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Ancestral state reconstruction with large numbers of sequences and edge-length estimation [PDF]

Journal of Mathematical Biology, 2022
Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that both the tree topology and edge lengths are known.
Lam Si Tung Ho, Edward Susko, Susko Edward   +2 more
exaly   +4 more sources

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Ancestral state reconstructions for genomes

Current Opinion in Genetics & Development, 2005
The recent expansion of phylogenetic analysis from the traditional field of molecular evolution, analyzing histories of genes, to the nascent field of "genomic evolution", analyzing histories of entire genomes, enables the construction of trees based on genome information, the quantification of the key processes that shape genome content and ...
openaire   +2 more sources

The Limitations of Ancestral State Reconstruction and the Evolution of the Ascus in the Lecanorales (Lichenized Ascomycota) [PDF]

Systematic Biology, 2008
Ancestral state reconstructions of morphological or ecological traits on molecular phylogenies are becoming increasingly frequent. They rely on constancy of character state change rates over trees, a correlation between neutral genetic change and phenotypic change, as well as on adequate likelihood models and (for Bayesian methods) prior distributions.
Stefan Ekman, Heidi Lie Andersen, Mats Wedin   +2 more
exaly   +3 more sources

Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction

Journal of Combinatorial Optimization, 2009
zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Bin Ma, Louxin Zhang, Zhang Louxin
exaly   +2 more sources

To the roots: reconstruction of the ancestral state of the dorid feeding apparatus

Zoology
Diet-driven ecological radiation has been proposed as a key factor in the diversification of Nudibranchia. Members of Doridina, one of the two major clades of nudibranchs, have a remarkably wide range of dietary preferences. The morphology of the feeding apparatus is related to prey preferences and feeding mechanisms.
Anna L. Mikhlina, Irina A. Ekimova, Dimitry M. Schepetov, Ángel Valdés, Elena V. Vortsepneva   +4 more
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RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography

Molecular Phylogenetics and Evolution, 2015
We announce the release of Reconstruct Ancestral State in Phylogenies (RASP), a user-friendly software package for inferring historical biogeography through reconstructing ancestral geographic distributions on phylogenetic trees. RASP utilizes the widely used Statistical-Dispersal Vicariance Analysis (S-DIVA), the Dispersal-Extinction-Cladogenesis (DEC)
Yan, Yu, Alan J, Harris, Christopher, Blair, Xingjin, He   +3 more
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Ancestral state reconstruction analysis of hymenopteran sex determination mechanisms

Journal of Evolutionary Biology, 2009
AbstractWe provide the first phylogenetic evidence supporting complementary sex determination (CSD) as the ancestral mechanism for haplodiploidy in the Hymenoptera. It is currently not possible, however, to distinguish the evolutionary polarity of single locus (sl) CSD and multiple‐locus (ml) CSD given the available data.
Asplen, M. K., Whitfield, J. B., de Boer, J. G., Heimpel, G. E.   +3 more
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Analyzing the Fitch Method for Reconstructing Ancestral States on Ultrametric Phylogenetic Trees

Bulletin of Mathematical Biology, 2010
The accuracy of the Fitch method for reconstructing ancestral states on ultrametric phylogenetic trees is studied. Two recurrence relations for computing the accuracy are given here. Using these relations, we analyze the convergence of the accuracy of the Fitch method for reconstructing the root state on a complete binary tree of 2( n ) leaves as n ...
Zhang, L., Shen, J., Yang, J., Li, G.
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Ancestral State Reconstruction of Phenotypic Characters

Evolutionary Biology
Ancestral state reconstruction involves estimating the unknown trait values of hypothetical ancestral species at internal nodes of a phylogenetic tree. In this review, I’ll illustrate the theory and practice of ancestral state reconstruction for both discrete and continuously-valued phenotypic traits, highlight several use cases via a set of empirical ...
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Evolutionary properties of sequences and ancestral state reconstruction

2007
AbstractA number of authors have recently stressed the importance of understanding the evolution of protein-protein interactions as an underlying cause of covarion-like patterns of evolution in ancestral sequences. Coevolution of interacting partners is seen as important, first in directing the evolution of proteins, and second in explaining why ...
Lesley J. Collins, Peter J. Lockhart
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