Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society

Abstract

Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the "source" taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.

Keywords: DNA barcoding; Neo-Darwinism; gene tree; genetic introgression; molecular evolution; mtDNA; nDNA; reticulation; species fate.

Figure 1

The scheme that illustrates the main steps and activities necessary to develop DNA barcoding and other associated fields of research.

Figure 2

Two histograms of the frequency distribution of the native species M. trossulus, hybrids, and the invasive species M. galloprovincialis in mussel settlements in the NWSJ (Peter the Great Bay and adjacent waters in the Sea of Japan). The left histogram (A) shows a hybrid genotypic group Fh simulated in the Structure software (8 biochemical-genetic loci, GBL, and two nDNA markers, GLU-5 and ITS-1,2). The Y-axis in both figures is the frequencies of genotypes in the total sample from the studied settlements. The right histogram (B) shows examples of hybrid occurrence with small or no gene introgression, as evidenced by the decreased score levels for F_b offspring. The three rows in figure (B) are examples of frequency variation of three types of hybrids (F_h, F_b, F₁) of the two mussel species. On the X-axis are the numbers of samples from mussel settlements in the NWSJ (Modified from [89,98]).

Figure 3

Summary of studies on hybrids and introgression in animal taxa.

Figure 4

(A) ANOVA of BIN score distribution in three fish taxa analyses that were retrieved from BOLD. BIN, barcode index number showing the frequency of concordant classifications (%, Y−axis) of a tested species-specimen by Co-1 mtDNA barcode records and its correspondence to the entire set of records in the BOLD data base that was named in an independent way. The comparison groups (X−axis) are specimens assigned to the certain species (1), genus (2), or family (3). Frequencies of concordant classifications do not differ among the analyzed research projects (see for details [28]); the same also applies to the three comparison groups in the plot (top). The overall average of concordant classifications by BIN estimates is over 82%. (B,C) Regression analysis of covariation of two variables in the BOLD projects of fish. LOG (BIN-ALL) values (a variable that designates zoologically identified specimens for intraspecies, intragenic, and intrafamily categories as recorded in BOLD, Y−axis) plotted against LOG (BIN-CONCRDANT) scores (all concordant OTU-clusters for Co−1 mtDNA barcode records or sequence-specimens for the same three categories, X−axis). Variations show a statistically significant positive linear dependence of the two variables for combined projects FERU/TZFPC (B) and SCFAA project (C). The overall covariation of the two variables for the data set, as estimated by the coefficient of determination on BIN scores, is R² = 98% and R² = 84%, respectively, for two analyses. More details of the analysis are provided elsewhere [28,29].

Figure 5

P-distance distribution in animal taxa for complete mitogenome in flatfish (A), 13 protein gene sequence data of mtDNA in minnow (B), and time-dependent variation for nDNA markers in a sample of 50,455 species/specimens of different taxa of Eukaryotes (C).