽  
Thin Walled ◽  
Inference Methods

A new wood-inhabiting fungal species, Gloeodontia yunnanensis, is proposed based on a combination of morphological features and DNA data. The species is characterized by an annual, resupinate basidiomata with smooth hymenial surface, a monomitic hyphal system with thin-walled, clamped generative hyphae and obclavate cystidia and subglobose to globose, hyaline, thick-walled, asperulate, strongly amyloid, acyanophilous basidiospores measuring 3.3–4.3 × 2.5–3.5 µm. Sequences of ITS and 28S gene regions of the studied samples were generated and phylogenetic analyses were performed with Maximum Likelihood, Maximum Parsimony and Bayesian Inference methods. The analyses based on ITS+28S sequences showed that G. yunnanensis nested in the Gloeodontia clade and formed a monophyletic lineage with strong support (100% BS, 100% BP, 1.00 BPP).

Neofavolus yunnanensis sp. nov. (Polyporales, Basidiomycota) from China: evidence from morphology and DNA sequence data

Phytotaxa ◽  
2019 ◽  
Vol 408 (2) ◽  
pp. 109-116 ◽  
Author(s):  
KAI-YUE LUO ◽  
XIANG MA ◽  
CHANG-LIN ZHAO
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequence ◽  
Maximum Parsimony ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Evidence ◽  
Dna Sequence Data ◽  
Thin Walled ◽  
Inference Methods

A new wood-inhabiting species, Neofavolus yunnanensis, is proposed based on a combination of morphological features and molecular evidence. The species is characterized by an annual growth, laterally stipitate basidiomata with reniform to semicircular pileus, dimitic hyphal system with clamped generative hyphae, IKI–, CB–, and cylindrical, hyaline, thin-walled, smooth, IKI–, CB– basidiospores. Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses showed that N. yunnanensis was nested into the genus Neofavolus and then was as a sister with N. mikawae and then grouped with N. alveolaris and N. cremeoalbidus.

A new karyological variant of Oecomys (Rodentia: Sigmodontinae) and its phylogenetic relationship based on molecular data

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 195-203 ◽  
Author(s):  
Ana Flávia Belchior de Andrade ◽  
Cibele Rodrigues Bonvicino
Keyword(s):  
Gene Flow ◽  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Maximum Parsimony ◽  
Sequence Data ◽  
Molecular Data ◽  
The Other ◽  
Morphological Attributes ◽  
Two Parameters ◽  
Brazilian Pantanal

A new karyological variant of the Sigmodontinae genus Oecomys was detected in specimens from Brazilian Pantanal. Karyologic analyses showed 2n = 72 and FN = 90, which differs from all known chromosomal complements of the genus. This new karyomorph showed distinctive morphological attributes and could not be attributed to any described Oecomys species. Molecular analysis using cytochrome-b sequence data suggested the monophyly of Oecomys. Maximum-likelihood analyses placed the Oecomys sp. haplotype clade as the sister branch to Oecomys bicolor, whereas maximum-parsimony analyses did not resolve its relationship with the other Oecomys species. Kimura's two parameters distance estimates between this and other Oecomys species are high, and active gene flow has been found not to coexist with these divergence estimates.Key words: Oecomys sp., rodent, Sigmodontinae, karyotype, molecular phylogeny.

Xylodon bambusinus and X. xinpingensis spp. nov. (Hymenochaetales) from southern China

Phytotaxa ◽  
2021 ◽  
Vol 511 (3) ◽  
Author(s):  
XIANG MA ◽  
CHANG-LIN ZHAO
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Growth Habit ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Two New Species ◽  
Thin Walled ◽  
Inference Methods

