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Simple Summary Experiences during infancy and as a juvenile are very influential on the lives of primates into adulthood. In this sense, the living conditions of chimpanzees kept as pets or performing in circuses cannot fulfil the three basic requirements needed for these animals to develop properly: adequate functioning of the organism (physical well-being); an optimal emotional state with the absence of sensations such as fear, pain, grief or apathy (mental well-being); and the ability to express species-specific behaviours (social well-being). In this study, we compare the activity budgets of three chimpanzees approximately one-decade post-rescue, to historical activity data before their rehabilitation. We found changes in behavior patterns in accordance with the sanctuary rehabilitation objectives. All chimpanzees improved their social competence by adding new members to their social network. Vigilance behavior also declined, and time spent resting increased when living at the sanctuary. Our results support previous studies conducted with rehabilitated chimpanzees in sanctuaries and highlight the important work of dedicated professionals during the rehabilitation process for these chimpanzees housed in captivity for the rest of their life. Abstract Chimpanzees used as pets and in the entertainment industry endure detrimental living conditions from early infancy onwards. The preferred option for ending their existence as pet or circus chimpanzees is their rescue and transfer to a primate sanctuary that will provide them with optimal living and social conditions, so that they can thrive. In this case study, we had the rare opportunity to compare the activity budgets of three chimpanzees from their time as pets in 2004 to their time living at the MONA sanctuary in 2020, after almost a decade in the centre. We found their behaviour patterns changed in accordance with the sanctuaries’ rehabilitation objectives. Resting periods increased considerably while vigilance simultaneously declined sharply. Moreover, the chimpanzees’ social competence increased as allogrooming became the predominant social behaviour, and agonistic interactions diminished even though they were living within a larger social group at the sanctuary. All three chimpanzees expanded their allogrooming and proximity networks at the sanctuary, which included new group members, but they maintained the closest relationships to those conspecifics who they were rescued with. In conclusion, these findings suggest that the sanctuary environment and social group setting made it possible for these three chimpanzees to improve their social competence and increase their well-being over time.

The genetic basis of phenotypes that have contributed to the adaptation of species and organisms to new environments is a central question in evolutionary genetics. The recent accumulation of genetic variability data has allowed a genome-wide search for different signatures of positive selection which has led to the discovery of hundreds of putative candidate genes that may have played a role in adaptation. However, such hypothesis-free approaches do not reveal either causal variants or the actual biological mechanisms that have made each adaptation possible. Furthermore, the detection of molecular signatures is limited both by the complex architecture of the genome and by the possible polygenic nature of the selected trait. In this thesis, through different evolutionary and functional approaches, we have disentangled the adaptive role of two non-synonymous variants in two different candidate genes encoding for a lymphocyte receptor and a zinc transporter, respectively. In past human adaptation, they were most likely selected as more effective means to fight pathogens. We have also revealed differences in the action of natural selection between different pathways and different coding and non-coding genomic elements in the chimpanzee lineage by analyzing polymorphisms and divergence data together. Thus, the results of this PhD thesis have contributed to detect new instances of genetic adaptation and provide biological explanation to them., La base genética de los carácteres que han contribuido a la adaptación de los organismos y las especies ha sido siempre una pregunta central en biología evolutiva. Gracias a la acumulación masiva de datos de variabilidad genética, en los últimos años se ha podido detectar en el genoma diferentes señales de selección positiva y también localizar cientos de genes candidatos que han podido tener un papel en la adaptación de las poblaciones a diferentes ambientes. Sin embargo en estos estudios, donde no hay una hipótesis a priori, se desconoce qué variantes dentro de estos genes fueron realmente las que proporcionaron una ventaja selectiva y por qué. Además, la compleja arquitectura del genoma y la naturaleza poligénica de muchos carácteres hace que sea difícil detectar casos más complejos de adaptación. En esta tesis se intenta resolver algunos de estos problemas. En primer lugar, mediante un enfoque evolutivo y funcional, hemos descifrado el rol adaptativo de dos variantes genéticas, una en un receptor linfocitario y la otra en un transportador de zinc, que probablemente fueron seleccionadas por conferir resistencia a patógenos. En segundo lugar, mediante el análisis de datos de polimorfismo y divergencia conjuntamente, también hemos detectado distintos mecanismos de acción de la selección natural en distintos pathways y entre elementos codificantes y elementos no codificantes reguladores en chimpancé.

En el gen de la proteïna priònica, o PRNP, hem observat que el particular patró de variació que hem trobat basant-nos en dades de seqüenciació en humans es deu a selecció positiva, i que el mètode utilitzat per detectar selecció és crític. Utilitzant dades basades en SNPs es pot introduir un biaix al aplicar tests de neutralitat basats en diversitat de seqüències, i això pot portar a conclusions errònies. A més, hem vist que els polimorfismes en els codons 129 i 219 presenten gran diferències de freqüència en diferents poblacions humanes i també hem vist que aquestes posicions estan fixades en ximpanzés. La variació trobada en controls ha estat comparada amb el patró de variació existent en pacients per la mateixa regió. La reseqüenciació del gen PRNP en un gran nombre de mostres humanes i de ximpanzés ens ha permès obtenir un gran nombre d´informació d´aquest gen., In the prion gene or PRNP, we have observed that the particular pattern of variation that we have found in this gene based on sequencing data in humans is due to positive selection, and that the method and the approach used to detect this selection critical. Ascertainment bias can be introduced by using SNP data and applying neutrality tests based on sequence diversity, therefore leading to anomalous conclusions being drawn. Moreover, we have seen that polymorphisms in codon 129 and 219 have big differences in frequency in different human populations and we have also seen that these positions are fixed in chimpanzees. The normal variation that we found in controls have been then compared with patients for the same region. The resequencing of PRNP in a very large sample of humans and chimpanzees has provided a great deal of information on this gene.