New insights into the phylogeny and taxonomy of Chinese Physospermopsis (Apiaceae)

Physospermopsis (Apiaceae) comprises about 10 species, but its taxonomy and phylogeny are disputed. The genus is mostly distributed in the Himalayas and Hengduan Mountains at high elevation. Earlier molecular studies involving six species of Physospermopsis indicated that this genus is not monophyletic and is nested in the East Asia Clade. Therefore, the aims of this study were to re-assess the phylogenetic position of, and interspecific relationships within, Physospermopsis based on two chloroplast loci (rpl16, rps16) and one nuclear region, the internal transcribed spacers of ribosomal DNA (ITS). Eight species involving 13 populations of Physospermopsis were collected. These were sequenced and analyzed with the sequences of 31 other Apiaceae species obtained from the NCBI to determine phylogenetic relationships using Bayesian inference (BI) and Maximum likelihood (ML). Our study found that Physospermopsis is monophyletic, nested in Pleurospermeae of Apiaceae, sister to Pleurospermum. And we propose that the Physospermopsis clade should be replaced by the East Asia Clade. However, the interspecific relationships within Physospermopsis were not well resolved and the positioning of species was unclear. Diagnostic characteristics to distinguish Physospermopsis species in the field and laboratory are provided for future Physospermopsis phylogenetic studies.

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Optimal markers for the identification ofColletotrichumspecies

10.1101/659177 ◽

2019 ◽

Cited By ~ 2

Author(s):

Willie Anderson dos Santos Vieira ◽

Priscila Alves Bezerra ◽

Anthony Carlos da Silva ◽

Josiene Silva Veloso ◽

Marcos Paz Saraiva Câmara ◽

...

Keyword(s):

Molecular Markers ◽

Species Complex ◽

Plant Pathogens ◽

Phylogenetic Signal ◽

Intergenic Spacer ◽

Internal Transcribed Spacers ◽

Type Locus ◽

Phylogenetic Studies ◽

Fungal Plant Pathogens ◽

Species Complexes

ABSTRACTColletotrichumis among the most important genera of fungal plant pathogens. Molecular phylogenetic studies over the last decade have resulted in a much better understanding of the evolutionary relationships and species boundaries within the genus. There are now approximately 200 species accepted, most of which are distributed among 13 species complexes. Given their prominence on agricultural crops around the world, rapid identification of a large collection ofColletotrichumisolates is routinely needed by plant pathologists, regulatory officials, and fungal biologists. However, there is no agreement on the best molecular markers to discriminate species in each species complex. Here we calculate the barcode gap distance and intra/inter-specific distance overlap to evaluate each of the most commonly applied molecular markers for their utility as a barcode for species identification. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone-3 (HIS3), DNA lyase (APN2), intergenic spacer between DNA lyase and the mating-type locusMAT1-2-1 (APN2/MAT-IGS), and intergenic spacer between GAPDH and a hypothetical protein (GAP2-IGS) have the properties of good barcodes, whereas sequences of actin (ACT), chitin synthase (CHS-1) and nuclear rDNA internal transcribed spacers (nrITS) are not able to distinguish most species. Finally, we assessed the utility of these markers for phylogenetic studies using phylogenetic informativeness profiling, the genealogical sorting index (GSI), and Bayesian concordance analyses (BCA). Although GAPDH, HIS3 and β-tubulin (TUB2) were frequently among the best markers, there was not a single set of markers that were best for all species complexes. Eliminating markers with low phylogenetic signal tends to decrease uncertainty in the topology, regardless of species complex, and leads to a larger proportion of markers that support each lineage in the Bayesian concordance analyses. Finally, we reconstruct the phylogeny of each species complex using a minimal set of phylogenetic markers with the strongest phylogenetic signal and find the majority of species are strongly supported as monophyletic.

