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.

scholarly journals Phylogeography of Nasutitermes ephratae (Termitidae: Nasutitermitinae) in Neotropical region

2022 ◽  
Author(s):  
Amanda de Faria Santos ◽  
Eliana Marques Cancello ◽  
Adriana Coletto Morales
Keyword(s):  
Genetic Structure ◽  
Central America ◽  
Divergence Time ◽  
Haplotype Network ◽  
Neotropical Region ◽  
Ancestral Area ◽  
Genetic Patterns ◽  
Dispersal Route ◽  
Ancestral Area Reconstruction ◽  
History Of

Abstract The neotropical region ranks third in the number of termites with five different families. Of these, Termitidae is the most diverse and includes the species Nasutitermes ephratae and is common in the neotropics. To date, only one study has been published about phylogeographic issues in neotropical termites (N. corniger). Here, we aimed to investigate and analyze the population genetic patterns of N. ephratae and then evaluated the phylogeographical processes involved in the evolutionary history of the species. We used the mitochondrial genes 16S rRNA and COII as molecular markers: These were sequenced for 128 samples of N. ephratae. We estimated the genetic diversity and divergence time as well as the demographic and genetic structure analyses. We also produced ancestral area reconstruction and a haplotype network. The results showed high genetic variability, recent demographic expansion, and strong genetic structure. We also inferred a dispersal route for the species that occurred in both directions between South and Central America. The results emphasize a temporary separation between the South and Central America population that affected the origin of the current Central America populations. These were formed form different phylogeographic histories.

Species delimitation and name application in Deyeuxia abnormis, Agrostis zenkeri, A. pleiophylla and related taxa (Poaceae: Agrostidinae)

Phytotaxa ◽  
2013 ◽  
Vol 111 (1) ◽  
pp. 1 ◽  
Author(s):  
BEATA PASZKO ◽  
ROBERT J. SORENG
Keyword(s):  
South Asia ◽  
Species Delimitation ◽  
Distinct Species ◽  
Species Group ◽  
New Synonyms

Historically tangled taxonomy and nomenclature of Deyeuxia abnormis, Agrostis zenkeri, A. pleiophylla and their allies is presented. Deyeuxia abnormis is recognized as a distinct species. Previous descriptions of this taxon were entangled with concepts of Agrostis zenkeri and Deyeuxia diffusa. The typification of Deyeuxia abnormis by Noltie is rejected in favor of the lectotype designated by Bor. The name Deyeuxia abnormis is applied to specimens of this species group with a tufted habit and callus hairs between 0.25 and 0.50 percent of their lemma in length. Specimens previously included in D. abnormis that are characterized by scrambling habit, simple or branched culms, and callus hairs between 0.6 and 1.0 percent of the lemma length, are assigned to D. diffusa. The taxonomy of Deyeuxia abnormis and its allies is clarified and new synonyms are provided, along with amended descriptions, and a key to the complex of D. abnormis and its allies. The distributions of Deyeuxia abnormis and D. diffusa in South Asia are updated. The previous typification of Agrostis pleiophylla is rejected and a new lectotype is selected. The names Anisachne gracilis (= Deyeuxia abnormis) and Agrostis continentalis (= Deyeuxia abnormis) are typified.

From the desert it came: evolution of the Australian paper daisy genus Leucochrysum (Asteraceae, Gnaphalieae)

2016 ◽  
Vol 29 (3) ◽  
pp. 176 ◽  
Author(s):  
Alexander N. Schmidt-Lebuhn ◽  
Kiarrah J. Smith
Keyword(s):  
Arid Zone ◽  
Nuclear Gene ◽  
Amplicon Sequencing ◽  
Success Rates ◽  
Ancestral Area ◽  
Biogeographic History ◽  
Molecular Phylogenetic ◽  
Ancestral Area Reconstruction ◽  
History Of ◽  
Australian Flora

