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      Resolved and Redeemed: A New Fleck to the Evolutionary Divergence in the Genus Scomberomorus Lacepède, 1801 (Scombridae) With Cryptic Speciation

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          Abstract

          The genus Scomberomorus, with 18 nominal species, sustains a significant heterogeneous fishery throughout its range. The sole molecular systematic study of this genus concerned the species group S. regalis, which contains the new world taxa. The species diversity of Scomberomorus in the northern Indian Ocean has not been studied at the molecular level, often leading to misidentifications. Here, novel genetic data are provided that reconfigure species boundaries from the region. We used single and multilocus data (eight mitochondrial and three nuclear genes) to infer phylogenetic relationships, species delimitation, and the resurrection of a time-calibrated phylogenetic tree. Our aim was also to verify the hypothesis of geographical races in S. guttatus predicated on variable vertebral counts. Interestingly, all species delimitation analyses have recovered another highly cryptic species in the nominal S. guttatus previously believed to have an Indo-Pacific distribution . Scomberomorus guttatus (Bloch and Schneider, 1801) in the sensu stricto, is redeemed from its type locality based on genetic data and preliminary morphomeristic investigations and has a restricted distribution in the Bay of Bengal. The cryptic species Scomberomorus aff. guttatus which exhibits >10% genetic divergence from S. guttatus is resurrected here from the synonymy of the latter as Scomberomorus leopardus (Shaw, 1803). Widespread in the Indo-Pacific, this species contains two major molecular operational taxonomic units (MOTUs) with a divergence threshold of over 2% between them. Our analysis suggests that vertebral counts must be coupled with other features to identify the species/lineages in the nominal S. guttatus. The heterogeneity in the S. guttatus species group is discussed in relation to the ecological diversity of the region which facilitates larval recruitment and niche specialization. The results also revealed two allopatric putative species in S. commerson, found primarily in the Pacific and Indian Oceans. This study added genetic data from S. lineolatus and S. koreanus, not previously represented in the sequence repositories. Estimation of divergence time indicated that the Indo-West Pacific species group undergoes multiple diversification events besides the recent splits detected within S. leopardus.

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          Basic local alignment search tool.

          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

            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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              MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

              Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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                Author and article information

                Journal
                Frontiers in Marine Science
                Front. Mar. Sci.
                Frontiers Media SA
                2296-7745
                June 9 2022
                June 9 2022
                : 9
                Article
                10.3389/fmars.2022.888463
                45e69589-f60d-4391-a1a3-bcc2aa2789e2
                © 2022

                Free to read

                https://creativecommons.org/licenses/by/4.0/

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