Project description:The great tit is a widely studied passerine bird species in ecology that, in the past decades, has provided important insights into speciation, phenology, behavior and microevolution. After completion of the great tit genome sequence, a customized high density 650k SNP array was developed enabling more detailed genomic studies in this species.
Project description:Ribosome profiling (Ribo-seq) and matched RNA sequencing (RNA-seq) data for three major mammalian organs (brain (cerebrum), liver, and testis) from five representatives of the three main mammalian lineages: human, rhesus macaque, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken; henceforth referred to as “chicken”), to be used as an evolutionary outgroup.
Project description:We use ZooMS to obtain secure species identifications of key specimens of early domesticated fauna from South Africa, dating to ca. 2000 BP. Because it can be difficult to distinguish between fragmentary remains of early domesticates (sheep) and similar-sized local wild bovids (grey duiker, grey rhebok, springbok) based on morphology alone, we explore the use of biomolecular methods to make these distinctions. As well as the traditional method of analysing bone fragments, we show the utility of minimally destructive sampling methods such as PVC eraser and polishing films for successful ZooMS identification. We also show that collagen extracted more than 25 years ago for the purpose of radiocarbon dating can yield successful ZooMS identification. Our study demonstrates the importance of developing appropriate regional frameworks of comparison for future research using ZooMS as a method of biomolecular species identification on archaeological faunal assemblages. We confirm that the specimen from the site of Spoegrivier dated to 2105±65 BP is indeed a sheep. This is the earliest directly dated evidence of domesticated animals in southern Africa.
Project description:RNA sequencing (RNA-seq) was used to annotate chimpanzee, gorilla, gibbon, and marmoset genome and transcript isoforms in adult testis. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
