An expanded concept of Madisonia including miscellaneous species of Pleurothallidinae (Orchidaceae): evidence from molecular analysis

Prior taxonomic studies in subtribe Pleurothallidinae have suggested a close relationship between miscellaneous species featuring long-repent, segmented rhizomes, abbreviated ramicauls, few-flowered inflorescences, and flowers with partially connate sepals and trilobed lip. The lack of phylogenetic information for most species has prevented further conclusions or changes in their taxonomy; and as a result, they are currently assigned to several unrelated genera: Anathallis, Madisonia, Pabstiella, Pleurothallis, Sansonia and Specklinia. We performed phylogenetic analyses using nuclear (nrITS) and five plastid (matK, psbD-trnT, rps16-trnQ, trnH-psbA and trnS-trnG) markers and demonstrated that these species form an isolated clade which requires generic recognition. The name Madisonia, previously a monotypic genus endemic of the Amazon basin, is re-circumscribed and expanded to include nine species distributed in the Atlantic Rainforest and the Caribbean. Eight new nomenclatural combinations are proposed.

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Genetic and morphological data support placement of Myrmotherula gularis (Spix) in the monotypic genus Rhopias Cabanis and Heine (Aves: Passeriformes: Thamnophilidae)

Zootaxa ◽

10.11646/zootaxa.3451.1.1 ◽

2012 ◽

Vol 3451 (1) ◽

pp. 1 ◽

Cited By ~ 7

Author(s):

RICARDO BELMONTE-LOPES ◽

GUSTAVO A. BRAVO ◽

MARCOS R. BORNSCHEIN ◽

GIOVANNI N. MAURÍCIO ◽

MARCIO R. PIE ◽

...

Keyword(s):

Morphological Traits ◽

Phylogenetic Analyses ◽

Morphological Data ◽

Character State ◽

Monotypic Genus ◽

Ancestral Reconstruction ◽

The Family ◽

Close Relationship ◽

Phylogenetic Resolution ◽

Phylogenetic Affinities

Recent DNA-based phylogenetic analyses of the family Thamnophilidae have shown that the genus Myrmotherula is polyphyletic. Traditional plumage-based taxonomy has been misleading in terms of identifying independently evolving lineages within the complex. Here, we integrate a molecular phylogeny with morphometric information and ancestral reconstruction of syringeal character states of the Musculi vocales ventrales, to investigate the taxonomic position of M. gularis, a species for which phylogenetic affinities have long been uncertain. We show that M. gularis represents a long branch in the tribe Thamnophilini that is not closely related to any other member of the Myrmotherula complex. Its relationships within the tribe remain uncertain because of the lack of phylogenetic resolution at the base of the tribe. M. gularis shares a derived character state of the M. vocalis ventralis with Taraba, Hypoedaleus, and Mackenziaena, which supports a close relationship between M. gularis and the large antshrikes. M. gularis can be diagnosed from Myrmotherula and Epinecrophylla by this condition of its M. vocalis ventralis, and from Isleria by plumage and other morphological traits. The phylogenetic and morphological distinctiveness of M. gularis does not warrant merging it into any other genus. We propose that this species be placed in a monotypic genus, for which the available name Rhopias applies.

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Biological and Molecular Properties of a Begomovirus from Dicliptera sexangularis

Phytopathology ◽

10.1094/phyto.2000.90.7.723 ◽

2000 ◽

Vol 90 (7) ◽

pp. 723-729 ◽

Cited By ~ 4

Author(s):

Pongtharin Lotrakul ◽

Rodrigo A. Valverde ◽

Angela D. Landry

Keyword(s):

Mosaic Virus ◽

Phylogenetic Analyses ◽

Amino Acid Sequences ◽

Yellow Mosaic Virus ◽

Bipartite Begomovirus ◽

Caribbean Basin ◽

Sequence Comparisons ◽

Close Relationship ◽

Yellow Mottle ◽

The Caribbean

Sixangle foldwing, Dicliptera sexangularis (Acanthaceae), showing severe yellow mottle and leaf distortion symptoms was collected from the shoreline of Calusa Island (Lee County, FL). The putative virus was transmitted from infected D. sexangularis to healthy seedlings by mechanical, whitefly (Bemisia tabaci biotype B), and graft-inoculations. Different forms of geminivirus-like DNAs were detected in total DNA extracted from infected plants by Southern blot hybridization analyses using DNA-A and -B of Bean golden mosaic virus (BGMV) from Guatemala as probes. Preliminary polymerase chain reaction experiments and sequence comparisons indicated that the virus was a distinct bipartite begomovirus. The virus was designated Dicliptera yellow mottle virus (DiYMV). Replicative dsDNAs of DiYMV were extracted, digested with selected restriction enzymes, and cloned into a plasmid vector. Both DNA-A and -B were sequenced and compared with those of other begomoviruses. Phylogenetic analyses using AV1, AC1, and BV1 nucleotide sequences indicated that DiYMV has a close relationship with the New World begomoviruses, especially those distributed in the nearby geographic areas of the Florida coast and the Caribbean Basin. However, different percent nucleotide sequence identities and phylogenetic relationships were detected when different open reading frames (ORFs) of DiYMV were compared with their counterparts from begomoviruses from the Caribbean Basin. Based on phylogenetic analyses of the AC1 and BV1 ORFs, DiYMV was closely related to BGMV type II isolates, whereas sequence comparisons of the common region and the AC4-derived amino acid sequences indicated its close relationship with Potato yellow mosaic virus from Venezuela.

