Genetic Differentiation and Divergence Time of Chinese Parnassius (Lepidoptera: Papilionidae) Species Based on Nuclear Internal Transcribed Spacer (ITS) Sequence Data

2020 ◽  
Vol 55 (4) ◽  
pp. 520-546
Author(s):  
Chengcai Si ◽  
Keke Chen ◽  
Ruisong Tao ◽  
Chengyong Su ◽  
Junye Ma ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Differentiation ◽  
Species Identification ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Divergence Time ◽  
Time Estimation ◽  
Western China ◽  
Tibet Plateau ◽  
Divergence Time Estimation

Abstract Parnassius (Lepidoptera: Papilionidae) is a genus of attractive butterflies mainly distributed in the mountainous areas of Central Asia, the Himalayas, and western China. In this study, we used the internal transcribed spacer (ITS1 and ITS2) sequence data as DNA barcodes to characterize the genetic differentiation and conduct the phylogenetic analysis and divergence time estimation of the 17 Parnassius species collected in China. Species identification and genetic differentiation analysis suggest that the ITS barcode is an effective marker for Parnassius species identification; additionally, a relatively high level of genetic diversity and low level of gene flow were detected in the five Parnassius species with diverse geographic populations. Phylogenetic analysis indicates that the 17 species studied were clustered in six clades (subgenera), with subgenus Parnassius at the basal position in the phylogenetic trees. Bayesian divergence time estimation shows that the genus originated about 18 million years ago during the early Miocene, correlated with orogenic events in the distribution region, probably southwestern China about 20–10 million years ago. Our estimated phylochronology also suggests that the Parnassius interspecific and intraspecific divergences were probably related with the rapid rising of the Qinghai-Tibet Plateau, the Tibet Movement, the Kunlun-Yellow River Tectonic Movement, and global cooling associated with intensified glaciation in the region during the Quaternary Period.

scholarly journals Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

2017 ◽  
Author(s):  
Mario dos Reis ◽  
Gregg F. Gunnell ◽  
José Barba-Montoya ◽  
Alex Wilkins ◽  
Ziheng Yang ◽  
...  
Keyword(s):  
Sequence Data ◽  
Divergence Time ◽  
Time Estimation ◽  
Test Case ◽  
Base Pairs ◽  
Molecular Sequence Data ◽  
Divergence Time Estimation ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Clock Models

AbstractPrimates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 61 thousand base pairs) that includes nine complete primate genomes (3.4 million base pairs). We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (auto-correlated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the auto-correlated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.

scholarly journals Bayesian Node Dating based on Probabilities of Fossil Sampling Supports Trans-Atlantic Dispersal of Cichlid Fishes

2016 ◽  
Author(s):  
Michael Matschiner ◽  
Zuzana Musilová ◽  
Julia M I Barth ◽  
Zuzana Starostová ◽  
Walter Salzburger ◽  
...  
Keyword(s):  
Sequence Data ◽  
Sampling Rate ◽  
Divergence Time ◽  
Time Estimation ◽  
Total Evidence ◽  
Teleost Fishes ◽  
New Approach ◽  
Divergence Time Estimation ◽  
Age Estimates ◽  
Birth Death

Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two non-exclusive alternative approaches have recently been developed, the "fossilized birth-death" model and "total-evidence dating". While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher-level taxa. We here develop a flexible new approach to Bayesian node dating that combines advantages of traditional node dating and the fossilized birth-death model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated datasets, and compare its performance to that of the fossilized birth death model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the fossilized birth-death model. By applying our approach to a large dataset including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for trans-oceanic dispersal of cichlids and other groups of teleost fishes.

The taxonomic placement of three fossil Fundulus species and the timing of divergence within the North American topminnows (Teleostei: Fundulidae)

Zootaxa ◽  
2017 ◽  
Vol 4250 (6) ◽  
pp. 577 ◽  
Author(s):  
MICHAEL J. GHEDOTTI ◽  
MATTHEW P. DAVIS
Keyword(s):  
Sequence Data ◽  
Divergence Time ◽  
Time Estimation ◽  
Species Group ◽  
Total Evidence ◽  
Morphological Data ◽  
Fossil Species ◽  
Divergence Time Estimation ◽  
Biogeographic History ◽  
Extant Species

The fossils species †Fundulus detillae, †F. lariversi, and †F. nevadensis from localities in the western United States are represented by well-preserved material with date estimations. We combined morphological data for these fossil taxa with morphological and DNA-sequence data to conduct a phylogenetic analysis and a tip-based divergence-time estimation for the family Fundulidae. The resultant phylogeny is largely concordant with the prior total-evidence phylogeny. The fossil species do not form a monophyletic group, and do not represent a discrete western radiation of Fundulus as previously proposed. The genus Fundulus diverged into subgeneric clades likely in the Eocene or Oligocene (mean age 34.6 mya, 53–23 mya), and all subgeneric and most species-group clades had evolved by the middle Miocene. †Fundulus lariversi is a member of subgenus Fundulus in which all extant species are found only in eastern North America, demonstrating that fundulids had a complicated biogeographic history. We confirmed †Fundulus detillae as a member of the subgenus Plancterus. †F. nevadensis is not classified in a subgenus but likely is related to the subgenera Plancterus and Wileyichthys. 

