Landscape Genomics Pipeline

Scripts for Landscape Genomics analyses, version 2. Scripts originally prepared by Carolina S. Carvalho, Jeronymo Dalapicolla, Luciana C. Resende-Moreira, Jamille C. Veiga, Brenda Forester, and Rodolfo Jaffé.

This pipeline was designed on Ubuntu 20.04 LTS, using RStudio v1.4.1717, VCFtools v.0.1.16, and R v4.1.0. It is organized in 4 parts:

PART 1 : GENETIC STRUCTURE AND GENETIC DIVERSITY

PART 2 : ISOLATION BY DISTANCE AND FINE-SCALE SPATIAL GENETIC STRUCTURE

PART 3 : ISOLATION BY RESISTANCE USING MLPE MODELS

PART 4 : LOCAL ADAPTATION ANALYSES; IDENTIFICATION OF CANDIDATES LOCI UNDER SELECTION

For a similar pipeline without using VCFtools v.0.1.16, check our Populational Genomics Pipeline

How to cite:

Part 1, 2 and 3:

Dalapicolla, J., do Prado, J. R., Percequillo, A. R., & Knowles, L. L. (2021). Functional connectivity in sympatric spiny rats reflects different dimensions of Amazonian forest‐association. Journal of Biogeography, 48(12), 3196-3209.

Genomic Datasets

Part 4:

Carvalho, C. S., Forester, B. R., Mitre, S. K., Alves, R., Imperatriz‐Fonseca, V. L., Ramos, S. J., ... & Jaffé, R. (2021). Combining genotype, phenotype, and environmental data to delineate site‐adjusted provenance strategies for ecological restoration. Molecular Ecology Resources, 21(1), 44-58.

Genomic Datasets