Intraspecific gene genealogies: trees grafting into networks.

By David Posada, Keith A. Crandall. Trends in Ecology & Evolution, 2001

1,542 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3de44e9dd29132972a7468c57ff20ada7b023ea4

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Citations in the corpus

The Iberian contribution to cryptic diversity in European bats (2006, methodology): “This approach combines the topology of a minimum spanning tree with a parsimony-based search of the absent nodes (median vectors) or haplotypes (Posada and Crandall, 2001).”
High genetic diversities and complex genetic structure in an Indo-Pacific tropical reef fish (Chlorurus sordidus): evidence of an unstable evolutionary past? (2004, background): “Nested clade analysis (NCA) uses the genealogical information implicit in the haplotype network to hypothesise on the roles of current and historical gene flow, range expansion, fragmentation, and the spatial and temporal scales at which these processes act (Templeton et al. 7995; Templeton 7998; Po”
Out of South America: multiple origins of non‐native apple snails in Asia (2008, methodology): “Intraspecifically, ancestral haplotypes may still be extant, violating assumptions of a bifurcating tree (Posada & Crandall, 2001), so we employed network methods using TCS 1.21 (Clement et al ., 2000).”
Population genetic structure reveals terrestrial affinities for a headwater stream insect (2007, methodology): “…using TCS 1.21 software (Clement, Posada & Crandall, 2000), and network reticulations that likely were caused by high mutation rates and saturation at specific nucleotide sites were resolved following common theoretical predictions (see Crandall & Templeton, 1993; Posada & Crandall, 2001).”
Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects (2003, background): “Second, as summarized recently by Posada & Crandall (2001), intraspecific DNA evolution does not in general follow a bifurcating process; instead multifurcation is the norm, with the additional complications of reticulate relationships produced by recombination, parallel mutations and recurrent…”
A rangewide phylogeography of Hermann's tortoise, Testudo hermanni (Reptilia: Testudines: Testudinidae): implications for taxonomy (2006, background): “In haplotypic data, loops can also indicate reverse or parallel mutations (Posada & Crandall 2001).”
Contrasting phylogeographical patterns for springtails reflect different evolutionary histories between the Antarctic Peninsula and continental Antarctica (2009, methodology): “A connection limit of 95% was used for all networks and predictions from coalescent theory were applied to resolve ambiguous loops (Crandall & Templeton, 1993; Crandall et al., 1994; Posada & Crandall, 2001).”
Phylogeography of the introduced species Rattus rattus in the western Indian Ocean, with special emphasis on the colonization history of Madagascar (2010, methodology): “A haplotypes network (an appropriate method for intraspecific data; Posada & Crandall, 2001) was constructed using the median-joining method available in the network version 4.1.1.2 software (http://www.fluxus-engineering.com/, Bandelt et al., 1999).”
DNA-based species delimitation in algae (2014, background): “Thus, although within-species gene genealogies differ in nature from among-species phylogenetic relationships (Posada & Crandall, 2001), young species reside in a boundary zone where both processes meet.”
A new cryptic species of pond turtle from southern Italy, the hottest spot in the range of the genus Emys (Reptilia, Testudines, Emydidae) (2005, background): “Moreover, the position of a haplotype in a network implies some information about its age because older haplotypes are thought to have a greater likelihood of being located internally in a network (Posada & Crandall 2001).”
Riverine and marine ecotypes of Sotalia dolphins are different species (2005, background): “NCA is a powerful tool that quantitatively and qualitatively investigates population structure and recent evolutionary history, including speciation (Templeton 1998, 2001; Clement et al. 2000; Posada and Crandall 2001; Sites and Marshall 2003).”
PHYLOGEOGRAPHIC HISTORY OF THE LAND SNAIL CANDIDULA UNIFASCIATA (HELICELLINAE, STYLOMMATOPHORA): FRAGMENTATION, CORRIDOR MIGRATION, AND SECONDARY CONTACT (2002, methodology): “For that purpose, and at least under neutrality, we can apply several empirical predictions derived from coalescent theory (Crandall and Templeton 1993; Crandall et al. 1994; Posada and Crandall 2001).”
Population structure and conservation implications for the loggerhead sea turtle of the Cape Verde Islands (2010, methodology): “We constructed statistical parsimony haplotype networks (Templeton et al. 1992; Posada and Crandall 2001 )t o depict patterns of genetic variation between the haplotypes using the software TCS v.1.21 (Clement et al. 2000).”
Species delimitation and relationships: The dance of the seven veils (2015, background): “Another possibility is to use networks, as advised by many authors (Posada & Crandall, 2001; Corl & Ellegren, 2013), to keep trace of reticulation events.”
Refugia within refugia: the case study of a canopy tree (Eurycorymbus cavaleriei) in subtropical China (2009, background): “Refugia and inference of demographic history Coalescent theory predicts that older alleles will occupy interior nodes of a haplotype network (Posada & Crandall, 2001).”