DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets

Abstract

We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new version of the popular tool for performing exhaustive population genetic analyses on multiple sequence alignments. This major upgrade incorporates novel functionalities to analyze large data sets, such as those generated by high-throughput sequencing technologies. Among other features, DnaSP 6 implements: 1) modules for reading and analyzing data from genomic partitioning methods, such as RADseq or hybrid enrichment approaches, 2) faster methods scalable for high-throughput sequencing data, and 3) summary statistics for the analysis of multi-locus population genetics data. Furthermore, DnaSP 6 includes novel modules to perform single- and multi-locus coalescent simulations under a wide range of demographic scenarios. The DnaSP 6 program, with extensive documentation, is freely available at http://www.ub.edu/dnasp.

The identity of the Sri Lankan Amblypharyngodon (Teleostei, Cyprinidae)

“…DNAsp v.6 (Rozas et al 2017) was used to compute the nucleotide diversity (π), haplotype diversity and neutrality tests: Tajima’s D (Tajima 1989) and Fu and Li’s F (Fu and Li 1993).…”

Evolutionary Rates and Phylogeographical Analysis of Odontoglossum Ringspot Virus Based on the 166 Coat Protein Gene Sequences

“…Nonsynonymous (d N ) and synonymous (d S ) differences that correlated with phylogenetic relationships were accessed separately using the Pamilo–Bianchi–Li method (Pamilo and Bianchi, 1993) in MEGA version 7 (Kumar et al, 2016). Nucleotide and haplotype diversity of ORSV CP sequences were estimated by DnaSP version 6.0 (Rozas et al, 2017). Haplotype diversity was calculated based on the frequency and number of haplotypes in the population.…”

“…To detect the level of gene flow between populations, the absolute value of the standardized variance in allele frequencies across populations ( Fst ) were estimated using DnaSP version 6.0 (Rozas et al, 2017). The absolute value of Fst ranges from 0 to 1 for undifferentiated to fully differentiated populations.…”

Suppressed Recombination of Sex Chromosomes Is Not Caused by Chromosomal Reciprocal Translocation in Spiny Frog (Quasipaa boulengeri)

“…Detailed sequence information is shown in Supplementary Table S1 . Sequence alignment and haplotype identification were conducted with MEGA7.0 (Kumar et al, 2016) and DnaSP v.6.10 (Rozas et al, 2017). Two species closely related to Q. boulengeri were chosen as outgroup taxa, Q. robertingeri and Q. spinosa .…”