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Chayote mosaic virus, a New Tymovirus Infecting Cucurbitaceae

Phytopathology ◽

10.1094/phyto.2000.90.10.1098 ◽

2000 ◽

Vol 90 (10) ◽

pp. 1098-1104 ◽

Cited By ~ 9

Author(s):

Juan J. Bernal ◽

Ignacio Jiménez ◽

Manuel Moreno ◽

Melanie Hord ◽

Carmen Rivera ◽

...

Keyword(s):

Mosaic Virus ◽

Protein Gene ◽

Phylogenetic Analyses ◽

Disease Symptoms ◽

Close Relationship ◽

Andean Potato ◽

The Caribbean ◽

Asymptomatic Infections ◽

Relationship Of ◽

Host Families

Chayote mosaic virus (ChMV) is a putative tymovirus isolated from chayote crops in Costa Rica. ChMV was characterized at the host range, serological, and molecular levels. ChMV was transmitted mechanically and induced disease symptoms mainly in Cucurbitaceae hosts. Asymptomatic infections were detected in other host families. Serologically, ChMV is related to the Andean potato latent virus (APLV) and the Eggplant mosaic virus (EMV), both members of the genus Tymovirus infecting solanaceous hosts in the Caribbean Basin and South America. The sequence of the genomic RNA of ChMV was determined and its genetic organization was typical of tymoviruses. Comparisons with other tymoviral sequences showed that ChMV was a new member of the genus Tymovirus. The phylogenetic analyses of the coat protein gene were consistent with serological comparisons and positioned ChMV within a cluster of tymoviruses infecting mainly cucurbit or solanaceous hosts, including APLV and EMV. Phylogenetic analyses of the replicase protein gene confirmed the close relationship of ChMV and EMV. Our results suggest that ChMV is related to two tymoviruses (APLV and EMV) of proximal geographical provenance but with different natural host ranges. ChMV is the first cucurbit-infecting tymovirus to be fully characterized at the genomic level.

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Linking morphological and molecular sources to disentangle the case of Xylodon australis

Scientific Reports ◽

10.1038/s41598-020-78399-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Javier Fernández-López ◽

M. Teresa Telleria ◽

Margarita Dueñas ◽

Mara Laguna-Castro ◽

Klaus Schliep ◽

...

Keyword(s):

New Zealand ◽

Phylogenetic Analyses ◽

Single Species ◽

R Package ◽

Molecular Data ◽

Historical Collections ◽

Close Relationship ◽

Kinship Relations ◽

History Of ◽

Different Sources

AbstractThe use of different sources of evidence has been recommended in order to conduct species delimitation analyses to solve taxonomic issues. In this study, we use a maximum likelihood framework to combine morphological and molecular traits to study the case of Xylodon australis (Hymenochaetales, Basidiomycota) using the locate.yeti function from the phytools R package. Xylodon australis has been considered a single species distributed across Australia, New Zealand and Patagonia. Multi-locus phylogenetic analyses were conducted to unmask the actual diversity under X. australis as well as the kinship relations respect their relatives. To assess the taxonomic position of each clade, locate.yeti function was used to locate in a molecular phylogeny the X. australis type material for which no molecular data was available using morphological continuous traits. Two different species were distinguished under the X. australis name, one from Australia–New Zealand and other from Patagonia. In addition, a close relationship with Xylodon lenis, a species from the South East of Asia, was confirmed for the Patagonian clade. We discuss the implications of our results for the biogeographical history of this genus and we evaluate the potential of this method to be used with historical collections for which molecular data is not available.

