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

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.

Hidden genomic evolution in a morphospecies-The landscape of rapidly evolving genes in Tetrahymena

A morphospecies is defined as a taxonomic species based wholly on morphology, but often morphospecies consist of clusters of cryptic species that can be identified genetically or molecularly. The nature of the evolutionary novelty that accompanies speciation in a morphospecies is an intriguing question. Morphospecies are particularly common among ciliates, a group of unicellular eukaryotes that separates 2 kinds of nuclei—the silenced germline nucleus (micronucleus [MIC]) and the actively expressed somatic nucleus (macronucleus [MAC])—within a common cytoplasm. Because of their very similar morphologies, members of the Tetrahymena genus are considered a morphospecies. We explored the hidden genomic evolution within this genus by performing a comprehensive comparative analysis of the somatic genomes of 10 species and the germline genomes of 2 species of Tetrahymena. These species show high genetic divergence; phylogenomic analysis suggests that the genus originated about 300 million years ago (Mya). Seven universal protein domains are preferentially included among the species-specific (i.e., the youngest) Tetrahymena genes. In particular, leucine-rich repeat (LRR) genes make the largest contribution to the high level of genome divergence of the 10 species. LRR genes can be sorted into 3 different age groups. Parallel evolutionary trajectories have independently occurred among LRR genes in the different Tetrahymena species. Thousands of young LRR genes contain tandem arrays of exactly 90-bp exons. The introns separating these exons show a unique, extreme phase 2 bias, suggesting a clonal origin and successive expansions of 90-bp–exon LRR genes. Identifying LRR gene age groups allowed us to document a Tetrahymena intron length cycle. The youngest 90-bp exon LRR genes in T. thermophila are concentrated in pericentromeric and subtelomeric regions of the 5 micronuclear chromosomes, suggesting that these regions act as genome innovation centers. Copies of a Tetrahymena Long interspersed element (LINE)-like retrotransposon are very frequently found physically adjacent to 90-bp exon/intron repeat units of the youngest LRR genes. We propose that Tetrahymena species have used a massive exon-shuffling mechanism, involving unequal crossing over possibly in concert with retrotransposition, to create the unique 90-bp exon array LRR genes.

Genomic comparison of ten morphologically very similar species of ciliate from the genus Tetrahymena reveals how parallel microevolutionary processes have shaped their genomes and created unique genes through retrotransposition.

MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification

Background

Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DNA analysis and has been addressed with several approaches, e.g., multiple alignments-, phylogenetic trees-, statistical- and character-based methods.

Results

We propose a supervised method based on a genetic algorithm to identify small genomic subsequences that discriminate among different species. The method identifies multiple subsequences of bounded length with the same information power in a given genomic region. The algorithm has been successfully evaluated through its integration into a rule-based classification framework and applied to three different biological data sets: Influenza, Polyoma, and Rhino virus sequences.

Conclusions

We discover a large number of small subsequences that can be used to identify each virus type with high accuracy and low computational time, and moreover help to characterize different genomic regions. Bounding their length to 20, our method found 1164 characterizing subsequences for all the Influenza virus subtypes, 194 for all the Polyoma viruses, and 11 for Rhino viruses. The abundance of small separating subsequences extracted for each genomic region may be an important support for quick and robust virus identification.

Finally, useful biological information can be derived by the relative location and abundance of such subsequences along the different regions.

Electronic supplementary material

The online version of this article (doi:10.1186/s13040-016-0116-2) contains supplementary material, which is available to authorized users.

Cohesion of Clonal Life History, Senescence and Rejuvenation Induced by Autogamy of the Histophagous Ciliate Tetrahymena rostrata

The histophagous ciliate Tetrahymena rostrata was found as a parasite in the renal organs of the land snails Zonitoides nitidus and Cochlicopa lubrica. A starvation medium induced encystment, meiosis, autogamy, and development of new macronuclei. The cell division rate declined linearly with number of divisions from the last autogamy until senescence. The senescing strains were rejuvenated by further encystment-induced autogamy. It is expected, that these processes contribute to genetic variability among the local, small, and isolated T. rostrata populations. Consistent with this expectation, small divergences in the cox-1 sequences appeared even among these strains, which had been isolated from different specimens of the same host species at the same site. The divergences in this gene between our T. rostrata strains from Z. nitidus and other strains from C. lubrica, Helix aspersa, and Deroceras reticulatum in Spain (Segade et al. 2009, Parasitology 136:771-782), were beyond the limits of intra-species variability within the genus Tetrahymena. However there is the lack of inter-strain differences in the life history and cytology among our, the Spanish, and those T.rostrata strains, that are not available for "barcoding" anymore. Therefore, variability in the life history and morphology within T .rostrata is constrained by natural selection.

