ASPM and mammalian brain evolution: a case study in the difficulty in making macroevolutionary inferences about gene–phenotype associations

Abstract

Identifying the genetic basis of adaptive phenotypes can be a significant step towards understanding how that phenotype evolved. With the increased availability of interspecific molecular data, an approach to uncover such genes has been to search for signatures of adaptive evolution at the molecular level. Many analyses have adopted a candidate gene approach, focusing on genes with important developmental roles. One such candidate gene is ASPM, which is involved in neurogenesis and associated with major neurological disorders [1]. The molecular evolution of ASPM has been investigated for a decade (see electronic supplementary material, table S1), under the hypothesis that it contributes to primate brain evolution. A recent study by Xu et al.[2] extends the taxonomic scope by demonstrating that ASPM evolved adaptively in cetaceans. However, descriptive studies of patterns of selection are now being supplanted by those that explicitly test for gene -phenotype associations. Using such an approach, we find that Xu et al.'s conclusion that ASPM is linked to increases in cetacean encephalization quotient (EQ), a measure of relative brain size, is not supported. We highlight developments in the analysis of molecular data and phylogenetic methods that are capable of resolving major issues in functional gene -phenotype coevolution, which we hope will provoke discussion and aid future studies.One approach for making gene -phenotype associations is to test for shifts in selection pressure acting on a gene in taxa that display the phenotype of interest. This frequently involves comparing estimates of dN/dS, a measure of the strength of selection acting on a protein-coding gene, using a range of tests implemented in software such as PAML (see electronic supplementary material, table S2) [3]. The results of these tests can be influenced by the nature of the data and, in particular, require sufficient evolutionary variation to make reliable estimates. Data with few substitutions or from a restricted number of taxa can lead to spurious results. These effects may be evident in Xu et al.'s analysis [2]. First, they suggest that a high proportion of branches in the cetacean phylogeny have an elevated dN/dS, which they interpret as evidence of increased positive selection, but do not perform explicit tests of this hypothesis. Further analysis (see the electronic supplementary material) suggests that none of these values are significantly greater than one, the threshold for accepting adaptive evolution. The apparent elevation in dN/dS is likely to be influenced by the low number of substitutions on short branches. This problem is particularly strong for cetaceans, which have low substitution rates [4]. Second, it is suggested that positive selection is limited to mammalian orders with high EQs. However, this result is likely to be influenced by sampling bias, and inclusion of further taxa provides evidence for positive selection across mammals (see the electronic supplementary material). Identifying robust shifts in selection pressur...

Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition

“…There are few human specific genes such as SRGAP2C 5 , ARHGAP11B 6 or NOTCH2NL 7 that recently appeared through gene duplication in the Homo lineage 8 and remarkably their expression in the mouse brain increases cortical development 6,7,9,10 . In addition, several genes involved in brain function display accelerated evolution of their coding regions in humans, for example FOXP2 has been associated with verbal apraxia and ASPM with microcephaly 11,12 . Functional studies also showed that mice carrying a "humanized" version of FOX2 display qualitative changes in ultrasonic vocalization 13 .…”

Genetic basis of brain size evolution in cetaceans: insights from adaptive evolution of seven primary microcephaly (MCPH) genes

“…Statistical association between selection on a functional gene and changes in phenotype are an important indication for exploring the genetic basis of adaptive phenotypes [ 21 , 48 ]. Regressions revealed a significant positive association between relative brain size (EQ) and evolutionary rates for ASPM and CDK5RAP2 but not for WDR62 and CEP152 (Fig.…”

“…Notably, no association was found in the ASPM gene when only the two exons (approx. 60% of the transcribed ASPM protein) were examined in our previous study [ 20 ], which was questioned by Montgomery et al [ 21 ]. However, when the 22 exons, accounting for 90.34% of the transcribed ASPM protein, were used in this study, it was striking and interesting to find a significant association between root-to-tip ω of ASPM and cetacean EQ ( R 2 = 0.304, P = 0.046, Fig.…”

“…Evidence of positive selection was determined on exons 3 and 18 of the ASPM gene in odontocetes, especially for species in the superfamily Delphinoidea, which was well matched with the two major events of relative brain size enlargement in cetaceans [ 20 ]. However, no significant association was identified between the evolutionary rate of the two ASPM exons and brain size phenotypes in cetaceans [ 21 ]. For MCPH1 gene, no compelling evidence of positive selection and association was examined between MCPH1 evolution and brain evolution in cetaceans [ 19 ].…”

Comparative genomics of brain size evolution

“…While initial studies did find evidence for positive selection across some primate lineages for several genes (reviewed in Gilbert et al, 2005), the correlation with changes in brain size was usually not explicitly tested, impeding the interpretation of these findings (Woods et al, 2005; Montgomery et al, 2014). …”