scholarly journals Old and Cosmopolite: Molecular Phylogeny of Tropical–Subtropical Kites (Aves: Elaninae) with Taxonomic Implications

Diversity ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 327
Author(s):  
Ivan J. Starikov ◽  
Michael Wink
Keyword(s):  
Molecular Phylogeny ◽  
Genetic Markers ◽  
Sequence Data ◽  
Cyt B ◽  
Ecological Data ◽  
Dna Sequence Data ◽  
Family Level ◽  
Taxonomic Implications ◽  
Rag 1 ◽  
Basal Position

Kites of the Elaninae group are small and medium-sized, mostly tropical raptors traditionally considered as an early diverged subfamily of the Accipitridae. We used nucleotide sequences of three genetic markers (mitochondrial Cyt b and COI, nuclear RAG-1) to reconstruct the phylogenetic relationships of the Elaninae, other kites, and representatives of different families of diurnal raptors. Our results confirm the basal position of Elaninae, separated the latest in Early Miocene, including Chelictinia riocourii, which was not sequenced before and belongs to this group. Not only DNA data but also cytological, morphological, and ecological data show the singularity of Elaninae. We suggest elevating this group to family level as Elanidae within the order Accipitriformes. It includes Gampsonyx swainsonii as a monotypic subfamily because of distinctive traits and DNA sequence data. Taxonomic implications for other macrogroups of Accipitriformes are discussed.

A phylogeny of the enigmatic Madagascan geckos of the genus Uroplatus (Squamata: Gekkonidae)

Zootaxa ◽  
2007 ◽  
Vol 1493 (1) ◽  
pp. 41-51 ◽  
Author(s):  
ELI GREENBAUM ◽  
AARON M. BAUER ◽  
TODD R. JACKMAN ◽  
MIGUEL VENCES ◽  
FRANK GLAW
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Phylogenetic Hypothesis ◽  
Cyt B ◽  
Undescribed Species ◽  
Dna Sequence Data ◽  
Center Of Diversity ◽  
Rag 1 ◽  
High Diversity

Since its discovery in the 17th century, the morphological peculiarities of the gekkonid lizard genus Uroplatus have generated a great deal of attention. A large number of skeletal, integumentary and visceral features are autapomorphic for the genus and some of the more well-known members of the group possess such aberrant characteristics that a separate family was once recognized to accommodate them. Recent phylogenetic analyses confirm that Uroplatus is a typical gekkonid gecko, but the specific affinities of the genus, as well as its intrageneric relationships have remained unresolved. Both nuclear (RAG-1 and PDC) and mitochondrial (ND2 and cyt b) genes (~3.2 Kb) were sequenced for 10 of 13 recognized species of Uroplatus, as well as two Madagascan and mainland African outgroups. The large-bodied forms of Uroplatus (U. fimbriatus, U. giganteus, U. henkeli, and U. sikorae) form a monophyletic group, and the smallbodied, short-tailed species are also monophyletic (U. ebenaui and U. phantasticus). Uroplatus alluaudi + U. pietschmanni comprise another distinct clade, whereas U. lineatus was weakly supported as the sister taxon of the largebodied clade and U. guentheri was sister to all other members of the genus. Our phylogenetic hypothesis based on combined DNA sequence data is mostly congruent with previous hypotheses based on morphological data. Based on a larger, more inclusive dataset, the closest relatives of Uroplatus are mainland African Afrogecko and Madagascan Matoatoa, suggesting that the diverse Malagasy gecko fauna does not comprise a single evolutionary lineage. A high diversity of new taxa (either representing synonyms to resurrect or undescribed species), morphologically similar either to U. ebenaui/phantasticus or to U. henkeli/sikorae, was apparent from our data. Many of these genetically highly divergent lineages originated from localities in northern Madagascar, which indicates this region as the possible center of diversity and endemism for several subgroups of Uroplatus.

