From Gene Trees to Species Trees

By Bin Ma, Ming Li, Louxin Zhang. SIAM journal on computing (Print), 2000

1,799 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/0792e097f8c879af36294e5d8469abcfc4e7ebea

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

Genealogical trees, coalescent theory and the analysis of genetic polymorphisms (2002, background): “Sexual organisms can be viewed as collections of genomic regions with different historie”
The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves (2016, background): “ILS is particularly prevalent when effective population size (Ne) is large and time between consecutive speciation events is short (Maddison 1997; Maddison & Knowles 2006).”
A review of long‐branch attraction (2005, methodology): “…simulation, the method has been quite popular and has been applied in several other studies in order to investigate possible LBA artifacts (Maddison et al., 1999; Tang et al., 1999; Tourasse and Gouy, 1999; Sanderson et al., 2000; Wiens and Hollingsworth, 2000; Omilian and Taylor, 2001;…”
How to fail at species delimitation (2013, background): “Seminal work by Maddison (1997) convinced a generation of researchers that they could not overlook the inherent stochasticity of genealogies when estimating phylogeny at the shallowest levels of diversification, and in time the basic coalescent model of Kingman (1982) was expanded to include…”
Phylogenetic Patterns in Northern Hemisphere Plant Geography (2001, background): “This is sometimes viewed as the biogeographic analog of lineage sorting (or deep coalescence) of gene trees with respect to a species tree (see Maddison 1997; Page and Charleston 1998).”
Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes. (2003, neutral): “Hybridization, incomplete lineage sorting or assortment of ancestral polymorphism are commonly cited as potential causes of incongruence between gene and species trees (Maddison, 1997).”
Phylogeny of the manta and devilrays (Chondrichthyes: mobulidae), with an updated taxonomic arrangement for the family (2018, background): “Coalescent variation and the potential for gene tree–species tree discordance (Maddison, 1997) are now well-documented and estimating phylogenies based on a small number of molecular markers is now considered insufficient for these purposes.”
ASTRAL: genome-scale coalescent-based species tree estimation (2014, background): “ILS is equivalent to ‘deep coalescence’, which occurs with high probability whenever the time between speciation events is short relative to the population size (Maddison, 1997).”
Delimiting species without monophyletic gene trees. (2007, background): “…Rannala and Yang, 2002; Rosenberg, 2002; Liu and Pearl, 2006; Carstens and Knowles, 2007a; Edwards et al., 2007), this approach focuses attention on the relationship between gene trees and the divergence of species lineages rather than equating gene trees with the species history (Maddison, 1997).”
Integrating ensemble species distribution modelling and statistical phylogeography to inform projections of climate change impacts on species distributions (2013, methodology): “To test the fit of our observed data to a model, we generated an expected distribution of discordance between gene trees and the population model, measured by deep coalescences (DC; Maddison, 1997).”
Inferring Phylogenetic Networks Using PhyloNet (2017, methodology): “Simple Counts of Extra Lineages: Maximum Parsimony Minimizing the number of deep coalescences, or MDC, is a criterion that was proposed originally by Maddison (Maddison, 1997) for species tree inference and later implemented and tested in both heuristic form (Maddison and Knowles, 2006) and exact al”