Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers

Abstract

Oaks are dominant forest tree species widely distributed across the Northern Hemisphere, where they constitute natural resources of economic, ecological, social and historical value. Hybridization and adaptive introgression have long been thought to be major drivers of their ecological success. Thus, the maintenance of species barriers remains a key question, given the extent of interspecific gene flow. In this study, we scanned the genomes of four European white oak species for reproductive barriers. We identified the ecological and phylogenic relationships of these species and inferred a long-term strict isolation followed by a recent and extensive postglacial contact. Then, we made use of the tremendous genetic variation among these species (31 million SNPs) to identify genomic regions for reproductive isolation. A literature-based functional annotation of the underlying genes highlighted important functions driving the reproductive isolation between these sister species. These functions were consistent with their ecological preferences and included tolerance to biotic and abiotic constraints. This study holds important implications for the renewal of European forests under global warming.

Comparing Pool‐seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster (Homarus americanus) as a case study

“…All of these factors may ultimately affect demographic inferences (Cutler & Jensen, 2010;Harvey, Smith, & Glenn, 2016). In such cases, Pool-seq has already proven to be an effective and accurate approach to investigate genomewide variations of terrestrial and marine high gene flow species such as oaks (Quercus spp., Leroy et al, 2018), poplar (Populus alba, Stölting et al, 2015;Populus alba, Populus tremula, Christe et al, 2016), Chinese chestnut (Castanea mollissima, LaBonte, Zhao, & Woeste, 2018), sticklebacks (Gasterosteus aculeatus, Guo, DeFaveri, & Sotelo, 2015), Atlantic herring (Clupea harengus, Guo, Li, & Merilä, 2016;Lamichhaney et al, 2012;Martinez Barrio et al, 2016), Atlantic cod (Gadus morhua, Karlsen et al, 2013), and the copepod (Tigriopus californicus, Lima & Willett, 2018). On the other hand, and pending on specific research objectives, quantifying genetic parameters where individual information is required may not always be necessary.…”

Adaptive introgression as a driver of local adaptation to climate in European white oaks

“…These two species display subtle differences in soil preferences when present in the same forest (Timbal & Aussenac, 1996;Eaton et al, 2016), but they also have different climate responses, as suggested by their allopatric (temperature-and precipitation-dependent) distributions at the edge of their ranges. Q. robur extends farther north (up to Finland) and east (up to the Ural Mountains) (see Leroy et al, 2018), and has a higher frequency in wetter climates (Eaton et al, 2016). We suspect that the introgression of Q. robur alleles for genes involved in these differential responses may have contributed to the expansion of Q. petraea populations to higher elevations in the Pyrenees and wetter climates in Ireland.…”

Hardwood Tree Genomics: Unlocking Woody Plant Biology

“…Shortlisted among the ‘botanical horror stories’ (Rieseberg et al, 2006), the Quercus genus constitutes an ideal taxon to investigate the dynamics of lineage diversification along a wide and fluid continuum of speciation. Several efforts to illuminate oak evolutionary histories using population genomic approaches have recently emerged (Ortego et al, 2016, 2018; Leroy et al, 2017, 2018). In European white oaks for example, the best-supported scenario of divergence is consistent with a long-term pervasive effect of interspecific gene flow, with the exception of some narrow genomic regions responsible for reproductive isolation.…”