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Appendices

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 4488 words.

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Bayesian computation (MCMC)

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 32739 words.

This chapter provides a detailed introduction to modern Bayesian computation. The Metropolis–Hastings algorithm is illustrated using a simple example of distance estimation between two...

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Bayesian phylogenetics

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 27279 words.

This chapter discusses the implementation of various models of genetic sequence evolution in Bayesian phylogenetic analysis. It discusses the specification of priors for parameters in such...

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Bayesian theory

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 18645 words.

This chapter summarizes the Frequentist–Bayesian controversy in statistics, and introduces the basic theory of Bayesian statistical inference, such as the prior, posterior, and Bayes’...

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Changes in allele and genotype frequency

Glenn-Peter Sætre and Mark Ravinet.

in Evolutionary Genetics

May 2019; p ublished online July 2019 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology; Genetics and Genomics. 11517 words.

Evolution is the change in heritable traits of populations over successive generations. At the molecular level this translates into changes in their genetic composition. A general...

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Coalescent theory and species trees

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 32207 words.

This chapter introduces Kingman’s coalescent process, which describes the genealogical relationships within a sample of DNA sequences taken from a population, and forms the basis for...

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Comparison of phylogenetic methods and tests on trees

Ziheng Yang.

in Molecular Evolution

May 2014; p ublished online August 2014 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology. 17404 words.

This chapter summarizes the criteria for comparing different tree reconstruction methods, such as consistency and efficiency, as well as computer simulation studies that evaluate the...

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Evolutionary Genetics

Glenn-Peter Sætre and Mark Ravinet.

May 2019; p ublished online July 2019 .

Book. Subjects: Biomathematics and Statistics; Evolutionary Biology; Genetics and Genomics. 336 pages.

Evolutionary genetics is the study of how genetic variation leads to evolutionary change. With the recent explosion in the availability of whole genome sequence data, vast quantities of...

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The foundations of evolutionary genetics

Glenn-Peter Sætre and Mark Ravinet.

in Evolutionary Genetics

May 2019; p ublished online July 2019 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology; Genetics and Genomics. 12468 words.

The fields of evolutionary biology and genetics were founded as separate disciplines in the mid-1800s, largely due to the works of Charles Darwin and Gregor Mendel respectively. It would,...

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Genetics and genomics of speciation

Glenn-Peter Sætre and Mark Ravinet.

in Evolutionary Genetics

May 2019; p ublished online July 2019 .

Chapter. Subjects: Biomathematics and Statistics; Evolutionary Biology; Genetics and Genomics. 24683 words.

The diversity of life on Earth is something that has long fascinated biologists. When we inspect all this variation, two striking patterns emerge. First, organisms appear as if they have...

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