Exploratory analysis of multiple traits co-adaptations in the population history

Abstract

18A variable environment affects the physiological states of individuals and, in the long run, 19 modifies their shapes. These changes, together with geographic barriers, generate 20 population structure. Here, we propose a graphical representation of significant associations 21 between genes, environments, and traits. A unique feature of the graph is the node of 22 genome FST. The subnetwork around this node suggests the cause and the effects of 23 population structure and segregation. A global structure of the graph enables to grasp a 24 comprehensive picture of adaptation to the environment. Focused look at the neighbors of 25 the environmental factors identifies the adaptive traits and the genetic background that 26 supported the adaptation of the traits. Isolated nodes express genetic differentiations that 27 are not explained by the population structure, implying the presence of some unrecognized 28 environmental factor. We show the potential usefulness of our graphical representation by a 29 detailed analysis of public dataset of wild poplar. 30 31 KEYWORDS 32 FST; environmental adaptation; genome scan; SNPs 33 34 35 3 Living organisms are adapted to their environment. This environmental adaptation can 36 create significant differences in phenotypes and traits among populations of a species. For 37 example, populations of sockeye salmon exhibit diversity in regards to life history traits 38 such as spawning time and habitat, adult body size and shape, rearing time in freshwater 39 and seawater, and adaptation to local spawning and rearing habitats within complex lake 40 systems (Hilborn et al. 2003). Populations of walking-stick insects have diverged in body 41 size, shape, host preference and behavior in parallel with the divergence of their host-plant 42 species (Nosil et al. 2002). Aridity gradients may be the cause of geographically structured 43 populations of Poaceae characterized by cytotype segregation of diploids and 44 allotetraploids (Manzaneda et al. 2012). When correlated with variation in environmental 45 factors over local populations, such variation in traits and phenotypes can offer an 46 opportunity for understanding natural selection processes (Coop et al. 2010). Adaptation to 47 environmental factors can change traits and phenotypes of a species, thereby creating 48 population structure. Geographical isolation, which can lead to reproductive isolation and 49 consequent differences in allele frequencies, also contributes to population structuring 50 (Wright 1965). Population structure needs to be considered when analyzing correlations 51 among genes, traits and environmental factors across population samples taken from a wide 52 range of geographical regions. 53 54Genome-wide association studies (GWASs) are widely used to identify associations 55 between genes and traits/environments (Visscher et al. 2017). When data are obtained from 56 a metapopulation exhibiting population structure, the effect of genotypes can be inferred by 57 eliminating population structure effects (Devlin a...