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.

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.

scholarly journals Evaluating the Performance of Probabilistic Algorithms for Phylogenetic Analysis of Big Morphological Datasets: A Simulation Study

2020 ◽  
Vol 69 (6) ◽  
pp. 1088-1105 ◽  
Author(s):  
Oksana V Vernygora ◽  
Tiago R Simões ◽  
Erin O Campbell
Keyword(s):  
Bayesian Inference ◽  
Missing Data ◽  
Maximum Likelihood ◽  
Evolutionary Biology ◽  
False Positives ◽  
Probabilistic Methods ◽  
Morphological Data ◽  
Global Optimality ◽  
Probabilistic Algorithms ◽  
Taxonomic Sampling

Abstract Reconstructing the tree of life is an essential task in evolutionary biology. It demands accurate phylogenetic inference for both extant and extinct organisms, the latter being almost entirely dependent on morphological data. While parsimony methods have traditionally dominated the field of morphological phylogenetics, a rapidly growing number of studies are now employing probabilistic methods (maximum likelihood and Bayesian inference). The present-day toolkit of probabilistic methods offers varied software with distinct algorithms and assumptions for reaching global optimality. However, benchmark performance assessments of different software packages for the analyses of morphological data, particularly in the era of big data, are still lacking. Here, we test the performance of four major probabilistic software under variable taxonomic sampling and missing data conditions: the Bayesian inference-based programs MrBayes and RevBayes, and the maximum likelihood-based IQ-TREE and RAxML. We evaluated software performance by calculating the distance between inferred and true trees using a variety of metrics, including Robinson-Foulds (RF), Matching Splits (MS), and Kuhner-Felsenstein (KF) distances. Our results show that increased taxonomic sampling improves accuracy, precision, and resolution of reconstructed topologies across all tested probabilistic software applications and all levels of missing data. Under the RF metric, Bayesian inference applications were the most consistent, accurate, and robust to variation in taxonomic sampling in all tested conditions, especially at high levels of missing data, with little difference in performance between the two tested programs. The MS metric favored more resolved topologies that were generally produced by IQ-TREE. Adding more taxa dramatically reduced performance disparities between programs. Importantly, our results suggest that the RF metric penalizes incorrectly resolved nodes (false positives) more severely than the MS metric, which instead tends to penalize polytomies. If false positives are to be avoided in systematics, Bayesian inference should be preferred over maximum likelihood for the analysis of morphological data.

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.

Entoloma lushanense (Entolomataceae, Basidiomycota), a new species of Entoloma subgenus Nolanea from Jiangxi Province, China

Phytotaxa ◽  
2020 ◽  
Vol 464 (1) ◽  
pp. 93-101
Author(s):  
JUN WANG ◽  
JUN-QING YAN ◽  
GUANG-HUA HUO ◽  
CHAO-YU CUI ◽  
LIN-PING ZHANG
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Jiangxi Province ◽  
A New Species

A new species, Entoloma lushanense, is described and illustrated from the Jiangxi Province of China. It is characterized by a small brownish grey pileus with obtuse umbo, heterodiametric spores, a pileipellis as a cutis with a subpellis, and the absence of cystidia and clamp-connections. These morphological characteristics and the phylogenetic analyses (Bayesian Inference and Maximum Likelihood) supported the uniqueness of the species and its taxonomic status within the subgenus Nolanea.

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.

scholarly journals Combination of nuclear and mitochondrial markers as a useful tool to identify Ctenophthalmus species and subspecies (Siphonaptera: Ctenophthalmidae)

2021 ◽  
Author(s):  
Antonio Zurita ◽  
Cristina Cutillas
Keyword(s):  
Taxonomic Status ◽  
Molecular Study ◽  
Molecular Data ◽  
Point Of View ◽  
Morphological Data ◽  
Molecular Approach ◽  
Nuclear Marker ◽  
Mitochondrial Markers ◽  
Morphological Criteria ◽  
Mtdna Markers

AbstractCtenophthalmus is considered the largest genus within the Order Siphonaptera. From a morphological point of view, only males of this genus can be identified at species and subspecies levels using morphological keys, whereas there are no morphological criteria in order to classify females at these taxonomical levels. Furthermore, the amount of available molecular and phylogenetic data for this genus is quite scarce so far. The main objective of this work was to assess the utility of the combination of nuclear and mitochondrial markers with respect to their ability to differentiate among different subspecies within the Ctenophthalmus genus. With this purpose, we carried out a comparative morphological and molecular study of three different subspecies (Ctenophthalmus baeticus arvernus, Ctenophthalmus nobilis dobyi, and Ctenophthalmus andorrensis catalaniensis) in order to clarify and discuss its taxonomic status. In addition, our study complemented the molecular data previously provided for Ctenophthalmus baeticus boisseauorum and Ctenophthalmus apertus allani subspecies. We sequenced five different molecular markers: EF1-α, ITS1, ITS2, cox1, and cytb. Our results confirmed that morphological data by themselves are not able to discriminate among Ctenophthalmus female taxa; however, the combination of the nuclear marker EF1-α together with mtDNA markers cytb and cox1 constituted a useful taxonomical and phylogenetic tool to solve this issue. Based on these results, we consider that the use of this molecular approach should be gradually used within Ctenophthalmus genus in order to complement its classical taxonomy and clarifying the complex taxonomy of other congeneric species of fleas.

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.