Present patterns of diversity in the Australian flora have been shaped by increasing seasonality since the Eocene, and by pronounced aridification in the past 3 million years. Arid-zone plants are commonly hypothesised to be the products of radiations of ancestrally temperate or coastal lineages, as in the case of the everlasting paper daisy tribe Gnaphalieae (Asteraceae). However, these inferences are often based on higher-level phylogenies, whereas evolutionary processes in the Australian Gnaphalieae have rarely been studied at the species level. Here, we reconstructed the phylogeny and biogeographic history of the small, but ecologically diverse, paper daisy genus Leucochrysum, to examine recent habitat shifts and character changes, at the same time exploring the feasibility of using amplicon sequencing of low-copy nuclear gene regions to resolve phylogenetic relationships in Australian Gnaphalieae. On the balance of evidence, outgroup comparison and ancestral-area reconstruction support an ancestral range in the arid zone with subsequent diversification towards the south-east, demonstrating a complex evolutionary history with a re-colonisation of temperate areas. Low amplification success rates suggest that methods other than amplicon sequencing of currently available primers will be more promising for molecular phylogenetic work at a larger scale.

A revision of the species group of Xenochrophis piscator (Schneider, 1799) (Squamata: Natricidae)

Zootaxa ◽  
2012 ◽  
Vol 3473 (1) ◽  
pp. 1 ◽  
Author(s):  
GERNOT VOGEL ◽  
PATRICK DAVID
Keyword(s):  
Sri Lanka ◽  
Distinct Species ◽  
Sensu Stricto ◽  
Species Group ◽  
Eastern India ◽  
Large Area ◽  
As Species ◽  
History Of ◽  
New Material ◽  
Univariate Analyses

Morphological variation was investigated across the entire geographic range of the snakes of the Xenochrophis piscatorspecies group. Our results, based on morphological univariate analyses, show the existence of several well-definedclusters identified as species. Xenochrophis flavipunctatus (Hallowell, 1861) is distinct from X. piscator (Schneider, 1799)and sympatric with it over a large area. Xenochrophis tytleri (Blyth, 1863) is confirmed as the valid combination for thepopulation living on the Andaman Islands. Xenochrophis asperrimus (Boulenger, 1891) is confirmed, with species status,for populations from Sri Lanka. Xenochrophis melanzostus (Gravenhorst, 1807) is accepted, as a distinct species mostprobably endemic to Java. Xenochrophis schnurrenbergeri Kramer, 1977 is confirmed for populations from Nepal,southeastern Pakistan, and northern and eastern India. Tropidonotus sanctijohannis Boulenger, 1891 seems to be amontane colour morph of X. piscator and is not regarded here as valid. The second population of “X. piscator“ on SriLanka is regarded as different from that of the mainland, but it is not named here due to the uncertain relationships amongpopulations of southern India and Sri Lanka. The variation of X. piscator sensu stricto is discussed. All taxa areredescribed on the basis of new material. The history of all synonyms is discussed and neotypes are designated for Hydruspalustris Schneider, 1799, Coluber melanzostus Gravenhorst, 1807 and Amphiesma flavipunctatum Hallowell, 1861. The holotype of Hydrus piscator Schneider 1799 has been rediscovered and is discussed.

scholarly journals Phylogeography, Population Structure, and Species Delimitation in Rockhopper Penguins (Eudyptes chrysocome and Eudyptes moseleyi)

2019 ◽  
Author(s):  
Herman L Mays ◽  
David A Oehler ◽  
Kyle W Morrison ◽  
Ariadna E Morales ◽  
Alyssa Lycans ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Species Delimitation ◽  
Diversity Index ◽  
Divergence Time ◽  
Distinct Species ◽  
Effective Population ◽  
Heuristic Approaches

Abstract Rockhopper penguins are delimited as 2 species, the northern rockhopper (Eudyptes moseleyi) and the southern rockhopper (Eudyptes chrysocome), with the latter comprising 2 subspecies, the western rockhopper (Eudyptes chrysocome chrysocome) and the eastern rockhopper (Eudyptes chrysocome filholi). We conducted a phylogeographic study using multilocus data from 114 individuals sampled across 12 colonies from the entire range of the northern/southern rockhopper complex to assess potential population structure, gene flow, and species limits. Bayesian and likelihood methods with nuclear and mitochondrial DNA, including model testing and heuristic approaches, support E. moseleyi and E. chrysocome as distinct species lineages with a divergence time of 0.97 Ma. However, these analyses also indicated the presence of gene flow between these species. Among southern rockhopper subspecies, we found evidence of significant gene flow and heuristic approaches to species delimitation based on the genealogical diversity index failed to delimit them as species. The best-supported population models for the southern rockhoppers were those where E. c. chrysocome and E. c. filholi were combined into a single lineage or 2 lineages with bidirectional gene flow. Additionally, we found that E. c. filholi has the highest effective population size while E. c. chrysocome showed similar effective population size to that of the endangered E. moseleyi. We suggest that the current taxonomic definitions within rockhopper penguins be upheld and that E. chrysocome populations, all found south of the subtropical front, should be treated as a single taxon with distinct management units for E. c. chrysocome and E. c. filholi.

