Genome sequencing and population genomics in non-model organisms

•Genome sequences of non-model organisms are accumulating at an unprecedented rate. •Expansion of gene families and positive selection underlie adaptive evolution. •Whole-genome resequencing reveals demography, local adaption, and speciation. High-throughput sequencing technologies are revolutionizing the life sciences. The past 12 months have seen a burst of genome sequences from non-model organisms, in each case representing a fundamental source of data of significant importance to biological research. This has bearing on several aspects of evolutionary biology, and we are now beginning to see patterns emerging from these studies. These include significant heterogeneity in the rate of recombination that affects adaptive evolution and base composition, the role of population size in adaptive evolution, and the importance of expansion of gene families in lineage-specific adaptation. Moreover, resequencing of population samples (population genomics) has enabled the identification of the genetic basis of critical phenotypes and cast light on the landscape of genomic divergence during speciation. High-throughput sequencing technologies are revolutionizing the life sciences. The past 12 months have seen a burst of genome sequences from non-model organisms, in each case representing a fundamental source of data of significant importance to biological research. This has bearing on several aspects of evolutionary biology, and we are now beginning to see patterns emerging from these studies. These include significant heterogeneity in the rate of recombination that affects adaptive evolution and base composition, the role of population size in adaptive evolution, and the importance of expansion of gene families in lineage-specific adaptation. Moreover, resequencing of population samples (population genomics) has enabled the identification of the genetic basis of critical phenotypes and cast light on the landscape of genomic divergence during speciation. the distribution of allele frequencies among a large set of polymorphic sites. An unfolded spectrum uses information on the ancestral state in that the frequency of derived alleles is depicted. If such information is not available, a folded spectrum simply depicts the frequency of the minor allele (and, hence, has 0.5 as its maximum frequency). a term mainly used in human biology that refers to the diversity of ideas an individual makes in any given situation or dilemma. incorrectly merged contigs (reads) that form a chimeric scaffold (contig). In the absence of independent means for the validation of scaffold structures, it might be that a certain fraction of chimeric scaffolds is unavoidable in assembly projects. the complete repertoire of proteases, involved in proteolytic degradation, present in a cell. the number of sequence reads covering a nucleotide site, often expressed as the mean across all sites in the genome. Depth of coverage is a critical parameter in population genomic analysis because the probability of obtaining reads from both alleles at a heterozygous site (i.e., to call a SNP) increases with number of reads covering that site. a measure of the size of an idealized population in which the effect of genetic drift on allele frequencies is similar to the population under consideration. the genetic background to phenotypic traits, including their number, effect sizes, and dominance. a metaphor for the spatial distribution (along chromosomes) of parameter values of a genomic feature, such as the abundance of genes and repeats, or measures of diversity and divergence. studies based on the use of large numbers of SNP markers genotyped in a group showing a particular trait, and in a control group, with the aim of finding association between trait and markers. the effect that natural selection has on linked sites. For example, the spread of an advantageous mutation in the population can be hindered by linkage to a disadvantageous mutation on the same background. Interference decreases with increasing genetic distance to selected loci. when the association between alleles at two or more loci is not random. the genomic distribution of nucleotide sites modified by the addition of methyl groups by methyltransferases. Methylation of cytosines preceding guanine is the most common form of methylation in many vertebrate genomes. Cytosines can also be methylated in other sequence contexts and, in plants, targets for methylation are more promiscuous. Methylation affects transcription and, thus, is implicated in several processes of gene regulation. the length of the scaffold in a genome assembly that, when scaffolds are sorted by size, all scaffolds larger than this size contain 50% of all assembled DNA. the average pairwise heterozygosity between two randomly drawn chromosomes from the population. At equilibrium and in the absence of selection, π should be the same as the expected value of the population genetic parameter theta estimated from the number of segregating sites. the complete repertoire of translated peptides (small proteins, such as hormones) in the genome. the complete repertoire of the phenotypes of an organism. natural selection for an advantageous allele, giving it an increased fixation probability. restriction site-associated DNA markers obtained by digesting genomic DNA with specific restriction enzymes, ligation of adaptors, amplification, and sequencing. This can reduce the complexity of genomic samples and enable sequencing of the same, targeted regions of the genome in multiple individuals. As a result, genotypes at specific SNPs can be obtained by sequencing, hence the term ‘genotyping by sequencing’ (GBS). an approach that uses signals in genetic data, such as locally reduced genetic diversity arising from a selective sweeps, to elucidate the phenotypic effects of the gene or genomic region in question. This is in contrast to forward genetics, in which the starting point is a phenotype and where one seeks to track its genetic basis. the selection coefficient (s, the relative fitness dis-/advantage of a derived allele) multiplied with Ne, to take into account the fact that the efficiency of selection is directly proportional to population size. natural selection for an advantageous allele that brings with it linked diversity at the haplotype background in which the advantageous allele resides (the region ‘hitch-hikes’ through the population). natural selection for advantageous alleles that are part of the standing genetic variation in a population (in practise, existing on different genetic background, due to recombination events). Under this scenario, the rate of adaptive evolution is not limited by the rate of supply of new mutations. polymorphism already existing in the population, in contrast to the appearance of new variants by mutation. Selection on standing genetic variation may, for instance, occur if environmental changes make a previously neutral variant non-neutral. the complete repertoire of transcribed sequences in the genome, including expression both from protein-coding genes and from noncoding RNAs.