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The genus Microniphargus (Crustacea, Amphipoda): evidence for three lineages distributed across northwestern Europe and transfer from Niphargidae to Pseudoniphargidae

Belgian Journal of Zoology ◽

10.26496/bjz.2021.92 ◽

2021 ◽

Vol 151 ◽

Author(s):

Dieter Weber ◽

Fabio Stoch ◽

Lee R.F.D. Knight ◽

Claire Chauveau ◽

Jean-François Flot

Keyword(s):

Cytochrome C ◽

Cytochrome C Oxidase ◽

Phylogenetic Analyses ◽

Ribosomal Gene ◽

Phylogenetic Position ◽

Mitochondrial Cytochrome ◽

Monotypic Genus ◽

Centre Of Origin ◽

Phylogenetic Studies ◽

The Family

Microniphargus leruthi Schellenberg, 1934 (Amphipoda: Niphargidae) was first described based on samples collected in Belgium and placed in a monotypic genus within the family Niphargidae. However, some details of its morphology as well as recent phylogenetic studies suggest that Microniphargus may be more closely related to Pseudoniphargus (Amphipoda: Pseudoniphargidae) than to Niphargus. Moreover, M. leruthi ranges over 1,469 km from Ireland to Germany, which is striking since only a few niphargids have confirmed ranges in excess of 200 km. To find out the phylogenetic position of M. leruthi and check whether it may be a complex of cryptic species, we collected material from Ireland, England and Belgium then sequenced fragments of the mitochondrial cytochrome c oxidase subunit 1 gene as well as of the nuclear 28S ribosomal gene. Phylogenetic analyses of both markers confirm that Microniphargus is closer to Pseudoniphargus than to Niphargus, leading us to reallocate Microniphargus to Pseudoniphargidae. We also identify three congruent mito-nuclear lineages present respectively in Ireland, in both Belgium and England, and in England only (with the latter found in sympatry at one location), suggesting that M. leruthi is a complex of at least three species with a putative centre of origin in England.

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The phylogenetic position of the enigmatic Assam day gecko Cnemaspis cf. assamensis (Squamata: Gekkonidae) demonstrates a novel biogeographic connection between Northeast India and south India-Sri Lanka

Amphibia-Reptilia ◽

10.1163/15685381-bja10062 ◽

2021 ◽

pp. 1-13

Author(s):

Ishan Agarwal ◽

Rachunliu G. Kamei ◽

Stephen Mahony

Keyword(s):

Sri Lanka ◽

Southeast Asia ◽

South Asian ◽

South India ◽

Northeast India ◽

Phylogenetic Position ◽

Phylogenetic Studies ◽

Molecular Phylogenetic ◽

Nd2 Gene ◽

Isolated Species

Abstract Northeast Indian biodiversity has long been considered to have a stronger affinity to Southeast Asian rather than Peninsular Indian fauna, however, few molecular phylogenetic studies have explored this hypothesis. In Asia, the polyphyletic gekkonid genus Cnemaspis sensu lato is comprised of two distantly related groups; one primarily from South Asia with some members in Southeast Asia, and the other exclusively from Southeast Asia. Cnemaspis assamensis is a systematically obscure and geographically isolated species (>1400 km from its nearest congeners) from the Brahmaputra River Valley in Northeast India. We provide the first molecular phylogenetic assessment of this species based on a partial ND2 gene fragment. Cnemaspis assamensis is determined to be a deeply divergent (Oligocene) member of the South Asian radiation and is sister to the podihuna clade which is endemic to Sri Lanka. The biogeographic implications of this find are discussed and this is suspected to represent a rare example of true disjunction between the wet zones of Northeast India and southern India/Sri Lanka. These results further emphasise the importance of Northeast India as a refuge for unique ancient faunal lineages.