In and out of the Qinghai-Tibet Plateau: divergence time estimation and historical biogeography of the large arctic-alpine genusSaxifragaL.

2016 ◽  
Vol 44 (4) ◽  
pp. 900-910 ◽  
Author(s):  
J. Ebersbach ◽  
A. N. Muellner-Riehl ◽  
I. Michalak ◽  
N. Tkach ◽  
M. H. Hoffmann ◽  
...  
Keyword(s):  
Divergence Time ◽  
Time Estimation ◽  
Historical Biogeography ◽  
Tibet Plateau ◽  
Divergence Time Estimation ◽  
Qinghai Tibet Plateau

scholarly journals The Complete Mitochondrial Genome of Platysternon megacephalum peguense and Molecular Phylogenetic Analysis

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 487 ◽  
Author(s):  
Hongdi Luo ◽  
Haijun Li ◽  
An Huang ◽  
Qingyong Ni ◽  
Yongfang Yao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Complete Mitochondrial Genome ◽  
Divergence Time ◽  
Time Estimation ◽  
Sister Group ◽  
Genetic Distances ◽  
The Tibetan Plateau ◽  
Evolutionary Analysis ◽  
Divergence Time Estimation ◽  
Molecular Features

Platysternon megacephalum is the only living representative species of Platysternidae and only three subspecies remain: P. m. megalorcephalum, P. m. shiui, and P. m. peguense. However, previous reports implied that P. m. peguense has distinct morphological and molecular features. The characterization of the mitogenome has been accepted as an efficient means of phylogenetic and evolutionary analysis. Hence, this study first determined the complete mitogenome of P. m. peguense with the aim to identify the structure and variability of the P. m. peguense mitogenome through comparative analysis. Furthermore, the phylogenetic relationship of the three subspecies was tested. Based on different tRNA gene loss and degeneration of these three subspecies, their rearrangement pathways have been inferred. Phylogenetic analysis showed that P. m. peguense is a sister group to (P. m. megalorcephalum and P. m. shiui). Furthermore, the divergence time estimation of these three subspecies coincided with the uplift of the Tibetan Plateau. This study shows that the genetic distances between P. m. peguense and the other two subspecies are comparable to interspecific genetic distances, for example within Mauremys. In general, this study provides new and meaningful insights into the evolution of the three Platysternidae subspecies.

scholarly journals Phylogenetic analysis of colubrid snakes based on 12S rDNA reveals distinct lineages of Dendrelaphis pictus (Gmelin, 1789) populations in Sumatra and Java

2018 ◽  
Vol 19 (1) ◽  
pp. 303-310 ◽  
Author(s):  
FITRA ARYA DWI NUGRAHA ◽  
FATCHIYAH FATCHIYAH ◽  
NIA KURNIAWAN ◽  
ERIC NELSON SMITH
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Time Estimation ◽  
Limited Data ◽  
Divergence Time Estimation ◽  
12S Rdna ◽  
The Subject ◽  
Molecular Relationships ◽  
Inference Methods

Nugraha FAD, Fatchiyah F, Smith EN, Nia Kurniawan N. 2018. Phylogenetic analysis of colubrid snakes based on 12S rDNA reveals distinct lineages of Dendrelaphis pictus (Gmelin, 1789) populations in Sumatra and Java. Biodiversitas 19: 303-310. The phylogenetic relationship among the major colubrid snakes, particularly those of the subfamily Colubrinae, has been the subject of much debate. Also, there was limited data on the molecular relationships of Sundaland colubrid snakes. This study aimed to examine the relationships among colubrid snakes from Sumatra and Java based on fragments of 12S rDNA gene. We sequenced 17 specimens of colubrid snakes representing 5 genera and 2 subfamilies: Colubrinae and Ahaetullinae. We used maximum likelihood, maximum parsimony and Bayesian inference methods for inferring phylogenetic relationships. The result of our phylogenetic analyses is in line with the previous findings for the separation between Colubrinae and Ahaetullinae. Interestingly, we found two distinct clades of Dendrelaphis pictus species with the high genetic divergence between them where D. pictus from Sumatra and West Java separated from Central and East Java clade. Our divergence time estimation showed that the differentiation between these clades of D. pictus occurred in the late Miocene epoch (8.9 Ma) when Sumatra and Java separated after being inundated in the early Miocene epoch.

