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Mitochondrial molecular markers (DNA sequences of D-loop, cytochrome b and cytochrome c oxidase I) were employed to characterize populations of the piranha Serrasalmus maculatus from Upper Paraná, Upper Paraguay and Tocantins River basins. D-loop sequences of S. maculatus population from Paraná-Paraguay River basin exhibited tandem repeats of short motifs (12 base pairs) and variable numbers depending on specimens, accounting for length variation. Concatenated mitochondrial sequences suggested that S. maculatus encompasses different mitochondrial DNA lineages. Although sampling was restricted to three river basins, phylogenetic analysis clearly indicated that the species currently recognized as S. maculatus presents high genetic variability. Maximum likelihood and Bayesian analysis clustered S. maculatus populations according to their locations. However, the highest genetic differentiation was identified between populations from Paraná-Paraguay system and Tocantins River basin. Three species delimitation analyses (PTP, GMYC, and ABGD) suggested that there are at least two species among the analyzed populations. The analysis of the mitochondrial sequences evidenced genetic differentiation among populations corresponding to related, but different species, suggesting that at least S. maculatus from the Tocantins River and Paraná-Paraguay River basins are most likely different species. Therefore, S. maculatus should be considered a species complex with morphologically cryptic diversity. An integrative revision is suggested.
Pubmed ID: 31454404
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Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.
View all literature mentionsA software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguad (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.
View all literature mentionsSoftware tool as biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7 and sequence analysis program. Provides sequence manipulation and analysis options and links to external analysis programs to view and manipulate sequences with simple point and click operations.
View all literature mentionsAn exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data). (entry from Genetic Analysis Software)
View all literature mentionsA cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
View all literature mentionsA peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.
View all literature mentionsSoftware Python program to discover optimal partitioning schemes for DNA sequences.Used for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data.
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