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The genus Euphorbia in Australia

Australian Journal of Botany ◽

10.1071/bt9770429 ◽

1977 ◽

Vol 25 (4) ◽

pp. 429 ◽

Cited By ~ 12

Author(s):

DC Hassall

Keyword(s):

New Species ◽

East Asia ◽

Papua New Guinea ◽

Chromosome Numbers ◽

New Guinea ◽

Sensu Stricto ◽

Indigenous Species ◽

South East Asia ◽

Interspecific Relationships ◽

New Hebrides

In Australia the genus Euphorbia L., sensu stricto, is represented by seven indigenous species in three subgenera. One species has been reported from Papua New Guinea and parts of South-east Asia, another from the New Hebrides; the remaining species are endemic to Australia. Two taxa are described as new species, viz. Euphorbia parvicaruncula and Euphorbia planiticola, and two former species are reduced to infraspecific rank, viz. Euphorbia tannensis subsp. eremophila, and Euphorbia tannensis subsp. eremophila var. finlaysonii. Observations are made on geographical distributions, interspecific relationships, and chromosome numbers.

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Molecular phylogeny of the Kosciuscola grasshoppers endemic to the Australian alpine and montane regions

Invertebrate Systematics ◽

10.1071/is12072 ◽

2013 ◽

Vol 27 (3) ◽

pp. 307 ◽

Cited By ~ 12

Author(s):

N. J. Tatarnic ◽

K. D. L. Umbers ◽

H. Song

Keyword(s):

Climate Change ◽

Body Temperature ◽

Molecular Phylogeny ◽

Colour Change ◽

Bayesian Analyses ◽

Phylogenetic Studies ◽

Australian Alps ◽

Molecular Studies ◽

Alpine Species ◽

Alpine Distribution

Diversity and speciation in Australia’s alpine biota are poorly understood. Here we present a molecular phylogeny of the Australian alpine grasshopper genus Kosciuscola (Sjösted) that currently includes five described species. These grasshoppers are of interest not only because of their alpine distribution but also for the extraordinary colour change exhibited by the species K. tristis, whose males turn turquoise when their body temperature exceeds 25°C. We reconstructed the phylogeny with two fragments of the mitochondrial genome using parsimony, maximum likelihood and Bayesian analyses and our data support the current taxonomy. Further, our data show little geographic structuring within some clades, which is puzzling since members of Kosciuscola are brachypterous. Finally, our data coupled with our observations on colouration provide evidence for a genetically distinct clade of K. tristis in the Victorian Alps. This is among the first molecular studies of an alpine invertebrate and one of a few on non-endangered, widespread Australian alpine species. More phylogenetic studies in the Australian Alps are required if we are to understand the evolution of alpine fauna and establish baseline data to monitor their response to climate change.

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Morphological study of fruits, seeds and embryo in the tropical tribe Dipterygeae (Leguminosae-Papilionoideae)

Rodriguésia ◽

10.1590/s2175-78602014000100007 ◽

2014 ◽

Vol 65 (1) ◽

pp. 89-97 ◽

Cited By ~ 5

Author(s):

Rafael Barbosa Pinto ◽

Vanessa Maria da Costa Rodrigues Francisco ◽

Vidal de Freitas Mansano

Keyword(s):

Morphological Study ◽

Morphological Analysis ◽

Morphological Characteristics ◽

The Other ◽

Embryo Morphology ◽

Phylogenetic Studies ◽

Dispersal Syndromes ◽

Diagnostic Characteristics ◽

First Time

This work analyses and describes fruit, seed and embryo morphology of 12 Dipterygeae species. The fruit is quite distinct among genera, being a legume in Taralea, a drupoid legume in Dipteryx and a cryptosamara in Pterodon. It was observed that the three genera present distinct morphological characteristics in the epicarp, mesocarp and endocarp. These structures are strongly associated with the dispersal syndromes presented by the genera. Embryonic descriptions are provided for the first time in this manuscript for the three genera presented here and the main diagnostic characteristics are: (1) a gradual extent of development of the hypocotyl-radicle axis from Taralea (undeveloped) to Dipteryx (the most developed); (2) the plumules are entire in Taralea and pinnate in Dipteryx and Pterodon; (3) a cleft below the hypocotyl-radicle axis in Taralea, absent in the other genera, because of the strongly cordate base of the cotyledonar leaves; (4) differences in the degree of development of the hypocotyl-radicle axis between D.alata, D.rosea and D.micrantha. Dipterygeae presents a noticeable diversity of fruit, seed and embryo, Taralea being the most distinct of all. The results of this morphological analysis suggest an evolutive path for the diaspores in the clade, based on phylogenetic studies which show Taralea as sister to the clade constituted by Dipteryx and Pterodon.