scholarly journals Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil–based model selection

2004 ◽  
Vol 359 (1450) ◽  
pp. 1477-1483 ◽  
Author(s):  
Thomas J. Near ◽  
Michael J. Sanderson
Keyword(s):  
Cross Validation ◽  
Sequence Data ◽  
Divergence Time ◽  
Evolutionary Model ◽  
Time Estimation ◽  
Optimal Estimation ◽  
Divergence Time Estimation ◽  
Fossil Calibration ◽  
Divergence Time Estimates ◽  
The Impact

Estimates of species divergence times using DNA sequence data are playing an increasingly important role in studies of evolution, ecology and biogeography. Most work has centred on obtaining appropriate kinds of data and developing optimal estimation procedures, whereas somewhat less attention has focused on the calibration of divergences using fossils. Case studies with multiple fossil calibration points provide important opportunities to examine the divergence time estimation problem in new ways. We discuss two cross–validation procedures that address different aspects of inference in divergence time estimation. ‘Fossil cross–validation’ is a procedure used to identify the impact of different individual calibrations on overall estimation. This can identify fossils that have an exceptionally large error effect and may warrant further scrutiny. ‘Fossil–based model cross–validation’ is an entirely different procedure that uses fossils to identify the optimal model of molecular evolution in the context of rate smoothing or other inference methods. Both procedures were applied to two recent studies: an analysis of monocot angiosperms with eight fossil calibrations and an analysis of placental mammals with nine fossil calibrations. In each case, fossil calibrations could be ranked from most to least influential, and in one of the two studies, the fossils provided decisive evidence about the optimal molecular evolutionary model.

Ebony and the Mascarenes: the evolutionary relationships and biogeography of Diospyros (Ebenaceae) in the western Indian Ocean

2019 ◽  
Vol 190 (4) ◽  
pp. 359-373 ◽  
Author(s):  
Alexander G Linan ◽  
George E Schatz ◽  
Porter P Lowry ◽  
Allison Miller ◽  
Christine E Edwards
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Time Estimation ◽  
Western Indian Ocean ◽  
Evolutionary Relationships ◽  
Ancestral Area ◽  
Molecular Analyses ◽  
Divergence Time Estimation ◽  
Mascarene Islands

Abstract Using analyses that exhaustively sampled Mascarene Diospyros and included representative taxa from Madagascar and other regions, we explored: (1) evolutionary relationships among Diospyros spp. across the WIO and (2) biogeographic connections of Malagasy taxa with those in surrounding regions, particularly focusing on connections with taxa in the Mascarene Islands. We obtained plastid sequence data for 146 Diospyros taxa, including 40 species not previously included in molecular analyses, and conducted Bayesian and maximum-likelihood phylogenetic analyses, divergence-time estimation and ancestral area reconstructions. Diospyros sampled from Madagascar fell into two clades, one of which contains all but two Malagasy species. Biogeographic analyses revealed that many clades probably originated in Madagascar and dispersed to locations in Africa and the Mascarenes, indicating that Madagascar may have acted as an important source of diversity for the region.

scholarly journals Conceptual issues in Bayesian divergence time estimation

2016 ◽  
Vol 371 (1699) ◽  
pp. 20150134 ◽  
Author(s):  
Bruce Rannala
Keyword(s):  
Bayesian Inference ◽  
Sequence Data ◽  
Divergence Time ◽  
Time Estimation ◽  
Statistical Problem ◽  
Divergence Times ◽  
Posterior Distributions ◽  
Divergence Time Estimation ◽  
Branch Lengths ◽  
Time Parameters

Bayesian inference of species divergence times is an unusual statistical problem, because the divergence time parameters are not identifiable unless both fossil calibrations and sequence data are available. Commonly used marginal priors on divergence times derived from fossil calibrations may conflict with node order on the phylogenetic tree causing a change in the prior on divergence times for a particular topology. Care should be taken to avoid confusing this effect with changes due to informative sequence data. This effect is illustrated with examples. A topology-consistent prior that preserves the marginal priors is defined and examples are constructed. Conflicts between fossil calibrations and relative branch lengths (based on sequence data) can cause estimates of divergence times that are grossly incorrect, yet have a narrow posterior distribution. An example of this effect is given; it is recommended that overly narrow posterior distributions of divergence times should be carefully scrutinized. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

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