Evolutionary history of the mediterranean Pinus halepensis-brutia species complex using gene-resequencing and transcriptomic approaches

Olsson, Sanna; Lorenzo, Zaida; Zabal‐Aguirre, Mario; Piotti, Andrea; Vendramin, Giovanni G.; González‐Martínez, Santiago C.; Grivet, Delphine

doi:10.1007/s11103-021-01155-7

Cited by 10 publications

(6 citation statements)

References 74 publications

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“…This provides a reference of how strong selection can be at the microgeographical scale for single loci. The differences among species are probably driven by the observed differences in genome-wide background diversity structure, as captured by our analysis of historical demography, as the two pines show historically smaller effective sample sizes and historical bottlenecks, unlike fir and cedar (see also Budde et al, 2017;Olsson et al, 2021). It is worth noting that the recently introduced (and therefore recently diverged) C. atlantica populations show as large estimates of selection as longer established populations, suggesting that selection operated indeed not only over short distances, but also at short timescales (Saleh et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

“…We sampled stands with strongly different demographic patterns: (i) likely to have been stable on the long term for A. alba , as these stands belong to a biogeographical sector with long‐standing presence of the species (Scotti‐Saintagne et al, 2021); (ii) recently introduced from a genetically diverse seed source and potentially having adapted to new conditions over few generations for C. atlantica (Lefèvre et al, 2004); and (iii) belonging to pioneer species, and therefore having probably undergone repeated colonization events ( P. halepensis : Ruiz Daniels et al, 2019, Olsson et al, 2021, Vendramin et al, 2021; P. pinaster : Bucci et al, 2007). To take these diverse stories into account in our analyses, we estimated historical demographic transitions and used them in population models to control for their effects on genetic diversity patterns as explained below.…”

Section: Methodsmentioning

confidence: 99%

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Common microgeographical selection patterns revealed in four European conifers

et al. 2022

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Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computationinferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains withinpopulation diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Common microgeographical selection patterns revealed in four European conifers

et al. 2022

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“…Pinus canariensis showed a gradual expansion starting c. 0.23 Ma, while P. halepensis declined sharply from 0.53 to 0.15 Ma followed by a recovery during the LGP. This strong bottleneck in P. halepensis is also discovered by Olsson et al (2021).…”

Section: Demographic Historymentioning

confidence: 71%

Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow

Zhao,

Gao,

Hall

et al. 2024

New Phytologist

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Summary Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers with 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil‐calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.

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“…This was shown in several species where the native genetic population structure was significantly altered as a consequence of intense seed exchanges (Jansen et al, 2017) and transfer of material among different regions or countries (Chen et al, 2019;Jansen et al, 2019;Raffl et al, 2018), which can pontentially affect adaptation (Milesi et al, 2019). By contrast, despite the use of FRM in afforestation, a clear structure of the genetic diversity of wild populations is still evident in others species (Bucci et al, 2007;Faivre-Rampant et al, 2016;Olsson et al, 2021;Scotti-Saintagne et al, 2019). In our study, the overall genetic diversity of the selected material slightly differed from that of the reference natural population, as in the study by Eklöf et al (2021).…”

Section: Discussionmentioning

confidence: 99%

“…For both species, a specific design was developed targeting 12,000 polymorphic positions available from previous studies. In particular, for P. halepensis we used SNP data in Olsson et al (2021) and the reference transcriptome in Pinosio et al (2014), while for P. nigra we used SNP data and the reference transcriptome in Olsson et al (2020) complemented with thirteen transcriptomic contigs corresponding to genes of interest used in Scotti-Saintagne et al (2019). Libraries were prepared following the standard protocol for the 'Ovation® Target Enrichment' (NuGEN Technologies).…”

Section: Genotypingmentioning

confidence: 99%