Two new species, Xylodon bambusinus and X. xinpingensis, are proposed based on morphological and molecular evidences. Both species share the annual growth habit, resupinate basidiomata and monomitic hyphal system with clamped, colorless generative hyphae, smooth, thin-walled basidiospores, but X. bambusinus is characterized by the smooth to tuberculate hymenial surface, presence of capitate and fusiform cystidia, broad ellipsoid basidiospores, while X. xinpingensis by the reticulate hymenophore with cream hymenial surface, and subglobose basidiospores (4.5–6 × 3.5–5 µm). Sequences of ITS and LSU nrRNA gene regions of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and Bayesian inference methods. The phylogenetic analyses based on molecular data of ITS and ITS+nLSU sequences showed that X. bambusinus was sister to X. subclavatus, while X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus. The nLSU dataset revealed that X. bambusinus grouped with X. asperus and X. brevisetus with lower supports, and that X. xinpingensis grouped with X. astrocystidiatus and X. paradoxus and then with X. rimosissimus without supports. Both morphological and molecular evidences confirmed the placement of two new species in Xylodon. Description and figures from the new species and a key to the known species of Xylodon from China are presented.

Systematics and phylogeography of the Australasian mangrove crabs Parasesarma semperi and P. longicristatum (Decapoda : Brachyura : Sesarmidae) based on morphological and molecular data

2018 ◽  
Vol 32 (1) ◽  
pp. 196 ◽  
Author(s):  
Adnan Shahdadi ◽  
Peter J. F. Davie ◽  
Christoph D. Schubart
Keyword(s):  
Genetic Data ◽  
Morphological Characters ◽  
Molecular Data ◽  
Geographic Range ◽  
The Philippines ◽  
Mitochondrial Genes ◽  
Width Ratio ◽  
Sister Relationship ◽  
Mangrove Crabs ◽  
Morphological And Molecular Data

Parasesarma semperi (Bürger, 1893) was first described from Bohol in the Philippines and is considered to be widely distributed in Southeast Asia. Parasesarma longicristatum (Campbell, 1967) was originally described as a subspecies of P. semperi from Queensland, Australia, and later recognised as a full species. In this study, we re-examine specimens of the two species from across their entire geographic range using genetic markers, a morphometric analysis, and traditional morphological characters. Previous taxonomic species diagnoses were found to be unreliable, but morphometric principle component analyses consistently separate the two species, with the length to width ratio of the propodus of the fourth pereiopod being of particular importance. Genetic data corresponding to the mitochondrial genes COI, ND1 and 16S confirmed a close sister relationship between the two species, forming reciprocally monophyletic groups. Both species have high haplotype diversities and high intraspecific gene flow.

Living and fossil placentals

2004 ◽  
Author(s):  
T.S. Kemp
Keyword(s):  
Sequence Data ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Molecular Sequence Data ◽  
Minor Characters ◽  
Molecular Sequence ◽  
Large Sets ◽  
Anterior Teeth ◽  
Basal Group

The vast majority of living and fossil mammals are placentals. Today there are about 4,400 species, which are traditionally organised into 18 Orders, with an extra one if the Pinnipedia are separated from the Carnivora, and a twentieth if the recently extinct Malagasy order Bibymalagasia is recognised as such. There have been many attempts to discover supraordinal groupings from amongst these Orders based on morphological characters, though few proposals have been universally accepted. It is only with the advent of increasingly large sets of molecular sequence data in the last few years that a reasonably robust resolution looks imminent, although these contemporary analyses are remarkably and controversially at odds with the traditional ones. Novacek et al. (1988) summarised the then current situation regarding supraordinal classification of placentals, a time at which morphology was still dominant but molecular data was at the threshold of significance. They accepted a basal group Edentata that combined the Xenarthra of the New World with the Pholidota of the Old, based on a few cranial characters, loss of the anterior teeth, and reduction of the enamel of the remaining ones. This left the rest of the living placentals as a monophyletic group Epitheria, sharing such apparently minor characters as the shape of the stapes bone in the ear. They found very little resolution within the Epitheria, and concluded that there was a polychotomy of no less than nine lineages arranged as a ‘star’ phylogeny. No remnant of the previously recognised taxon Ferungulata, created by Simpson (1945) for the Carnivora plus the ungulate orders Artiodactyla, Perissodactyla, Proboscidea, Hyracoidea, Sirenia, and Tubulidentata remained. On the other hand, three supra ordinal taxa of earlier authors did survive. One was Gregory’s (1910) Archonta, consisting of generally conservative forms and by now composed of the Primates, Dermoptera, Scandentia, and Chiroptera, but excluding the Lipotyphla. The second was Glires, originating with Linnaeus (1758) and widely accepted ever since, for the Rodentia and Lagomorpha; Novacek et al. (1988) tentatively placed the Macroscelidea as the sister-group of the Glires. The third supraordinal taxon recognised was, like Glires, well-established if not universally accepted.

