DnaSP, DNA polymorphism analyses by the coalescent and other methods

By Julio Rozas, Juan C. Sánchez-DelBarrio, Xavier Messeguer, Ricardo Rozas. Bioinform., 2003

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View Paper: https://www.semanticscholar.org/paper/6fa99e64380484c08acad8117b464dfe8af32c6a

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In Genetics

Citations in the corpus

Mitochondrial DNA and electronic tracking reveal population structure of Atlantic bluefin tuna (Thunnus thynnus) (2008, methodology): “To further test for population subdivision, the nearest neighbor statistic (Snn, Hudson 2000) was calculated using the program DNASP 4.0 ( Rozas et al. 2003 ).”
seqphase: a web tool for interconverting phase input/output files and fasta sequence alignments (2010, methodology): “Since its version 4.50, the versatile Windows program DnaSP (Rozas & Rozas 1995, 1997, 1999; Rozas et al. 2003) includes an implementation of PHASE that takes as input a FASTA alignment (of one sequence per individual, with heterozygous positions represented by IUPAC ambiguity codes), and can write…”
A deficit of detoxification enzymes: pesticide sensitivity and environmental response in the honeybee (2006, methodology): “Silent site nucleotide comparisons were calculated using DNAsp Version 4 (Rozas et al., 2003).”
Historical climate modelling predicts patterns of current biodiversity in the Brazilian Atlantic forest (2008, methodology): “DNA sequences were downloaded from GenBank or obtained from authors (see Appendix S1 in Supplementary Material) and analysed in DNAsp (Rozas et al., 2003) to compare levels of genetic diversity in refuge and non-refuge areas as defined by the models.”
High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography (2008, methodology): “We first entered the NEXUS-formatted sequence output of DnaSP into PAUP, and ran a heuristic search for a maximumparsimony tree with M. canettii strain K116 set as the outgroup.”
Tomato SNP Discovery by EST Mining and Resequencing (2005, methodology): “DnaSP (Rozas et al. 2003) was used to estimate h for all sites and also separately for untranslated regions (UTRs), exons, and introns (Table 1).”
The genetic structure of the loggerhead sea turtle (Caretta caretta) in the Mediterranean as revealed by nuclear and mitochondrial DNA and its conservation implications (2007, methodology): “Haplotype diversity (h), nucleotide diversity (p) and the genetic distance (cst) (Nei 1982) between each pair of populations were calculated using the program DNAsp (Rozas et al. 2003).”
Beyond the beneficial effects of translocations as an effective tool for the genetic restoration of isolated populations (2009, methodology): “To evaluate the effectiveness of the translocation program in recovering microsatellite levels of genetic diversity prior to the population bottleneck, we used a clustering method that allowed the identification of distinct subgroups based on multilocus genotype data, as implemented in the computer ”
Complete mitochondrial genomes and a novel spatial genetic method reveal cryptic phylogeographical structure and migration patterns among brown bears in north‐western Eurasia (2013, methodology): “10 (Rozas et al., 2003).”
Cryptic speciation in the giant Antarctic isopod Glyptonotus antarcticus (Isopoda: Valvifera: Chaetiliidae) (2005, methodology): “The number of unique mitochondrial haplotypes was determined with the computer program DnaSP 4 (Rozas et al., 2003).”
The Sunflower High-oleic Mutant Ol Carries Variable Tandem Repeats of FAD2-1, a Seed-specific Oleoyl-phosphatidyl Choline Desaturase (2006, positive): “The 10 allele sequences were aligned using Clustal-W and screened for single nucleotide polymorphisms (SNPs) and INDEL and SSR polymorphisms using DNAsp (Rozas and Rozas 1999; Rozas et al. 2003; http://www.ub.es/ dnasp).”
Genome Microevolution of Chikungunya Viruses Causing the Indian Ocean Outbreak (2006, methodology): “]. Both analyses yielded exactly the same consensus sequence for all strains. A single contig was obtained for the six isolates. Sequence alignments and computation of substitution tables were performed using programs BioNumerics, DNASP version 4.10 [”
Lack of population structure in the fiddler crab Uca annulipes along an East African latitudinal gradient: genetic and morphometric evidence (2010, methodology): “Number of mtDNA haplotypes, haplotype diversity (h), and nucleotide diversity () were calculated for each location as well as for the pooled samples using DNASP version 4.50 ( Rozas et al. 2003 ).”
DNA bar-coding reveals source and patterns of Thaumastocoris peregrinus invasions in South Africa and South America (2010, background): “the past 7 years (2001‐2008) the haplotype diversity in Sydney has thus remained relatively constant, indicating the absence of evolutionary forces such as drift, immigration or genetic bottlenecks that would result in temporal changes in population structure ( Roderick 1996; Sakai et al. 2001).”
Worldwide sequence conservation of transmission-blocking vaccine candidate Pvs230 in Plasmodium vivax (2011, neutral): “9 software [47].”
Phylogeography of the pool frog Rana (Pelophylax) lessonae in the Italian peninsula and Sicily: multiple refugia, glacial expansions and nuclear–mitochondrial discordance (2008, background): “4.0 (Rozas et al., 2003).”
Evolution in a tropical archipelago: comparative phylogeography of Philippine fauna and flora reveals complex patterns of colonization and diversification (2008, methodology): “Basic attributes of DNA variation were calculated with DnaSP, verison 4.10 ( Rozas et al., 2003 ).”