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Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

Genome Biology and Evolution ◽

10.1093/gbe/evz209 ◽

2019 ◽

Vol 11 (10) ◽

pp. 2824-2849 ◽

Cited By ~ 6

Author(s):

Paweł Mackiewicz ◽

Adam Dawid Urantówka ◽

Aleksandra Kroczak ◽

Dorota Mackiewicz

Keyword(s):

Phylogenetic Analyses ◽

Mitochondrial Genes ◽

The Other ◽

Phylogenetic Position ◽

Evolutionary Relationships ◽

Mitochondrial Genomes ◽

Ancestral State ◽

Phylogenetic Information ◽

Long Time ◽

Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

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Phylogenetic analyses of nucleotide sequences confirm a unique plant intercontinental disjunction between tropical Africa, the Caribbean, and the Hawaiian Islands

Journal of Plant Research ◽

10.1007/s10265-009-0258-0 ◽

2009 ◽

Vol 123 (1) ◽

pp. 57-65 ◽

Cited By ~ 13

Author(s):

Sandra Namoff ◽

Quentin Luke ◽

Francisco Jiménez ◽

Alberto Veloz ◽

Carl E. Lewis ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Hawaiian Islands ◽

Nucleotide Sequences ◽

Tropical Africa ◽

The Caribbean

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Is urban bushmeat trade in Colombia really insignificant?

Oryx ◽

10.1017/s0030605315001118 ◽

2016 ◽

Vol 51 (2) ◽

pp. 305-314 ◽

Cited By ~ 3

Author(s):

Nathalie van Vliet ◽

Maria Quiceno ◽

Jessica Moreno ◽

Daniel Cruz ◽

John E. Fa ◽

...

Keyword(s):

Urban Areas ◽

Amazon Basin ◽

Sustainable Use ◽

The Pacific ◽

Hydrochoerus Hydrochaeris ◽

Wild Meat ◽

The Caribbean ◽

Alternative Sources ◽

Bushmeat Trade ◽

Brocket Deer

AbstractThe bushmeat trade in ecosystems in South America other than those within the Amazon basin is presumed to be insignificant, as alternative sources of protein (e.g. beef, chicken, fish) are considered to be more readily available in non-moist forests. However, studies and confiscation reports from countries such as Colombia suggest that bushmeat is consumed in a variety of ecosystems, although the nature of market chains, particularly in urban areas, is still unknown. We studied the urban bushmeat trade in markets in the five main ecoregions in Colombia. We recorded a total of 85 species, the most frequently traded being the paca Cuniculus paca, red brocket deer Mazama americana, grey brocket deer Mazama gouazoubira, capybara Hydrochoerus hydrochaeris, armadillo Dasypus spp. and black agouti Dasyprocta fuliginosa. Most sales of wild meat occur through clandestine channels and involve a limited number of stakeholders. Bushmeat is a luxury product in urban areas of the Caribbean, the Pacific and the Andean regions. Further work is needed to quantify and monitor the volumes of bushmeat traded, comprehend motivations, explore ways of reducing threats, and engage with stakeholders to organize legal and sustainable use of bushmeat.

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Tigridiopalma longmenensis (Melastomataceae), a new species from Guangdong, China

Phytotaxa ◽

10.11646/phytotaxa.500.3.8 ◽

2021 ◽

Vol 500 (3) ◽

pp. 241-247

Author(s):

HUI-FENG WANG ◽

ZHENG-FENG WANG ◽

QIAO-MEI QIN ◽

HONG-LIN CAO ◽

XIAO-MING GUO

Keyword(s):

New Species ◽

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Monotypic Genus ◽

Distribution Map ◽

Complete Chloroplast Genome ◽

Chloroplast Genomes ◽

A New Species

Tigridiopalma longmenensis, a new species from Guangdong, China, is described. This species differs from its ally, T. magnifica, by the polychasium consisting of scorpioid cymes, hypanthium with carinas on angles, and longer stamens with a conspicuously white or pink spur at the connective base of anther. A diagnosis and a distribution map of the two species are also provided. The complete chloroplast genome of T. longmenensis was reported here. Phylogenetic analyses based on complete chloroplast genomes from T. longmenensis and other 15 Melastomataceae species indicated that T. longmenensis is sister to T. magnifica. The discovery of T. longmenensis terminates Tigridiopalma as a monotypic genus.

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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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A new species of Cleistocybe (Agaricales, Basidiomycota) from the Tibetan Plateau, China

Phytotaxa ◽

10.11646/phytotaxa.336.3.7 ◽

2018 ◽

Vol 336 (3) ◽

pp. 286 ◽

Cited By ~ 2

Author(s):

HONG-MEI WU ◽

JIA-QI LUO ◽

KE WANG ◽

RUN-CHAO ZHANG ◽

YI LI ◽

...

Keyword(s):

New Species ◽

Tibetan Plateau ◽

Phylogenetic Analyses ◽

Morphological Observation ◽

Morphological Description ◽

The Tibetan Plateau ◽

Sequence Analyses ◽

The North ◽

Close Relationship ◽

A New Species

During field expeditions to the Tibetan Plateau, a collection of an undescribed species with several basidiomes was found. Morphological observation and DNA sequence analyses of the collection revealed a close relationship with Cleistocybe vernalis, the type species of the genus Cleistocybe. Therefore, a new species is proposed for the fungus with full morphological description accompanied by phylogenetic analyses. The discovery of the species extends the reported distribution of the genus from the north of America and Europe to Asia.

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