scholarly journals Phylogenetic Reconstruction and Divergence Time Estimation of Blumea DC. (Asteraceae: Inuleae) in China Based on nrDNA ITS and cpDNA trnL-F Sequences

Plants ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 210
Author(s):  
Ying-bo Zhang ◽  
Yuan Yuan ◽  
Yu-xin Pang ◽  
Fu-lai Yu ◽  
Chao Yuan ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Reconstruction ◽  
Divergence Time ◽  
Herbal Medicines ◽  
Time Estimation ◽  
Nuclear Ribosomal Dna ◽  
Posterior Density ◽  
Divergence Time Estimation ◽  
Explosive Expansion ◽  
Highest Posterior Density

The genus Blumea is one of the most economically important genera of Inuleae (Asteraceae) in China. It is particularly diverse in South China, where 30 species are found, more than half of which are used as herbal medicines or in the chemical industry. However, little is known regarding the phylogenetic relationships and molecular evolution of this genus in China. We used nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) trnL-F sequences to reconstruct the phylogenetic relationship and estimate the divergence time of Blumea in China. The results indicated that the genus Blumea is monophyletic and it could be divided into two clades that differ with respect to the habitat, morphology, chromosome type, and chemical composition of their members. The divergence time of Blumea was estimated based on the two root times of Asteraceae. The results indicated that the root age of Asteraceae of 76–66 Ma may maintain relatively accurate divergence time estimation for Blumea, and Blumea might had diverged around 49.00–18.43 Ma. This common ancestor had an explosive expansion during the Oligocene and Miocene and two major clades were differentiated during these epochs 29.60 Ma (17.76–45.23 Ma 95% HPD (Highest Posterior Density). Evidence from paleogeography and paleoclimate studies has confirmed that Blumea experienced differentiation and an explosive expansion during the Oligocene and Miocene.

scholarly journals Phylogenetic reconstruction and divergence time estimation of Blumea DC. (Asteraceae: Inuleae) in China based on nrDNA ITS and cpDNA trnL-F sequences

2018 ◽  
Author(s):  
Yingbo Zhang ◽  
Yuan Yuan ◽  
Yu-xin Pang ◽  
Fu-lai Yu ◽  
Dan Wang ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Reconstruction ◽  
Divergence Time ◽  
Time Estimation ◽  
Nuclear Ribosomal Dna ◽  
Recent Common Ancestor ◽  
Chromosome Type ◽  
Divergence Time Estimation ◽  
Most Recent Common Ancestor ◽  
Explosive Expansion

The genus Blumea DC. is one of the economically most important genera of Inuleae (Asteraceae) in China. It is particularly diverse in south China, where 30 species occur, more than half of which are used as herbal medicine or in the chemical industry. However, little is known about the phylogenetic relationships and molecular evolution of this genus in China. We used nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) trnL-F sequences to reconstruct the phylogenetic relationship and estimate the divergence time of Blumea DC. in China. Results indicated the genus of Blumea DC. was monophyletic and could be divided into two clades, the two clades were resolved that differ with respect to habitat, morphology, chromosome type and chemical composition, of their members. Furthermore, based on the two root time of Asteraceae, the divergence time of Blumea DC. were compare estimated. Results indicated the most recent common ancestor of Asteraceae maybe originated from 76-66 Ma, and Blumea DC. maybe originated from 72.71-52.42 Ma, and had an explosive expansion during Oligocene and Miocene (30.09-11.44 Ma), two major clades were differentiated during the Palaeocene and Oligocene (66.29-46.72 Ma), also the evidence from paleogeography and paleoclimate also supported Blumea DC. had an differentiation and explosive expansion during Oligocene and Miocene.

scholarly journals The Implications of Lineage-Specific Rates for Divergence Time Estimation

2019 ◽  
Vol 69 (4) ◽  
pp. 660-670 ◽  
Author(s):  
Tom Carruthers ◽  
Michael J Sanderson ◽  
Robert W Scotland
Keyword(s):  
Estimation Error ◽  
Divergence Time ◽  
Time Estimation ◽  
Rate Variation ◽  
Data Set ◽  
Divergence Time Estimation ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
The Impact ◽  
Highest Posterior Density

Abstract Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates—defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates—defined as variation in the average rate across all branches at each sampled locus. We show that lineage-specific rates lead to erroneous divergence time estimates, regardless of how many loci are sampled. Further, we show that stronger lineage-specific rates lead to increasing error. This contrasts to residual rates and gene-specific rates, where sampling more loci significantly reduces error. If divergence times are inferred in a Bayesian framework, we highlight that error caused by lineage-specific rates significantly reduces the probability that the 95% highest posterior density includes the correct value, and leads to sensitivity to the prior. Use of a more complex rate prior—which has recently been proposed to model rate variation more accurately—does not affect these conclusions. Finally, we show that the scale of lineage-specific rates used in our simulation experiments is comparable to that of an empirical data set for the angiosperm genus Ipomoea. Taken together, our findings demonstrate that lineage-specific rates cause error in divergence time estimates, and that this error is not overcome by analyzing genomic scale multilocus data sets. [Divergence time estimation; error; rate variation.]

scholarly journals Mahonia vs. Berberis Unloaded: Generic Delimitation and Infrafamilial Classification of Berberidaceae Based on Plastid Phylogenomics

