Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals

Abstract

Background: In response to ecological niche of domestication, domesticated mammals and birds developed adaptively phenotypic homoplasy in behavior modifications like fearlessness, altered sociability, exploration and cognition, which partly or indirectly result in consequences for economic productivity. Such independent adaptations provide an excellent model to investigate molecular mechanisms and patterns of evolutionary convergence driven by artificial selection. Results: First performing population genomic and brain transcriptional comparisons in 68 wild and domesticated chickens, we revealed evolutionary trajectories, genetic architectures and physiologic bases of adaptively behavioral alterations. To extensively decipher molecular convergence on behavioral changes thanks to domestication, we investigated selection signatures in hundreds of genomes and brain transcriptomes across chicken and 6 other domesticated mammals. Although no shared substitution was detected, a common enrichment of the adaptive mutations in regulatory sequences was observed, presenting significance to drive adaptations. Strong convergent pattern emerged at levels of gene, gene family, pathway and network. Genes implicated in neurotransmission, semaphorin, tectonic protein and modules regulating neuroplasticity were central focus of selection, supporting molecular repeatability of homoplastic behavior reshapes. Genes at nodal positions in trans-regulatory networks were preferably targeted. Consistent down-regulation of majority brain genes may be correlated with reduced brain size during domestication. Up-regulation of splicesome genes in chicken rather mammals highlights splicing as an efficient way to evolve since avian-specific genomic contraction of introns and intergenics. Genetic burden of domestication elicits a general hallmark. The commonly selected genes were relatively evolutionary conserved and associated with analogous neuropsychiatric disorders in human, revealing trade-off between adaption to life with human at the cost of neural changes affecting fitness in wild.

On taming the effect of transcript level intra-condition count variation during differential expression analysis: a story of dogs, foxes and wolves

“…Up until recently, almost no gene overlap had been observed between gene expression profiles involving pairs of domesticated and wild animals [34]. However, a recently published paper performing population genomic and brain transcriptional comparisons in seven bird and mammal domesticated species has revealed a strong convergent pattern in genes implicated in neurotransmission and neuroplasticity [68]. These functions are compatible with those found in our analysis.…”

“…The copyright holder for this preprint this version posted January 24, 2022. ; https://doi.org/10.1101/2022.01.24.477470 doi: bioRxiv preprint performing population genomic and brain transcriptional comparisons in seven bird and mammal domesticated species has revealed a strong convergent pattern in genes implicated in neurotransmission and neuroplasticity [68]. These functions are compatible with those found in our analysis.…”

“…All the samples were downloaded from the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EMBL-EBI), covering a wide range of ages, both sex as well as multiple replicate and sequencing strategies (Table S1). We selected these specific case studies because, firstly we were interested in evaluating the effects of TVscript both at intra and inter-study levels and the domestic dog, being a model organism, has an available high-quality reference transcriptome as well as several high-quality RNA-seq datasets generated across different studies; while secondly, we sought to perform a brief exploratory inter-study scan to investigate if the domestication of both dogs and foxes has resulted in the co-expression of a set of common brain genes, relative to their “wild/aggressive” type, since behavioural modifications are considered to have been the first target in domestication [42].…”

Population Genomic Sequencing Delineates Global Landscape of Copy Number Variations that Drive Domestication and Breed Formation of in Chicken

“…Nine RNA sequencing data of cerebrum samples from LXG, SILK, RW, and WL male chickens (two for LXG, RW, and WL respectively and three for SILK) ( Hou et al, 2020 ), as well as two transcriptomes of cerebrum samples from RJFs (one male and one female) with accession numbers SRR306710-306711 ( Brawand et al, 2011 ) were downloaded and analyzed together. The clean sequencing data were mapped to the reference genome (galGal4) by TopHat v2.0.13 ( Trapnell et al, 2009 ).…”

Novel 61-bp Indel of RIN2 Is Associated With Fat and Hatching Weight Traits in Chickens

“…In this study, we analyzed whole-genome sequence data, which has been deposited in the archive of the Beijing Institute of Genomics 1 under accession number CRA000005 ( Hou et al, 2020 ). Chicken RIN2 is located on chromosome 3 and consists of 20 exons, encoding an 836 amino acid protein.…”