Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

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A molecular phylogenetic and DNA barcode assessment of the tribe Pterosiphonieae (Ceramiales, Rhodophyta) emphasizing the Northeast Pacific

Botany ◽

10.1139/cjb-2016-0083 ◽

2016 ◽

Vol 94 (10) ◽

pp. 917-939 ◽

Cited By ~ 18

Author(s):

Amanda M. Savoie ◽

Gary W. Saunders

Keyword(s):

South African ◽

North American ◽

New Genus ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Dna Barcode ◽

Sensu Stricto ◽

North American Species ◽

African Species ◽

Molecular Phylogenetic

Sequence data (COI-5P and rbcL) for North American members of the tribe Pterosiphonieae were compared with collections from around the world. Phylogenetic analyses resolved Pterosiphonia as polyphyletic and many species required transfer to other genera. In our analyses Pterosiphonia sensu stricto included only the type species P. cloiophylla (C. Agardh) Falkenberg and P. complanata (Clemente) Falkenberg, as well as the South African species P. stegengae sp. nov. A new genus, Xiphosiphonia gen. nov., was described for X. ardreana (Maggs & Hommersand) comb. nov., X. pennata (C. Agardh) comb. nov., and X. pinnulata (Kützing) comb. nov. Some Asian, European and North American species previously attributed to Pterosiphonia were transferred to Symphyocladia including S. baileyi (Harvey) comb. nov., S. dendroidea (Montagne) comb. nov., S. plumosa nom. nov. (for P. gracilis Kylin), and S. tanakae (S. Uwai & M. Masuda) comb. nov. We also described two new North American species, Symphyocladia brevicaulis sp. nov. and S. rosea sp. nov. Other species formed a well-supported clade for which the genus name Polyostea Ruprecht was resurrected. Included in Polyostea were P. arctica (J. Agardh) comb. nov., P. bipinnata (Postels & Ruprecht) Ruprecht, P. hamata (E.S. Sinova) comb. nov., and P. robusta (N.L. Gardner) comb. nov.

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Molecular phylogenetics of the Onobrychis genus (Fabaceae: Papilionoideae) using ITS and trnL–trnF DNA sequence data

Australian Journal of Botany ◽

10.1071/bt13279 ◽

2014 ◽

Vol 62 (3) ◽

pp. 235 ◽

Cited By ~ 2

Author(s):

S. Safaei Chaei Kar ◽

F. Ghanavati ◽

M. R. Naghavi ◽

H. Amirabadi-zade ◽

R. Rabiee

Keyword(s):

Dna Sequence ◽

Molecular Phylogenetics ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Dna Sequence Data ◽

Group I ◽

Molecular Phylogenetic ◽

Nuclear Its ◽

Cultivated Species ◽

Relationship Of

Onobrychis, comprising more than 130 species, is a genus of the family Fabaceae. At this time, the interspecies relationship of this biologically important genus is still a subject of great discussion and debate. To help resolve this disagreement, we used molecular phylogeny to analyse internal transcribed spacer (ITS) and trnL–trnF sequences of 76 species of Onobrychis. Bayesian interference, maximum parsimony and maximum likelihood analyses of nuclear ITS and plastid trnL–trnF DNA sequence data generated trees with strong posterior probability for two groups: Onobrychis subgen. Sisyrosema (including: Heliobrychis, Hymenobrychis, Afghanicae and Anthyllium sections) along with Laxiflorae section in Group I and Onobrychis subgen. Onobrychis (except Laxiflorae section) in the other (Group II). The Laxiflorae section roots back to the ancestral node for Sisyrosema subgen. O. viciifolia (cultivated species), which is closely associated with O. cyri var. cyri, suggesting that the latter may be a wild progenitor of O. viciifolia. The present study supported the paraphyly of subgenera Onobrychis and Sisyrosema. The study proposed the paraphyletic nature of the sections Onobrychis, Dendrobrychis, Heliobrychis and Hymenobrychis. Together with our molecular phylogenetic analyses we present a review of Onobrychis morphology and discuss and compare our results with those of earlier morphological and molecular phylogenetic analyses.

