On Phylogenetic Uncertainty and Ancestral Sequence Reconstruction
نویسندگان
چکیده
منابع مشابه
Robustness of Ancestral Sequence Reconstruction to Phylogenetic Uncertainty
Ancestral sequence reconstruction (ASR) is widely used to formulate and test hypotheses about the sequences, functions, and structures of ancient genes. Ancestral sequences are usually inferred from an alignment of extant sequences using a maximum likelihood (ML) phylogenetic algorithm, which calculates the most likely ancestral sequence assuming a probabilistic model of sequence evolution and ...
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Ancestral reconstruction is the extrapolation back in time from measured characteristics of individuals (or populations) to their common ancestors. It is an important application of phylogenetics, the reconstruction and study of the evolutionary relationships among individuals, populations, or species to their ancestors. In the context of biology, ancestral reconstruction can be used to recover...
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Hypotheses about the functions of ancient proteins and the effects of historical mutations on them are often tested using ancestral protein reconstruction (APR)-phylogenetic inference of ancestral sequences followed by synthesis and experimental characterization. Usually, some sequence sites are ambiguously reconstructed, with two or more statistically plausible states. The extent to which the ...
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The ancestral sequence reconstruction problem asks to predict the DNA or protein sequence of an ancestral species, given the sequences of extant species. Such reconstructions are fundamental to comparative genomics, as they provide information about extant genomes and the process of evolution that gave rise to them. Arguably the best method for ancestral reconstruction is maximum likelihood est...
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Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse pl...
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