Landscape genomics

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Introduction

« Landscape genomics » sounds like a work by Eduardo Kac. This somewhat post-modern term actually refers to a scientific field that has expanded over the past decade.

Environmental conservation issues have urged a need to better understand and describe species and populations on Earth. Recently, progress in sequencing technologies made it possible to refine this understanding through genomics. Understanding and describing populations of living organisms in a given environment by exploiting sequencing data is the ultimate goal of landscape genomics. So this article is an introduction of this field.

Populations : an ambiguous definition

Individuals from a same species, unless they are clones, are all slightly differents from each others. In breeding conditions where parents and genotypes are known, it is possible to idendificate accurately relationships between genetic diversity and phenotype. However, in other conditions where these information about pedigree are not available (for instance a study about a wild species with few related information) so it is necessary to infer this genetic structure.

Indeed, a species - let's take the example of an animal species - can be composed of several populations.

Speaking of populations, two very thorough researchers, Oscar Gaggiotti & Robin Waples, have listed 17 very exact definitions of this concept. The two authors concluded that with so many definitions for the same concept, based on the same observations, different researchers could reach different or even contradictory results. What is a population? There is no correct answer, the definition depends on the context. In the context of landscape genomics, a population is a group of individuals of the same species capable of interacting at the time of reproduction. A population is therefore defined according to spatial, genetic and temporal criteria. Indeed, not all individuals will have the opportunity to interbreed due to geographic distance, habitat heterogeneity or other factors.

Hardy and Weinberg defined the equilibrium state of an ideal population in which genetic diversity would tend towards a constant value. The conditions necessary for such an equilibrium are:

In reality, the ideal population does not exist, but the knowledge of this theoretical equilibrium state of a population's genetic diversity makes it possible to determine the effects of external factors on a real population's genetic diversity. In other words, the way in which a population is not ideal allows to know how the natural habitat affects the genetic structure of this population.