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A revision of the Leptogium saturninum group in North America

The Lichenologist ◽

10.1017/s0024282916000323 ◽

2016 ◽

Vol 48 (5) ◽

pp. 387-421 ◽

Cited By ~ 6

Author(s):

Daphne F. STONE ◽

James W. HINDS ◽

Frances L. ANDERSON ◽

James C. LENDEMER

Keyword(s):

North American ◽

Morphological Study ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Lower Surface ◽

Molecular Data ◽

The North ◽

Molecular Phylogenetic ◽

Nrits Sequence

AbstractA revision of the North American members of the Leptogium saturninum group (i.e. species with long lower-surface hairs, isidia, and usually smooth upper surface) is presented based on molecular phylogenetic analyses of mtSSU and nrITS sequence data, together with an extensive morphological study. Three species supported by both molecular and morphological characteristics are recognized: L. acadiense sp. nov. (distinguished by granular saturninum-type isidia, medulla composed of irregularly arranged or perpendicular hyphae), L. cookii sp. nov. (distinguished by cylindrical saturninum-type isidia) and L. hirsutum (distinguished by hirsutum-type isidia and medulla composed of loosely intertwined hyphae). One species supported by morphological characteristics, but for which no molecular data could be generated, is also recognized: L. compactum sp. nov. (distinguished by hirsutum-type isidia and medulla composed of tightly packed hyphae). Finally, L. saturninum (distinguished by granular saturninum-type isidia and medulla composed of perpendicular and parallel hyphae) is supported by morphological characteristics but molecular data from geographically diverse populations, including those near the type locality, indicate that the morphologically defined species is paraphyletic. Leptogium burnetiae is excluded from North American based on morphological study of the type. The species are described and illustrated in detail, and are distinguished morphologically by their isidium development, morphology of mature isidia, and pattern of hyphae in the medulla in transverse sections near lobe margins. A key to the members of the L. saturninum group and related species is also presented.

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Across Lydekker's Line - first report of mite harvestmen (Opiliones : Cyphophthalmi : Stylocellidae) from New Guinea

Invertebrate Systematics ◽

10.1071/is06046 ◽

2007 ◽

Vol 21 (3) ◽

pp. 207 ◽

Cited By ~ 28

Author(s):

Ronald M. Clouse ◽

Gonzalo Giribet

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

New Guinea ◽

Single Male ◽

Molecular Sequence Data ◽

Molecular Sequence ◽

The Family ◽

Biogeographic Region ◽

Molecular Phylogenetic ◽

History Of

Opiliones (harvestmen) in the suborder Cyphophthalmi are not known to disperse across oceans and each family in the suborder is restricted to a clear biogeographic region. While undertaking a revisionary study of the South-east Asian family Stylocellidae, two collections of stylocellids from New Guinea were noted. This was a surprising find, since the island appears never to have had a land connection with Eurasia, where the rest of the family members are found. Here, 21 New Guinean specimens collected from the westernmost end of the island (Manokwari Province, Indonesia) are described and their relationships to other cyphophthalmids are analysed using molecular sequence data. The specimens represent three species, Stylocellus lydekkeri, sp. nov., S. novaguinea, sp. nov. and undescribed females of a probable third species, which are described and illustrated using scanning electron microscope and stereomicroscope photographs. Stylocellus novaguinea, sp. nov. is described from a single male and it was collected with a juvenile and the three females of the apparent third species. Molecular phylogenetic analyses indicate that the new species are indeed in the family Stylocellidae and they therefore reached western New Guinea by dispersing through Lydekker’s line – the easternmost limit of poor dispersers from Eurasia. The New Guinean species may indicate at least two episodes of oceanic dispersal by Cyphophthalmi, a phenomenon here described for the first time. Alternatively, the presence in New Guinea of poor dispersers from Eurasia may suggest novel hypotheses about the history of the island.

