The loci of evolution: how predictable is genetic evolution?

Abstract

Is genetic evolution predictable? Evolutionary developmental biologists have argued that, at least for morphological traits, the answer is a resounding yes. Most mutations causing morphological variation are expected to reside in the cis-regulatory, rather than the coding, regions of developmental genes. This "cis-regulatory hypothesis" has recently come under attack. In this review, we first describe and critique the arguments that have been proposed in support of the cis-regulatory hypothesis. We then test the empirical support for the cis-regulatory hypothesis with a comprehensive survey of mutations responsible for phenotypic evolution in multicellular organisms. Cis-regulatory mutations currently represent approximately 22% of 331 identified genetic changes although the number of cis-regulatory changes published annually is rapidly increasing. Above the species level, cis-regulatory mutations altering morphology are more common than coding changes. Also, above the species level cis-regulatory mutations predominate for genes not involved in terminal differentiation. These patterns imply that the simple question "Do coding or cis-regulatory mutations cause more phenotypic evolution?" hides more interesting phenomena. Evolution in different kinds of populations and over different durations may result in selection of different kinds of mutations. Predicting the genetic basis of evolution requires a comprehensive synthesis of molecular developmental biology and population genetics.

Figure 1

Gene structure and definitions of cis-regulatory and coding regions and cis-regulatory and coding mutations. (A) A single gene encodes a complex set of instructions in the DNA sequence. The final gene product can either be a protein, via an mRNA intermediate, or a mature RNA molecule itself (transfer RNA, ribosomal RNA, micro RNA, etc.). Gray boxes indicate DNA regions that encode a protein product. The mRNA molecule is transcribed from the transcription initiation site to the polyadenylation signal and introns are spliced out. Many genes encode alternative mRNA splice variants that can be generated by alternative use of different exons (Graveley 2001; Xing and Lee 2006). This is indicated in the figure by lines above the gene connecting alternative exons. Alternative splice variants are usually expressed in different tissues and at different times in development. The mechanisms regulating splicing are not fully understood, but at least some of the information is encoded in the introns and must be recognized by cell-type-specific splicing factors (Lopez 1998). The mRNA contains 5′ and 3′ untranslated regions (UTRs), which are involved in mRNA stability, mRNA localization, and translation. The basal transcription apparatus binds upstream of the gene-coding region, often at a TA-rich sequence motif called a TATA box. Two enhancer modules are indicated to the left of the exons. Each module can contain binding sites for multiple transcription factors. In some cases, transcription factor binding sites are not clustered into discrete modules. (B) Genes can therefore be divided into coding regions, encompassing all of the exons, and cis-regulatory sequences, which include all other DNA that regulates gene expression. Cis-regulatory sequences include sequences that regulate transcription, RNA stability and splicing, and translation. (C) We define coding mutations as mutations that alter the amino acid sequence encoded by the mRNA or that alter the nucleotide sequence of a mature RNA molecule. (D) Cis-regulatory mutations can occur anywhere in the gene region, including noncoding sequence and coding sequence. In rare cases, synonymous mutations in coding regions alter gene regulation in cis, for example through modification of transcription factor binding sites or through modification of RNA stability (see text for further details). In principle, nonsynonymous mutations could alter both the polypeptide sequence and gene regulation, but no such examples have been reported yet. The regulation of gene expression operates at multiple levels: translation, alternative splicing variants, mRNA stability, mRNA cell localization, translation, etc. (Stern 2003; Alonso and Wilkins 2005). All of these levels of gene regulation are, potentially, available for evolutionary modification (Alonso and Wilkins 2005). However, by far the majority of variation in the distribution of gene products during development is controlled at the transcriptional level (Davidson 2006).

Figure 2

Cumulative number of coding mutations, cis-regulatory mutations and other types of mutations (gene amplification, gene loss, etc.) that have been identified over time as responsible for phenotypic evolution. Results are from data in Appendix 1. Note that the slope for cis-regulatory mutations has increased in recent years. The current discovery rate of cis-regulatory mutations approximately equals the discovery rate of coding mutations. If this reflects the long-term trend, then we expect ultimately to observe approximately equal numbers of cis-regulatory and coding mutations.

Figure 3

Evolutionarily relevant cis-regulatory mutations are more frequently found in interspecific comparisons than in intraspecific comparisons or among domesticated races. (A) The proportion of all mutations that are cis-regulatory mutations for morphological and physiological traits in the complete dataset. (B) Proportion of cis-regulatory mutations for morphological and physiological traits in the restricted dataset, where only one or two mutations per gene were included. Two mutations were included only if both coding and cis-regulatory mutations were found for a single gene. (C) Proportion of cis-regulatory mutations for DGB versus non-DGB genes in the complete dataset. (D) Proportion of cis-regulatory mutations for DGB versus non-DGB genes in the restricted dataset. The total number of mutations for each category is shown above the bars.

Figure 4

Scanning electron micrograph of trichomes and bristles on a leg of Drosophila melanogaster. Trichomes are nonsensory cuticular extensions. Bristles are sensory organs innervated by single neurons.

Figure 5

Partial regulatory networks patterning (A) trichomes (modified from results in Chanut-Delalande et al. 2006; Overton et al. 2007) and (B) bristles in Drosophila melanogaster (modified from Calleja et al. 2002; Hartenstein 2004).