Taxonomic status and phylogenetic position of Oxymycterus juliacae Allen 1900 (Rodentia: Cricetidae)

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Dennisse Ruelas ◽  
Víctor Pacheco
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Cytochrome B ◽  
Morphological Traits ◽  
Genetic Material ◽  
Taxonomic Status ◽  
Valid Species ◽  
Phylogenetic Position ◽  
Congeneric Species ◽  
Morphological Distinction

Abstract The phylogenetic position of the “Upper yungas inca hocicudo” Oxymycterus juliacae, one of the lesser-known species of the genus Oxymycterus, is still unresolved. Several authors considered it a subspecies or synonym of Oxymycterus inca, but more recently, it was recognized as a valid species based on morphometric analysis and morphological traits. The objectives of this study were then to substantiate the morphological distinction of O. juliacae and evaluate its phylogenetic position using cytochrome b sequences. We evaluated the morphology of O. juliacae and compared it with congeneric species. In addition, a Cytochrome b gene matrix was subjected to analyses of maximum likelihood and Bayesian inference. Our results support the morphometric and morphological distinction of O. juliacae and found that this species is more closely related to Oxymycterus willkaurco than to O. inca. Therefore, the recognition of O. juliacae as a full species is supported and a rediagnosis is provided. In addition, we found O. inca is more related to other lowland species from Argentina, Brazil, and Uruguay, than to central Andean species. More efforts are needed to secure genetic material of Oxymycterus species, mainly the Andean species, for a better understanding of their phylogenetic relationship.

Phylogenetic position of the Ancash leaf-eared mouse Phyllotis definitus Osgood 1915 (Rodentia: Cricetidae)

Mammalia ◽  
2018 ◽  
Vol 82 (2) ◽  
pp. 153-166
Author(s):  
Edgardo M. Rengifo ◽  
Victor Pacheco
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Cytochrome B ◽  
Maximum Parsimony ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Base Pairs

AbstractThe phylogenetic position of the Ancash leaf-eared mousePhyllotis definitusremains unresolved, as this species has been considered to be related toPhyllotis magister,Phyllotis xanthopygusorPhyllotis andiumby several authors. The objective of this study was to clarify the phylogenetic position ofP. definitususing 801 base pairs of cytochrome b sequences. A matrix constituted by 43 specimens was subjected to maximum likelihood, maximum parsimony and Bayesian inference analyses. Our results indicate thatP. definitusis a member of the “andium/amicus” group and is closely related toPhyllotis pearsoni, supporting a set of chromosomal and morphological characters previously identified for this group.

scholarly journals Molecular phylogeny of common sun skink, Eutropis (Squamata: Scincidae), of northwestern part of Bangladesh

2019 ◽  
Vol 47 (1) ◽  
pp. 13-25
Author(s):  
Mosharrof Hossain ◽  
Che Jing
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
16S Rrna ◽  
Molecular Phylogeny ◽  
Posterior Probability ◽  
Common Ancestor ◽  
Northwestern Part ◽  
Congeneric Species ◽  
Relationship Of ◽  
Posterior Probability Support

A study on the phylogenetic relationship of Bangladeshi Skink confirmed species as Eutropis multifasciata by Bayesian inference (BI) (100%) and 98% node support to maximum likelihood (ML) tree topology, respectively. The sequence divergences between Eutropis multifasciata and other congeneric species were significant, ranging from 0.1 to 13.6% for 16S rRNA. Intraspecific genetic divergence within E. multifasciata was estimated 10.3%. E. multifasciata formed a distinct clade with high posterior probability support. This maiden study on Bangladeshi Skink results support that one monophyletic subgroup containing all specimens of E. multifasciata and all recently recognized E. multifasciata populations have evolved from one common ancestor. Bangladesh J. Zool. 47(1): 13-25, 2019

Delving deeper into the phylogenetics of the herbaceous bamboos (Poaceae, Bambusoideae, Olyreae): evaluation of generic boundaries within the Parodiolyra/Raddiella clade uncovers a new genus

2019 ◽  
Vol 192 (1) ◽  
pp. 61-81 ◽  
Author(s):  
Iasmin L C Oliveira ◽  
Andreza O Matos ◽  
Christian Silva ◽  
Maria Luiza S Carvalho ◽  
Christopher D Tyrrell ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Morphological Evidence ◽  
Taxon Sampling ◽  
Plastid Genomes ◽  
Herbaceous Bamboos

