Two levels of information in DNA: relationship of Romanes' "intrinsic" variability of the reproductive system, and Bateson's "residue" to the species-dependent component of the base composition, (C+G)%

Speciation, natural selection, and networks: three historians versus theoretical population geneticists

In 1913, the geneticist William Bateson called for a halt in studies of genetic phenomena until evolutionary fundamentals had been sufficiently addressed at the molecular level. Nevertheless, in the 1960s, the theoretical population geneticists celebrated a "modern synthesis" of the teachings of Mendel and Darwin, with an exclusive role for natural selection in speciation. This was supported, albeit with minor reservations, by historians Mark Adams and William Provine, who taught it to generations of students. In subsequent decades, doubts were raised by molecular biologists and, despite the deep influence of various mentors, Adams and Provine noted serious anomalies and began to question traditional "just-so-stories." They were joined in challenging the genetic orthodoxy by a scientist-historian, Donald Forsdyke, who suggested that a "collective variation" postulated by Darwin's young research associate, George Romanes, and a mysterious "residue" postulated by Bateson, might relate to differences in short runs of DNA bases (oligonucleotides). The dispute between a small network of historians and a large network of geneticists can be understood in the context of national politics. Contrasts are drawn between democracies, where capturing the narrative makes reversal difficult, and dictatorships, where overthrow of a supportive dictator can result in rapid reversal.

Information theoretic perspective on genome clustering

Shannon’s information theoretic perspective of communication helps one to understand the storage and processing of information in one-dimensional sequences. An information theoretic analysis of 937 available completely sequenced prokaryotic genomes and 238 eukaryotic chromosomes is presented. Information content (Id) values were used to cluster these chromosomes. Chargaff’s second parity rule i.e compositional self-complementarity, an empirical fact is observed in all the genomes, except for the proteobacteria Candidatus Hodgkinia cicadicola. High information content, arising out of biased base composition in all the 14 chromosomes of Plasmodium falciparum is found among two other genomes of prokaryotes viz. Buchnera aphidicola str. Cc (Cinara cedri) and Candidatus Carsonella ruddii PV. Despite size and compositional variations, both prokaryotic and eukaryotic genomes do not deviate significantly from an equiprobable and random situation. Eukaryotic chromosomes of an organism tend to have similar informational restraints as seen when a simple distance based method is used to cluster them. In eukaryotes, in certain cases, Id values are also similar for the two arms (p and q arm) of the chromosomes. The results of this current study confirm that the information content can provide insights into the clustering of genomes and the evolution of messaging strategies of the genomes. An efficient and robust Perl CGI standalone tool is created based on this information theory algorithm for the analysis of the whole genomes and is made available at https://github.com/AlagurajVeluchamy/InformationTheory.

When acting as a reproductive barrier for sympatric speciation, hybrid sterility can only be primary

Animal gametes unite to form a zygote that develops into an adult with gonads that, in turn, produce gametes. Interruption of this germinal cycle by prezygotic or postzygotic reproductive barriers can result in two cycles, each with the potential to evolve into a new species. When the speciation process is complete, members of each species are fully reproductively isolated from those of the other. During speciation a primary barrier may be supported and eventually superceded by a later-appearing secondary barrier. For those holding certain cases of prezygotic isolation to be primary (e.g. elephant cannot copulate with mouse), the onus is to show that they had not been preceded over evolutionary time by periods of postzygotic hybrid inviability (genically determined) or sterility (genically or chromosomally determined). Likewise, the onus is upon those holding cases of hybrid inviability to be primary (e.g. Dobzhansky–Muller epistatic incompatibilities) to show that they had not been preceded by periods, however brief, of hybrid sterility. The latter, when acting as a sympatric barrier causing reproductive isolation, can only be primary. In many cases, hybrid sterility may result from incompatibilities between parental chromosomes that attempt to pair during meiosis in the gonad of their offspring (Winge-Crowther-Bateson incompatibilities). While such incompatibilities have long been observed on a microscopic scale, there is growing evidence for a role of dispersed finer DNA sequence differences (i.e. in base k-mers).