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Two new species of the Phimochirus holthuisi complex from the Gulf of Mexico, supported by morphology, color, and genetics (Crustacea: Anomura: Paguridae)

Zootaxa ◽

10.11646/zootaxa.4683.4.4 ◽

2019 ◽

Vol 4683 (4) ◽

pp. 531-551

Author(s):

DARRYL L. FELDER ◽

RAFAEL LEMAITRE ◽

CATHERINE CRAIG

Keyword(s):

New Species ◽

Gulf Of Mexico ◽

Continental Shelf ◽

Gene Sequence ◽

Sequence Data ◽

Phylogenetic Analyses ◽

The Other ◽

Two New Species ◽

Molecular Phylogenetic ◽

Gene Sequence Data

Coloration, gene-sequence data (H3, 12s, 16s), and subtle features in morphology support the description of two new species, both formerly regarded to represent accepted variants of Phimochirus holthuisi s.l. While color in life consistently separates these species from P. holthuisi s.s. and from each other, morphological distinctions are subtle and less than absolute in small specimens, being based on ventral spine counts of walking leg dactyls and relative development of the superior crest on the major chela. Molecular phylogenetic analyses clearly support the separation of sister clades, representing two new species, from P. holthuisi s.s. as well as other congeners available for analysis. Both of the new species are presently known to occur widely throughout the northern Gulf of Mexico, though one occurs more commonly in the northeastern and southeastern Gulf, and may range as far south as Suriname. The other has been taken primarily in the northwestern Gulf, and is not known from outside Gulf waters. While both of the new species appear restricted to relatively deep subtidal waters of the continental shelf, Phimochirus holthuisi s.s. is instead more commonly found in shallow nearshore tropical waters on or near coral reefs. Previous literature reports of P. holthuisi usually represent, at least in part, one or both of these two new species.

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Urocystis cumminsii sp. nov., a smut fungus on Themidaceae from Arizona

Mycotaxon ◽

10.5248/134.591 ◽

2020 ◽

Vol 134 (4) ◽

pp. 591-599

Author(s):

Kyryll G. Savchenko ◽

Sylena R. Harper ◽

Lori M. Carris ◽

Lisa A. Castlebury

Keyword(s):

United States ◽

Sequence Data ◽

Phylogenetic Analyses ◽

First Record ◽

Smut Fungi ◽

Its Sequence ◽

Sequence Analyses ◽

Molecular Phylogenetic ◽

A New Species ◽

Basal Position

The morphology and phylogenetic relationships of a species of Urocystis on Dichelostemma capitatum (Themidaceae, Asparagales) collected in the Tucson Mountains in Arizona, United States, were studied using microscopy and ITS rDNA sequence analyses. This is a first record for smut fungi on hosts from Themidaceae. Molecular phylogenetic analyses based on ITS sequence data revealed its basal position in relation to species on Poaceae. As a result, the smut in leaves of Dichelostemma capitatum is described and illustrated here as a new species, Urocystis cumminsii.

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The genus Phillipsia from China and Thailand

Phytotaxa ◽

10.11646/phytotaxa.316.2.3 ◽

2017 ◽

Vol 316 (2) ◽

pp. 138 ◽

Cited By ~ 1

Author(s):

ANUSHA H. EKANAYAKA ◽

D. J. BHAT ◽

KEVIN D. HYDE ◽

E. B. GARETH JONES ◽

QI ZHAO

Keyword(s):

New Species ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Morphological Examination ◽

Phylogenetic Studies ◽

Molecular Phylogenetic ◽

A New Species

The genus Phillipsia (Sarcoscyphaceae) is characterized by large, bright-coloured, sub-stipitate apothecia, sub-operculate asci and asymmetrical ascospores with longitudinal striations. Morphological and phylogenetic studies were carried out on new collections of Phillipsia from China and Thailand. Phillipsia subpurpurea are recorded from China and Phillipsia gelatinosa from Thailand is introduced as a new species to science. Our new collections are confirmed to be divergent from other species of Phillipsia based on morphological examination and molecular phylogenetic analyses of ITS and LSU sequence data. Descriptions and figures are provided for the taxa which are also compared with allied taxa.