Abstract The present study aims to expand the knowledge of phylogenetic relationships in Olyrinae, a subtribe of herbaceous bamboos (Poaceae: Bambusoideae: Olyreae). Our focus is on Parodiolyra and Raddiella, two historically related genera that, with their sister Diandrolyra, form one of the four main lineages in the subtribe. Previous phylogenetic analyses suggested that Parodiolyra is not monophyletic, but its taxonomic boundaries and its relationship with Raddiella remain uncertain due to low sampling. We increased the taxon sampling and sequenced five regions of the nuclear and plastid genomes for this lineage and other representatives of Olyreae. We used maximum parsimony, maximum likelihood, Bayesian inference and coalescence analysis. Our results corroborate the paraphyly of Parodiolyra, with P. micrantha sister to a clade including the remaining Parodiolyra and Raddiella. All remaining Parodiolyra form a well-supported clade, but Raddiella had conflicting resolutions, being either monophyletic or not. Thus, based on phylogenetic and morphological evidence, we here recircumscribe Parodiolyra, transferring P. micrantha and P. colombiensis to the new genus Taquara (described here). Regarding Raddiella, sampling is still not comprehensive and does not allow a decision on to its taxonomic status to be made at this time. Inclusion of other phreatophytic species may be crucial to resolve the problem of conflicting topologies.

Taxonomic reassessment of species within the chrysaoros group of Calisto (Lepidoptera : Nymphalidae : Satyrinae)

2017 ◽  
Vol 31 (6) ◽  
pp. 747 ◽  
Author(s):  
Rayner Núñez Aguila ◽  
Antonio R. Pérez-Asso ◽  
Julio A. Genaro
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Taxonomic Status ◽  
Haplotype Network ◽  
Morphological Data ◽  
Putative Species

The taxonomic status of the Hispaniolan species of Calisto Hübner, 1823 included in the chrysaoros group is reassessed. Morphological data and COI barcode sequences were analysed through different methods: Neighbour-Joining clustering, ABGD, Median-Joining Haplotype Network, Maximum Likelihood, and Bayesian Inference. Analyses yielded two deeply separated groups or putative species: C. clydoniata and C. chrysaoros. A shallower split was found, except in the Bayesian Inference approach, among populations of southern and northern Hispaniola palaeo-islands. In light of these findings we propose the recognition of two species: C. clydoniata and C. chrysaoros. Within the latter, the populations of the southern and northern Hispaniola palaeo-islands should be recognised as different subspecies: C. chrysaoros chrysaoros Bates and C. chrysaoros galii Schwartz, respectively. Calisto clenchi, syn. nov. is a synonym of C. chrysaoros chrysaoros whereas C. galii galli, syn. nov. and C. galii choneupsilon, syn. nov. are synonyms of C. chrysaoros galii.

Phylogenetic Relationships in the Salicornioideae / Suaedoideae / Salsoloideae s.l. (Chenopodiaceae) Clade and a Clarification of the Phylogenetic Position of Bienertia and Alexandra Using Multiple DNA Sequence Datasets

2006 ◽  
Vol 31 (3) ◽  
pp. 571-585 ◽  
Author(s):  
Maxim V. Kapralov ◽  
Hossein Akhani ◽  
Elena V. Voznesenskaya ◽  
Gerald Edwards ◽  
Vincent Franceschi ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Kranz Anatomy ◽  
Statistical Support ◽  
Chloroplast Dna Regions