Success of alignment-free oligonucleotide (k-mer) analysis confirms relative importance of genomes not genes in speciation and phylogeny

The utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many 21st century practitioners. A path from the 19th century recognition of the informational basis of heredity to the modern era can be discerned. Crick’s DNA ‘unpairing postulate’ predicted that recombinational pairing of homologous DNAs during meiosis would be mediated by short k-mers in the loops of stem-loop structures extruded from classical duplex helices. The complementary ‘kissing’ duplex loops – like tRNA anticodon–codon k-mer duplexes – would seed a more extensive pairing that would then extend until limited by lack of homology or other factors. Indeed, this became the principle behind alignment-based methods that assessed similarity by degree of DNA–DNA reassociation in vitro. These are now seen as less sensitive than alignment-free methods that are closely consistent, both theoretically and mechanistically, with chromosomal anti-recombination models for the initiation of divergence into new species. The analytical power of k-mer differences supports the theses that evolutionary advance sometimes serves the needs of nucleic acids (genomes) rather than proteins (genes), and that such differences can play a role in early speciation events.

Simple Deviation Analysis of Two-Dimensional Viral DNA Walks

We consider the method of two-dimensional DNA walks based on three independent groups of mapping rules for 21 DNA sequences of animal and plant viruses, and for the sequences of irrational and random numbers. This method provides a visualization tool for the determination of the regional abundance of nucleotides in DNA sequences. By defining a statistical deviation and a maximum-deviation ratio for a DNA walk, we find that the maximum-deviation ratios for the 21 viral DNA sequences are generally larger than those of the random-number sequences of same lengths. It is shown that the viral DNA sequences generally have the smallest maximum-deviations with the same mapping group, and that greater difference between CG and AT contents is associated with larger maximum-deviation ratio. Also it is possible to distinguish a viral DNA sequence from a random-number sequence if the lengths of the sequences are longer than 2000 base-pairs. Other possible applications of the two-dimensional DNA walks are mentioned.

William Bateson, Richard Goldschmidt, and Non-Genic Modes of Speciation

Sometimes a cross between two individuals that appear to belong to the same species produces a sterile offspring (i.e., their hybrid is sterile). Thus, the two individuals appear reproductively isolated from each other. If each could find a compatible mate, then new species might emerge. At issue is whether the form of hybrid sterility that precedes sympatric differentiation into species is, in the general case, of genic or non-genic origin. Several recent papers lend the authority of William Bateson to the genic hypothesis, referring to the "Bateson–Dobzhansky–Muller hypothesis". All these papers cite a 1996 paper that, in turn, cites a 1909 paper of Bateson. However, from 1902 until 1926 the latter espoused a non-genic hypothesis that today would be classified as "chromosomal". Analysis of Bateson's 1909 text reveals no recantation. Bateson's non-genic view was similar to that advanced by Richard Goldschmidt in the 1940s. However, Bateson proposed a contribution from parents of abstract factors that, together in their hybrids, complement to bring about a negative effect (hybrid sterility). In contrast, Goldschmidt proposed that normally parents contribute complementary factors making parental chromosomes compatible at meiosis in their hybrids, which hence are fertile (i.e., the parental factors work together to produce a positive effect). When the factors are not sufficiently complementary the parental chromosomes are incompatible in their hybrids, which hence are sterile. The non-genic Batesonian–Goldschmidtian abstractions are now being fleshed-out chemically in terms of DNA base-composition differences.

