Talk:Genetic variation in nature

Reviewer B

In 1988 Nevo wrote"Environmental stress, through extreme temperatures or humididty may affect ... species abundances and boundaries, hence affecting biodiversity at all levels, of genes, genomes, individuals, populations, species, communities and biota "

Such broad activities are rare for one individual especially when specialization is dividing science into increasingly small semi-isolated disciplines. Eviatar Nevo has spent his life countering this trend. He has become one of the pivotal evolutionary biologists of his era, whose work should be cited for many decades to come. These multidisciplinary achievements have been developed by Nevo at the University of Haifa with internal and world-wide collaborations.

The present article on Genetic Variation in Nature is a progress report of these achievements. Predictably, the direction is becoming increasingly molecular, however the authors (Nevo, Beiles) skilfully incorporate the consequences of environmental stress in the context of habitats of organisms. I have therefore no hesitation in recommending publication of this review as it stands. For me, it is a well-presented up-to-date summary of a diverse literature with an indication of likely future developments.

Reviewer A

This article, "Genetic variation in nature" addresses a fundamental question in evolutionary biology : What is genetic variation, how large it is and what is its significance in nature. The present view focuses on the relationships between variation and selection in the context of environmental stresses or changes. The basic intent of this article is excellent and worthwile, providing a summary of multidisciplinary achievements in this domain on different organisms or different level of biological organization studied. We recommend the publication of this article, however, the authors should lighten the paper by making some changes as indicated below.

The title, "genetic variation in nature", is too general according to the content of this article. As it is, it refers to all types of genetic variation and thus should deals not only with selection and adaptation but also with the evolutionary history of species and populations especially as long as molecular approaches are considered (demographic history, population structure, migration,...). There is a clear choice of the authors to focus on one side of the question, we suggest to revise the current title to something like "Genetic variation in nature mediated through selection and adaptation" .

Our main concern is that the article is organised in a succession of points considering variation description (single nucleotide polymorphism for example), however some of these points refer to mechanisms that produce or maintain variation (transposons, horizontal transfer, alternative splicing,..). This distinction is important and should be indicated clearly.

A number of sentences are too long or incomplete making reading tedious and unclear :

• Section 7.1 , "SNP diversity" and later in the text. Why italics for "coding" and "non coding" genomes or sequences ? ("SNP is the most common sequence variation in coding and non coding parts of genomes")

• section "Isa gene : bifunctional amylase /subtilism inhibitor:" delete events, in "indicate high recombination within this gene regardless....".

• insert a comma after low diversity "this association suggests selective sweeps in the wetter climates with resulting low diversity, and weaker selection or ...".

• section Adaptive dehydrin-1 SNP evolution in "Evolution Canyon": "Dhn1 expression under dehydration displayed interslope divergence between the opposite slopes....". How is the expression quantified ? mRNA estimates ?

• The statement is that significant Interslope divergence is found between the african and the european slopes with only an haplotype commun to both. How is the variation at the level of the whole species ?

• section "Adaptive selected SNPs widespread across life". This paragraph is a list of examples. Reading would be easier by presenting one or two examples in detail, the others may be summarized in a table.

• Section "copy number variation": at the end, "Significant temporal fluctutations in the copy number of Tes provide new insight into genome evolution...", what are these new insights ?

• Section "Mobile elements". (Last subsection): "Mobile DNA and evolution in the 21st century....blueprint". The meaning of this sentence is not clear. "Likewise, the rapid emergence of adaptive novel complexes.... the origin of species", the verb is missing in this sentence.

• Section "Whole genome sequencing": The "Human genome" subsection should be separated in "Genomic diversity of humans" for the first part and "genomic functional divergence" starting from Comparative genomics becomes a powerful approach.... To the end of the section, which refers to human but also Drosophila and others.

• Section "The relative importance of evolutionary forces": Vertebrates should be preferred to mammals in the sentence "Natural selection appears to overrule migration and stochasticity in the dynamic evolution of population genetic structure in diverse taxa across life from bacteria to mammals, challenging Wrights’s promotion of genetic drift as a major evolutionary factor even in very small populations" . Especially instead of even seems more appropriate as the effects of drift are stronger in small populations. At the end of the second sub-section, it seems that a reference to Lynch’s work would be useful.