Pyrosequencing as a tool for rapid fish species identification and commercial fraud detection

The increased consumption of fish products, as well as the occurrence of exotic fish species in the Mediterranean Sea and in the fish market, has increased the risk of commercial fraud. Furthermore, the great amount of processed seafood products has greatly limited the application of classic identification systems. DNA-based identification allows a clear and unambiguous detection of polymorphisms between species, permitting differentiation and identification of both commercial fraud and introduction of species with potential toxic effects on humans. In this study, a novel DNA-based approach for differentiation of fish species based on pyrosequencing technology has been developed. Raw and processed fish products were tested, and up to 25 species of fish belonging to Clupeiformes and Pleuronectiformes groups were uniquely and rapidly identified. The proper identification based on short and unique genetic sequence signatures demonstrates that this approach is promising and cost-effective for large-scale surveys.

Revisiting species delimitation within the genus Oxystele using DNA barcoding approach

The genus Oxystele, a member of the highly diverse marine gastropod superfamily Trochoidea, is endemic to southern Africa. Members of the genus include some of the most abundant molluscs on southern African shores and are important components of littoral biodiversity in rocky intertidal habitats. Species delimitation within the genus is still controversial, especially regarding the complex O. impervia / O. variegata. Here, we assessed species boundaries within the genus using DNA barcoding and phylogenetic tree reconstruction. We analysed 56 specimens using the mitochondrial gene COI. Our analysis delimits five molecular operational taxonomic units (MOTUs), and distinguishes O. impervia from O. variegata. However, we reveal important discrepancies between MOTUs and morphology-based species identification and discuss alternative hypotheses that can account for this. Finally, we indicate the need for future study that includes additional genes, and the combination of both morphology and genetic techniques (e.g. AFLP or microsatellites) to get deeper insight into species delimitation within the genus.

Potential use of DNA barcodes in regulatory science: identification of the U.S. Food and Drug Administration's "Dirty 22," contributors to the spread of foodborne pathogens

The U.S. Food, Drug, and Cosmetic Act prohibits the distribution of food that is adulterated, and the regulatory mission of the U.S. Food and Drug Administration (FDA) is to enforce this Act. FDA field laboratories have identified the 22 most common pests that contribute to the spread of foodborne disease (the "Dirty 22"). The current method of detecting filth and extraneous material (tails, legs, carcasses, etc.) is visual inspection using microscopy. Because microscopy can be time-consuming and may yield inaccurate and/or nonspecific results due to lack of expertise, an alternative method of detecting these adulterants is needed. In this study, we sequenced DNA from the 5' region of the cytochrome oxidase I gene of these 22 common pests that contribute to the spread of foodborne pathogens. Here, we describe the generation of DNA barcodes for all 22 species. To date, this is the first attempt to develop a sequence-based regulatory database and systematic primer strategy to identify these FDA-targeted species. DNA barcoding can be a powerful tool that can aid the FDA in promoting the protection and safety of the U.S. food supply.

An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding

DNA barcoding has become a well-funded, global enterprise since its proposition as a technique for species identification, delimitation and discovery in 2003. However, the rapid development of next generation sequencing (NGS) has the potential to render DNA barcoding irrelevant because of the speed with which it generates large volumes of genomic data. To avoid obsolescence, the DNA barcoding movement must adapt to use this new technology. This review examines the DNA barcoding enterprise, its continued resistance to improvement and the implications of this on the future of the discipline. We present the consistent failure of DNA barcoding to recognize its limitations and evolve its methodologies, reducing the usefulness of the data produced by the movement and throwing into doubt its ability to embrace NGS.

