On the genetic basis of tail-loss evolution in humans and apes [RNA-seq]

The loss of the tail is one of the main anatomical evolutionary changes to have occurred along the lineage leading to humans and to the “anthropomorphous apes”. This morphological evolution in the ancestral hominoids has long been considered to have accommodated a characteristic style of locomotion and contributed to the evolution of bipedalism in humans. Yet, the genetic mechanism that facilitated tail-loss evolution in hominoids remains unknown. Primate genome sequencing projects have made possible the inference of causal links between genotypic and phenotypic changes, and enabled the search for hominoid-specific genetic elements controlling tail development. Here, we present evidence that an individual Alu element insertion in the genome of the hominoid ancestor may have contributed to tail-loss evolution. We demonstrate that this Alu element – inserted into an intron of the TBXT gene (also called T or Brachyury ) – pairs with a neighboring ancestral Alu element encoded in the reverse genomic orientation and leads to a hominoid-specific alternative splicing event. To study the effect of this splicing event, we generated multiple mouse models that express both full length and exon-skipped isoforms of mouse Tbxt, mimicking expression pattern of its hominoid ortholog TBXT. We found that mice expressing both Tbxt isoforms can exhibit a complete absence of the tail or a shortened tail, depending on the relative abundance of Tbxt isoforms expressed at the embryonic tail bud, supporting the notion that the exon-skipped transcript is sufficient to induce a tail-loss phenotype. We further noted that mice expressing the exon-skipped Tbxt isoform – both in heterozygous and homozygous forms – may develop a neural tube defect condition, which affects ~1/1,000 human neonates. We speculate that tail loss evolution along the hominoid lineage may be associated with an adaptive cost of potential neural tube defects that may continue to affect human health today. Total RNA isolated from day-1 in vitro differentiated mESC lines across wild-type, TbxtinsASAY/insASAY, TbxtΔexon6/+, and TbxtΔexon6/Δexon6 genotypes was used for bulk RNA-seq. Each genotype has two replicates. WT mESC lines are controls.