# Natural selection and recombination rate variation shape nucleotide polymorphism across the genomes of three related Populus species

## TL;DR

This study compares genetic variation and evolutionary forces in three Populus tree species to understand how they shape genomic diversity.

## Contribution

The first comparative population genomic study among closely related forest tree species, revealing how evolutionary forces shape genomic variation.

## Key findings

- P. tremuloides shows the highest genome-wide variation and fastest linkage disequilibrium decay.
- Pervasive natural selection correlates neutral polymorphism with recombination rate in all three species.
- Linked selection patterns differ between genic and intergenic regions within each species.

## Abstract

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome re-sequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum and population-scaled recombination rates in three species of Populus: P. tremula, P. tremuloides and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, both due to purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination are largely explaining the disparate magnitudes and signatures of linked selection we observe among species. The present work provides the first phylogenetic comparative study at genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.