Genomic analysis of wild and captive chimpanzee populations from non-invasive samples using target capture methods

Resumen

Abstract Wild chimpanzee populations are considered to be under threat of extinction due to the damaging consequences of human impact into their natural habitat and illegal trade. Conservation genomics is an emerging field that has the potential to guide conservation efforts not only in the wild (in situ) but also outside their natural range (ex situ). In this thesis, we have explored to which extent target capture methods on specific genomic regions can provide insights into chimpanzee genetic diversity in captive and wild populations. Specifically, we have characterized the ancestry and inbreeding of 136 European captive chimpanzees to aid their management in captivity and inferred the origin of 31 confiscated individuals from illegal trade by sequencing ancestry informative SNPs. Also, we have examined molecular strategies to maximize the library complexity in target capture methods from fecal samples so they can be applied in large-scale genomic studies. Finally, we have captured the chromosome 21 from 828 fecal samples collected across the entire extant chimpanzee range. As a result of our high-density sampling scheme, we have found strong evidence of population stratification in chimpanzee populations and we have discovered new local genetic diversity that is linked to its geographic origin. Finally, with this newly generated dataset and fine-grained geogenetic map, we have implemented a strategy for the geolocalization of chimpanzees which has a direct conservation application.