Molecular Footprints of Local Adaptation in Two Mediterranean Conifers

Abstract

This study combines neutrality tests and environmental correlations to identify nonneutral patterns of evolution in candidate genes related to drought stress in two closely related Mediterranean conifers, Pinus pinaster Ait. and P. halepensis Mill. Based on previous studies, we selected twelve amplicons covering six candidate genes that were sequenced in a large sample spanning the full range of these two species. Neutrality tests relatively robust to demography (DHEW compound test and maximum likelihood multilocus Hudson-Kreitman-Aguadé test) were used to detect selection events at different temporal scales. Environmental associations between variation at candidate genes and climatic variables were also examined. These combined approaches detected distinct genes that may be targeted by selection, most of them specific to only one of the two conifers, despite their recent divergence (<10 Ma). An exception was 4-coumarate: CoA ligase, a gene involved in the production of various important secondary products that appeared to play a role in local adaptation processes of both pines. Another remarkable result was that all significant environmental correlations involved temperature indices, highlighting the importance of this climatic factor as a selective driver on Mediterranean pines. The ability to detect natural selection at the DNA sequence level depends on the nature and the strength of the selection events, on the timescale at which they occurred, and on the sensitivity of the methods to other evolutionary forces that can mimic selection (e.g., demography and population structure). Using complementary approaches can help to capture different aspects of the evolutionary processes that govern molecular variation at both intra-and interspecific levels.

Signatures of volcanism and aridity in the evolution of an insular pine (Pinus canariensis Chr. Sm. Ex DC in Buch)

“…It is noteworthy that two genes involved in the responses to drought (lp3-3) and lignin development showed two SNPs each, potentially subjected to balancing selection. These SNPs did not show any correlation with aridity gradients in agreement with the lack of selection evidence found for this candidate gene in the Mediterranean pines P. pinaster and P. halepensis (Grivet et al, 2011).…”

“…Genomic DNA was extracted from the needles using the Invisorb Spin Plant Mini Kit (STRATEC Molecular, Berlin, Germany). Amplicons from eight nuclear genes (Table 2) were obtained using previously published primer pairs transferred from P. pinaster (Grivet et al, 2011), P. sylvestris (Palmé et al, 2008), P. taeda (Brown et al, 2004) and from several species of subgenus Strobus (Tsutsui et al, 2009 …”

“…One way to demonstrate the action of selection and thus local adaptation is to test for clinal genetic variation along environmental gradients (Grivet et al, 2011;Mosca et al, 2012). Genetic patterns of local adaptation can be detected by identifying correlations between patterns of allele frequencies and environmental variables, which can act as selective agents promoting natural selection (Hancock et al, 2010).…”

Considering evolutionary processes in adaptive forestry

“…Nowadays, thanks to the emergence and evolution of the so-called next generation sequencing techniques and related bioinformatics (Metzker 2009;Kircher and Kelso 2010), full-genome sequencing, reduced-representation sequencing and targeted sequencing are in progress not only for model species but also for nonmodel species where molecular monitoring is becoming worth considering from scratch. Evidence of genetic changes at molecular level in trees has recently emerged from the direct study of genome wide DNA polymorphisms: evidence of the correlations between genotype frequencies and environmental gradients (Eckert et al 2010) or climaterelated traits (Grivet et al 2011), sometimes completed with functional information on the detected genes (Holliday et al 2010). See also Alberto et al (2013) for a recent review of single nucleotide polymorphisms associated to climate related traits in trees.…”

The population genomic signature of environmental selection in the widespread insect-pollinated tree species Frangula alnus at different geographical scales

“…In contrast, tree genera for which genomic resources are available (for example, Pinus sp., Picea sp., Eucalyptus sp., and Populus sp.) have been frequently examined for patterns of environmental selection (for example, Grivet et al, 2011;Prunier et al, 2011;Keller et al, 2011, Bradbury et al, 2013Steane et al, 2014). Hence, although genomic markers provide valuable information on the capacity of tree species to respond to climatic cues, little is known about the relative effects of climate and geographical scale on the genomic differentiation in non-model tree species.…”