Coalescent Theory

Nordborg, M.

doi:10.1002/9780470061619.ch25

Cited by 60 publications

(38 citation statements)

References 44 publications

(43 reference statements)

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“…The stochastic process known as the coalescent was first introduced by Kingman (1982), while Hudson (1983) and Tajima (1983) also independently described this process in biological journals with discussions on the statistical issues involved in the analysis of polymorphism data. Since then, a number of population geneticists have contributed to further development of the coalescent theory (reviewed by Tavaré (1984), Hudson (1990), Fu and Li (1999), Nordborg (2001), Hein et al (2005)). …”

Section: Single Nucleotide Polymorphisms In Duplicated Genesmentioning

confidence: 98%

Population genetic models of duplicated genes

Innan¹

2009

Genetica

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Various population genetic models of duplicated genes are introduced. The problems covered in this review include the fixation process of a duplicated copy, copy number polymorphism, the fates of duplicated genes and single nucleotide polymorphism in duplicated genes. Because of increasing evidence for concerted evolution by gene conversion, this review introduces recently developed gene conversion models. In the first half, models assuming independent evolution of duplicated genes are introduced, and then the effect of gene conversion is considered in the second half.

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Section: Single Nucleotide Polymorphisms In Duplicated Genesmentioning

confidence: 98%

Population genetic models of duplicated genes

Innan¹

2009

Genetica

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“…After the regression, the adjusted values were backtransformed taking their exponential so that posterior densities were expressed in the original scale. The simulated data was obtained using a standard coalescent process (Hudson 1990;Nordborg 2001). We used the stepwise mutation model (Kimura and Ohta 1978) for the microsatellite data and an infinite sites model (Kimura 1969) for sequence data.…”

Section: Methodsmentioning

confidence: 99%

The use of approximate Bayesian computation in conservation genetics and its application in a case study on yellow-eyed penguins

Lopes

Boessenkool

2009

Conserv Genet

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The inference of demographic parameters from genetic data has become an integral part of conservation studies. A group of Bayesian methods developed originally in population genetics, known as approximate Bayesian computation (ABC), has been shown to be particularly useful for the estimation of such parameters. These methods do not need to evaluate likelihood functions analytically and can therefore be used even while assuming complex models. In this paper we describe the ABC approach and identify specific parts of its algorithm that are being the subject of intensive studies in order to further expand its usability. Furthermore, we discuss applications of this Bayesian algorithm in conservation studies, providing insights on the potentialities of these tools. Finally, we present a case study in which we use a simple IsolationMigration model to estimate a number of demographic parameters of two populations of yellow-eyed penguins (Megadyptes antipodes) in New Zealand. The resulting estimates confirm our current understanding of M. antipodes dynamic, demographic history and provide new insights into the expansion this species has undergone during the last centuries.

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“…Seven individuals of C. melanosterna, three C. palearis, 13 C. bakeri, three C. oedirhina, and one C. similis (outgroup) were included. For nuclear markers, diploid individuals do not correspond to the tips of a gene tree because each individual contains two alleles that may or may not be identical by state and formally cannot be identical by descent from the previous generation (Nordborg 2001). Construction of a concatenated file such as that required by BEST is equivalent to randomly sampling one allele per individual.…”

Section: Bayesian Estimation Of Species Trees (Best) Analysismentioning

confidence: 99%

Gene trees, species and species trees in the Ctenosaura palearis clade

2010

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The growing use of molecular systematics in conservation has increased the importance of accurate resolution of taxonomic units and relationships. DNA data relate most directly to genealogies, which need not have perfect relationships with species limits and phylogenies. We used a multilocus gene tree approach to elucidate the relationships between four endangered Central American iguanas. We found support for the proposition that the described species taxa correspond to distinct evolutionary lineages warranting individual protection. We combined gene trees to estimate a phylogeny using Bayesian Estimation of Species Trees (BEST), minimizing deep coalescence, Species Trees from Average Ranks (STAR), and traditional concatenation. The estimate from concatenation conflicted with the other methods, likely owing to the disproportionate effect of mtDNA on concatenated analyses. This illustrates the importance of appropriate treatment of multilocus sequence data in phylogenetics. Our results indicate that these species have gone through recent and rapid speciation, resulting in four closely related narrowrange endemics.

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Coalescent Theory

Cited by 60 publications

References 44 publications

Population genetic models of duplicated genes

Population genetic models of duplicated genes

The use of approximate Bayesian computation in conservation genetics and its application in a case study on yellow-eyed penguins

Gene trees, species and species trees in the Ctenosaura palearis clade

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