Barcode index number, taxonomic rank and modes of speciation: examples from fish

Abstract

Species delimitation by DNA sequence data or DNA barcoding is successful, as confirmed by the vast BOLD data base. However, the theory that would explain this fact has not been developed yet. An approach based on Barcoding Index Number (BIN), suggested in the assignment, allows delimiting of taxa of three ranks (species, genera, and families) and statistical validation with a high precision of delimiting (over 80%), as well as shows for majority of Co-1-based single gene trees good correspondence between their topology and conventional taxa content for analyzed fish species (R² ≈ 0.84–0.98). Knowledge of deviations from these data can help to find out new taxa and improve biodiversity description. It is concluded that delimiting is successful for bulk of cases because the geographic mode of speciation prevails in nature. It takes a long time for new taxa to form in isolation, which allows accumulation of random mutations and many different nucleotide substitutions between them that can be detected by molecular markers and give unique DNA barcodes. The use of BIN approach, described here, can aid greatly in making this important question clearer especially under wider examination of other organisms.

Keywords:

• mtDNA and nDNA
• DNA barcoding
• BIN
• gene tree reticulation
• gene introgression
• species fate
• molecular evolution
• Neo-Darwinism

Acknowledgements

I am very thankful to Dr. R. Ward for proofreading of this manuscript and his fruitful editorial comments, as well to E. Shvetsov and T. Koznova for editing English in the paper.

Disclosure statement

The author gratefully acknowledges the financial support received from the Russian Science Foundation (Grant #14-50-00034 connected with the section of molecular phylogenetics and tree reticulation) and, in part, from the Russian Foundation for Basic Research (Grant #14-04-00758 and #15-29-02456 as regards gene introgression between species). Also, funding was partly obtained from the Far Eastern Branch of the Russian Academy of Sciences in the framework of the Federal Program of Base Research (Grant #15-I-6-014 о). No other financial, consulting, or personal relationships have influenced this work, and no writing assistance was obtained.

Additional information

Funding

The author gratefully acknowledges the financial support received from the Russian Science Foundation (Grant #14-50-00034 connected with the section of molecular phylogenetics and tree reticulation) and, in part, from the Russian Foundation for Basic Research (Grant #14-04-00758 and #15-29-02456 as regards gene introgression between species). Also, funding was partly obtained from the Far Eastern Branch of the Russian Academy of Sciences in the framework of the Federal Program of Base Research (Grant #15-I-6-014 о).