Evolutionary Genomics

Evolution has created an astonishing array of morphological diversity. A striking example is the adaptation of limbs during evolution. The transformation of fins into limbs was fundamental to the transition from aquatic to terrestrial life. However, since then, the tetrapod limb has been subject to extensive evolutionary adaptation to generate functional diversity. Darwin highlighted the differences in limb morphology among living creatures to support his argument for evolution by natural selection and descent in the often quoted statement “what can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include the same bones, in the same relative positions?” (The origin of species; 1859). The common skeletal blueprint for paired appendages that he referred to includes the single proximal long bone of the upper arm/leg, the middle paired long bones of forearm/shin, and the distal hand/foot plate with digits comprising the autopod.

This project focuses on how such diversity emerges and is codified in the genome. We compare genomic sequences from different species and search for changes that are related to morphological diversity. Based on our knowledge about mutational mechanisms in human disease, we hypothesize that similar processes can lead to evolutionary changes, neofunctionalization and the development of novel traits. In the past years, we have extensively shown that structural variations (deletions, duplications, inversions) can alter gene regulatory landscapes, thereby resulting in ectopic enhancer-promoter contacts and gene misexpression. In an evolutionary context, the rewiring of regulatory information can confer new expression domains and new functions to a gene without changing the specificities of the protein itself. Such changes can have drastic effects and are thus prime candidates for natural selection.

We use the Iberian mole, Talpa occidentalis, as a model of study because it presents very specific and unique traits, including high tolerance to low O2 levels, very small hypoplastic eyes, forelimb polydactyly and the presence of testis-like tissue in females. In fact, moles are the only case of true hermaphroditism in mammals (females develop testes and ovaries (ovotestis)).

We use genomic approaches, including whole genome sequencing with short and long read technologies and a variety of functional assays (RNAseq, ChIP-seq for histone modifications, ATAC-seq) to investigate genetic changes that occur through evolution and to detect those that might be linked to the phenotype of interest. In a more global context, by comparing non-model species, like moles, with other close-related or more distant organisms, we want to investigate common mechanisms of changes in gene regulation and their contribution to evolution and the acquisition of traits.

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