Towards a monophyletic classification of Lejeuneaceae III: the systematic position of Leiolejeunea

Phytotaxa ◽  
2014 ◽  
Vol 170 (3) ◽  
pp. 187 ◽  
Author(s):  
ALFONS SCHÄFER-VERWIMP ◽  
KATHRIN FELDBERG ◽  
SHANSHAN DONG ◽  
HUUB VAN MELICK ◽  
DENILSON F. PERALTA ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Dna Sequences ◽  
Its Region ◽  
Systematic Position ◽  
Leaf Cell ◽  
Oil Bodies ◽  
Sister Relationship ◽  
First Time

The derived liverwort Leiolejeunea grandiflora was recollected at the type locality in Jamaica after more than 100 years. The characteristics of its oil bodies were described for the first time based on the new collections. Each leaf cell possesses 2-4(-6) rather small, subhomogeneous to very finely segmented, subglobose to ellipsoidal, colorless oil bodies. The plants were either dioicous or autoicous. DNA sequences of two chloroplast regions (trnL-trnF, rbcL) and the nuclear ribosomal ITS region were obtained for two accessions of Leiolejeunea to enable the inference of the phylogenetic relationships of these plants. Based on Bayesian inference of phylogeny as well as maximum parsimony and maximum likelihood analyses of a dataset including 87 representatives of Lejeuneaceae, Leiolejeunea was found as the putative sister to either Echinolejeuneinae or Cheilolejeuneinae. Thus, we propose the new monogeneric subtribe Leiolejeuneinae with relationships to Cheilolejeuneinae and Echinolejeuneinae. The analyses included also one accession of the generitype of Cheilolejeunea, C. decidua [= Cheilolejeunea adnata]. This species was found in a well supported sister relationship with Cystolejeunea. To avoid nomenclatural confusion, we propose a wide genus concept for Cheilolejeunea including Aureolejeunea, Cyrtolejeunea, Cystolejeunea, Evansiolejeunea, Leucolejeunea, and Omphalanthus.

scholarly journals A revised taxonomy of Asian snail-eating snakes Pareas (Squamata, Pareidae): evidence from morphological comparison and molecular phylogeny

ZooKeys ◽  
2020 ◽  
Vol 939 ◽  
pp. 45-64
Author(s):  
Ping Wang ◽  
Jing Che ◽  
Qin Liu ◽  
Ke Li ◽  
Jie Qiong Jin ◽  
...  
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Molecular Phylogeny ◽  
Morphological Data ◽  
Multivariate Morphometrics ◽  
Cryptic Diversity ◽  
Cyt B ◽  
Morphological Comparison ◽  
The Family ◽  
Two New Species

The Asian snail-eating snakes Pareas is the largest genus of the family Pareidae (formerly Pareatidae), and widely distributed in Southeast Asia. However, potential diversity remains poorly explored due to their highly conserved morphology and incomplete samples. Here, on basis of more extensive sampling, interspecific phylogenetic relationships of the genus Pareas were reconstructed using two mitochondrial fragments (cyt b and ND4) and two nuclear genes (c-mos and Rag1), and multivariate morphometrics conducted for external morphological data. Both Bayesian Inference and Maximum Likelihood analyses consistently showed that the genus Pareas was comprised of two distinct, monophyletic lineages with moderate to low support values. Based on evidences from molecular phylogeny and morphological data, cryptic diversity of this genus was uncovered and two new species were described. In additional, the validity of P. macularius is confirmed.

scholarly journals Taxonomic status of Flexopecten glaber ponticus (Bucquoy, Dautzenberg & Dollfus, 1889) – the Black Sea Flexopecten glaber (Linnaeus, 1758) (Bivalvia: Pectinidae)

2018 ◽  
Vol 3 (4) ◽  
pp. 14-28 ◽  
Author(s):  
I. P. Bondarev
Keyword(s):  
Comparative Analysis ◽  
Black Sea ◽  
Taxonomic Status ◽  
Morphological Data ◽  
Valid Species ◽  
The Black Sea ◽  
Marmara Sea ◽  
History Of ◽  
The Mediterranean ◽  
The Republic

The name Flexopecten glaber ponticus (Bucquoy, Dautzenberg & Dollfus, 1889) is generally used for the only Pectinidae representative inhabiting the Black Sea. It is registered in the Red Book of the Republic of Crimea as endemic subspecies reducing in amount. F. glaber ponticus is listed in WoRMS MolluscaBase as the only accepted subspecies of Flexopecten glaber (Linnaeus, 1758). In the past its taxonomic status has been changed from a geographic variety to valid species. The purpose of this study is to establish its correct taxonomic status. The study is based on a comparative analysis of conchological features of Flexopecten glaber and F. glaber ponticus in relation with the brief natural history of population in the Black Sea. Sampling was performed by snorkel equipment in Kazach’ya Bay (Black Sea, Crimea, Sevastopol) at 2–6 m depths. A total of 100 scallop specimens were sampled in September 2017. To assure a better understanding in a broader context those results are compared with the previously published morphological data based on the analysis of a large amount of material from the Black Sea and the Mediterranean Sea – Marmara Sea regions. Comparative analysis of conchological features of F. glaber ponticus from the Black Sea with F. glaber from the Mediterranean region has not revealed any distinct differences between them. Thus, there are no evidenced data for the diagnosis of F. glaber ponticus as a subspecies. Species F. glaber appeared in the Black Sea not earlier than 7,000 years ago and formed a well developed population less than 3,000 years ago. We have to conclude that the specified divergence period is not long enough to form a subspecies. As a result of the present survey the subspecific status of F. glaber ponticus is not retained and the name is placed in synonymy of the parent species Flexopecten glaber.

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