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Phylogenetic relationships of the nematode subfamily Phascolostrongylinae from macropodid and vombatid marsupials inferred using mitochondrial protein sequence data

Parasites & Vectors ◽

10.1186/s13071-021-05028-2 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Tanapan Sukee ◽

Ian Beveridge ◽

Anson V. Koehler ◽

Ross Hall ◽

Robin B. Gasser ◽

...

Keyword(s):

Amino Acid ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Mitochondrial Protein ◽

Amino Acid Sequences ◽

Internal Transcribed Spacers ◽

Nuclear Ribosomal Dna ◽

Phylogenetic Position ◽

Data Sets ◽

Sister Relationship

Abstract Background The subfamily Phascolostrongylinae (Superfamily Strongyloidea) comprises nematodes that are parasitic in the gastrointestinal tracts of macropodid (Family Macropodidae) and vombatid (Family Vombatidae) marsupials. Currently, nine genera and 20 species have been attributed to the subfamily Phascolostrongylinae. Previous studies using sequence data sets for the internal transcribed spacers (ITS) of nuclear ribosomal DNA showed conflicting topologies between the Phascolostrongylinae and related subfamilies. Therefore, the aim of this study was to validate the phylogenetic relationships within the Phascolostrongylinae and its relationship with the families Chabertiidae and Strongylidae using mitochondrial amino acid sequences. Methods The sequences of all 12 mitochondrial protein-coding genes were obtained by next-generation sequencing of individual adult nematodes (n = 8) representing members of the Phascolostrongylinae. These sequences were conceptually translated and the phylogenetic relationships within the Phascolostrongylinae and its relationship with the families Chabertiidae and Strongylidae were inferred from aligned, concatenated amino acid sequence data sets. Results Within the Phascolostrongylinae, the wombat-specific genera grouped separately from the genera occurring in macropods. Two of the phascolostrongyline tribes were monophyletic, including Phascolostrongylinea and Hypodontinea, whereas the tribe Macropostrongyloidinea was paraphyletic. The tribe Phascolostrongylinea occurring in wombats was closely related to Oesophagostomum spp., also from the family Chabertiidae, which formed a sister relationship with the Phascolostrongylinae. Conclusion The current phylogenetic relationship within the subfamily Phascolostrongylinae supports findings from a previous study based on ITS sequence data. This study contributes also to the understanding of the phylogenetic position of the subfamily Phascolostrongylinae within the Chabertiidae. Future studies investigating the relationships between the Phascolostrongylinae and Cloacininae from macropodid marsupials may advance our knowledge of the phylogeny of strongyloid nematodes in marsupials. Graphical Abstract

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Phylogenetic position and evolution of glandular structures of the unusual and narrowly distributed genus Rhytidanthera (Ochnaceae)

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boaa008 ◽

2020 ◽

Vol 193 (1) ◽

pp. 84-99 ◽

Cited By ~ 2

Author(s):

Sandra Reinales ◽

Carlos Parra-O

Keyword(s):