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Phylogenetic relationships of Australian Scirtidae (Coleoptera) based on mitochondrial and nuclear sequences

Invertebrate Systematics ◽

10.1071/is13046 ◽

2014 ◽

Vol 28 (6) ◽

pp. 628 ◽

Cited By ~ 3

Author(s):

Steven J. B. Cooper ◽

Christopher H. S. Watts ◽

Kathleen M. Saint ◽

Remko Leijs

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Elongation Factor ◽

Nuclear Gene ◽

Species Complexes ◽

Close Relationship ◽

Molecular Phylogenetic ◽

Coi Sequences ◽

Elongation Factor 1 ◽

Combined Data

Scirtidae is a cosmopolitan group of beetles with aquatic or saproxylic larvae. A large diversity of species has recently been described from Australia, but their systematics is uncertain. There is evidence that current genera are polyphyletic and that Australian species were wrongly placed in northern hemisphere genera. Here we investigate the systematics of Australian Scirtidae using molecular phylogenetic analyses of combined data from the mitochondrial cytochrome c oxidase subunit 1 (COI) and nuclear gene elongation factor 1-α (EF1-α) genes. We also assess the current taxonomy of Australian Scirtidae using partial COI sequences. Bayesian phylogenetic analyses of COI and EF1-α sequence data from 81 taxa show that the Australian genera Contacyphon, Pseudomicrocara and Prionocyphon are polyphyletic. There is no close relationship between Australian and Eurasian genera, with the exception of Scirtes. Phylogenetic analyses of partial COI data from Australian Scirtidae generally support the current α taxonomy, with the exception of several species that may be associated with species complexes. Geographically a high proportion of species lineages are restricted to relict patches of wet forest suggesting that they may be relict populations. The phylogeny and sequence data presented here provide a sound basis for further systematic and biogeographical studies of the Scirtidae.

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A revision of the genus Seligeria (Seligeriaceae, Bryophyta) in Russia inferred from molecular data

Phytotaxa ◽

10.11646/phytotaxa.323.1.2 ◽

2017 ◽

Vol 323 (1) ◽

pp. 27 ◽

Cited By ~ 5

Author(s):

VLADIMIR E. FEDOSOV ◽

ALINA V. FEDOROVA ◽

ELENA A. IGNATOVA ◽

MICHAEL S. IGNATOV

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Phylogenetic Group ◽

Undescribed Species ◽

Dna Sequence Data ◽

Molecular Phylogenetic ◽

Nuclear Its ◽

Sister Relationships ◽

Central Strand

The genus Seligeria is revised based on morphological and DNA sequence data of nuclear ITS and chloroplastic trnL-F. Fifteen species from most infrageneric units of the genus are recovered in two well supported phylogenetic clusters that are also distinctive in morphology. The clade with the type species of the genus, S. pusilla, includes also S. donniana, S. brevifolia, S. calcarea, S. patula, S. tristichoides, S. trifaria, and S. oelandica. These species are characterized by short, cupulate or turbinate capsules widened towards the mouth, and the lack of a stem central strand. Another clade includes species with rather long, mainly ovate to cylindrical capsules and more or less developed stem central strand: S. campylopoda, S. recurvata, S. subimmersa, S. diversifolia, and S. polaris. These two clusters do not show sister relationships, but the second one appears more closely related to the Blindia clade. To resolve the apparent paraphyly, the latter phylogenetic group is segregated in a genus Blindiadelphus. In some aspects of morphology and ecology it is intermediate between Seligeria s. str. and Blindia, but differs from both genera in subquadrate upper leaf cells and thin- to moderately thick-walled rectangular exothecial cells. Molecular phylogenetic analyses revealed heterogeneity within the specimens previously referred to Blindiadelphus campylopodus, indicating a presence in Asian Russia of an undescribed species that is described here as Blindiadelphus sibiricus. It differs from B. campylopodus by the larger spores and typically rounded leaf apices. The isotype specimen of S. galinae appeared to be nearly identical to S. donniana in the sequences of ITS and trnL-F, and examination of morphology revealed no substantial differences between these species. Thus, we consider S. galinae as a synonym of S. donniana. The genus Blindiadelphus includes species of Seligeria subg. Blindiadelphus and S. subg. Cyrtoseligeria, which however are found intermingled in the molecular phylogenetic analysis. Thus the genus Blindiadelphus is accepted without any infrageneric taxa. The phylogenetic tree is congruent with the subdivision of the genus Seligeria s.str into subg. Seligeria, subg. Anodon, subg. Megalosporia and one newly established subgenus Robustidontia for S. brevifolia.

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