Ecological genomics and molecular adaptation: state of the Union and some research goals for the near future.

Transcription

1 Ecological genomics and molecular adaptation: state of the Union and some research goals for the near future. Louis Bernatchez Genomics and Conservation of Aquatic Resources Université LAVAL!

2 Molecular ecology: an ever growing field tracking markers development Ecological genetics Population structure Phylogeography Genome scans Mating systems Reproductive success Ecological genomics Modified from Schöterrer 2004

3 Molecular ecology: an ever growing field tracking markers development issues 24 issues 258 pages 5358 pages

4 Ecological genomics and molecular adaptation: back to the future Ecological genetics Population structure Phylogeography Genome scans Mating systems Reproductive success Ecological genomics Modified from Schöterrer 2004

5 Ecological genomics and molecular adaptation: back to the future Richard C. Lewontin

6 What is Ecological genomics? An field of research that seeks to understand the processes by which organisms adapt to their environment. Feder and Mitchell-Olds Studying the biological mechanisms that underlie ecologically important traits. Investigate how these traits affect fitness. Examine the evolutionary processes through which specific traits arise and persist.

7 What is Ecological genomics? Progress from genes to funcitons Generation time (or size)

8 What is Ecological genomics? Gordon Research Conference on Ecological genomics Number of presentations Microbes Plants Invertebrates Fish Others Vertebrates

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10 Ecological genomics : success stories

11 Ecological genomics : success stories

12 The promises of GENOMICS in the NGS era A plethora of SNP studies for the next few years... With SNP development Without SNP development RRL RADseq GBS

13 The promises of GENOMICS in the NGS era and whole genome re-sequencing...

14 The promises of GENOMICS in the NGS era and transcriptomics studies (RNA-seq, microarrays)

15 The promises of GENOMICS in the NGS era and transcriptomics studies (RNA-seq, microarrays) Langfelder et al Biochem. Biophyc. Acta.

16 The challenges ahead I. The way from gene to protein: Structural gene polymorphism Transcription regulation (transcription factors) Slicing regulation (alternative splicing)? RNA transport regulation RNA degradation (interference RNA) Translation regulation (microrna) Proteins modification

17 The challenges ahead II. From protein to function : Phototransduction network in Drosophila: Landry et al.

18 The challenges ahead III. From protein networks to phenotype : Growth metabolism network (simplified)

19 The challenges ahead

20 The challenges ahead Mechanisms of Phenotypic Change Migration Selection Ultimate Drift Mutation Processes that drive the evolution of proximate mecanisms Gene X Environment Proximate Gene X Gene Mechanisms that change phenotype within the lifespan of the individual Phenotype AaBb AaBb

21 A few unsolved issues at the mechanistic molecular level : What are the molecular bases of quantitative genetic variance? Variance in: - Allelic diversity? - Number of real genes? - Levels of gene expression? - Effect of each gene? What is phenotypic plasticity? Environmental effects on: - Switch of genes controlling phenotypes? - Change of gene expression of same genes?

22 A few unsolved issues at the mechanistic molecular level : What are the molecular bases of quantitative genetic variance? Variance in: - Allelic diversity? - Number of real genes? - Levels of gene expression? - Effect of each gene? What is phenotypic plasticity? Environmental effects on: - Switch of genes controlling phenotypes? - Change of gene expression of same genes?

23 Where is the predictive theory about the evolutionary causes and consequences of: - The molecular complexity linking the genotype to the phenotype. - Phenotypic plasticity and reaction norms. - Non genetic inheritance (Epigenetic inheritance, parental effects) Priority no. 1: The need for an extended theory of evolution beyond DNA

24 Ecological genomics and molecular adaptation: some research goals for the near future. Priority no. 2: The need for gene ecological annotation. No matter how much you sequence, annotation of genes currently remains the main limiting factor in making functional infererence. Solution 1. Better data integration to enable ecological associations of genes and genomes. Solution 2. Functional analyses. Pavey, Bernatchez, Aubin-Orth, Landry, TREE (in rev.).

25 Ecological genomics and molecular adaptation: some research goals for the near future.. What are the roles of post-transcriptional regulatory mechanisms to phenotypic diversity and plasticity?. Is there variation in gene network architecture within and between closely related species?. Are the same genes and pathways involved in plastic responses within species and phenotypic divergence among populations? Pavey, Bernatchez, Aubin-Orth, Landry, TREE (in rev.).

26 Ecological genomics and molecular adaptation: some research goals for the near future. Priority no. 3: Phenomics Linking genotype, environment and phenotype Phenotyping across biological diversity The genotype-environment-phenotype map Houle et al Nat. Rev. Gen.

27 Ecological genomics and molecular adaptation: some research goals for the near future. Priority no. 4. Becoming predictive about organismal solutions to cope with environmental heterogeneity Solution 1: Local adaptation Solution 2: Phenotypic plasticity Solution 3 : Balanced polymorphism maintained by spatially varying selection

28 Ecological genomics and molecular adaptation: some research goals for the near future.

29 Ecological genomics and molecular adaptation: some research goals for the near future. Priority no. 5: Ecological systems biology : A holistic approach towards the full integration of multi-dimensional high throughput «omics» measurements

30 Ecological genomics and molecular adaptation: some research goals for the near future. Billions of data points/individual The Holy Trinity of Biology The network of networks

31 Thanks Harry!