Exome Resequencing Reveals Evolutionary History, Genomic Diversity, and Targets of Selection in the ConifersPinus taedaandPinus elliottii

Abstract

Loblolly pine ( Pinus taeda ) and slash pine ( Pinus elliottii ) are ecologically and economically important pine species that dominate many forest ecosystems in the southern United States, but like all conifers, the study of their genetic diversity and demographic history has been hampered by their large genome size. A small number of studies mainly based on candidate-gene sequencing have been reported for P. taeda to date, whereas none are available for P. elliottii . Targeted exome resequencing has recently enabled population genomics studies for conifers, approach used here to assess genomic diversity, signatures of selection, population structure, and demographic history of P. elliottii and P. taeda . Extensive similarities were revealed between these species: both species feature rapid linkage disequilibrium decay and high levels of genetic diversity. Moreover, genome-wide positive correlations for measures of genetic diversity between the species were also observed, likely due to shared structural genomic constraints. Also, positive selection appears to be targeting a common set of genes in both pines. Demographic history differs between both species, with only P. taeda being affected by a dramatic bottleneck during the last glacial period. The ability of P. taeda to recover from a dramatic reduction in population size while still retaining high levels of genetic diversity shows promise for other pines facing environmental stressors associated with climate change, indicating that these too may be able to adapt successfully to new future conditions even after a drastic population size contraction.

Genomics of Clinal Local Adaptation inPinus sylvestrisUnder Continuous Environmental and Spatial Genetic Setting

“…Earlier work has shown that LD decays very rapidly within the P. sylvestris genome ( Dvornyk et al 2002 ; Pyhäjärvi et al 2007 ; Wachowiak et al 2009 ) and also in other conifers such as P. taeda ( Lu et al 2016 ; Acosta et al 2019 ). This study allows for examining longer range patterns of LD than before as in many cases multiple target sequences are positioned within the same scaffold.…”

Genomics of clinal local adaptation inPinus sylvestrisunder continuous environmental and spatial genetic setting

“…Earlier work has shown that LD decays very rapidly within the P. sylvestris genome (Dvornyk, Sirviö, Mikkonen, & Savolainen, 2002;Tanja Pyhäjärvi et al, 2007;Wachowiak et al, 2009) and also in other conifers such as P. taeda (Acosta et al, 2019;Lu et al, 2016). This study allows for examining longer range patterns of LD than before as in many cases multiple target sequences are positioned within the same scaffold.…”

Champions of winter survival: cold acclimation and molecular regulation of cold hardiness in evergreen conifers

“…These historical clues, based on fossil and pollen records, receive further support from and are complemented by the genomic studies now possible due to recent advancements in next-generation sequencing. For example, Pinus taeda and Pinus elliottii, two species that survived in North American Pleistocene refugia, exhibit different levels of genetic diversity, indicating that P. taeda experienced a drastic bottleneck event probably associated with severe freezing during the late Wisconsin glacial interval (30 000-11 000 yr ago), whereas P. elliottii survived relatively unscathed (Acosta et al, 2019). Picea rubens is another North American species with low genetic diversity as well as poor winter cold tolerance, which probably survived in a warm coastal refugium (DeHayes & Hawley, 1992).…”