scholarly journals Population divergence time estimation using individual lineage label switching

2019 ◽  
Author(s):  
Peter Beerli ◽  
Haleh Ashki ◽  
Somayeh Mashayekhi ◽  
Michal Palczewski
Keyword(s):  
Divergence Time ◽  
Time Estimation ◽  
Random Variable ◽  
Recent Common Ancestor ◽  
Population Divergence ◽  
Inference Method ◽  
Divergence Time Estimation ◽  
Most Recent Common Ancestor ◽  
Wide Range ◽  
Truncated Normal

AbstractDivergence time estimation from multilocus genetic data has become common in population genetics and phylogenetics. We present a new Bayes inference method that treats the divergence time as a random variable. The divergence time is calculated from an assembly of splitting events on individual lineages in a genealogy. The waiting time for such a splitting event is drawn from a hazard function of the truncated normal distribution. This allows easy integration into the standard coalescence framework used in programs such as MIGRATE. We explore the accuracy of the new inference method with simulated population splittings over a wide range of divergence time values and with a dataset of the Zika virus; the geographic analyses of the expansion of the pathogen follows a trajectory from Africa to Asia to America, corroborating analyses based only on the dates of incidences. Evaluations of simple divergence models show high accuracy, whereas the accuracy of the results of isolation with migration (IM) models depend on the magnitude of the immigration rate and potentially on the number of samples. High immigration rates lead to a time of the most recent common ancestor of the sample that predates the divergence time, thus loses any potential signal of the divergence event in the sample data. This reduced accuracy with high immigration rates is problematic for all IM methods, including ours.

scholarly journals Ghosts of a Structured Past: Impacts of Ancestral Patterns of Isolation-by-Distance on Divergence-Time Estimation

2020 ◽  
Vol 111 (6) ◽  
pp. 573-582
Author(s):  
Zachary B Hancock ◽  
Heath Blackmon
Keyword(s):  
Population Size ◽  
Isolation By Distance ◽  
Divergence Time ◽  
Time Estimation ◽  
Ancestral Population ◽  
Recent Common Ancestor ◽  
Divergence Times ◽  
Population Divergence ◽  
Divergence Time Estimation ◽  
Coalescent Time

Abstract Isolation-by-distance is a widespread pattern in nature that describes the reduction of genetic correlation between subpopulations with increased geographic distance. In the population ancestral to modern sister species, this pattern may hypothetically inflate population divergence time estimation due to allele frequency differences in subpopulations at the ends of the ancestral population. In this study, we analyze the relationship between the time to the most recent common ancestor and the population divergence time when the ancestral population model is a linear stepping-stone. Using coalescent simulations, we compare the coalescent time to the population divergence time for various ratios of the divergence time over the population size. Next, we simulate whole genomes to obtain single nucleotide polymorphisms (SNPs), and use the Bayesian coalescent program SNAPP to estimate divergence times. We find that as the rate of migration between neighboring demes decreases, the coalescent time becomes significantly greater than the population divergence time when sampled from end demes. Divergence-time overestimation in SNAPP becomes severe when the divergence-to-population size ratio < 10 and migration is low. Finally, we demonstrate the impact of ancestral isolation-by-distance on divergence-time estimation using an empirical dataset of squamates (Tropidurus) endemic to Brazil. We conclude that studies estimating divergence times should be cognizant of the potential ancestral population structure in an explicitly spatial context or risk dramatically overestimating the timing of population splits.

scholarly journals Ghosts of a structured past: Impacts of ancestral patterns of isolation-by-distance on divergence-time estimation

2020 ◽  
Author(s):  
Zachary B. Hancock ◽  
Heath Blackmon
Keyword(s):  
Population Size ◽  
Isolation By Distance ◽  
Divergence Time ◽  
Time Estimation ◽  
Ancestral Population ◽  
Recent Common Ancestor ◽  
Divergence Times ◽  
Population Divergence ◽  
Divergence Time Estimation ◽  
Coalescent Time

AbstractIsolation by distance is a widespread pattern in nature that describes the reduction of genetic correlation between subpopulations with increased geographic distance. In the population ancestral to modern sister species, this pattern may hypothetically inflate population divergence time estimation due to the potential for allele frequency differences in subpopulations at the ends of the ancestral population. In this study, we analyze the relationship between the time to the most recent common ancestor and the population divergence time when the ancestral population model is a linear stepping-stone. Using coalescent simulations, we compare the coalescent time to the population divergence time for various ratios of the divergence time over the product of the population size and the deme number. Next, we simulate whole genomes to obtain SNPs, and use the Bayesian coalescent program SNAPP to estimate divergence times. We find that as the rate of migration between neighboring demes decreases, the coalescent time becomes significantly greater than the population divergence time when sampled from end demes. Divergence-time overestimation in SNAPP becomes severe when the divergence-to-population size ratio < 10 and migration is low. We conclude that studies estimating divergence times be cognizant of the potential ancestral population structure in an explicitly spatial context or risk dramatically overestimating the timing of population splits.