Genomic conflict settled in favour of the species rather than the gene at extreme GC percentage values

Wada and colleagues have shown that, whether prokaryotic or eukaryotic, each gene has a "homostabilising propensity" to adopt a relatively uniform GC percentage (GC%). Accordingly, each gene can be viewed as a "microisochore" occupying a discrete GC% niche of relatively uniform base composition amongst its fellow genes. Although first, second and third codon positions usually differ in GC%, each position tends to maintain a uniform, gene-specific GC% value. Thus, within a genome, genic GC% values can cover a wide range. This is most evident at third codon positions, which are least constrained by amino acid encoding needs. In 1991, Wada and colleagues further noted that, within a phylogenetic group, genomic GC% values can also cover a wide range. This is again most evident at third codon positions. Thus, the dispersion of GC% values among genes within a genome matches the dispersion of GC% values among genomes within a phylogenetic group. Wada described the context-independence of plots of different codon position GC% values against total GC% as a "universal" characteristic. Several studies relate this to recombination. We have confirmed that third codon positions usually relate more to the genes that contain them than to the species. However, in genomes with extreme GC% values (low or high), third codon positions tend to maintain a constant GC%, thus relating more to the species than to the genes that contain them. Genes in an extreme-GC% genome collectively span a smaller GC% range, and mainly rely on first and second codon positions for differentiation as "microisochores". Our results are consistent with the view that differences in GC% serve to recombinationally isolate both genome sectors (facilitating gene duplication) and genomes (facilitating genome duplication, e.g. speciation). In intermediate-GC% genomes, conflict between the needs of the species and the needs of individual genes within that species is minimal. However, in extreme-GC% genomes there is a conflict, which is settled in favour of the species (i.e. group selection) rather than in favour of the gene (genic selection).

Chromosomal speciation: a reply

The "genic" and the "non-genic" (chromosomal) hypotheses for the predominant mechanism by which species diverge into two have long been in contention. In 1998 Coyne and Orr attacked certain formulations of the chromosomal hypothesis on the grounds that they required macromutations (structural changes in chromosomes). In 1999 I replied that numerous independent micromutations (single DNA base changes) should suffice (GC% hypothesis). Kliman et al., with the support of Coyne and Charlesworth, have presented various counterarguments, to which the present paper responds with evidence that GC% differences are primary to genic differences and would operate by changing the structure of stem-loops extruded from duplex DNAs. Chromosomes attempting to align by means of complementary loop-loop interactions would fail if GC% differences exceeded a critical threshold. This would disrupt meiosis (hybrid sterility) and the parents of organisms with failed meiosis would be reproductively isolated from each other. If they could find new mates with which they were GC-compatible, then new species could emerge. The model leads to predictions consistent with several lines of evidence. The GC% version of the chromosomal hypothesis has a sound basis and deserves at least as much attention as its genic rival.

Optimum growth temperature and the base composition of open reading frames in prokaryotes

The purine-loading index (PLI) is the difference between the numbers of purines (A+G) and pyrimidines (T+C) per kilobase of single-stranded nucleic acid. By purine-loading their mRNAs organisms may minimize unnecessary RNA-RNA interactions and prevent inadvertent formation of "self" double-stranded RNA. Since RNA-RNA interactions have a strong entropy-driven component, this need to minimize should increase as temperature increases. Consistent with this, we report for 550 prokaryotic species that optimum growth temperature is related to the average PLI of open reading frames. With increasing temperature prokaryotes tend to acquire base A and lose base C, while keeping bases T and G relatively constant. Accordingly, while the PLI increases, the (G+C)% decreases. The previously observed positive correlation between (G+C)% and optimum growth temperature, which applies to RNA species whose structure is of major importance for their function (ribosomal and transfer RNAs) does not apply to mRNAs, and hence is unlikely to apply generally to genomic DNA.

Selective pressures that decrease synonymous mutations in Plasmodium falciparum

Rich and Ayala propose that the zero rate of non-amino-acid-changing (synonymous) mutations in some proteins of Plasmodium falciparum reflects a recent population bottleneck. Alternatively, Arnot and Saul propose sequence conservation in response to selective pressures other than the pressure to encode protein. Among these are fold pressure and purine-loading pressure. Genomes adapt to these by acquisition of introns and/or low-complexity (simple-sequence) segments in proteins. Adaptive explanations include facilitation of intragenic recombination (and hence diversification of the encoded protein) by DNA stem-loop secondary structures.