Learning to classify species with barcodes

Background

According to many field experts, specimens classification based on morphological keys needs to be supported with automated techniques based on the analysis of DNA fragments. The most successful results in this area are those obtained from a particular fragment of mitochondrial DNA, the gene cytochrome c oxidase I (COI) (the "barcode"). Since 2004 the Consortium for the Barcode of Life (CBOL) promotes the collection of barcode specimens and the development of methods to analyze the barcode for several tasks, among which the identification of rules to correctly classify an individual into its species by reading its barcode.

Results

We adopt a Logic Mining method based on two optimization models and present the results obtained on two datasets where a number of COI fragments are used to describe the individuals that belong to different species. The method proposed exhibits high correct recognition rates on a training-testing split of the available data using a small proportion of the information available (e.g., correct recognition approx. 97% when only 20 sites of the 648 available are used). The method is able to provide compact formulas on the values (A, C, G, T) at the selected sites that synthesize the characteristic of each species, a relevant information for taxonomists.

Conclusion

We have presented a Logic Mining technique designed to analyze barcode data and to provide detailed output of interest to the taxonomists and the barcode community represented in the CBOL Consortium. The method has proven to be effective, efficient and precise.

Potential use of DNA barcodes in regulatory science: applications of the Regulatory Fish Encyclopedia

The use of a DNA-based identification system (DNA barcoding) founded on the mitochondrial gene cytochrome c oxidase subunit I (COI) was investigated for updating the U.S. Food and Drug Administration Regulatory Fish Encyclopedia (RFE; http://www.cfsan.fda.gov/-frf/rfe0.html). The RFE is a compilation of data used to identify fish species. It was compiled to help regulators identify species substitution that could result in potential adverse health consequences or could be a source of economic fraud. For each of many aquatic species commonly sold in the United States, the RFE includes high-resolution photographs of whole fish and their marketed product forms and species-specific biochemical patterns for authenticated fish species. These patterns currently include data from isoelectric focusing studies. In this article, we describe the generation of DNA barcodes for 172 individual authenticated fish representing 72 species from 27 families contained in the RFE. These barcode sequences can be used as an additional identification resource. In a blind study, 60 unknown fish muscle samples were barcoded, and the results were compared with the RFE barcode reference library. All 60 samples were correctly identified to species based on the barcoding data. Our study indicates that DNA barcoding can be a powerful tool for species identification and has broad potential applications.

The diversity of microbes: resurgence of the phenotype

The introduction of molecular genetic methods has caused confusion about the nature of microbial species. Environmental DNA extraction has indicated the existence of a vast diversity of genotypes, but how this relates to functional and phenotypic diversity has not been sufficiently explored. It has been implied that genetic distance per se correlates with phenotypic differentiation and thus reflects subtle (but undiscovered) adaptive fine-tuning to the environment, and that microbes may show biogeographic patterns at the genetic level. Here, we argue that no theoretically based species concept exists; species represent only the basic unit in the taxonomic hierarchy. The significance of naming species is that it organizes biological information. The reason why microbial species collectively represent large genetic differences is owing to huge absolute population sizes, absence of allopatric speciation and low extinction rates. Microbial phenotypes are, therefore, ancient in terms of the geological time-scale and have been maintained through stabilizing selection. These problems are discussed with special reference to eukaryotic micro-organisms.

Evolution of branched regulatory genetic pathways: directional selection on pleiotropic loci accelerates developmental system drift

Developmental systems are regulated by a web of interacting loci. One common and useful approach in studying the evolution of development is to focus on classes of interacting elements within these systems. Here, we use individual-based simulations to study the evolution of traits controlled by branched developmental pathways involving three loci, where one locus regulates two different traits. We examined the system under a variety of selective regimes. In the case where one branch was under stabilizing selection and the other under directional selection, we observed "developmental system drift": the trait under stabilizing selection showed little phenotypic change even though the loci underlying that trait showed considerable evolutionary divergence. This occurs because the pleiotropic locus responds to directional selection and compensatory mutants are then favored in the pathway under stabilizing selection. Though developmental system drift may be caused by other mechanisms, it seems likely that it is accelerated by the same underlying genetic mechanism as that producing the Dobzhansky-Muller incompatibilities that lead to speciation in both linear and branched pathways. We also discuss predictions of our model for developmental system drift and how different selective regimes affect probabilities of speciation in the branched pathway system.

