A LIKELIHOOD FRAMEWORK FOR INFERRING THE EVOLUTION OF GEOGRAPHIC RANGE ON PHYLOGENETIC TREES

By Richard H. Ree, Brian R. Moore, Campbell O. Webb, Michael J. Donoghue. Evolution; international journal of organic evolution, 2005

850 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Paleontology

View Paper: https://www.semanticscholar.org/paper/9774e20de16b663656add6329c3f9e12a24ed52c

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Citations in the corpus

Biogeography and diversification of colletid bees (Hymenoptera: Colletidae): emerging patterns from the southern end of the world (2012, methodology): “These included parsimony-based DIVA (dispersal–vicariance analysis; Ronquist, 1997), a likelihood-based DEC model (Ree et al., 2005; Ree & Smith, 2008) and a Bayesian model for biogeographical reconstruction (Sanmartı́n et al., 2008).”
Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement (2012, methodology): “Likelihood analysis of ancestral area reconstruction was conducted using the software LAGRANGE (Ree et al ., 2005; Ree & Smith, 2008).”
Taking into account phylogenetic and divergence‐time uncertainty in a parametric biogeographical analysis of the Northern Hemisphere plant clade Caprifolieae (2009, neutral): “…group, Lonicera, is typically separated into two subgenera (Caprifolium, Lonicera), the largest of which, Lonicera subgenus Lonicera, is typically separated into four sections, Coeloxylosteum, Isoxylosteum, Nintooa and Isika (Rehder, 1903; Hara, 1983; Hsu & Wang, 1988), and a number of subsections.”
Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. (2008, methodology): “In this paper, we describe how to refine the method of Ree et al. (2005) to overcome this drawback, showing how instantaneous rates of dispersal and local extinction can be used to construct a rate matrix for transitions between geographic ranges that is directly analogous to the rate matrix Q…”
Use of dispersal–vicariance analysis in biogeography – a critique (2009, background): “Perhaps information from phylogeographic data (Riddle & Hafner, 2006; Riddle, 2009) or metapopulation studies can be integrated, wherever it is available, to specify such costs.”
Can the tropical conservatism hypothesis explain temperate species richness patterns? An inverse latitudinal biodiversity gradient in the New World snake tribe Lampropeltini (2009, methodology): “The ancestral area of the lampropeltinines was estimated using the ML dispersal‐extinction‐cladogenesis model implemented in the program L agrange 2.0.1 ( Ree et al ., 2005; Ree & Smith, 2008).”
A new basal rebbachisaurid (Sauropoda, Diplodocoidea) from the Early Cretaceous of the Neuquén Basin; evolution and biogeography of the group (2012, positive): “Phylogenetic analysis of rebbachisaurids using DEC (Ree et al. 2005; Ree and Smith 2008).”
Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini) (2010, neutral): “Thus, DIVA assumes constant rates across the tree and requires short branch lengths if the minimum number of historical events is assumed (Ree et al., 2005).”
Model selection in historical biogeography reveals that founder-event speciation is a crucial process in Island Clades. (2014, methodology): “Probabilistic modeling of geographic range evolution (Ree et al. 2005; Ree and Smith 2008; Ree and Sanmartín 2009) was a major advance in historical biogeography, making biogeographical problems accessible to modelbased maximum-likelihood (ML) and Bayesian inference methodologies (reviewed by…”
Origin of Mediterranean insular endemics in the Boraginales: integrative evidence from molecular dating and ancestral area reconstruction (2009, methodology): “improved methods of ancestral area inference (Ree et al., 2005) that allow for the explicit incorporation of a priori estimates of the probability of dispersal dependent on the”
Estimating ancestral distributions of lineages with uncertain sister groups: a statistical approach to Dispersal–Vicariance Analysis and a case using Aesculus L. (Sapindaceae) including fossils (2009, methodology): “…advantageous when working with groups for which little or unreliable prior information is available, for its ease of use and freedom from potential error associated with model selection and model parameter determination required for the model-based methods (Ree et al., 2005; Nylander et al., 2008).”
Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. II. Diversification history and origin of regional assemblages (2013, methodology): “Ancestral area reconstructions inferred using a maximum likelihood method under the dispersal–extinction–cladogenesis (DEC) model (Ree et al., 2005; Ree & Smith, 2008) were taken from Baker & Couvreur (2012) and incorporated dispersal probability constraints reflecting geological history (model M1: ”
Temporal and spatial origin of Gesneriaceae in the New World inferred from plastid DNA sequences (2013, methodology): “We produced a calibrated tree using a relaxed molecular clock approach (Drummond et al., 2006), and the biogeographical history of the family was inferred using a maximum-likelihood method that implements the dispersal–extinction–cladogenesis model (Ree et al., 2005; Ree & Smith, 2008).”
Phylogeny and Biogeography of Tsuga (Pinaceae) Inferred from Nuclear Ribosomal Its and Chloroplast DNA Sequence Data (2008, methodology): “This method incorporates phylogeny, divergence times, fossil data, rates of lineage dispersal and extinction, and an independent model of the probability of connection among geographic areas over time (Ree et al. 2005; Moore et al. in press).”
An evaluation of new parsimony‐based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae (2011, methodology): “Cladogenetic evolution at speciation nodes is modelled as three alternative range inheritance scenarios (Ree et al. , 2005).”