Differences in (G+C) content between species: a commentary on Forsdyke's "chromosomal viewpoint" of speciation

Forsdyke (1999) has recently argued that differences in (G+C)%, or G+C content, may trigger new species formation. He further argues that the genic model has shortcomings that can be overcome by his "chromosomal" (hereafter, "G+C") model. We disagree on several counts. First, we do not accept that the genic model has the shortcomings suggested by Forsdyke. There is an abundance of empirical support for the contribution of individual genes, as well as of mapped chromosomal regions, to post-zygotic reproductive isolation (and Haldane's rule). Further, we argue that the G+C model suffers from the same theoretical difficulties as other speciation models based on underdominance. We also question the evidence Forsdyke uses to support his model. Finally, we describe analyses of G+C content in a well-studied model system of speciation (the Drosophila melanogaster species complex), the results of which are incompatible with the G+C model. Thus, while Forsdyke's G+C model cannot be explicitly ruled out, it is not directly supported by empirical data. In contrast, the genic model is well supported by empirical data, holds up on theoretical grounds, and does not require any assistance from the G+C model.

Chargaff's legacy

Of Chargaff's four rules on DNA base composition, only his first parity rule was incorporated into mainstream biology as the DNA double helix. Now, the cluster rule, the second parity rule, and the GC rule, reveal the multiple levels of information in our genomes and potential conflicts between them. In these terms we can understand how double-stranded RNA became an intracellular alarm signal, how potentially recombining nucleic acids can distinguish between 'self' and 'not-self' so leading to the origin of species, how isochores evolved to facilitate gene duplication, and how unlikely it is that any mutation can ever remain truly neutral.

Haldane's rule: hybrid sterility affects the heterogametic sex first because sexual differentiation is on the path to species differentiation

Prevention of recombination is needed to preserve both phenotypic differentiation between species and sexual phenotypic differentiation within species. For species differentiation (speciation), isolating barriers preventing recombination may be pre-zygotic (gamete transfer barriers), or post-zygotic (either a developmental barrier resulting in hybrid inviability, or a chromosomal-pairing barrier resulting in hybrid sterility). The sterility barrier is usually the first to appear and, although often initially only manifest in the heterogametic sex (Haldane's rule), is finally manifest in both sexes. For sexual differentiation, the first and only barrier is chromosomal-pairing, and always applies to the heterogametic sex. For regions of sex chromosomes affecting sexual differentiation there must be something analogous to the process generating the hybrid sterility seen when allied species cross. Explanations for Haldane's rule have generally assumed that the chromosomal-pairing barrier initiating evolutionary divergence into species is due to incompatibilities between gene products ("genic), or sets of gene products ("polygenic), rather than between chromosomes per se ("chromosomal"). However, if chromosomal incompatibilities promoting incipient sexual differentiation could also contribute to the process of incipient speciation, then a step towards speciation would have been taken in the heterogametic sex. Thus, incipient speciation, manifest as hybrid sterility when "varieties" are crossed, would appear at the earliest stage in the heterogametic sex, even in genera with homomorphic sex chromosomes (Haldane's rule for hybrid sterility). In contrast, it has been proposed that Haldane's rule for hybrid inviability needs differences in dosage compensation, so could not apply to genera with homomorphic sex chromosomes.

Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine

When transcription is to the right of the promoter, the "top," mRNA-synonymous strand of DNA tends to be purine-rich. When transcription is to the left of the promoter, the top, mRNA-template strand tends to be pyrimidine-rich. This transcription-direction rule suggests that there has been an evolutionary selection pressure for the purine-loading of RNAs. The politeness hypothesis states that purine-loading prevents distracting RNA-RNA interactions and excessive formation of double-stranded RNA, which might trigger various intracellular alarms. Because RNA-RNA interactions have a distinct entropy-driven component, the pressure for the evolution of purine-loading might be greater in organisms living at high temperatures. In support of this, we find that Chargaff differences (a measure of purine-loading) are greater in thermophiles than in nonthermophiles and extend to both purine bases. In thermophiles the pressure to purine-load affects codon choice, indicating that some features of their amino acid composition (e.g., high levels of glutamic acid) might reflect purine-loading pressure (i.e., constraints on mRNA) rather than direct constraints on protein structure and function.