Premise of the Study Successful establishment of neopolyploids, and therefore polyploid speciation, is thought to be contingent on environmental niche shifts from their progenitors. We explore this niche shift hypothesis in the obligate outcrosser Arabidopsis arenosa complex, which includes diploid and recently formed autotetraploid populations. Methods To characterize the climatic niches for both cytotypes in Arabidopsis arenosa, we first gathered climatic data from localities with known ploidy types. We then estimated the climatic niches for diploids and autotetraploids and calculated niche overlap. Using this niche overlap statistic, we tested for niche equivalency and similarity. We explored differences in niches by estimating and comparing niche optimum and breadth and then calculated indices of niche expansion and unfilling. Key Results Climatic niche overlap between diploids and autotetraploids is substantial. Although the two niche models are not significantly divergent, they are not identical as they differ in both optimum and breadth along two environmental gradients. Autotetraploids fill nearly the entire niche space of diploids and have expanded into novel environments. Conclusions We find climatic niche expansion but not divergence, together with a moderate change in the niche optimum, in the autotetraploid lineage of Arabidopsis arenosa. These results indicate that the climatic niche shift hypothesis alone cannot explain the coexistence of tetraploid and diploid cytotypes.

Reinforcement is the process by which selection against hybridization increases reproductive isolation between taxa. Much research has focused on demonstrating the existence of reinforcement, yet relatively little is known about the genetic basis of reinforcement or the evolutionary conditions under which reinforcement can occur. Inspired by reinforcement’s characteristic phenotypic pattern of reproductive trait divergence in sympatry but not in allopatry, we discuss whether reinforcement also leaves a distinct genomic pattern. First, we describe three patterns of genetic variation we expect as a consequence of reinforcement. Then, we discuss a set of alternative processes and complicating factors that may make the identification of reinforcement at the genomic level difficult. Finally, we consider how genomic analyses can be leveraged to inform if and to what extent reinforcement evolved in the face of gene flow between sympatric lineages and between allopatric and sympatric populations of the same lineage. Our major goals are to understand if genome scans for particular patterns of genetic variation could identify reinforcement, isolate the genetic basis of reinforcement, or infer the conditions under which reinforcement evolved.

Although polyploidy is widespread across the plant Tree of Life, its long-term evolutionary significance is still poorly understood. Here, we examine the effects of polyploidy in explaining the large-scale evolutionary patterns within angiosperms by focusing on a single family exhibiting extensive interspecific variation in chromosome numbers. We inferred ploidy from haploid chromosome numbers for 80% of species in the most comprehensive species-level chronogram for the Brassicaceae. After evaluating a total of 94 phylogenetic models of diversification, we found that ploidy influences diversification rates across the Brassicaceae. We also found that despite diversifying at a similar rate to diploids, polyploids have played a significant role in driving present-day differences in species richness among clades. Overall, in addition to highlighting the complexity in the evolutionary consequences of polyploidy, our results suggest that rare successful polyploids persist while significantly contributing to the long-term evolution of clades. Our findings further indicate that polyploidy has played a major role in driving the long-term evolution of the Brassicaceae and highlight the potential of polyploidy in shaping present-day diversity patterns across the plant Tree of Life.

Although polyploidy, or whole-genome duplication, is widespread across the Plant Tree of Life, its long-term evolutionary significance is still poorly understood. Here we examine the effects of polyploidy in driving macroevolutionary patterns within the angiosperm family Brassicaceae, a speciose clade exhibiting extensive inter-specific variation in chromosome numbers. We inferred ploidal levels from haploid chromosome numbers for 80% of species in the most comprehensive species-level chronogram for the Brassicaceae published to date. After evaluating a total of 54 phylogenetic models of diversification, we found that ploidy drives diversification rates across the Brassicaceae, with polyploids experiencing faster rates of speciation and extinction, but relatively slower rates of diversification. Nevertheless, diversification rates are, on average, positive for both polyploids and diploids. We also found that despite diversifying significantly slower than diploids, polyploids have played a significant role in driving present-day differences in species richness among clades. Overall, although most polyploids go extinct before sustainable populations are established, rare successful polyploids persist and significantly contribute to the long-term evolution of lineages. Our findings suggest that polyploidy has played a major role in shaping the long-term evolution of the Brassicaceae and highlight the importance of polyploidy in shaping present-day diversity patterns across the plant Tree of Life. Significance statementAlthough polyploidy is a source of innovation, its long-term evolutionary significance is still debated. Here we analyze the evolutionary role of polyploidy within the Brassicaceae, a diverse clade exhibiting extensive variation in chromosome numbers among species. We found that, although polyploids diversify slower than diploids, polyploids have faster extinction and speciation rates. Our results also suggest that polyploidy has played an important role in shaping present-day differences in species richness within the Brassicaceae, with potential implications in explaining diversity patterns across the plant Tree of Life.\body IntroductionAlthough polyploidy-the heritable condition of carrying more than two complete sets of chromosomes-is widespread across the plant phylogeny (1), its evolutionary significance is still debated (2-6). Discussions on the evolutionary role of polyploidy date back to Stebbins (7,8) and Wagner (9) who considered polyploidy to have negligible effects on the long-term evolution of plants. This idea, later known as the 'dead-end' hypothesis, was recently reframed as an expectation that polyploid species will undergo extinction more frequently than diploids (4, 5, 10-12). However, polyploidy can influence the long-term evolution of lineages (1,(13)(14)(15)(16)(17) regardless of whether polyploids are more likely to go extinct than diploids (4,5, 10-12). Both interpretations of the 'dead-end' hypothesis are thus not equivalent to each other. The original hypothesis focused on t...

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