DOI: 10.5061/dryad.280gb5mth
title: Environmental and serotiny data of Pinus halepensis

description: Many plants undergo adaptation to fire. Yet, as global change is
 increasing fire frequency worldwide, our understanding of the genetics of
 adaptation to fire is still limited. We studied the genetic basis of
 serotiny (the ability to disseminate seed exclusively after fire) in the
 widespread, pioneer Mediterranean conifer Pinus halepensis Mill., by
 linking individual variation in serotiny presence and level to fire
 frequency and to genetic polymorphism in natural populations. After
 filtering steps, 885 Single Nucleotide Polymorphisms (SNPs) out of 8,000
 SNPs used for genotyping were implemented to perform an in situ
 association study between genotypes and serotiny presence and level. To
 identify serotiny-associated loci, we performed random forest analyses of
 the effect of SNPs on serotiny levels, while controlling for tree size,
 frequency of wildfires, and background environmental parameters. Serotiny
 showed a bimodal distribution, with serotinous trees more frequent in
 populations exposed to fire in their recent history. Twenty-two SNPs found
 in genes involved in stress tolerance were associated with
 presence-absence of serotiny while thirty-seven found in genes controlling
 for flowering were associated with continuous serotiny variation. This
 study shows the high potential of P. halepensis to adapt to changing fire
 regimes, benefiting from a large and flexible genetic basis of trait
 variation.
description: Overall, 10 populations of
 <em>P.
 halepensis</em> were
 selected according to two fire modalities, half located in areas that were
 fire-free from 1959 until 2018 (“No-Fire” modality populations, PHNF) and
 the other half in areas having suffered at least one fire (“Fire” modality
 populations, PHF) during the same time period. The pairs “Fire” -
 “No-Fire” were located between 5 and 25 kilometers apart in order to
 minimize genetic divergence caused solely by drift (Lotterhos &
 Whitlock, 2015). The populations were sampled in sites where the past land use was the same in order to
 mitigate the impact of soil conditions on trait variation (See Romero
 & Ganteaume 2020). In the current work, the sampling occurred in
 recent forests (as opposed to ancient forests that could have already been
 mapped in the 18th–19th centuries), mostly resulting from land abandonment
 that can provide adequate conditions for regeneration in the absence of
 fire. In each population,
 19 to 20 mature and dominant trees, between 15 and 30 years old (on
 average 22.03 ± 3.1 years old), were sampled. In areas undergoing fires
 during the past 60 years, we only sampled populations when at least 10
 years had elapsed since the last fire event in order to be sure of the
 sexual maturity of the trees that have grown post-fire (Santos del Blanco
 et al., 2010). Furthermore, in order to reduce environmental differences between populations, we selected sample sites with as homogeneous environmental conditions as possible (slope, exposure, elevation, and past land use; see Table S1). However, Romero & Ganteaume (2020) found a significant effect on trait variation, working on the same database as the one used in the current study. This effect has therefore to be accounted for in the analyses (see below).  Serotiny measurements were carried out following Budde et al. (2014). Using binoculars, we counted, on each tree, 20 mature cones (older than three years) on healthy branches, avoiding dominated trees and those with a diameter smaller than 10 cm. Measurements were performed during the summer (June – July 2018), at least 48 h after a rain event occurred to avoid counting cones closed due to high relative humidity. Tree serotiny level was calculated as the number of closed cones divided by the total number of cones (on 192 trees).