ReviewTrends in ecology & evolution2013
Computational approaches to species phylogeny inference and gene tree reconciliation.
Review in Trends in ecology & evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
54 citing papers in PubMed.
- Phylogenomics of Marine Angelfishes: Diagnosing Sources of Systematic Discordance for an Iconic Reef Fish Family (F: Pomacanthidae).Systematic biology · 2025Article
- Leveraging Weighted Quartet Distributions for Enhanced Species Tree Inference from Genome-Wide Data.Genome biology and evolution · 2025Article
- Teasing apart the sources of phylogenetic tree discordance across three genomes in the oak family (Fagaceae).BMC plant biology · 2025Article
- Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning.Molecular biology and evolution · 2024Article
- Filtration of Gene Trees From 9,000 Exons, Introns, and UCEs Disentangles Conflicting Phylogenomic Relationships in Tree Frogs (Hylidae).Genome biology and evolution · 2023Article
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- A stochastic Farris transform for genetic data under the multispecies coalescent with applications to data requirements.Journal of mathematical biology · 2022Article
- Transcriptome analysis provides new insights into cold adaptation of corsac fox (Ecology and evolution · 2022Article
- Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs.Systematic biology · 2022Article
- Phylogenomic assessment of the role of hybridization and introgression in trait evolution.PLoS genetics · 2021Article
- Genome-wide analysis reveals signatures of complex introgressive gene flow in macaques (genusZoological research · 2021Article
- Chromosome-scale genome assembly of Cucumis hystrix-a wild species interspecifically cross-compatible with cultivated cucumber.Horticulture research · 2021Article
- Migratory routes, domesticated birds and cercarial dermatitis: the distribution of Trichobilharzia franki in Northern Iran.Parasite (Paris, France) · 2021Article
- Biased Gene Retention in the Face of Introgression Obscures Species Relationships.Genome biology and evolution · 2020Article
- Phylogenetic double placement of mixed samples.Bioinformatics (Oxford, England) · 2020Article
- Unblended disjoint tree merging using GTM improves species tree estimation.BMC genomics · 2020Article
- Novel phylogenetic methods are needed for understanding gene function in the era of mega-scale genome sequencing.Nucleic acids research · 2020Article
- Evolution of the extracytoplasmic function σ factor protein family.NAR genomics and bioinformatics · 2020Article
- Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study.Genome biology and evolution · 2020Article
- Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure.Genome biology and evolution · 2020Article
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Abstract
An intricate relation exists between gene trees and species phylogenies, due to evolutionary processes that act on the genes within and across the branches of the species phylogeny. From an analytical perspective, gene trees serve as character states for inferring accurate species phylogenies, and species phylogenies serve as a backdrop against which gene trees are contrasted for elucidating evolutionary processes and parameters. In a 1997 paper, Maddison discussed this relation, reviewed the signatures left by three major evolutionary processes on the gene trees, and surveyed parsimony and likelihood criteria for utilizing these signatures to elucidate computationally this relation. Here, I review progress that has been made in developing computational methods for analyses under these two criteria, and survey remaining challenges.
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