Coalescent methods for estimating phylogenetic trees.
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Summary
Recent models to estimate phylogenetic trees under the multispecies coalescent review shows that species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount.
- Type
- review
- Published
- 2009-10-01
- Cited by
- 385
- References
- 95
- OpenAlex
- https://openalex.org/W2084761838
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:15627254
Keywords
Coalescent theory, Supertree, Phylogenetic tree, Biology, Tree rearrangement
References
- Coalescent Theory: An Introduction
- Phylogeography — The History and Formation of Species
- Maximum-likelihood methods for phylogeny estimation.
- Algorithms and Data Structures
- Phylogenetic identification of lateral genetic transfer events
- A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
- Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.
- Gene genealogy in three related populations: consistency probability between gene and population trees.
- Gene trees, species trees and the segregation of ancestral alleles.
- Origins of the coalescent. 1974-1982.
- Majority-rule supertrees.
- From a comb to a tree: phylogenetic relationships of the comb-footed spiders (Araneae, Theridiidae) inferred from nuclear and mitochondrial genes.
- Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony
- TESTING FOR PHYLOGENETIC SIGNAL IN COMPARATIVE DATA: BEHAVIORAL TRAITS ARE MORE LABILE
- Efficient algorithms for lateral gene transfer problems
- Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy
- Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny.
- Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci?
- Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
- Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting
Cited by
- Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping.
- Multispecies Coalescent Analysis of the Early Diversification of Neotropical Primates: Phylogenetic Inference under Strong Gene Trees/Species Tree Conflict
- Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)
- Rooting phylogenetic trees under the coalescent model using site pattern probabilities
- Species Delimitation and Phylogenetic Relationships. A study of Silene sections Atocion and Cryptoneurae
- Phylogenetics and diversification of Escallonia (Escalloniaceae)
- Multigene phylogenetic analyses to delimit new species in fungal plant pathogens.
- Managing and analyzing phylogenetic databases
- Confusions in Fungal Systematics
- Using the Birth-Death Process to Infer Changes in the Pattern of Lineage Gain and Loss
- Phylogenetic Inference for Multidomain Proteins
- Exploring the Evolutionary History of North American Prairie Grouse (Genus: Tympanuchus) Using Multi-locus Coalescent Analyses
- Algorithms for constructing more accurate and inclusive phylogenetic trees
- From Gene Trees to Species Trees: Algorithms for Parsimonious Reconciliation
- Phylogeography and species limits of the Aspidoscelis hyperythra complex of Baja California, Mexico
- Bayesian Computational Inference of Species Trees and Population Sizes
- Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased.
- Statistics in the Billera-Holmes-Vogtmann treespace
- Desenvolvimento e aplicações de DArT (Diversity Arrays Technology) e genotipagem por sequenciamento (Genotyping-by-Sequencing) para análise genética em eucalyptus
- The Forest for the Trees: Evaluating Molecular Phylogenies with an Emphasis on Higher-Level Decapoda
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