Plastid Dna ◽

Phylogenetic Position ◽

Primary Forest ◽

Phylogenetic Study ◽

Pollinator Attraction ◽

Phylogenetic Studies ◽

Nuclear Its ◽

Glandular Structures ◽

Floral Bud ◽

African Genus

Abstract Rhytidanthera is the only genus of Ochnaceae with compound leaves, and it forms sparse, small populations restricted to the primary forest of the Colombian and Venezuelan Andes and the sandstone hills of La Macarena and Chiribiquete. It has been suggested to be related to Godoya, Cespedesia and Krukoviella in taxonomic and phylogenetic studies. However, the relationships in this group remain poorly resolved, due to the lack of a wider molecular and taxonomic sampling. We present a phylogenetic study of tribe Sauvagesieae including three Rhytidanthera spp. and one species each of Godoya and Cespedesia, using sequences from one nuclear (ITS) and four plastid DNA regions (matK, ndhF, rbcL and trnL-F), in order to clarify the relationships among these four genera. We recover a new and well-supported phylogenetic hypothesis, with Rhytidanthera as sister to a clade comprising Godoya and the clade formed by Cespedesia and Krukoviella. This Neotropical clade was recovered as sister to the monotypic and African genus Fleurydora. The clade comprising Rhytidanthera, Godoya, Cespedesia and Krukoviella is supported by the presence of glandular structures (colleters) at the base of stipules and bracts. The colleters also evolved at the base of the sepals in this clade, with a secondary loss in Cespedesia and Krukoviella. We suggest that the combination of unequal-sized sepals enclosing the floral bud and the presence of colleters in members of this clade could have a role in the protection of leaves and flowers in the early stages of development, instead of acting in pollinator attraction.

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First report of Leptostraca from South-east Asia: Nebalia cambodiana sp. nov. (Crustacea: Malacostraca)

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315416000618 ◽

2016 ◽

Vol 97 (6) ◽

pp. 1343-1349 ◽

Cited By ~ 1

Author(s):

Ji-Hun Song ◽

Taeseo Park ◽

Gi-Sik Min

Keyword(s):

New Species ◽

East Asia ◽

Compound Eye ◽

Fine Sand ◽

Distal Margin ◽

South East Asia ◽

Light Traps ◽

Diagnostic Characteristics ◽

Sand And Gravel ◽

A New Species

A new species of Leptostraca, Nebalia cambodiana sp. nov. (Crustacea: Malacostraca), is described from Cambodia. The specimen was collected by light traps on a diving deck where the bottom consisted of fine sand and gravel. The new species is distinguished from all other known species of Nebalia by the following characteristics: rostrum very long, length nearly 3.5 times width; a compound eye with one distinct dorsal papilla and four small lobes on distal margin; an antennular flagellum with nine articles; the fourth article of the antennular peduncle with only one distal thick seta; the antennular scale is elliptical, with a length that is 2 times the width; exopod of the second maxilla is the same length as first article of its endopod; pleonites 5 to 7 with rounded denticles along their posterior dorsal margins; the protopod of pleopod 4 lacks serration along the posterior margin; and anal plates with distinct lateral ‘shoulder’.The new species is the first species of Leptostraca found in South-east Asia. In this paper, we provide illustrations and a detailed description of the diagnostic characteristics of N. cambodiana sp. nov.

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Phylogenetic position of Coronastrum ellipsoideum and description of Parachlorella hussii sp. nov.

Biologia ◽

10.2478/s11756-011-0056-8 ◽

2011 ◽

Vol 66 (4) ◽

Cited By ~ 14

Author(s):

Christina Bock ◽

Marie Pažoutová ◽

Lothar Krienitz

Keyword(s):

Molecular Data ◽

Phylogenetic Position ◽

Rrna Gene ◽

Combined Approach ◽

Molecular Analyses ◽

Phylogenetic Studies ◽

The Family ◽

Its Rrna Gene ◽

Molecular Phylogenetic ◽

First Time

AbstractFollowing traditional morphological concepts, the genus Coronastrum is considered to be a rare member of the Scenedesmaceae (Chorophyceae). This classification may be called into question when molecular data are taken into account as well. Recent molecular phylogenetic studies revealed the polyphyletic origin of the family Scenedesmaceae within the Chlorophyceae and Trebouxiophyceae. In a combined approach of morphological analyses, SSU/ITS rRNA gene phylogeny and comparison of the ITS secondary structure, we analysed the systematics of Coronastrum strains available in public strain collections. Our molecular analyses revealed a new subclade within the Chlorella clade of the Chlorellaceae consisting of Coronastrum ellipsoideum, two strains with Dictyosphaerium-like morphology and one strain which fits the description of the genus Parachlorella. Four additional strains formed together a new lineage within the genus Parachlorella in the Parachlorella clade of the Chlorellaceae. These strains differ from the already known Parachlorella species in complementary base changes within the ITS2 and are here described for the first time as Parachlorella hussii sp. nov.

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