Ancestral inference on gene trees under selection

2004 ◽  
Vol 66 (3) ◽  
pp. 219-232 ◽  
Author(s):  
Graham Coop ◽  
Robert C. Griffiths
Keyword(s):  
Gene Trees ◽  
Ancestral Inference

Importance sampling on coalescent histories. II: Subdivided population models

2004 ◽  
Vol 36 (2) ◽  
pp. 434-454 ◽  
Author(s):  
Maria De Iorio ◽  
Robert C. Griffiths
Keyword(s):  
Importance Sampling ◽  
Dna Sequences ◽  
Sampling Technique ◽  
Population Models ◽  
Gene Trees ◽  
Gene Frequencies ◽  
Sample Distribution ◽  
Subdivided Population ◽  
Importance Sampling Technique ◽  
Ancestral Inference

De Iorio and Griffiths (2004) developed a new method of constructing sequential importance-sampling proposal distributions on coalescent histories of a sample of genes for computing the likelihood of a type configuration of genes in the sample by simulation. The method is based on approximating the diffusion-process generator describing the distribution of population gene frequencies, leading to an approximate sample distribution and finally to importance-sampling proposal distributions. This paper applies that method to construct an importance-sampling algorithm for computing the likelihood of samples of genes in subdivided population models. The importance-sampling technique of Stephens and Donnelly (2000) is thus extended to models with a Markov chain mutation mechanism between gene types and migration of genes between subpopulations. An algorithm for computing the likelihood of a sample configuration of genes from a subdivided population in an infinitely-many-alleles model of mutation is derived, extending Ewens's (1972) sampling formula in a single population. Likelihood calculation and ancestral inference in gene trees constructed from DNA sequences under the infinitely-many-sites model are also studied. The Griffiths-Tavaré method of likelihood calculation in gene trees of Bahlo and Griffiths (2000) is improved for subdivided populations.

Importance sampling on coalescent histories. II: Subdivided population models

2004 ◽  
Vol 36 (02) ◽  
pp. 434-454 ◽  
Author(s):  
Maria De Iorio ◽  
Robert C. Griffiths
Keyword(s):  
Importance Sampling ◽  
Dna Sequences ◽  
Sampling Technique ◽  
Population Models ◽  
Gene Trees ◽  
Gene Frequencies ◽  
Sample Distribution ◽  
Subdivided Population ◽  
Importance Sampling Technique ◽  
Ancestral Inference

De Iorio and Griffiths (2004) developed a new method of constructing sequential importance-sampling proposal distributions on coalescent histories of a sample of genes for computing the likelihood of a type configuration of genes in the sample by simulation. The method is based on approximating the diffusion-process generator describing the distribution of population gene frequencies, leading to an approximate sample distribution and finally to importance-sampling proposal distributions. This paper applies that method to construct an importance-sampling algorithm for computing the likelihood of samples of genes in subdivided population models. The importance-sampling technique of Stephens and Donnelly (2000) is thus extended to models with a Markov chain mutation mechanism between gene types and migration of genes between subpopulations. An algorithm for computing the likelihood of a sample configuration of genes from a subdivided population in an infinitely-many-alleles model of mutation is derived, extending Ewens's (1972) sampling formula in a single population. Likelihood calculation and ancestral inference in gene trees constructed from DNA sequences under the infinitely-many-sites model are also studied. The Griffiths-Tavaré method of likelihood calculation in gene trees of Bahlo and Griffiths (2000) is improved for subdivided populations.

Gene trees: A powerful tool for exploring the evolutionary biology of species and speciation

2000 ◽  
Vol 15 (3) ◽  
pp. 211-222 ◽  
Author(s):  
Alan R. Templeton ◽  
Stephanie D. Maskas ◽  
Mitchell B. Cruzan
Keyword(s):  
Evolutionary Biology ◽  
Gene Trees

scholarly journals Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1645-1656 ◽  
Author(s):  
Bruce Rannala ◽  
Ziheng Yang
Keyword(s):  
Dna Sequences ◽  
Gene Tree ◽  
Species Tree ◽  
Bayes Estimation ◽  
Ancestral Population ◽  
Divergence Times ◽  
Gene Trees ◽  
Species Divergence ◽  
Multiple Loci ◽  
Population Sizes

Abstract The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be ∼20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.

scholarly journals PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees

2014 ◽  
Vol 15 (1) ◽  
pp. 268 ◽  
Author(s):  
Joseph MEX Lucas ◽  
Matthieu Muffato ◽  
Hugues Crollius
Keyword(s):  
Gene Trees ◽  
Synteny Blocks ◽  
Tandem Duplications

scholarly journals Gene Trees versus Species Trees: Reassessing Life-History Evolution in a Freshwater Fish Radiation

2010 ◽  
Vol 59 (5) ◽  
pp. 504-517 ◽  
Author(s):  
Jonathan M. Waters ◽  
Diane L. Rowe ◽  
Christopher P. Burridge ◽  
Graham P. Wallis
Keyword(s):  
Life History ◽  
Freshwater Fish ◽  
Life History Evolution ◽  
Gene Trees ◽  
Species Trees ◽  
History Evolution

scholarly journals Phylogenomic Discordance in the Eared Seals is best explained by Incomplete Lineage Sorting following Explosive Radiation in the Southern Hemisphere

2020 ◽  
Author(s):  
Fernando Lopes ◽  
Larissa R Oliveira ◽  
Amanda Kessler ◽  
Yago Beux ◽  
Enrique Crespo ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Molecular Data ◽  
Species Tree ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Data Types ◽  
High Coverage ◽  
Sea Lions ◽  
The Family

Abstract The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance because of strong gene-tree species tree discordance. Divergence times estimates in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here we used high-coverage genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 to 2.5 Ma. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be non-monophyletic, with California (Z. californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Z. wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family.

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