2022 ◽  
Vol 12 ◽  
Author(s):  
Chia-Lun Hsieh ◽  
Chih-Chieh Yu ◽  
Yu-Lan Huang ◽  
Kuo-Fang Chung
Keyword(s):  
Incomplete Lineage Sorting ◽  
Divergence Time ◽  
Time Estimation ◽  
Nuclear Ribosomal Dna ◽  
Length Variation ◽  
Lineage Sorting ◽  
Divergence Time Estimation ◽  
Generic Delimitation ◽  
History Of

The early-diverging eudicot family Berberidaceae is composed of a morphologically diverse assemblage of disjunctly distributed genera long praised for their great horticultural and medicinal values. However, despite century-long studies, generic delimitation of Berberidaceae remains controversial and its tribal classification has never been formally proposed under a rigorous phylogenetic context. Currently, the number of accepted genera in Berberidaceae ranges consecutively from 13 to 19, depending on whether to define Berberis, Jeffersonia, and Podophyllum broadly, or to segregate these three genera further and recognize Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Dysosma, Diphylleia, and Sinopodophyllum, respectively. To resolve Berberidaceae’s taxonomic disputes, we newly assembled 23 plastomes and, together with 85 plastomes from the GenBank, completed the generic sampling of the family. With 4 problematic and 14 redundant plastome sequences excluded, robust phylogenomic relationships were reconstructed based on 93 plastomes representing all 19 genera of Berberidaceae and three outgroups. Maximum likelihood phylogenomic relationships corroborated with divergence time estimation support the recognition of three subfamilies Berberidoideae, Nandinoideae, and Podophylloideae, with tribes Berberideae and Ranzanieae, Leonticeae and Nandineae, and Podophylleae, Achlydeae, Bongardieae tr. nov., Epimedieae, and Jeffersonieae tr. nov. in the former three subfamilies, respectively. By applying specifically stated criteria, our phylogenomic data also support the classification of 19 genera, recognizing Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Diphylleia, Dysosma, and Sinopodophyllum that are morphologically and evolutionarily distinct from Berberis, Jeffersonia, and Podophyllum, respectively. Comparison of plastome structures across Berberidaceae confirms inverted repeat expansion in the tribe Berberideae and reveals substantial length variation in accD gene caused by repeated sequences in Berberidoideae. Comparison of plastome tree with previous studies and nuclear ribosomal DNA (nrDNA) phylogeny also reveals considerable conflicts at different phylogenetic levels, suggesting that incomplete lineage sorting and/or hybridization had occurred throughout the evolutionary history of Berberidaceae and that Alloberberis and Moranothamnus could have resulted from reciprocal hybridization between Berberis and Mahonia in ancient times prior to the radiations of the latter two genera.

scholarly journals Out of the Qinghai-Tibetan Plateau (QTP) and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

AoB Plants ◽  
2021 ◽  
Author(s):  
Min-Jie Li ◽  
Huan-Xi Yu ◽  
Xian-Lin Guo ◽  
Xing-Jin He
Keyword(s):  
Evolutionary History ◽  
Divergence Time ◽  
Time Estimation ◽  
Adjacent Region ◽  
Rapid Radiation ◽  
Divergence Time Estimation ◽  
Species Diversification ◽  
The Third ◽  
Evolutionary Line ◽  
History Of

Abstract The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

scholarly journals Reliable confidence intervals for RelTime estimates of evolutionary divergence times

2019 ◽  
Author(s):  
Qiqing Tao ◽  
Koichiro Tamura ◽  
Beatriz Mello ◽  
Sudhir Kumar
Keyword(s):  
Confidence Intervals ◽  
Divergence Time ◽  
Simulated Data ◽  
Molecular Dating ◽  
Divergence Times ◽  
Rate Variation ◽  
Evolutionary Divergence ◽  
Posterior Density ◽  
Divergence Time Estimates ◽  
Highest Posterior Density

AbstractConfidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs. However, current non-Bayesian methods may produce unreliable CIs because they do not incorporate rate variation among lineages and interactions among clock calibrations properly. Here, we present a new analytical method to calculate CIs of divergence times estimated using the RelTime method, along with an approach to utilize multiple calibration uncertainty densities in these analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density (HPD) intervals. In the analysis of computer-simulated data, we found that RelTime CIs show excellent average coverage probabilities, i.e., the true time is contained within the CIs with a 95% probability. These developments will encourage broader use of computationally-efficient RelTime approach in molecular dating analyses and biological hypothesis testing.

Taxonomy, phylogeny, and divergence time estimation for Apiosphaeria guaranitica, a Neotropical parasite on bignoniaceous hosts

Mycologia ◽  
2018 ◽  
Vol 110 (3) ◽  
pp. 526-545 ◽  
Author(s):  
Debora Cervieri Guterres ◽  
Samuel Galvão-Elias ◽  
Bruno Cézar Pereira de Souza ◽  
Danilo Batista Pinho ◽  
Maria do Desterro Mendes dos Santos ◽  
...  
Keyword(s):  
Divergence Time ◽  
Time Estimation ◽  
Divergence Time Estimation

scholarly journals Correction: Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes)

PLoS ONE ◽  
2019 ◽  
Vol 14 (5) ◽  
pp. e0217959 ◽  
Author(s):  
Hussam Zaher ◽  
Robert W. Murphy ◽  
Juan Camilo Arredondo ◽  
Roberta Graboski ◽  
Paulo Roberto Machado-Filho ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Fossil Record ◽  
Large Scale ◽  
Divergence Time ◽  
Time Estimation ◽  
Divergence Time Estimation
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