Australasian orchid diversification in time and space: molecular phylogenetic insights from the beard orchids (Calochilus, Diurideae)

2018 ◽  
Author(s):  
Katharina Nargar ◽  
Sarah Molina ◽  
Natascha Wagner ◽  
Lars Nauheimer ◽  
Claire Micheneau ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Divergence Time ◽  
Clock Model ◽  
Infrageneric Classification ◽  
Ancestral Area ◽  
Molecular Clock Model ◽  
Molecular Phylogenetic ◽  
Spatio Temporal ◽  
Vegetative Characters ◽  
Relaxed Molecular Clock

Phylogenetic relationships in Calochilus (~30 species) were inferred based on a supermatrix of 81 loci including 22 species. To examine the spatio-temporal evolution of Calochilus, divergence-time estimations were conducted within a Bayesian framework using an uncorrelated relaxed molecular-clock model, followed by maximum-likelihood ancestral-range reconstructions comparing four biogeographic models. To trace the evolution of key floral and vegetative characters, maximum-likelihood ancestral-character reconstructions were carried out. The stem age of Calochilus was dated to ~12.0 million years ago in the mid-Miocene. Divergence of Calochilus into a tropical and a temperate clade was inferred to have occurred ~7.6 million years ago in the late Miocene. Northern Australia was reconstructed as the ancestral area of the tropical clade and the Euronotian region for the temperate clade. Range expansions from Australia to other Australasian regions, such as New Zealand and New Guinea, were inferred to have occurred only in recent geological times, commencing in the Pleistocene. The infrageneric classification for Calochilus was revised, erecting two subgenera, subgenus Calochilus and subgenus Tropichilus subgen. nov. Section Calochilus Szlach. was recircumscribed, and sect. Abrochilus sect. nov., and section Placochilus sect. nov. were erected. Identification keys to subgenera and sections and a taxonomic synopsis of the genus are provided.

scholarly journals Phylogeography of hepatitis B: The role of Portugal in the early dissemination of HBV worldwide

2022 ◽  
Author(s):  
Rute Marcelino ◽  
Ifeanyi J Ezeonwumelu ◽  
Andre Janeiro ◽  
Paula Mimoso ◽  
Sonia Matos ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Hbv Genotype ◽  
Hbv Genotypes ◽  
Molecular Clock Model ◽  
Global Spread ◽  
History Of ◽  
Spatio Temporal ◽  
Relaxed Molecular Clock ◽  
Nucleotide Substitution Model

In Portugal, the genetic diversity, origin of HBV, and the Portuguese role in the dissemination of HBV worldwide were never investigated. In this work, we studied the epidemic history and transmission dynamics of HBV genotypes that are endemic in Portugal. HBV pol gene was sequenced from 130 patients followed in Lisbon. HBV genotype A (HBV/A) was the most prevalent (n=54, 41.5%), followed by D [HBV/D; (n=44, 33.8%)], and E [HBV/E; (n=32, 24.6%)]. Spatio-temporal evolutionary dynamics was reconstructed in BEAST using a Bayesian Markov Chain Monte Carlo method, with a GTR nucleotide substitution model, an uncorrelated lognormal relaxed molecular clock model, a Bayesian skyline plot, and a continuous diffusion model. HBV/D4 was the first subgenotype to be introduced in Portugal around 1857 (HPD 95% 1699-1931) followed by HBV/D3 and A2 a few decades later. HBV/E and HBV/A1 were introduced in Portugal later, almost simultaneously. Our results also indicate a very important role of Portugal in the exportation of HBV/D4 and A2 to Brazil and Cape Verde, respectively, at the beginning of the XX century. This work clarifies the epidemiological history of HBV in Portugal and shows that Portugal had an important role in the global spread of this virus.

scholarly journals A revised infrageneric classification and synopsis of the Afro-Eurasian genus Moraea (Iridaceae: Irideae)

Bothalia ◽  
2013 ◽  
Vol 43 (1) ◽  
pp. 29-42 ◽  
Author(s):  
P. Goldblatt ◽  
J. C. Manning ◽  
J. Schnitzler
Keyword(s):  
New Species ◽  
Current Data ◽  
Infrageneric Classification ◽  
The Past ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Molecular Phylogenies ◽  
Vegetative Characters

Molecular phylogenetic studies of Moraea Mill. and the inclusion of Barnardiella Goldblatt, Galaxia Thunb., Gynandriris Parl., Hexaglottis Vent., Homeria Vent. and Roggeveldia Goldblatt in the genus have rendered the existing infrageneric classification, dating from 1976, in need of substantial revision. In particular, subg. Moraea and subg. Vieusseuxia have been shown to be paraphyletic. We propose a new infrageneric classification, based, as far as current data permit, on phylogenetic principles. Monophyletic subgenera and sections are circumscribed based on molecular phylogenies alone or in combination with morphological considerations. We recognize 11 subgenera, 15 sections and three series, arranged as follows in phylogenetic sequence: Plumarieae; Visciramosae (with sect. Multifoliae and sect. Visciramosae); Moraea (with sect. Moraea and sect. Polyphyllae); Galaxia (with ser. Unguiculatae, ser. Eurystigma and ser. Galaxia); Monocephalae; Acaules; Polyanthes (with sect. Serpentinae, sect. Deserticola, sect. Hexaglottis, sect. Gynandriris, sect. Polyanthes and sect. Pseudospicatae); Grandifl orae; Vieusseuxia (with sect. Integres, sect. Vieusseuxia and sect. Villosae); and Homeria (with sect. Stipanthera, sect. Flexuosae, sect. Homeria and sect. Conantherae). Most are moderately to well circumscribed at the morphological level either by floral or vegetative characters, except subg. Moraea, which includes a small number of unspecialized species apparently not linked by any apomorphic features. With over 27 new species described in the past 25 years and another 60 transferred to the genus, Moraea now includes 214 species. We provide a full taxonomic synopsis of the genus.