The Chenopodiaceae includes taxa with both C3 and C4 photosynthesis with diverse kinds of Kranz anatomy and single-celled C4 species without Kranz anatomy; thus, it is of key importance for understanding evolution of C4 photosynthesis. All of the C4 genera except Atriplex, which belongs to Chenopodioideae, are in the Salicornioideae / Suaedoideae / Salsoloideae s.l. (including Camphorosmeae and Sclerolaeneae) clade. Our study focused on the relationships of the main lineages within this clade with an emphasis on the placement of the single cell functioning C4 genus Bienertia using maximum parsimony, maximum likelihood, and Bayesian inference phylogenetic analyses of the nuclear ribosomal ITS and five chloroplast DNA regions (atpB-rbcL, matK, psbB-psbH, rbcL, and trnL-trnF). Further we provide a detailed phylogeny of Alexandra and Suaeda based on ITS, atpB-rbcL, and psbB-psbH. Our molecular data provide strong statistical support for the monophyly of: (1) a Salicornioideae / Suaedoideae / Salsoloideae s.l. clade; (2) a Salicornioideae / Suaedoideae clade; (3) the subfamilies Salicornioideae, Suaedoideae (including Bienertia) and Salsoloideae s.l.; (4) the tribes Suaedeae, Salsoleae, and Camphorosmeae; (5) the Salicornieae if Halopeplideae is included; and (6) Suaeda if Alexandra is included. Alexandra lehmannii is therefore reclassified as Suaeda lehmannii and a new section of Suaeda is created, section Alexandra. There are four independent origins of C4 photosynthesis within the Suaedoideae including two parallel origins of Kranz C4 anatomy (in Suaeda sections Salsina s.l. and Schoberia) and two independent origins of C4 systems without Kranz anatomy (in Bienertia and in Suaeda section Borszczowia).

Redescription of Acanthogyrus (Acanthosentis) maroccanus (Dollfus, 1951) (Acanthocephala: Quadrigyridae), a parasite of the Algerian barb Luciobarbus callensis (Valenciennes) (Cyprinidae) in Algeria, and first molecular data

2019 ◽  
Vol 94 ◽  
Author(s):  
A. Menasria ◽  
D. Barčák ◽  
N. Kaouachi ◽  
M. Bensouilah ◽  
T. Scholz ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Molecular Data ◽  
Morphological Features ◽  
Phylogenetic Position ◽  
Reproductive Structures ◽  
Rdna Sequences ◽  
Northwest Africa ◽  
28S Rdna Sequences ◽  
Cyprinid Fishes

Abstract Acanthogyrus (Acanthosentis) maroccanus (Dollfus, 1951), an insufficiently described quadrigyrid acanthocephalan of cyprinid fishes from Northwest Africa, is redescribed based on recently collected specimens from the Algerian barb Luciobarbus callensis (Valenciennes) in Algeria. Newly observed morphological features for A. (A.) maroccanus include the arrangement of proboscis hooks (not in regular circles), the male reproductive structures extending into the copulatory bursa and the presence of a para-receptacle structure and vaginal sleeve. The mechanism of copulation of this acanthocephalan is described based on several copulating pairs. The phylogenetic position of A. (A.) maroccanus within Eoacanthocephala was assessed based on partial 28S rDNA sequences. Maximum likelihood and Bayesian inference analyses placed A. (A.) maroccanus in a clade with Palliolisentis (Demidueterospinus) ophiocephalus (Thapar, 1931), both species included in the Quadrigyridae, the only family within the Gyracanthocephala.

scholarly journals Phylogenetic relationships within the genus Cynanthus (Aves: Trochilidae), with emphasis on C. doubledayi

Zootaxa ◽  
2008 ◽  
Vol 1742 (1) ◽  
pp. 61 ◽  
Author(s):  
GABRIELA M. GARCÍA-DERAS ◽  
NANDADEVI CORTÉS-RODRÍGUEZ ◽  
MAGALI HONEY ◽  
ADOLFO G. NAVARRO-SIGÜENZA ◽  
JAIME GARCÍA-MORENO ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Coastal Plain ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Taxonomic Status ◽  
Full Species ◽  
Preliminary Support

We investigated the phylogeny of the genus Cynanthus and the taxonomic status of C. doubledayi using partial sequences of the mitochondrial DNA gene ND2 and three phylogenetic approaches: maximum parsimony, maximum likelihood, and Bayesian inference. Our results corroborate the monophyly of the genus and provide preliminary support for the validity of C. doubledayi as a full species (not a subspecies of C. latirostris, as traditionally considered). As an endemic of the coastal plain of southwestern Mexico, C. doubledayi corroborates the importance of this region for in situ speciation of birds and other taxa.