scholarly journals Mountains as Islands: Species Delimitation and Evolutionary History of the Ant-Loving Beetle Genus Panabachia (Coleoptera, Staphylinidae) from the Northern Andes

Insects ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 64
Author(s):  
Sofía Muñoz-Tobar ◽  
Michael Caterino
Keyword(s):  
Species Delimitation ◽  
Divergence Time ◽  
Morphological Characters ◽  
Protein Coding ◽  
Widespread Species ◽  
Mitochondrial Coi ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Putative Species ◽  
History Of

The ant-loving beetle genus Panabachia Park 1942 is a poorly studied beetle lineage from the new world tropics. We recently collected Panabachia from several previously unrecorded locations in the páramo biome of the high Ecuadorian Andes, with males exhibiting great morphological variation in the distribution of the foveae and depressions in the pronotum, as well as aspects of the male genitalia. Here, we employ phylogenetic and species delimitation methods with mitochondrial (COI) and nuclear protein-coding (wingless) gene sequences to examine the concordance of morphological characters and geography with hypothesized species boundaries. Three methods of species delimitation (bPTP, GMYC and Stacey) were used to estimate the number of species, and divergence times between putative species using molecular clock calibration. Phylogenetic analysis revealed two parallel radiations, and species delimitation analyses suggest there are between 17 and 22 putative species. Based on clade support and concordance across species delimitation methods we hypothesize 17 distinct clusters, with allopatric speciation consistent with most geographic patterns. Additionally, a widespread species appears to be present in northern páramo sites, and some sister species sympatry may indicate other diversification processes have operated on certain lineages of Panabachia. Divergence time estimates suggest that Panabachia originated in the Miocene, but most species analyzed diverged during the Pliocene and Pleistocene (5.3–0.11 Mya), contemporaneous with the evolution of páramo plant species.

Age estimation for the genus Cymbidium (Orchidaceae: Epidendroideae) with implementation of fossil data calibration using molecular markers (ITS2 & matK) and phylogeographic inference from ancestral area reconstruction

2016 ◽  
Vol 14 (06) ◽  
pp. 1660001 ◽  
Author(s):  
Ruchishree Konhar ◽  
Manish Debnath ◽  
Jean Valrie Marbaniang ◽  
Devendra Kumar Biswal ◽  
Pramod Tandon
Keyword(s):  
Life Forms ◽  
Ancestral Area ◽  
Tropical Regions ◽  
Ancestral Area Reconstruction ◽  
History Of ◽  
Public Repositories ◽  
Bayesian Relaxed Clock ◽  
The Tropics ◽  
Fossil Data ◽  
Relaxed Clock

Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and biogeographers. One such family belonging to angiosperms is Orchidaceae with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and biogeographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are distinctly distributed in tropical to temperate regions. Much is not known about correlations among the level of CAM activity (one of the photosynthetic pathways often regarded as an adaptation to water stress in land plants), habitat, life forms, and phylogenetic relationships of orchids from an evolutionary perspective. A relatively well-resolved and highly supported phylogeny for Cymbidium orchids is reconstructed based on sequence analysis of ITS2 and matK regions from the chloroplast DNA available in public repositories viz. GenBank at NCBI. This study examines a genus level analysis by integrating different molecular matrices to existing fossil data on orchids in a molecular Bayesian relaxed clock employed in BEAST and assessed divergence times for the genus Cymbidium with a focus on evolutionary history of photosynthetic characters. Our study has enabled age estimations (45Ma) as well as ancestral area reconstruction for the genus Cymbidium using BEAST by addition of previously analyzed two internal calibration points.

scholarly journals Phylogenomic insights into biogeographic diversification and character evolution of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)