scholarly journals Morphological and molecular phylogenetic analyses of Zepedanulus ishikawai (Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

2021 ◽  
pp. 1-28
Author(s):  
Yoshimasa Kumekawa ◽  
Haruka Fujimoto ◽  
Osamu Miura ◽  
Ryo Arakawa ◽  
Jun Yokoyama ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Ryukyu Archipelago ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Polymerase Chain

Abstract Harvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestman Zepedanulus ishikawai (Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based on CO1 and 16S rRNA sequences of mtDNA, the 28S rRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals of Z. ishikawai were monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades of Z. ishikawai.

Species Delimitation and evolutionary history of tree frogs in the Hyla chinensis-group (Hylidae, Amphibian)

2019 ◽  
Author(s):  
Tao Pan ◽  
Guiyou Wu ◽  
Xing Kang ◽  
Peng Yan ◽  
Izaz Ali ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Divergence Time ◽  
Distinct Species ◽  
Species Group ◽  
Early Miocene ◽  
Evolutionary Divergence ◽  
Dabie Mountains ◽  
Ancestral Area ◽  
Ancestral Area Reconstruction ◽  
History Of

Abstract Background Species are the cornerstone in many domains of biology research, which made the accurate species delimitation became critically important. In this study, the systematics and biogeography of the Hyla chinensis -group were analyzed based on phylogeny, species delimitation and ancestral area reconstruction methods.Results The phylogenetic results showed six specific clusters existed in the H. chinensis- group. BPP analysis indicated that six distinct species exist due to the high probability values (>0.95), which were also supported by the BF analysis. The divergence time of the H. chinensis -group is estimated to date back to 18.84 Mya in the early Miocene. Combining the results of ancestral area reconstruction, the H. chinensis -group might have originated from Guangxi-Hainan, then spread eastwardly and reached Nanling mountains, Wuyi mountains, Huangshan mountains and Taiwan. In rightabout colonization, it is gradually extended to the Yunnan-Guizhou Plateau, Sichuan basin, Qinling mountains and Dabie mountains. Considering the geological movement from early Miocene to Pliocene, the colonization pattern of the H. chinensis -group maybe closely related to the progressive uplift of Qinghai-Tibetan Plateau (QTP) and historical climate change.Conclusions Our study provides evidence for species delimitation and speciation process within the H. chinensis -group. Our study supports the hypothesis that the evolutionary divergence in this species group was a consequence of the progressive uplift of QTP and environmental change.

Phylogenetic relationships and a new sectional classification of Croton (Euphorbiaceae) in Australia

2015 ◽  
Vol 28 (4) ◽  
pp. 219 ◽  
Author(s):  
Benjamin W. van Ee ◽  
Paul I. Forster ◽  
Paul E. Berry
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Pacific Islands ◽  
Australian Species ◽  
Molecular Phylogenetic ◽  
Species Lists ◽  
Nuclear Its ◽  
Australian Flora ◽  
Sectional Classification

A molecular phylogeny, morphological descriptions, species lists and a key to the sections of Croton L. (Euphorbiaceae) recognised for Australia are presented. The molecular phylogenetic results supported the recognition of six sections, to account for the 29 native Australian species. The monophyly of each of these sections was highly supported in the Bayesian and maximum-likelihood analyses of nuclear ITS and plastid trnL–F DNA sequences, whereas their relationships to each other and to other groups were less well resolved. Croton may represent one, two or three separate arrivals to Australia, with support for hypotheses of subsequent dispersals from Australia to Pacific islands and to Asia. Croton sections Argyrati, Arnhemici, Caudati, Dockrilliorum and Insulares are newly described. Croton section Gymnocroton Baill., previously placed in synonymy, is again recognised. Croton armstrongii S.Moore is excluded from the Australian flora.

An infrageneric classification of Thesium (Santalaceae) based on molecular phylogenetic data

Taxon ◽  
2020 ◽  
Vol 69 (1) ◽  
pp. 100-123
Author(s):  
Daniel A. Zhigila ◽  
G. Anthony Verboom ◽  
A. Muthama Muasya
Keyword(s):  
Infrageneric Classification ◽  
Phylogenetic Data ◽  
Molecular Phylogenetic ◽  
Molecular Phylogenetic Data
Sign in / Sign up

Export Citation Format

Share Document