Biological identifications through DNA barcodes

Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.

The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law

Before the Darwinian revolution many biologists considered organic forms to be determined by natural law like atoms or crystals and therefore necessary, intrinsic and immutable features of the world order, which will occur throughout the cosmos wherever there is life. The search for the natural determinants of organic form-the celebrated "Laws of Form"-was seen as one of the major tasks of biology. After Darwin, this Platonic conception of form was abandoned and natural selection, not natural law, was increasingly seen to be the main, if not the exclusive, determinant of organic form. However, in the case of one class of very important organic forms-the basic protein folds-advances in protein chemistry since the early 1970s have revealed that they represent a finite set of natural forms, determined by a number of generative constructional rules, like those which govern the formation of atoms or crystals, in which functional adaptations are clearly secondary modifications of primary "givens of physics." The folds are evidently determined by natural law, not natural selection, and are "lawful forms" in the Platonic and pre-Darwinian sense of the word, which are bound to occur everywhere in the universe where the same 20 amino acids are used for their construction. We argue that this is a major discovery which has many important implications regarding the origin of proteins, the origin of life and the fundamental nature of organic form. We speculate that it is unlikely that the folds will prove to be the only case in nature where a set of complex organic forms is determined by natural law, and suggest that natural law may have played a far greater role in the origin and evolution of life than is currently assumed.

Laboratory and evolutionary history of Tetrahymena thermophila

An account is given of the early efforts to domesticate tetrahymenas as laboratory instruments for genetics. The rationale for developing a new organismic technology was the comparative leverage provided by a eukaryotic microorganism at a large evolutionary distance from both prokaryotic microbes and multicellular organisms. The tetrahymenine ciliates were considered more favorable materials than paramecia because of their ability to grow on simple media, though in fact their simpler nutritional needs have never been fully exploited. The first task was to sort the large set of phenotypically similar but evolutionarily and molecularly diverse ciliates referred to at the time as T. pyriformis. Then a species amenable to genetic manipulation was identified and its culture and cytogenetics were brought under control. Fortunately, the very first breeding system investigated--that in the species now called T. thermophila--has proved to be suitable for a wide range of studies. A large factor in the program's success was its use of the foundation previously established by studies on paramecia. However, serious unforeseen difficulties were encountered on the way to "domestication." These included inbreeding deterioration associated with their outbreeding life-style and germinal deterioration (mutational erosion) in the unexpressed micronuclear genome after long maintenance in vegetative culture. Cryogenic preservation was an important means of escaping these organismic limitations, and somatic (macronuclear) assortment has proved a valuable supplement to meiotic recombination.

The global diversity of protozoa and other small species

It is widely believed that the number of species of micro-organisms in the world is extremely large. Here, we offer the contrasting view--that the number may be quite modest. Most of the work reviewed refers to the ciliated protozoa. As with all microbial groups, we must define our concept of "species", and for ciliates, the "morphospecies" concept appears to be at least as robust as any other. Critical examination of published descriptions of ciliates provides a "best estimate" of 3744 for the global number of free-living morphospecies. Of these, 793 are associated with marine sediments, and 1370 with freshwater sediments. In an independent analysis based on extrapolation (assuming the ubiquity of species) from ecological datasets, we estimate the numbers of species in marine and freshwater sediments as 597 and 732, respectively (i.e. within a factor of two of the figures obtained from taxonomic analysis). This apparent convergence of independent estimates will strengthen if, as is likely, the number of nominal species is further reduced by taxonomic revision. These relatively low numbers of species are consistent with (a) the vast amount of published information indicating typically cosmopolitan distributions for ciliates and other microbes, and (b) recent experimental evidence that most free-living ciliates are rare or cryptic--seldom detectable, but present, and "waiting" for suitable conditions to arrive. In summary, most ciliates (and other micro-organisms) are probably ubiquitous, endemics are rare, global species richness is relatively low, and, at least in the case of the ciliates, most species have already been discovered.