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 initiation of metamorphosis as an ancient polyphenic trait and its role in metazoan life-cycle evolution

2010 ◽  
Vol 365 (1540) ◽  
pp. 641-651 ◽  
Author(s):  
Sandie M. Degnan ◽  
Bernard M. Degnan
Keyword(s):  
Life Cycle ◽  
Dispersal Distance ◽  
Recent Common Ancestor ◽  
Population Divergence ◽  
Juvenile Form ◽  
Larval Phase ◽  
Most Recent Common Ancestor ◽  
Wide Range ◽  
Settlement And Metamorphosis ◽  
Life Cycle Evolution

Comparative genomics of representative basal metazoans leaves little doubt that the most recent common ancestor to all modern metazoans was morphogenetically complex. Here, we support this interpretation by demonstrating that the demosponge Amphimedon queenslandica has a biphasic pelagobenthic life cycle resembling that present in a wide range of bilaterians and anthozoan cnidarians. The A. queenslandica life cycle includes a compulsory planktonic larval phase that can end only once the larva develops competence to respond to benthic signals that induce settlement and metamorphosis. The temporal onset of competence varies between individuals as revealed by idiosyncratic responses to inductive cues. Thus, the biphasic life cycle with a dispersing larval phase of variable length appears to be a metazoan synapomorphy and may be viewed as an ancestral polyphenic trait. Larvae of a particular age that are subjected to an inductive cue either maintain the larval form or metamorphose into the post-larval/juvenile form. Variance in the development of competence dictates that only a subset of a larval cohort will settle and undergo metamorphosis at a given time, which in turn leads to variation in dispersal distance and in location of settlement. Population divergence and allopatric speciation are likely outcomes of this conserved developmental polyphenic trait.

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.

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 Chromosomal dynamics in space and time: evolutionary history of Mycetophylax ants across past climatic changes in the Brazilian Atlantic coast

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ricardo Micolino ◽  
Maykon Passos Cristiano ◽  
Natália Martins Travenzoli ◽  
Denilce Meneses Lopes ◽  
Danon Clemes Cardoso
Keyword(s):  
Evolutionary History ◽  
Chromosomal Rearrangements ◽  
Atlantic Coast ◽  
Ecological Impact ◽  
Divergence Time ◽  
Molecular Data ◽  
Recent Common Ancestor ◽  
Integrative Approach ◽  
Most Recent Common Ancestor ◽  
History Of

AbstractFungus-farming ants of the genus Mycetophylax exhibit intra and interspecific chromosome variability, which makes them suitable for testing hypotheses about possible chromosomal rearrangements that endure lineage diversification. We combined cytogenetic and molecular data from Mycetophylax populations from coastal environments to trace the evolutionary history of the clade in light of chromosomal changes under a historical and geographic context. Our cytogenetic analyses revealed chromosomal differences within and among species. M. morschi exhibited three distinct karyotypes and considerable variability in the localization of 45S rDNA clusters. The molecular phylogeny was congruent with our cytogenetic findings. Biogeographical and divergence time dating analyses estimated that the most recent common ancestor of Mycetophylax would have originated at about 30 Ma in an area including the Amazon and Southern Grasslands, and several dispersion and vicariance events may have occurred before the colonization of the Brazilian Atlantic coast. Diversification of the psammophilous Mycetophylax first took place in the Middle Miocene (ca. 18–10 Ma) in the South Atlantic coast, while “M. morschi” lineages diversified during the Pliocene-Pleistocene transition (ca. 3–2 Ma) through founder-event dispersal for the Northern coastal regions. Psammophilous Mycetophylax diversification fits into the major global climatic events that have had a direct impact on the changes in sea level as well as deep ecological impact throughout South America. We assume therefore that putative chromosomal rearrangements correlated with increased ecological stress during the past climatic transitions could have intensified and/or accompanied the divergence of the psammophilous Mycetophylax. We further reiterate that “M. morschi” comprises a complex of at least three well-defined lineages, and we emphasize the role of this integrative approach for the identification and delimitation of evolutionary lineages.

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