Revision of the Nepalese genus Microplinthus Zherichin, 1987 (Coleoptera: Curculionidae: Molytinae), with description of 25 new species

Zootaxa ◽  
2020 ◽  
Vol 4794 (1) ◽  
pp. 1-63
Author(s):  
MASSIMO MEREGALLI
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Bayesian Inference ◽  
Maximum Parsimony ◽  
Morphological Characters ◽  
Type Locality ◽  
Central Nepal

The Nepalese genus Microplinthus Zherichin, 1987 is revised. The following 25 new species are described (type locality in parentheses): M. annapurnae (Annapurna Himal, Rambrong Danda, 28°23’N 84°13’E), M. arunensis (Khandbari Distr., forest S. Mansimgma, 27°30’N 87°20’E), M. brevipennis (Manaslu Himal, Bhara Pokhari, 28°18’N 84°28’E), M. durga (W Pokhara, near Ghorepani, 28°24’N 83°42’E), M. franzi (Kaligandakhi valley, between Lethe and Tukuche, 28°36’N 83°38’E), M. ganesha (Ganesh Himal, Rupchet, 28°05’N 85°09’E), M. godawaricus (Kathmandu, Phulchowki, 27°34’N 85°24’E), M. gupta (Helambu Himal, upper Chipling, 27°53’N 85°28’E), M. helambuensis (Central Nepal, between Mulkharka and Thare Pati, 28°08’N 85°22’E–28°02’N 85°29’E), M. jaegeri (W Pokhara, Mt. Panchase, 28°13’N 83°48’E), M. karnalicus (Karnali Distr. 5 km E Charta, 29°18’N 82°20’E), M. kaskianus (Kaski Distr., above Pothana, 28°19’N 83°51’E), M. kaumarya (Karnali Distr., Gotichaur valley, 29°12’10”N 82°18’56”E), M. khandbariensis (Khandbari Distr., above Seduwa, 27°34’N 87°15’E), M. koshianus (Koshi Prov., SW Chichilla, 27°27.01’N 87°13.13’E), M. letheensis (Kaligandakhi valley, between Lethe and Tukuche, 28°36’N 83°38’E), M. longipennis (Manaslu Himal, Bhara Pokhari lekh, 28°18’24”N 84°28’06”E), M. messneri (Panchtar Distr., Dhorpar Kharka, 27°05’N 87°55’E), M. newarorum (Phulchowki Distr., Lalitpur, 27°34’N 85°24’E), M. phulchowkianus (Kathmandu, Phulchowki, 27°34’N 85°24’E), M. rugosus (Solokhumbu Distr., Lamiura Danda, 27°34’N 86° 30’E), M. schmidti (Manaslu Himal, Dudh Pokhari lekh, 28°20’N 84°35’E), M. sherpa (Khandbari Distr., Bakan, 27°38’N 87°12’E), M. tamanus (Rolwaling Himal, upper Simigau, 27°51’N 86°15’E), M. yeti (Hinku Distr., Drangka Khola bridge, 27°35’N 86°47’E). A key for the identification of all species of Microplinthus is given. A phylogenetic analysis based on morphological characters of the species referable to the genera Falsanchonus, Microniphades and Microplinthus was carried out, implementing Bayesian Inference and Maximum Parsimony. Results indicate that the genera Falsanchonus and Microniphades are paraphyletic and are here treated as junior synonyms of Microplinthus. 

