Massive haplotypes underlie ecotypic differentiation in sunflowers.

Species often include multiple ecotypes that are adapted to different environments1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations2-4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37 large (1-100 Mbp in size), non-recombining haplotype blocks that are associated with numerous ecologically relevant traits, as well as soil and climate characteristics. Limited recombination in these haplotype blocks keeps adaptive alleles together, and these regions differentiate sunflower ecotypes. For example, haplotype blocks control a 77-day difference in flowering between ecotypes of the silverleaf sunflower H. argophyllus (probably through deletion of a homologue of FLOWERING LOCUS T (FT)), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, frequently associated with structural variants and often appear to represent introgressions from other-possibly now-extinct-congeners. These results highlight a pervasive role of structural variation in ecotypic adaptation.

Effects of genotype identity and diversity on the invasiveness and invasibility of plant populations.

Genetic diversity within species is a potentially important, but poorly studied, determinant of plant community dynamics. Here we report experiments testing the influence of genotype identity and genotypic diversity both on the invasibility of a foundation, matrix-forming species (Kentucky bluegrass, Poa pratensis), and on the invasiveness of a colonizing species (dandelion, Taraxacum officinale). Genotypes of Kentucky bluegrass in monoculture showed significant variation in productivity and resistance to dandelion invasion, but the productivity and invasion resistance of genotypic mixtures were not significantly different from those of genotypic monocultures. Indirect evidence suggested temporal shifts in the genotypic composition of mixtures. Dandelion genotypes in monoculture showed striking and significant variation in productivity and seed production, but there was no significant tendency for these variables in mixtures to deviate from null expectations based on monocultures. However, productivity and seed production of dandelion mixtures were consistently greater than those of the two least productive genotypes, and statistically indistinguishable from those of the three most productive genotypes, suggesting the possibility of greater invasiveness of genotypically diverse populations in the long run due to dominance by highly productive genotypes. In both experiments, the identity of genotypes was far more important than genetic diversity per se.

A novel post hoc method for detecting index switching finds no evidence for increased switching on the Illumina HiSeq X.

High-throughput sequencing using the Illumina HiSeq platform is a pervasive and critical molecular ecology resource, and has provided the data underlying many recent advances. A recent study has suggested that "index switching," where reads are misattributed to the wrong sample, may be higher in new versions of the HiSeq platform. This has the potential to invalidate both published and in-progress work across the field. Here, we test for evidence of index switching in an exemplar whole-genome shotgun data set sequenced on both the Illumina HiSeq 2500, which should not have the problem, and the Illumina HiSeq X, which may. We leverage unbalanced heterozygotes, which may be produced by index switching, and ask whether the undersequenced allele is more likely to be found in other samples in the same lane than expected based on the allele frequency. Although we validate the sensitivity of this method using simulations, we find that neither the HiSeq 2500 nor the HiSeq X has evidence of index switching. This suggests that, thankfully, index switching may not be a ubiquitous problem in HiSeq X sequence data. Lastly, we provide scripts for applying our method so that index switching can be tested for in other data sets.

Genotypic diversity effects on the performance of Taraxacum officinale populations increase with time and environmental favorability.

Within-population genetic diversity influences many ecological processes, but few studies have examined how environmental conditions may impact these short-term diversity effects. Over four growing seasons, we followed experimental populations of a clonal, ubiquitous weed, Taraxacum officinale, with different numbers of genotypes in relatively favorable fallow field and unfavorable mowed lawn environmental treatments. Population performance (measured as total leaf area, seed production or biomass) clearly and consistently increased with diversity, and this effect became stronger over the course of the experiment. Diversity effects were stronger, and with different underlying mechanisms, in the fallow field versus the mowed lawn. Large genotypes dominated in the fallow field driving overyielding (via positive selection effects), whereas in the mowed lawn, where performance was limited by regular disturbance, there was evidence for complementarity among genotypes (with one compact genotype in particular performing better in mixture than monoculture). Hence, we predict stronger genotypic diversity effects in environments where intense intraspecific competition enhances genotypic differences. Our four-year field experiment plus seedling establishment trials indicate that genotypic diversity effects have far-reaching and context-dependent consequences across generations.