Ecological genomics of local adaptation and speciation of bromeliads from neotropical mountains

Abstract

Local adaptation can cause population genetic divergence and culminate in events of ecological speciation. Despite the growing literature on the role of local adaptation in population divergence, the number of these studies in the Neotropics is still incipient, where most of the terrestrial biodiversity is concentrated. The objective of this project is to understand how the process of local adaptation to an altitudinal gradient has contributed to the genetic divergence of bromeliads that occur in mountains in Southeast Brazil. Therefore, we first intend to assemble and annotate the genome on a chromosomal scale, using sequences of PacBio HiFi and OmniC, from a model taxa of our research group, Pitcairnia flammea (Bromeliaceae). Subsequently, individuals from populations distributed along an altitudinal gradient in the Atlantic Forest will be re-sequenced in a medium coverage (15 to 30X) to detect the genomic variation of the species' gene pool, that is, the pangenome. By using a perspective of combining population genomics and pangenome we aim: 1) To understand the role of natural selection, genetic drift and gene flow in population divergence and consequent speciation of the Pitcairnia flammea complex distributed along an altitudinal gradient in the Atlantic Forest;2) to infer the genetic and molecular bases responsible for the local adaptations to the altitudinal gradient and their contribution to the structuring and genetic divergence of these populations of Pitcairnia flammea; 3) To comprehend how variations in SNPs (Single Nucleotide Polymorphism) and in chromosomal structure - SVs (Structural Variation) and PAVs (Presence-Absense Variations) - have contributed to the local adaptation and genetic divergence of Pitcairnia flammea populations. In this way, this project aims to understand how the environment can promote the genomic divergence of locally adapted populations, contributing to the elucidation of the first steps of the speciation process in one of the most biodiverse areas in the world and to make predictions about the resilience of species in the face of changes climate. (AU)