Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.

By Bruce Rannala, Ziheng Yang. Genetics, 2003

1,122 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/5f15a8de588010e3174ddbb8789facf4236e92ac

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Citations in the corpus

A roadmap for island biology: 50 fundamental questions after 50 years of The Theory of Island Biogeography (2017, background): “…include comparing the fit of data among the predictions of competing phylogenetic and population genetic simulation models (e.g. Chan et al., 2014; Pati~no et al., 2015), or combining phylogenetic and population genetic perspectives into unified statistical frameworks (e.g. Rannala & Yang, 2003).”
Phylogenetic tree building in the genomic age (2020, unknown): “The framework for accommodating ILS is the multi-species coalescent (MSC) model 158,159 , an extension of the single-population coalescent 160 to the case of multiple species.”
The role of molecular genetics in sculpting the future of integrative biogeography (2008, methodology): “a Temporal congruence: Estimating lineage divergence times with an appropriate statistical model derived from coalescent theory (Tajima, 1983; Knowles and Maddison, 2002) can be accomplished using a variety of wellestablished approaches (Rannala and Yang, 2003; Yoder and Yang, 2004; Edwards et al., ”
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING? (2009, background): “Such likelihoods have appeared in several forms recently and provide a solid foundation for developing new species tree methods (Rannala and Yang 2003; Degnan and Salter 2005; Steel and Rodrigo 2008).”
The fossilized birth–death process for coherent calibration of divergence-time estimates (2013, unknown): “calibration of divergence-time estimates”
Species Delimitation: A Decade After the Renaissance (2013, unknown): “A multi-species or ‘censored’ model was formulated to account for this discordance by considering each branch of the species tree as a separate coalescent model and by connecting them into a population-level genealogy fol‐ lowing the topology of the species tree [62,63].”
BEST: Bayesian estimation of species trees under the coalescent model (2008, unknown): “BEST takes advantage of the information from multiple gene trees and performs a Bayesian analysis to estimate the topology of the species tree, divergence times and population sizes, while another popular program, MCMCcoal (Rannala and Yang, 2003), can only estimate species divergence times and popu”
Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent (2018, background): “ILS is most prominent if the species arose in a rapid succession of speciation events (a species radiation), creating short internal branches on the species tree, and if the ancestral species had large population sizes.”
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees (2018, methodology): “For each replicate, 1000 true gene trees are simulated under the MSCM (exact commands shown in Additional file 1: Appendix C and parameters given in Additional file 1: Table S2).”
How to fail at species delimitation (2013, background): “…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 multiple species (e.g. Rannala & Yang 2003).”
Isolation with migration models for more than two populations. (2010, background): “The discernment of recent evolutionary history for closely related populations or species presents challenges that fall in the area of population genetics (Gillespie and Langley 1979; Pamilo and Nei 1988; Hudson 1992; Nielsen 1998; Rannala and Yang 2003; Degnan and Salter 2005), and evolutionary bio”
Inferring phylogeny despite incomplete lineage sorting. (2006, methodology): “The discord between inferred gene trees and species trees has been used to extract information about species histories, and in particular estimates of species divergence times and ancestral population sizes (e.g., Edwards and Beerli, 2000; Hey and Nielsen, 2004; Rannala and Yang, 2003; Takahata and ”
The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times (2015, methodology): “The true times and the mutation rate are used to calculate the relative ages, τ, needed by the program MCCOAL in the simulation.”
ASAP: assemble species by automatic partitioning (2020, methodology): “We used a “multispecies coalescent” framework (Rannala & Yang, 2003) with different options and parameters using Monte-Carlo simulations, as described previously (Puillandre, et al., 2012).”