A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, †Mascarinus) with taxonomic implications 

Zootaxa ◽  
2019 ◽  
Vol 4563 (3) ◽  
pp. 547 ◽  
Author(s):  
MICHAEL P. BRAUN ◽  
THOMAS DATZMANN ◽  
THOMAS ARNDT ◽  
MATTHIAS REINSCHMIDT ◽  
HEINZ SCHNITKER ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Genetic Markers ◽  
Related Species ◽  
Phylogenetic Relationships ◽  
Nucleotide Sequences ◽  
Monophyletic Group ◽  
Closely Related Species ◽  
Psittacula Krameri ◽  
Taxonomic Implications ◽  
Rag 1

The long-tailed parakeets of the genus Psittacula Cuvier, 1800 have thus far been regarded as a homogeneous and monophyletic group of parrots. We used nucleotide sequences of two genetic markers (mitochondrial CYTB, nuclear RAG-1) to reconstruct the phylogenetic relationships of Psittacula and closely related species. We found that the Asian genus Psittacula is apparently paraphyletic because two genera of short-tailed parrots, Psittinus Blyth, 1842 and Tanygnathus Wagler, 1832, cluster within Psittacula, as does †Mascarinus Lesson, 1830. To create monophyletic genera, we propose recognition of the following genera: Himalayapsitta Braun, 2016 for P. himalayana, P. finschii, P. roseata, and P. cyanocephala; Nicopsitta Braun, 2016 for P. columboides and P. calthrapae; Belocercus S. Müller, 1847 for P. longicauda; Psittacula Cuvier, 1800 for P. alexandri and P. derbiana; Palaeornis Vigors, 1825 for †P. wardi and P. eupatria; and Alexandrinus Braun, 2016 for P. krameri, †P. exsul, and P. (eques) echo. Additionally, Psittacula krameri and P. alexandri are paraphyletic species, which should be split to form monophyletic species. 

Molecular phylogeny and systematics of the centipede genus Ethmostigmus Pocock (Chilopoda : Scolopendromorpha) from peninsular India

2018 ◽  
Vol 32 (6) ◽  
pp. 1316 ◽  
Author(s):  
Jahnavi Joshi ◽  
Gregory D. Edgecombe
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Indian Plate ◽  
Eastern Ghats ◽  
Integrative Approach ◽  
Phylogenetic Position ◽  
Ecological Data ◽  
Peninsular India ◽  
Dna Sequence Data

Integrative taxonomy assesses the congruence between different lines of evidence for delimiting species, such as morphological, molecular or ecological data. Herein molecular phylogenetics is used to test monophyly and determine the phylogenetic position of the Old World tropical centipede genus Ethmostigmus Pocock, 1898, and to define species boundaries for Ethmostigmus in peninsular India. A phylogeny of the family Scolopendridae based on DNA sequence data for three markers from 427 specimens sampling in all major lineages (144 individuals generated in this study) recovers Ethmostigmus as a monophyletic group, but relationships among the genera in its subfamily Otostigminae are poorly supported. Two species delimitation methods for DNA sequence data and phylogeny are integrated with morphology and geographic data to propose a well-supported species hypothesis for Ethmostigmus on the peninsular Indian plate. Five species of Ethmostigmus are recognised in peninsular India, of which E. coonooranus Chamberlin, 1920 and three new species, namely, E. agasthyamalaiensis, sp. nov., E. sahyadrensis, sp. nov. and E. praveeni, sp. nov., occur in the Western Ghats, a biodiversity hotspot. The lesser-known Eastern Ghats harbour one species, E. tristis (Meinert, 1886), which has been nearly unreported for 130 years. This study highlights the value of an integrative approach to systematics, especially in underexplored, high biodiversity regions and where morphological variation is limited among closely related species.

Species delimitation of Hymenasplenium obliquissimum group (Aspleniaceae) in southwestern China

Phytotaxa ◽  
2021 ◽  
Vol 480 (1) ◽  
pp. 29-44
Author(s):  
GUO-CHENG ZHANG ◽  
HUA-FENG HONG ◽  
GE-HONG CHEN ◽  
SHU-GANG LU ◽  
YAN-FEN CHANG
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Reticulate Evolution ◽  
Southwestern China ◽  
Natural Classification ◽  
Ploidy Levels ◽  
Dna Sequence Data ◽  
Taxonomic Implications ◽  
Taxonomic Approach ◽  
Locus Classicus

