Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness

Abstract

Domestication has resulted in immense phenotypic changes in animals despite their relatively short evolutionary history. The European rabbit is one of the most recently domesticated animals, but exhibits distinct morphological, physiological and behavioural differences from their wild conspecifics. A previous study revealed that sequence variants with striking allele frequency differences between wild and domestic rabbits were enriched in conserved non-coding regions, in the vicinity of genes involved in nervous system development. This suggests that a large proportion of the genetic changes targeted by selection during domestication might affect gene regulation. Here, we generated RNA-sequencing data for four brain regions (amygdala, hypothalamus, hippocampus and parietal/temporal cortex) sampled at birth and revealed hundreds of differentially expressed genes (DEGs) between wild and domestic rabbits. DEGs in amygdala were significantly enriched for genes associated with dopaminergic function and all 12 DEGs in this category showed higher expression in domestic rabbits. DEGs in hippocampus were enriched for genes associated with ciliary function, all 21 genes in this category showed lower expression in domestic rabbits. These results indicate an important role of dopamine signalling and ciliary function in the evolution of tameness during rabbit domestication. Our study shows that gene expression in specific pathways has been profoundly altered during domestication, but that the majority of genes showing differential expression in this study have not been the direct targets of selection.

Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation

“…In this work, we utilized publicly available independent experimental RNA-Seq datasets from transcriptomes of domestic animals compared with their wild congeners [23][24][25][26][27][28][29]; these data were statistically significant according to Fisher's Z-test, with corrections for multiple comparisons (P ADJ < 0.05), as published by their authors (see, the PubMed database [52]) and outlined in Table 2. As a result, 2347 DEGs were analyzed, which represented seven tissues of seven domestic animal species and seven of their wild congeners, as readers can see in in the last row of Table 2.…”

Did Dog Domestication Contribute to Language Evolution?

“…In turn, low cortisol levels increase social learning capabilities and promote the activity of the prefrontal cortex, contributing to improving executive functions like cognitive inhibition, ToM, working memory, and language skills (see Pörtl and Jung, 2017 , 2019 for details). A second mechanism of interest concerns the dopamine reward system, which exhibits differences in domesticated animals compared to their wild conspecifics ( Komiyama et al, 2014 ; Sato et al, 2020 ). Changes in dopamine signaling might have thus contributed not only to more diverse and complex vocal signals in both dogs and humans as noted in the Introduction, but also to potentiating dog-human co-adaptation, and perhaps co-evolution.…”

Positive selection of skeleton-related genes during duck domestication revealed by whole genome sequencing

“…Domestication is the process in which a wild species is artificially selected to be domestic, with many traits changed to meet human requirements. Various features distinguish domestic animals from their wild ancestors, and it is well-documented that the genetic architecture underlying variations in phenotypic traits (such as morphology in chickens [ 1 , 2 ], pigs [ 3 – 5 ], and pigeons [ 6 , 7 ]; feather color [ 8 , 9 ]; neurological aspects such as tameness in companion animals [ 10 – 12 ]; and physiological aspects such as starch digestibility in dogs [ 13 ] and reproduction in chickens [ 14 , 15 ]) are altered dramatically in domestic animals compared to those in their wild ancestors.…”