FOXP2, initially identified for its role in human speech, contains two nonsynonymous substitutions derived in the human lineage. Evidence for a recent selective sweep in Homo sapiens, however, is at odds with the presence of these substitutions in archaic hominins. Here, we comprehensively reanalyze FOXP2 in hundreds of globally distributed genomes to test for recent selection. We do not find evidence of recent positive or balancing selection at FOXP2. Instead, the original signal appears to have been due to sample composition. Our tests do identify an intronic region that is enriched for highly conserved sites that are polymorphic among humans, compatible with a loss of function in humans. This region is lowly expressed in relevant tissue types that were tested via RNA-seq in human prefrontal cortex and RT-PCR in immortalized human brain cells. Our results represent a substantial revision to the adaptive history of FOXP2, a gene regarded as vital to human evolution.

Introduction

Przeworski et al., 2005 Przeworski M.

Coop G.

Wall J.D. The signature of positive selection on standing genetic variation. Krause et al. (2007) Krause J.

Lalueza-Fox C.

Orlando L.

Enard W.

Green R.E.

Burbano H.A.

Hublin J.-J.

Hänni C.

Fortea J.

de la Rasilla M.

et al. The derived FOXP2 variant of modern humans was shared with Neandertals. Coop et al. (2008) Coop G.

Bullaughey K.

Luca F.

Przeworski M. The timing of selection at the human FOXP2 gene. Ptak et al., 2009 Ptak S.E.

Enard W.

Wiebe V.

Hellmann I.

Krause J.

Lachmann M.

Pääbo S. Linkage disequilibrium extends across putative selected sites in FOXP2. Several alternative hypotheses have been proposed to reconcile these findings. The haplotype carrying the two derived amino acids could have been present as standing variation in the common ancestor of humans and other ancient hominins and then positively selected in humans after species divergence ∼500 kya. However, for this to be the case, the haplotype would have had to be at high frequency in the ancestral population, which would dramatically reduce the ability to detect a recent selective signal in modern genomes ().instead suggested a very old sweep targeted these two amino acids beginning before the split of humans and Neanderthals 300–400 kya, with the alleles reaching fixation ∼260 kya. However, aspoint out, the observed pattern of an excess of high-frequency derived alleles in the intron preceding the exonic substitutions is indicative of a recent fixation of the linked allele, as low-frequency variation is quickly lost from populations. The ancestral alleles would have had to remain segregating at low frequency for over 300,000 years of human and Neanderthal history, which is unlikely. Gene conversion has been demonstrated to be insufficient for explaining how these two substitutions could be in Neanderthals ().

Enard et al., 2002 Enard W.

Przeworski M.

Fisher S.E.

Lai C.S.L.

Wiebe V.

Kitano T.

Pa A.P.M.

Pääbo S. Molecular evolution of FOXP2, a gene involved in speech and language. Maricic et al., 2013 Maricic T.

Günther V.

Georgiev O.

Gehre S.

Curlin M.

Schreiweis C.

Naumann R.

Burbano H.A.

Meyer M.

Lalueza-Fox C.

et al. A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Ptak et al., 2009 Ptak S.E.

Enard W.

Wiebe V.

Hellmann I.

Krause J.

Lachmann M.

Pääbo S. Linkage disequilibrium extends across putative selected sites in FOXP2. Maricic et al. (2013) Maricic T.

Günther V.

Georgiev O.

Gehre S.

Curlin M.

Schreiweis C.

Naumann R.

Burbano H.A.

Meyer M.

Lalueza-Fox C.

et al. A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Maricic et al., 2013 Maricic T.

Günther V.

Georgiev O.

Gehre S.

Curlin M.

Schreiweis C.

Naumann R.

Burbano H.A.

Meyer M.

Lalueza-Fox C.

et al. A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Despite extensive discussion over the past 15 years, the initial hypothesis of a recent selective sweep at exon 7 of FOXP2 has not been systematically reevaluated. This is especially concerning given that the model was based on a limited Sanger sequencing dataset of only three introns and a small sample of humans (n = 20) (). It has been suggested that alternative targets could be responsible for the sweep apart from these two substitutions (). By comparing Neanderthal and Denisovan sequences to a panel of 50 modern humans,identify a nearly fixed, derived polymorphism (rs114972925) in intron 9 that affects the binding of an upstream transcription factor, POU3F2, in HeLa cells. The derived version of this variant was found to be less efficient at binding POU3F2 compared to the ancestral version, in addition to binding a different proportion of POU3F2 dimers versus monomers, which they argue is suggestive of an effect on subsequent FOXP2 expression (). We are not aware of any additional investigations of the selective history of this or other areas of FOXP2 since the initial work or examination of this region in human brain cells, which is the tissue type most relevant to FOXP2′s presumed primary function.