Statistical phylogeography: methods of evaluating and minimizing inference errors

By Alan R. Templeton. Molecular Ecology, 2004

653 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/e6646b3112fc57bfffe5ab70c11d0816b68ae412

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Citations in the corpus

THE MOLECULAR TOOLBOX: GENETIC TECHNIQUES IN WILDLIFE ECOLOGY AND MANAGEMENT (2005, background): “…based on both nuclear microsatellite DNA markers (tests for genetic bottlenecks; Cornuet and Luikart 1996, Luikart et al. 1998) and DNA sequence data (changes in population size and geographic distribution over time; Templeton 1998, Emerson et al. 2001, Strimmer and Pybus 2001, Templeton 2004).”
Genetic structure and phylogeography of the lined shore crab, Pachygrapsus crassipes, along the northeastern and western Pacific coasts (2006, methodology): “A biological key provided by Templeton (2004) was used to guide inference of these models (e.g.”
Comparative phylogeography of unglaciated eastern North America (2006, methodology): “Although debate continues on how best to test phylogeographical hypotheses (Knowles & Maddison 2002; Templeton 2004), we suggest here, briefly, a number of methods that bring hypothesis testing, including the application of confidence intervals and likelihood ratio tests (e.g. Beerli & Felsenstein…”
Phylogeographic information systems: putting the geography into phylogeography (2006, background): “In NCA, the spatial distribution of clades and the spatial relationships between clades are quantified with two indices of spatial proximity; the clade distance and nested clade distance.”
Phylogeographic studies of plants in China: Advances in the past and directions in the future (2012, methodology): “The nested clade phylogeographic analysis was widely applied to test and infer demographic history previously (Templeton, 1998, 2004).”
Markers, old and new, for examining Phytophthora infestans diversity (2004, methodology): “Improved sequencing chemistry and reduced costs, combined with new concepts (Carbone & Kohn, 2001b; Templeton, 2004) and analysis tools (Clement et al.”
Incongruent patterns of genetic connectivity among four ophiuroid species with differing coral host specificity on North Atlantic seamounts (2010, methodology): “2008), it can be a practical and appropriate method to identify evolutionary processes and geographical patterns in population genetic data (Templeton 1998; Templeton et al. 2000; Templeton 2004; Panchal and Beaumont 2007; Beaumont and Panchal 2008; Garrick et al. 2008; Petit 2008a; Petit 2008b; Tem”
The role of molecular genetics in sculpting the future of integrative biogeography (2008, background): “…Smith, 2008) – and on the other hand, within the increasingly sophisticated realm of single-taxon or comparative phylogeography (e.g., Knowles, 2004; Templeton, 2004; Lapointe and Rissler, 2005; Hickerson et al., 2006; Kidd and Ritchie, 2006; Carstens and Richards, 2007; Hickerson et al., 2007).”
Multiple periglacial refugia in the Patagonian steppe and post‐glacial colonization of the Andes: the phylogeography of Calceolaria polyrhiza (2010, methodology): “For significant associations, the latest version of the inference key of Templeton (2004) was used to recognize probable demographic processes and/or historical events of the clades.”
Phylogeography of the widespread marine invader Microcosmus squamiger (Ascidiacea) reveals high genetic diversity of introduced populations and non‐independent colonizations (2008, background): “Thus, the results of this analysis should be taken with some caution until cross-validation with other DNA regions can be performed (Templeton, 2004).”
OPERATIONAL CRITERIA FOR DELIMITING SPECIES (2004, methodology): “TEMPLETON’S TESTS OF COHESION Extensions of Templeton’s (1989) original, general hypotheses about genotypic and phenotypic cohesion have rendered both operational (Templeton 1994, 1998, 1999; Templeton et al. 1995) and include tests of species boundaries (Templeton 2001).”
Phylogeographic patterning in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes) reveals the signature of historical climatic oscillations (2006, methodology): “NCA is a powerful statistical method that allows for a rigorous assessment of the relationship between geography and haplotype distribution and discriminates between processes that have influenced population structure (Templeton et al., 1995; Templeton, 2004).”
Phylogeography: retrospect and prospect (2009, background): “The net goal should be a robust ‘statistical phylogeography’ (Knowles & Maddison, 2002; Templeton, 2004; Knowles, 2008) that reflects a realistic integration of population genetic and phylogenetic methods.”
Implications of life history for genetic structure and migration rates of southern African coastal invertebrates: planktonic, abbreviated and direct development (2007, neutral): “The most likely phylogeographic scenario explaining the observed phylogeographic patterns was inferred using the latest version of the inference key for the nested haplotype tree analysis of geographic distances (Templeton 2004; latest version posted on November 11, 2005).”