Comparison of sequence differences in a variable 23S rRNA domain among sets of cryptic species of ciliated protozoa

Studies were undertaken to discover the relative molecular distances separating some familiar forms of ciliated protozoa, and the genetic species they include. Sequences of 190 bases of the D2 domain of the large ribosomal nucleic acid molecule were obtained by polymerase chain reaction from protists of three distinctive groups of ciliated protozoa-Colpoda, Paramecium and Tetrahymena. Evolutionary trees were constructed for each set of sequences using the PHYLOGEN 1.0 string programs. All three groups of ciliates manifested large molecular diversity among strains difficult or impossible to distinguish morphologically. The largest single evolutionary distance within a group was the 75 differences separating Tetrahymena paravorax from the other tetrahymenids. The largest mean distance for a group was the 21.2 for the colpodids. In all the protist groups the large molecular diversity is obscured by morphological conservatism associated with constraints of ancient designs. The molecular diversity within morphotypes argues for long evolutionary coexistence of species differentiated from each other in significant physiological, ecological, or nutritional ways.

Linear genetics, non-linear epigenetics: complementary approaches to understanding complex diseases

Recent discoveries and rediscoveries in molecular and cell biology, in population and evolutionary biology, and in disease natural history raise new doubts about the ability of genetic analysis alone to predict multifactorial (polygenic) human diseases and other complex phenotypes. These doubts serve to redirect our attention to epigenetic regulation as a second informational system in parallel with the genome. Epigenetic regulation is now viewed by many biologists as a process that includes mechanisms capable of constraining the genome and providing for new patterns of gene expression. Epigenetic networks, both intra- and inter-cellular, provide a basis for nonlinear and chaotic views of cellular and tissue level differentiation and organization, and thus provide a more dynamic approach to understanding the creation of complex phenotypes, even from isogeneic conditions. The reality of regulatory networks within cells inserted, as it were, between genome and phenome, also helps explain the difficulties now encountered when prediction and diagnosis of complex disease omits epigenetic considerations and depends entirely on gene causality.

Epigenesis: the missing beat in biotechnology?

The range of human phenotypes/diseases for which our burgeoning bio-molecular data base is sufficient to provide understanding, diagnosis, and therapy is small. Only 2 percent of our total disease load is related to monogenic causality, and even here the final phenotype is modulated by many factors. Monogenic logic cannot, moreover, be applied to the 98 percent of our most important sources of premature disability and death. This article provides an analysis of the limits of genetic thinking in biotechnology and describes the outline for another approach to understanding complex cellular/physiological systems. In this outline, rules governing physiological regulation and cellular and higher levels of organization are located not in the genome, but in interactive epigenetic networks which themselves organize genomic response to environmental signaling.

The 5S and 5.8S ribosomal RNA sequences of Tetrahymena thermophila and T. pyriformis

The nucleotide sequences of the 5S rRNAs of Tetrahymena thermophila and two strains of T. pyriformis have been determined to be identical. The 5.8S rRNA sequences have also been determined; these sequences correct several errors in an earlier report. The 5.8S rRNAs of the two species differ at a single position. The sequencing results indicate that the species are of recent common ancestry. Molecular evidence that has been interpreted in the past as suggestive of an ancient divergence has been reviewed and found to be consistent with a T. pyriformis complex radiation beginning approximately 30-40 million years ago.

New wild Tetrahymena from Southeast Asia, China, and North America, including T. malaccensis, T. asiatica, T. nanneyi, T. caudata, and T. silvana n. spp

Tetrahymena of the T. pyriformis complex collected from varied habitats in Malaysia, Thailand, and The People's Republic of China include strains of the micronucleate species T. americanis and T. canadensis and the amicronucleate T. pyriformis and T. elliotti. Two new breeding species are described-T. malaccensis from Malaysia and T. asiatica from China and Thailand. Two wild selfers from China and some of the amicronucleate strains from all three countries fall into isozymic groups similar to named micronucleate and amicronucleate species. The T. patula complex is represented by two groups of clones from Malaysia that fit the morphological description of T. vorax. They, however, have radically different isozymic electrophoretic patterns and both groups differ from those of previously described T. vorax. As their molecules indicate relationships to other "T. vorax" strains as distant as that between T. vorax and T. leucophrys, they are considered to be new species, T. caudata and T. silvana. A third new breeding species, T. nanneyi, was identified among strains previously collected in North America. Viable immature progeny were obtained from the new strains of the five breeding species. Maximum temperature tolerances were determined for the new strains of four of the breeding species.