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Gene trees, species and species trees in the Ctenosaura palearis clade
Conservation Genetics, 2010The growing use of molecular systematics in conservation has increased the importance of accurate resolution of taxonomic units and relationships. DNA data relate most directly to genealogies, which need not have perfect relationships with species limits and phylogenies.
Stesha A. Pasachnik +2 more
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Synthesizing Species Trees from Unrooted Gene Trees
Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics, 2017Synthesizing species trees from a collection of smaller gene trees is a widely used approach for inferring credible species tree estimates. While corresponding computational problems are typically NP-hard, several of these problems have been effectively addressed by using the parameterized Strict Consensus Approach.
Jucheol Moon, Oliver Eulenstein
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From Gene Trees to Species Trees II: Species Tree Inference by Minimizing Deep Coalescence Events
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011When gene copies are sampled from various species, the resulting gene tree might disagree with the containing species tree. The primary causes of gene tree and species tree discord include incomplete lineage sorting, horizontal gene transfer, and gene duplication and loss.
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Maximum tree: a consistent estimator of the species tree
Journal of Mathematical Biology, 2009We propose a model based approach to use multiple gene trees to estimate the species tree. The coalescent process requires that gene divergences occur earlier than species divergences when there is any polymorphism in the ancestral species. Under this scenario, speciation times are restricted to be smaller than the corresponding gene split times.
Liu, Liang, Yu, Lili, Pearl, Dennis K.
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Coalescent histories for discordant gene trees and species trees
Theoretical Population Biology, 2010Given a gene tree and a species tree, a coalescent history is a list of the branches of the species tree on which coalescences in the gene tree take place. Each pair consisting of a gene tree topology and a species tree topology has some number of possible coalescent histories.
Noah A, Rosenberg, James H, Degnan
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Reconciling Gene Trees to a Species Tree
2003In this paper we deal with the general problem of recombining the information from evolutionary trees representing the relationships between distinct gene families. First we solve a problem from [8] regarding the construction of a minimum reconciled tree by giving an efficient algorithm. Then we show that the exemplar problem, arising from the exemplar
BONIZZONI, PAOLA +2 more
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Gene trees and species trees are not the same
Trends in Ecology & Evolution, 2001The relationship between species is usually represented as a bifurcating tree with the branching points representing speciation events. The ancestry of genes taken from these species can also be represented as a tree, with the branching points representing ancestral genes.
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Leptospermum Species (Tea Trees)
1996The genus Leptospermum is a member of the family Myrtaceae, which is subdivided into a number of tribes. The Leptospermeae contains genera in which the ovary generally is divided into two to five cells. The capsules open by partitions visible at the apex of the fruit, and contain one or two seeds. Rarely, the capsules fail to open.
W. A. Shipton, B. R. Jackes
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Paeonia Species (Tree Peonies)
1996Tree peonies are largely grown for their large and showy flowers (P. suffruticosa cultivars and hybrids) and ornamental foliage (Plutea and P. delavayi). In China and Japan extracts made from the fleshy roots of P. suffruticosa are used in traditional medicinal preparations and cosmetics. Figure 1 shows a mature plant of P. suffruticosa subsp.
A. C. James, R. A. Harris, S. H. Mantell
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Gene trees, species trees, and species networks
2009Luay Nakhleh, Derek Ruths, Hideki Innan
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