The Hymenasplenium obliquissimum group contains the widespread H. obliquissimum and several geographically restricted species, including H. retusulum, H. wuliangshanense, H. latidens, H. changputungense, H. quercicola, H. szechuanense, H. furfuraceum, H. adiantifrons, and H. filipes. However, the taxonomy of this group is still unclear and needs to be revised because some entities were treated infraspecifically or as synonyms and the validation of some species still needs to be assessed. To formulate a natural classification and investigate the relationships in this group, we collected and studied specimens of species related to the H. obliquissimum group and obtained specimens of species described by Ching at their locus classicus in southwestern China. An integrative taxonomic approach was taken to delimit species in the group using cytological, morphological, and DNA sequence data. Specifically, in the phylogenetic analyses, the H. obliquissimum group was recovered as a monophyletic group, comprising five principal chloroplast lineages. Based on our inferences, we provided taxonomic implications of chloroplast lineages discovered in this study and suggested possible reticulate evolution in the H. obliquissimum group which was interpreted by the incongruence of chloroplast and nuclear phylogenies. Further studies to strengthen the taxonomic of taxa especially those with the co-existence of different ploidy levels are still warranted.

The Macroptilium gracile species complex (Fabaceae, Papilionoideae): an integrative taxonomic study based on morphological, molecular and ecological data

2020 ◽  
Vol 194 (1) ◽  
pp. 118-139
Author(s):  
Chiara Berlingeri ◽  
Manuel B Crespo ◽  
Teodardo Calles
Keyword(s):  
Sequence Data ◽  
Ecological Data ◽  
Multivariate Statistical ◽  
Dna Sequence Data ◽  
Diverse Species ◽  
History Of ◽  
Potential Habitats ◽  
Nuclear Its ◽  
Nmds Analysis ◽  
New Nomenclatural Combinations

Abstract Macroptilium gracile (Phaseolinae, Fabaceae) sensu lato is an extremely diverse species distributed from Mexico to Argentina. The taxonomic and nomenclatural history of the species is confusing, due to existing contrasting treatments. All 15 names corresponding to 12 taxa that have often been considered akin to M. gracile were selected here to clarify the identity of this taxonomic aggregate, using morphological, molecular and biogeographical analyses. Univariate and multivariate statistical analyses (nMDS and cluster) of 67 morphological traits were performed on a sample of 109 herbarium sheets. Maximum parsimony and Bayesian inference analyses were conducted using plastid (rpl32-trnL(UAG), trnK-matK-trnK) and nuclear (ITS/5.8S) DNA sequence data on a sample of 31 accessions belonging to taxa of the M. gracile complex and other Macroptilium spp., using three members of related genera (Phaseolus and Vigna) as outgroups. A database with plant locations per taxa was used to elaborate a distribution map, and the potential habitats were estimated through nMDS analysis. Our morphological, molecular and biogeographic results suggest that members of the M. gracile complex belong to three taxonomic entities, for which a new arrangement is proposed accepting Macroptilium gracile (with two varieties) and M. campestre, including two new nomenclatural combinations (M. gracile var. subcoriaceum and M. campestre). Types for all cited names are indicated where available (with a new lectotype designation). Morphological, ecological and distributional data are reported for each accepted taxon.

A new species of Youngia (Asteraceae, tribe Cichorieae) from Yunnan, China

Phytotaxa ◽  
2016 ◽  
Vol 275 (2) ◽  
pp. 140 ◽  
Author(s):  
RUI KE ◽  
YOU-SHENG CHEN
Keyword(s):  
New Species ◽  
Molecular Phylogeny ◽  
Dna Sequence ◽  
Yunnan Province ◽  
Sequence Data ◽  
Strong Support ◽  
Corolla Tube ◽  
Dna Sequence Data ◽  
A New Species

Youngia gongshanensis, a new species of Youngia sect. “Mesomeris” from Yunnan province of China is described and illustrated based on evidence from morphology and molecular phylogeny. The new species is superficially very similar to Y. atripappa having a solitary and erect stem and more or less lyrately pinnatisect leaves, but can be distinguished by capitula with 5–6 (vs. 12–15) florets, corolla tube glabrous (vs. sparsely pubescent with short white spreading hairs), pappus white (vs. grayish), bracts ovate to elliptic, distinct large (vs. very small, subulate). Parsimony analyses based on DNA sequence data of the nuclear ribosomal ITS shows that the new species is sister to Y. cineripappa with strong support, but the new species differs from the latter in having a glabrous corolla tube, smaller capitula with a lesser number of florets, and especially the white pappus.

scholarly journals Hymenochaetaceae (Basidiomycota, Hymenochaetales) from the Guineo-Congolian phytochorion: Phylloporia rinoreae sp. nov., an additional undescribed species from the Forest Global Earth Observatory Plot in Gabon

