Unique signals of clinal and seasonal allele frequency change at eQTLs in Drosophila melanogaster

Populations of short-lived organisms can respond to spatial and temporal environmental heterogeneity through local adaptation. Local adaptation can be reflected on both phenotypic and genetic levels, and it has been documented in many organisms. Although some complex fitness-related phenotypes have been shown to vary across latitudinal clines and seasons in similar ways in Drosophila melanogaster populations, we lack a general understanding of the genetic architecture of local adaptation across space and time. To address this problem, we examined patterns of allele frequency change across latitudinal clines and between seasons at previously reported expression quantitative trait loci (eQTLs). We divided eQTLs into groups by utilizing differential expression profiles of fly populations collected across a latitudinal cline or exposed to different environmental conditions. We also examined clinal and seasonal patterns of allele frequency change at eQTLs grouped by tissues. In general, we find that clinally varying polymorphisms are enriched for eQTLs, and that these eQTLs change in frequency in predictable ways across the cline and in response to starvation tolerance. The enrichment of eQTL among seasonally varying polymorphisms is more subtle, and the direction of allele frequency change at eQTL appears to be somewhat idiosyncratic. Taken together, we suggest that clinal adaptation at eQTLs is distinct than that of seasonal adaptation.

Effects of latitudinal variation on field and common garden comparisons between native and introduced groundsel (Senecio vulgaris) populations

Aims Field and common garden comparisons are commonly performed to test the rapid evolution of increased vigor in introduced plant populations. Latitudinal clines in phenotypic traits can obscure such evolutionary inferences, particularly when native or introduced populations are distributed across large geographic ranges. We tested whether the latitudinal clines influence comparisons between introduced and native populations of Senecio vulgaris. Methods Senecio vulgaris is native to Europe but has been introduced in northeastern and southwestern China. To evaluate the performance in terms of growth and reproduction between native European populations and introduced Chinese populations, we compared plant height, number of branches and number of capitula in field populations in native and introduced ranges and in a common garden in Switzerland. Important Findings The introduced Chinese populations performed better than the native European populations in the field in terms of plant height and number of capitula, which was consistent with the prediction of the evolution of the increased competitive ability (EICA) hypothesis. The Chinese populations produced more capitula than the European populations when the latitudinal cline was considered in the common garden comparison. When we compared the traits of the northeastern Chinese, southwestern Chinese and European populations in both the field and common garden, the northeastern Chinese populations, at latitudes similar to those of the European populations, exhibited greater plant size and more capitula than the European populations in both the field and common garden. However, the southwestern Chinese populations, at latitudes much lower than those of the European populations, did not perform better than the native populations in terms of reproduction. In conclusion, our results suggest that latitudinal clines in phenotypic traits should be considered in field and common garden comparisons when introduced populations are geographically structured.

Florida Drosophila melanogaster genomes sampled 13 years apart show increases in warm-associated SNP alleles

ABSTRACTWe studied genetic change in Drosophila melanogaster using whole-genome SNP data from samples taken 13 years apart in Homestead, FL. This population is at the southern tip of a well-studied US latitudinal cline. On the non-inversion-carrying chromosome arms, 11-16% of SNPs show significant frequency changes. These are enriched for latitudinal clines and genic sites. For clinal SNPs each allele is either the northern- or southern-favored. Seventy-eight to 95 percent with significant frequency increase are southern-favored. Five to seven percent of SNPs also show significant seasonal change and involve increases in the northern-favored allele during the season. On the 2L and 3R chromosome arms there are significant seasonal shifts for common inversions. We identify regions and genes that are candidates for selection. These regions also show correspondence with those associated with soft sweeps in Raleigh, NC. This shift towards southern-favored alleles may be caused by climate shifts or increased African-European admixture.

Global variation in the thermal tolerances of plants

Thermal macrophysiology is an established research field that has led to well-described patterns in the global structuring of climate adaptation and risk. However, since it was developed primarily in animals, we lack information on how general these patterns are across organisms. This is alarming if we are to understand how thermal tolerances are distributed globally, improve predictions of climate change, and mitigate effects. We approached this knowledge gap by compiling a geographically and taxonomically extensive database on plant heat and cold tolerances and used this dataset to test for thermal macrophysiological patterns and processes in plants. We found support for several expected patterns: Cold tolerances are more variable and exhibit steeper latitudinal clines and stronger relationships with local environmental temperatures than heat tolerances overall. Next, we disentangled the importance of local environments and evolutionary and biogeographic histories in generating these patterns. We found that all three processes have significantly contributed to variation in both heat and cold tolerances but that their relative importance differs. We also show that failure to simultaneously account for all three effects overestimates the importance of the included variable, challenging previous conclusions drawn from less comprehensive models. Our results are consistent with rare evolutionary innovations in cold acclimation ability structuring plant distributions across biomes. In contrast, plant heat tolerances vary mainly as a result of biogeographical processes and drift. Our results further highlight that all plants, particularly at mid-to-high latitudes and in their nonhardened state, will become increasingly vulnerable to ongoing climate change.