Morphological and Molecular Characterization of Anisakid Nematode Larvae (Nematoda: Anisakidae) in the Black Cusk eel Genypterus maculatus from the Southeastern Pacific Ocean off Peru

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Abstract

The back cusk eel, Genypterus maculatus (Tschudi, 1846), (Ophiidiformes: Ophiididae) is one of the benthic-demersal fish usually consumed in northern Peru. Here, we identified the third stage (L3) Anisakidae sampled from 29 specimens of G. maculatus captured off the south American Pacific coast, Lambayeque Region, Peru. A total of 20 anisakid nematode larvae were collected on the visceral surface and divided morphologically into three types (Type I–III). These larvae were identified by mtDNA Cox2 sequences analysis, which indicated that corresponded to Anisakis pegreffii Campana-Rouget and Biocca, 1955, Skrjabinisakis physeteris (Baylis, 1923) and S. brevispiculata (Dollfus, 1966) Safonova, Voronova, and Vainutis, 2021, respectively. This is the first record of S. brevispiculata in Peru. The results obtained in this study provide knowledge on the diversity and distribution of Anisakis Dujardin, 1845 and Skrjabinisakis Mozgovoi, 1951, species in the south American Pacific waters and their relevance for public health. In addition, we suggest that combined use of molecular and morphological approaches is needed to characterize L3 anisakid larvae.

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Basic local alignment search tool.

Stephen F Altschul, Warren Gish, Webb Miller … (1990)

A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen, Heiko Schmidt, Arndt von Haeseler … (2014)

Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.

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MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

Koichiro Tamura, Glen Stecher, Daniel Walter Peterson … (2013)

We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.