scholarly journals DNA Barcoding: Mixed results for big-headed flies (Diptera: Pipunculidae)

Zootaxa ◽  
2007 ◽  
Vol 1423 (1) ◽  
pp. 1-26 ◽  
Author(s):  
JEFFREY H. SKEVINGTON ◽  
CHRISTIAN KEHLMAIER ◽  
GUNILLA STÅHLS
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Base Pairs ◽  
Data Set ◽  
Taxonomic Decision ◽  
Morphological Species

Sequence data from 658 base pairs of mitochondrial cytochrome c oxidase I (cox1) were analysed for 28 described species of Pipunculidae (Diptera) in an effort to test the concept of DNA Barcoding on this family. Two recently revised but distantly related pipunculid lineages with presumed different evolutionary histories were used for the test (Clistoabdominalis Skevington, 2001 and Nephrocerus Zetterstedt, 1838). An effort was made to test the concept using sister taxa and morphologically similar sibling species swarms in these two genera. Morphological species concepts for Clistoabdominalis taxa were either supported by cox1 data or found to be too broad. Most of the discordance could be accounted for after reassessing morphological characters. In these cases, the molecular data were invaluable in assisting taxonomic decision-making. The radiation of Nearctic species of Nephrocerus could not be diagnosed using cox1. The ability of cox1 to recover phylogenetic signal was also tested on Clistoabdominalis. Morphological data for Clistoabdominalis were combined with the molecular data set. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology. Partitioned Bremer support is used to localize areas of conflict between the datasets.

Description of a new pygmy chameleon (Chamaeleonidae: Brookesia) from central Madagascar

Zootaxa ◽  
2012 ◽  
Vol 3490 (1) ◽  
pp. 63 ◽  
Author(s):  
ANGELICA CROTTINI ◽  
AURÉLIEN MIRALLES ◽  
FRANK GLAW ◽  
D. JAMES HARRIS ◽  
ALEXANDRA LIMA ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Morphological Characters ◽  
Molecular Data ◽  
The Other ◽  
Western Slope ◽  
Forest Fragment ◽  
High Plateau ◽  
Central High ◽  
Nd2 Gene

We describe a new Brookesia species from a forest fragment located 13 km south of Ambalavao in the southern part ofMadagascar's central high plateau. Brookesia brunoi sp. nov. is one of the few arid-adapted Brookesia species inhabitingdeciduous forests on the western slope of the central high plateau of the island (around 950 m a.s.l.). So far the species hasonly been observed in the private Anja Reserve. The species belongs to the Brookesia decaryi group formed by arid-adapt-ed Brookesia species of western Madagascar: B. bonsi Ramanantsoa, B. perarmata (Angel), B. brygooi Raxworthy &Nussbaum and B. decaryi Angel. Brookesia brunoi differs from the other four species of the group by a genetic divergenceof more than 17.6% in the mitochondrial ND2 gene, and by a combination of morphological characters: (1) nine pairs oflaterovertebral pointed tubercles, (2) absence of enlarged pointed tubercles around the vent, (3) presence of poorly definedlaterovertebral tubercles along the entire tail, (4) by the configuration of its cephalic crest, and (5) hemipenial morphology.Based on our molecular phylogeny this species is sister to a clade containing B. brygooi, B. decaryi, and probably B. bonsifor which no ND2 sequences were available. Our molecular data also confirm the presence of a divergent mitochondriallineage in the Tsingy de Bemaraha, which might be assigned to either B. bonsi or B. decaryi, and point to the need of more research on this population.

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