2019 ◽  
Vol 152 (3) ◽  
pp. 531-538
Author(s):  
Matthieu Jerusalem ◽  
Prudence Yombiyeni ◽  
Gabriel Castillo ◽  
Cony Decock
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Dna Sequence ◽  
Rain Forest ◽  
Sequence Data ◽  
Central Africa ◽  
Undescribed Species ◽  
Ecological Data ◽  
Dna Sequence Data ◽  
A New Species

Background and aims – The aim of this study is the continuation of an ongoing survey of Hymenochaetaceae (Basidiomycota, Hymenochaetales) from the lower Guinean sub-region in Central Africa. In this frame, a new species of Phylloporia is described from Gabon, based on morphological, ecological and phylogenetic data. Methods – The species is described using morphological methods, and ecological data. DNA-based phylogenetic analysis are also used to search for affinities.Key results – A new species of Phylloporia, P. rinoreae, is described based on specimens collected on living twigs of a shrubby Rinorea species (Violaceae), occurring in the Guineo-Congolian rain forest. Phylogenetic inferences using DNA sequence data from partial nuc 28S (region including the D1/D2/D3 domains) resolved this species as a distinct clade within the Phylloporia lineage. An identification key to the species reported from the Guineo-Congolian phytochorion is provided.Conclusion – Phylloporia rinoreae is the seventh species of the genus described from and so far only known from Gabon in the Lower Guinean phytogeographical sub-region.

Inferring evolutionary processes from DNA sequence data

2019 ◽  
pp. 145-172
Author(s):  
Glenn-Peter Sætre ◽  
Mark Ravinet
Keyword(s):  
Molecular Evolution ◽  
Dna Sequence ◽  
Genetic Markers ◽  
Dna Sequences ◽  
Sequence Data ◽  
Neutral Theory ◽  
Evolutionary Genetics ◽  
Haplotype Structure ◽  
Dna Sequence Data ◽  
Neutrality Tests

The allelic evolutionary genetic models explored so far are applicable to genetic markers. However, DNA sequences harbor a lot of information about the evolutionary past that would be missed if different sequences were simply treated as different alleles. This chapter introduces some important methods and concepts applicable to the analysis of DNA-sequence data. The null models for analyzing sequence data are derived from the neutral theory of molecular evolution. Historically, however, the neutral theory has made a large impact on evolutionary genetics. Therefore, this chapter starts by reviewing its important contribution. Then, important parameters and statistics for analyzing sequence variation are introduced, including a plethora of neutrality tests. The chapter ends with a cautious focus on the powerful tool of genome scan analysis and its utility for identifying regions of the genomes potentially under selection. This includes a section on more recently derived statistics which incorporate information on haplotype structure.

Is the horned pitviper Ceratrimeresurus shenlii Liang and Liu, 2003 from China a valid Protobothrops?

2011 ◽  
Vol 32 (1) ◽  
pp. 132-135
Author(s):  
Ellen Hitschfeld ◽  
Anna Hundsdörfer ◽  
Markus Auer ◽  
Fumin Wang ◽  
Lihua Zhou ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
Sequence Data ◽  
Isolation By Distance ◽  
Guangdong Province ◽  
Distinct Species ◽  
Cyt B ◽  
Dna Sequence Data ◽  
Phylogenetic Placement ◽  
Close Relationship

AbstractPrevious records of horned pitvipers from Vietnam and China are reviewed and the phylogenetic placement of four snakes from two sites in Tianjingshan Forest, China (Ruyan County, Guangdong Province; 24°43′N, 113°03′E, 563 m a.s.l.; 24°43′N, 113°02′E, 585 m a.s.l.) is examined. Using mitochondrial DNA sequence data (12S, 16S, ND4, cyt b; 2306 bp) and Bayesian and Maximum Likelihood analyses, the Tianjingshan pitvipers are revealed as sister to Protobothrops cornutus with a differentiation resembling those of P. flavoviridis and P. tokarensis. This indicates a close relationship with P. cornutus and suggests that Ceratrimeresurus shenlii Liang and Liu, 2003, previously considered a junior synonym of P. cornutus (Smith, 1930), could be a valid subspecies of P. cornutus or a recently split distinct species. However, further studies and samples from intermediate localities are needed to decide whether the observed differentiation reflects a pattern of isolation-by-distance or a phylogeographic, and thus perhaps taxonomically relevant, break.

Sign in / Sign up

Export Citation Format

Share Document