The Foundations of Genodynamics: The Development of Metrics for Genomic-Environmental Interactions

TL;DR

This paper develops a quantitative framework using information theory and thermodynamics to analyze genomic-environment interactions, focusing on SNPs and haploblocks in stable populations.

Contribution

It introduces a normalized information content metric and a thermodynamic analogy to characterize genomic diversity and environmental influences.

Findings

NIC correlates inversely with environmental driving forces

Genomic energies can be assigned to alleles and haplotypes

Framework enables comparison of population genomes across environments

Abstract

Single nucleotide polymorphisms (SNPs) represent an important type of dynamic sites within the human genome. These common variants often locally correlate into more complex multi-SNP haploblocks that are maintained throughout generations in a stable population. The information encoded in the structure of common SNPs and SNP haploblock variation can be characterized through a normalized information content (NIC) metric. Such an intrinsic measure allows disparate regions of individual genomes and the genomes of various populations to be quantitatively compared in a meaningful way. Using our defined measures of genomic information, the interplay of maintained statistical variations due to the environmental baths within which stable populations exist can be interrogated. We develop the analogous "thermodynamics" characterizing the state variables for genomic populations that are stable under stochastic environmental stresses. Since living systems have not been found to develop in the absence of environmental influences, we focus on describing the analogous genomic free energy measures in this development. The intensive parameter describing how an environment drives genomic diversity is found to depend inversely upon the NIC of the genome of a stable population within that environment. Once this environmental potential has been determined from the whole genome of a population, additive state variables can be directly related to the probabilities of the occurrence of given viable SNP based units (alleles) within that genome. This formulation allows the determination of both population averaged state variables as well as the genomic energies of individual alleles and their combinations. The determination of individual allelic potentials then should allow the parameterization of specific environmental influences upon shared alleles across populations in varying environments.