Statistical properties of new neutrality tests against population growth.

By Sebastián Ramos-Onsins, Julio Rozas. Molecular biology and evolution, 2002

2,109 citations recorded by the source corpus.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/3641094ecc9f7638740c61c8f8a733505dbc8234

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In Genetics

1. Julio Rozas
2. R. Zink
3. G. Barrowclough
4. C. Miyaki
5. Daniele Canestrelli
6. G. Nascetti
7. P. Balk
8. W. Wachowiak

Citations in the corpus

• Phylogeography of the pool frog Rana (Pelophylax) lessonae in the Italian peninsula and Sicily: multiple refugia, glacial expansions and nuclear–mitochondrial discordance (2008, methodology): “For the Sicilian clade, the small and not significant value of Fu’s (1997) FS statistic and the large and not significant value of the R2 statistic (Ramos-Onsins & Rozas, 2002) both suggest a history of prolonged demographic stability, although a good fitting of the observed and expected mismatch…”
• ABGD, Automatic Barcode Gap Discovery for primary species delimitation (2012, background): “…growth (Rogers & Harpending 1992) or to build up a test of neutrality (Harpending et al. 1993), although because of the large variance of the gap widths, it is of limited use because it has strong bias for estimators and low power for statistics (Ramos-Onsins & Rozas 2002; Rosenberg & Hirsh 2003).”
• Circumpolar dispersal by rafting in two subantarctic kelp-dwelling crustaceans (2010, background): “…addition to selection, a historical population size contraction and subsequent expansion is also predicted to result in an excess of singleton mutations in a population relative to a historically constant-size population; both are indicated by negative values of Fu’s FS (Ramos-Onsins & Rozas 2002).”
• Phylogeny and comparative phylogeography of Sclerurus (Aves: Furnariidae) reveal constant and cryptic diversification in an old radiation of rain forest understorey specialists (2013, methodology): “In addition, we used Tajima’s D (Tajima, 1989), Fu’s FS test (Fu, 1997) and R2 (Ramos-Onsins & Rozas, 2002) to test the scenarios of population expansion.”
• Eurythoe complanata (Polychaeta: Amphinomidae), the ‘cosmopolitan’ fireworm, consists of at least three cryptic species (2010, methodology): “2003) was employed to test the neutrality of nucleotide substitutions or possible historical population size changes, using Tajima’s D, Fu’s Fs, and Ramos-Onsins with Rozas’ R2 tests (Tajima 1989; Nei and Kumar 2000; Ramos-Onsins and Rozas 2002).”
• Phylogeography of the introduced species Rattus rattus in the western Indian Ocean, with special emphasis on the colonization history of Madagascar (2010, positive): “FS (Fu, 1997) and R2 (Ramos-Onsins & Rozas, 2002) statistics were estimated.”
• PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R (2014, background): “2006), Strobeck’s S (Strobeck 1987), Achaz’s Y (Achaz 2009), Fu’s FS (Fu 1997), Ramos-Onsins’ and Rozas’ R2 (Ramos-Onsins and Rozas 2002), as well as all corresponding theta values Linkage disequilibrium ZnS (Kelly 1997), B/Q (Wall 1999), ZA/ZZ (Rozas et al.”
• DNA sequence polymorphism analysis using DnaSP. (2009, background): “In spite of the popular nature and usefulness of these statistics in the analysis of past demographic events, they are very conservative, especially for recombining DNA regions (19).”
• Phylogeography of Xiphorhynchus fuscus (Passeriformes, Dendrocolaptidae): vicariance and recent demographic expansion in southern Atlantic forest (2007, methodology): “Demographic expansion was inferred by calculating Fs (Fu, 1997) and R2 (Ramos-Onsins & Rozas, 2002) using DnaSP, version 4 (Rozas & Sánchez-Del Barrio, 2003).”
• Mitochondrial DNA under siege in avian phylogeography (2008, methodology): “In addition, we subjected the data to the R2 analysis for population growth (Ramos-Onsins & Rozas 2002) and found it highly significant.”
• DnaSP, DNA polymorphism analyses by the coalescent and other methods (2003, methodology): “DnaSP also computes a number of statistical tests for detecting population growth including the recently developed R2 test (Ramos-Onsins and Rozas, 2002).”
• Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.) (2008, methodology): “Deviations of particular genes from the frequency distribution spectrum under standard neutral model of evolution were assessed with Tajima’s D (Tajima 1989), Fay and Wu H (Fay and Wu 2000), and Ramos–Onsins and Rozas R2 tests (Ramos-Onsins and Rozas 2002).”