The phylogenetic position and taxonomic status of the Southeast and South Asian bamboo genera Neohouzeaua and Ochlandra (Poaceae: Bambusoideae) 

Phytotaxa ◽  
2020 ◽  
Vol 472 (2) ◽  
pp. 107-122
Author(s):  
WEI LIM GOH ◽  
SARAWOOD SUNGKAEW ◽  
ATCHARA TEERAWATANANON ◽  
DIETER OHRNBERGER ◽  
ELIZABETH A. WIDJAJA ◽  
...  
Keyword(s):  
South Asian ◽  
Morphological Traits ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Generic Type ◽  
Staminal Tube ◽  
Specimen Material ◽  
Molecular Phylogenetic ◽  
Woody Bamboos

Among the tropical woody bamboos, the Melocanninae is one of the most clearly recognized subtribes morphologically and has also been consistently well delimited in molecular phylogenetic work. The relationships among those genera in this subtribe, however, have been contentious because of poorly understood generic delimitations, in part due to poor specimen material or insufficiently assessed morphological traits, sometimes exacerbated by poorly accessible provenances. We address the phylogenetic and taxonomic status of two groups which together include the largest number of species in this subtribe: the Neohouzeaua-Schizostachyum complex, distributed from India to South China, Southeast Asia and southwest Pacific, and the endemic Indian genus Ochlandra. Three Neohouzeaua species (including the generic type), 12 Schizostachyum species (including the generic type and several species of uncertain placement), together with five species of Ochlandra and representatives of Cephalostachyum, Melocanna and Pseudostachyum were assessed in a molecular phylogenetic analysis together with members of other well-distinguished subtribes. Members of Neohouzeaua and Schizostachyum align into two main groups that were not completely well-supported statistically but which members possess mostly reflexed culm leaf blades, or mostly erect culm leaf blades. Other characters which provide obvious differences between taxa, such as the number of flowers in a pseudospikelet, fusion of filaments into a staminal tube, and presence of lodicules, were inconsistent between these groups. Neohouzeaua and Schizostachyum cannot be clearly distinguished in either morphological or molecular terms, and thus are united under the latter name, which takes precedence. In reviewing names in Neohouzeaua and their basionyms, several lectotypifications are designated. Three new combinations in Schizostachyum are proposed. On the other hand, Ochlandra forms a distinct clade and its monophyly is demonstrated, supported by clear morphological characters.

scholarly journals The Afro–Oriental Genus Yaeprimus Sasa et Suzuki (Diptera: Chironomidae: Chironomini): Phylogeny, New Species and Expanded Diagnoses

Diversity ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 31
Author(s):  
Wu Han ◽  
Jinxing Wei ◽  
Xiaolong Lin ◽  
Hongqu Tang
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Genetic Markers ◽  
Mixed Model ◽  
Phylogenetic Position ◽  
Life Stages ◽  
Likelihood Methods ◽  
Maximum Likelihood Methods ◽  
A New Species

Expanded generic diagnoses of all life stages of Yaeprimus Sasa et Suzuki, 2000 (Lunditendipes Harrison, 2000, syn. n.) are given. Yaeprimus tropicus comb. n. is redescribed as an adult based on type material. Additionally, a new species Y. balteatus sp. n. from Oriental China is described based on the adult male and pupa. The phylogenetic position of Yaeprimus within Chironomini and the validity of the new species are explored based on concatenated five genetic markers (18S, 28S, CAD1, CAD4, and COI-3P) through both mixed–model Bayesian inference and maximum likelihood methods. The results strongly support Yaeprimus as sister to Imparipecten Freeman, 1961, which counters a previously proposed systematical position based solely on morphology.

scholarly journals On the identity and phylogenetic position of Dero indica (Clitellata: Naididae)

Biologia ◽  
2020 ◽  
Vol 75 (10) ◽  
pp. 1685-1689
Author(s):  
Sivabalan Srinivasan ◽  
Svante Martinsson ◽  
Mohammed Ibrahim Naveed
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Cryptic Species ◽  
Phylogenetic Position ◽  
Close Relationship

Abstract The identity and validity of the freshwater worm Dero indica (Clitellata: Naididae; Naidinae) has been debated, and it has been suggested that it is likely to be identical with D. digitata. In this study we combine a newly generated COI sequence of D. indica with available sequences from GenBank, to estimate the phylogeny of Dero using both Bayesian Inference and Maximum Likelihood. The trees show that D. indica is well separated from D. digitata, instead it is closest to D. vaga, but with low support. Furthermore, the analyses confirm the close relationship between Dero and Branchiodrilus found in previous studies, and indicates the presence of cryptic species in D. furcata and D. digitata.

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