Opioid receptors

Östergård, Maria

doi:10.1186/gb-2001-2-9-reports0028

Genome Biol

2001

DOI: 10.1186/gb-2001-2-9-reports0028

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Opioid receptors

Maria Östergård¹

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Cited by 7 publications

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Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony

et al. 2006

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Gene duplication and gene loss as well as other biological events can result in multiple copies of genes in a given species. Because of these gene duplication and loss dynamics, in addition to variation in sequence evolution and other sources of uncertainty, different gene trees ultimately present different evolutionary histories. All of this together results in gene trees that give different topologies from each other, making consensus species trees ambiguous in places. Other sources of data to generate species trees are also unable to provide completely resolved binary species trees. However, in addition to gene duplication events, speciation events have provided some underlying phylogenetic signal, enabling development of algorithms to characterize these processes. Therefore, a soft parsimony algorithm has been developed that enables the mapping of gene trees onto species trees and modification of uncertain or weakly supported branches based on minimizing the number of gene duplication and loss events implied by the tree. The algorithm also allows for rooting of unrooted trees and for removal of in-paralogues (lineage-specific duplicates and redundant sequences masquerading as such). The algorithm has also been made available for download as a software package, Softparsmap.

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Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony

et al. 2006

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Selecton: a server for detecting evolutionary forces at a single amino-acid site

et al. 2005

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Sequence Divergence, Functional Constraint, and Selection in Protein Evolution

Fay

2003

Annu. Rev. Genom. Hum. Genet.

258

160

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The genome sequences of multiple species has enabled functional inferences from comparative genomics. A primary objective is to infer biological functions from the conservation of homologous DNA sequences between species. A second, more difficult, objective is to understand what functional DNA sequences have changed over time and are responsible for species' phenotypic differences. The neutral theory of molecular evolution provides a theoretical framework in which both objectives can be explicitly tested. Development of statistical tests within this framework has provided insight into the evolutionary forces that constrain and in some cases change DNA sequences and the resulting patterns that emerge. In this article, we review recent work on how functional constraint and changes in protein function are inferred from protein polymorphism and divergence data. We relate these studies to our understanding of the neutral theory and adaptive evolution.

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Opioid receptors

Cited by 7 publications

References 1 publication

Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony

Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony

Selecton: a server for detecting evolutionary forces at a single amino-acid site

Sequence Divergence, Functional Constraint, and Selection in Protein Evolution

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