2021 ◽  
Author(s):  
Xiurong Ke ◽  
Diego F Morales-Briones ◽  
Hongxin Wang ◽  
Qinghui Sun ◽  
Landis B Jacob ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
East Asian ◽  
Divergence Time ◽  
Time Estimation ◽  
Distribution Patterns ◽  
Ancestral Area ◽  
Divergence Time Estimation ◽  
Network Analyses ◽  
Ancestral Area Reconstruction

Disjunctive distribution patterns and drivers of the Sino-Japanese flora in East Asia have attracted much attention in the past decades, which is also served as an important glacial sanctuary during the quaternary glacial period. However, few studies have focused on the phylogeography, diversification and evolution of morphological character at the genus level with both nuclear and plastid data. Diabelia (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across China, Japan and Korea, serving as an ideal group to explore the mechanism of East Asian flora speciation and diversification. However, the phylogenetic relationships among Diabelia remain elusive and species delimitation within the genus (three species or four species) are still controversial. In this study, we reconstructed the phylogenetic relationships among Diabelia based on nuclear and cpDNA by using target enrichment and genome skimming approaches, respectively. We found that the main clades within Diabelia were discordant between nuclear and plastid genome trees. Both nuclear and plastid phylogenetic analyses supported five main clades: D. serrata, D. tetrasepala, D. spathulata var. sanguinea, D. spathulata var. stenophylla and D. spathulata var. spathulata. Diabelia tetrasepala was inferred to be the result of a hybridization event from the species network analyses. The result of divergence time estimation and ancestral area reconstruction showed that Diabelia originated in Japan during the early Miocene, with subsequent gene flow between China, Japan and Korea. Overall, our results support the division of Diabelia into five main clades and this research provides new insights for the speciation process and taxonomy within Diabelia.

scholarly journals Phylogeny and species delimitation based on molecular approaches on the species of the Australoheros autrani group (Teleostei, Cichlidae), with biogeographic comments

2019 ◽  
Vol 95 (1) ◽  
pp. 49-64 ◽  
Author(s):  
Felipe Polivanov Ottoni ◽  
José L. O. Mattos ◽  
Axel M. Katz ◽  
Pedro H.N. Bragança
Keyword(s):  
Phylogenetic Analysis ◽  
Species Delimitation ◽  
Species Recognition ◽  
Mitochondrial Gene ◽  
Divergence Time ◽  
Morphological Characters ◽  
Species Group ◽  
Nucleotide Substitutions ◽  
Divergence Time Estimates ◽  
Late Neogene

Three distinct and independent molecular-based species delimitation analyses were performed among the species and populations included within theAustraloherosautranigroup, based on sequences of the mitochondrial gene Cytochrome b: a tree-based method proposed by Wiens and Penkrot (WP), a Character-based DNA Barcoding (CBB) and coalescent species delimitation method termed the Bayesian Implementation of the Poisson tree processes (bPTP). The congruence of WP and CBB delimited 11 independent lineages (species), while the bPTP delimited just nine lineages. We did not favour any of the methods, and we considered the possibility of two slightly variant scenarios. A time-calibrated phylogenetic analysis is proposed based on the predominant congruence of the results of these three species delimitation methods herein applied. The monophyly of theA.autranispecies group was highly supported with maximum node support value and diagnosed by 11 nucleotide substitutions. The sister clade of theA.autranispecies group is the clade comprisingA.sp. Timbé do Sul andA.minuano. The phylogenetic analysis supports three main clades within theA.autranispecies group, supported by maximum node support value, with the Southern Mata Atlântica clade as the most basal clade. Divergence time estimates indicate that the diversification of theAustraloherosoriginated during the early Neogene, but only in the late Neogene did the processes of diversification in the southeast and north regions occur. Diversification within theAustraloherosautranispecies group occurred synchronically for the three main clades during the beginning of the Quaternary. It is demonstrated that molecular characters are valuable tools for species recognition, particularly in speciose groups with inconspicuous or difficult to record morphological characters. The resulting phylogeny of theAustraloherosautranigroup is highly compatible with the geological and biogeographic scenarios proposed for the Neogene and Quarternary shaping of the extant river basins of eastern Brazil. Despite the origin of theA.autranigroup being dated to the late Miocene, species level diversification occurred in the Pleistocene and was probably driven by headwater capture events and sea-level fluctuations.

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