Abstract
The genetic variation found in small regions of the genomes of many species can be arranged into haplotype trees that reflect the evolutionary genealogy of the DNA lineages found in that region and the accumulation of mutations on those lineages. This review demonstrates some of the many ways in which clades (branches) of haplotype trees have been applied in recent years, including the study of genotype/phenotype associations at candidate loci and in genome-wide association studies, the phylogeographic history of species, human evolution, the conservation of endangered species, and the identification of species.
Highlights
Clade comes from the Greek word for “branch”
This review focuses upon how clades of haplotypes in haplotype trees have been used to analyze a variety of data types in biology
Biology is different from disciplines such as chemistry or physics because all living forms have a history, and that history has played a critical role in shaping the present
Summary
Clade comes from the Greek word for “branch”. In evolutionary biology, clade refers to a branch of an evolutionary tree. What is observable is whether or not two copies in the current sample of DNA sequences differ or not If they differ, one or more mutations had occurred in one or both of the DNA lineages before they coalesced into a common ancestral molecule. In a haplotype tree each current DNA sequence and each node in the tree represents a distinct and unique sequence state called a haplotype Every branch in this evolutionary tree of haplotypes is marked by one or more mutational events. The haplotype tree is a map that shows how all the current array of genetic variation found in the diverse haplotypes in the sample arose by the accumulation of mutations in DNA lineages over evolutionary history This history can be obscured if recombination occurs, so haplotype trees are restricted to areas of the genome showing little to no recombination. This review focuses upon how clades of haplotypes in haplotype trees have been used to analyze a variety of data types in biology
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