Crassulacean acid metabolism (CAM) is a water‐efficient photosynthetic strategy involving a coordinated suite of complex traits including metabolic, anatomical and regulatory aspects that shift across the diel cycle. While CAM has evolved repeatedly in land plants, the evolutionary routes enabling this convergence remain elusive. Whereas the same core CAM (de)carboxylation genes are consistently involved, a key question is whe...

Speciation, the continuous process by which new species form, is often investigated by looking at the variation of nucleotide diversity and differentiation across the genome (hereafter genomic landscapes). A key challenge lies in how to determine the main evolutionary forces at play shaping these patterns. One promising strategy, albeit little used to date, is to comparatively investigate these genomic landscapes as progressio...

Introgression can introduce novel genetic variation at a faster rate than mutation alone and result in adaptive introgression when adaptive alleles are maintained in the recipient genome over time by natural selection. A previous study from our group demonstrated adaptive introgression from Populus balsamifera into P. trichocarpa in a target genomic region. Here we expand our local ancestry analysis to the whole genome of both...

Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro‐ and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine th...

Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land‐use change have affected contemp...

Speciation often involves repeated episodes of genetic contact between divergent populations before reproductive isolation ( RI ) is complete. Whole‐genome sequencing ( WGS ) holds great promise for unravelling the genomic bases of speciation. We have studied two ecologically divergent, hybridizing species of the ‘model tree’ genus Populus (poplars, aspens, cottonwoods), Populus alba and P. tremula , using >8.6 million single...

Asexual reproduction is a common and fundamental mode of reproduction in plants. Although persistence in adverse conditions underlies most known cases of clonal dominance, proximal genetic drivers remain unclear, in particular for populations dominated by a few large clones. In this study, we studied a clonal population of the riparian tree Populus alba in the Douro river basin (northwestern Iberian Peninsula) where it hybridi...

Natural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies in Populus trichocarpa , a keystone tree species, indicated genomic footprints of admixture with its sister species Populus balsamifera and identified candidate genes for local adaptation. Here, we explored the patterns of introgression and signals of local adaptation in...

Natural hybrid zones have proven to be precious tools for understanding the origin and maintenance of reproductive isolation ( RI ) and therefore species. Most available genomic studies of hybrid zones using whole‐ or partial‐genome resequencing approaches have focused on comparisons of the parental source populations involved in genome admixture, rather than exploring fine‐scale patterns of chromosomal ancestry across the ful...

In the context of potential interspecific gene flow, the integrity of species will be maintained by reproductive barriers that reduce genetic exchange, including traits associated with prezygotic isolation or poor performance of hybrids. Hybrid zones can be used to study the importance of different reproductive barriers, particularly when both parental species and hybrids occur in close spatial proximity. We investigated the i...

The co‐occurrence of geographical structure in herbivore communities, metabolomes and defence genes in forest trees has been analysed in the context of ‘geographical mosaics’ of coevolution. A deeper understanding of these important issues will require full integration of a ‘genomic mosaic’ view of species into community ecology.

The drivers of species diversification and persistence are of great interest to current biogeography, especially in those global biodiversity ‘hotspots’ harbouring most of Earth's animal and plant life. Classical multispecies biogeographical work has yielded fascinating insights into broad‐scale patterns of diversification, and DNA ‐based intraspecific phylogeographical studies have started to complement this picture at much f...

Interspecific hybridization may enhance the capacity of populations to adapt to changing environments, and has practical implications for reforestation. We use genome‐wide estimates of admixture and phenotypic traits for trees in a common garden to examine the extent and direction of gene flow across a P icea hybrid zone, testing assumptions of the bounded hybrid superiority and tension zone models of hybrid zone maintenance....

Recent advances in population genomics have triggered great interest in the genomic landscape of divergence in taxa with ‘porous’ species boundaries. One important obstable of previous studies of this topic was the low genomic coverage achieved. This issue can now be overcome by the use of ‘next generation’ or short‐read DNA ‐sequencing approaches capable of assaying many thousands of single nucleotide polymorphisms ( SNP s) i...

The maintenance of species barriers in the face of gene flow is often thought to result from strong selection against intermediate genotypes, thereby preserving genetic differentiation. Most speciation genomic studies thus aim to identify exceptionally divergent loci between populations, but divergence will be affected by many processes other than reproductive isolation ( RI ) and speciation. Through genomic studies of recombi...

The hypothesis of gene flow between species with large differences in chromosome numbers has rarely been tested in the wild, mainly because species of different ploidy are commonly assumed to be reproductively isolated from each other because of instantaneous and strong postzygotic barriers. In this study, a broad‐scale survey of molecular variation was carried out between two orchid species with different ploidy levels: Epide...

The two species of the palm genus Howea (Arecaceae) from Lord Howe Island, a minute volcanic island in the Tasman Sea, are now regarded as one of the most compelling examples of sympatric speciation, although this view is still disputed by some authors. Population genetic and ecological data are necessary to provide a more coherent and comprehensive understanding of this emerging model system. Here, we analyse data on abundanc...