Project description:How does environmental change drive phenotypic evolution? We addressed this question using Daphnia genotypes separated by ~1600-years of evolution in a Minnesota lake using methods in resurrection ecology (i.e., reviving dormant eggs from sediments) and found substantial genetic and physiological differentiation. These shifts are highly correlated with anthropogenic environmental change, specifically phosphorus (P)-driven eutrophication. Here, we explore transcriptomic changes that may underlie the observed shifts in P use physiology (see poster by Fricsh et al for a detailed explanation). We compared the transcriptomes of two ancient and two contemporary genotypes in ancient (i.e., low P; LP) and contemporary (i.e., high P; HP) conditions using an 11000-gene microarray. Ancient and contemporary genotypes differed in the number of differentially expressed genes in the HP (mean ± SD; 645 ± 112.95) and LP (1071 ± 211.63) treatments. These results indicate considerable transcriptomic variation between ancient and contemporary genotypes in both dietary treatments, with stressful (LP) conditions invoking differential expression of more genes (t= -2.51; P= 0.04). Moreover, ancient and contemporary genotypes exhibited markedly different transcriptomic responses to dietary treatments. Contemporary genotypes upregulated 84.5 ± 28.99 while ancient genotypes upregulated 413.5 ± 26.16 genes (t= 164.5; P= 0.003). Similarly, ancient (127.5 ± 101.1) and contemporary (316 ± 98.99) genotypes differed significantly in the number of genes downregulated between the HP and LP treatments (t= 125.66; P= 0.005). These results indicate substantial regulatory shifts may underlie the striking physiological differences observed. Further analyses of gene families that were differentially expressed (DE) between ancient and contemporary genotypes revealed several gene families already known to be important in mitigating stoichiometric imbalances driven by P availability. Agglomerative hierarchical cluster analyses of DE loci between ancient and contemporary genotypes indicating age-based clustering will be presented. Together, our theoretical framework based on elemental supply, and unique model system enabled a millennial-scale exploration of the environmental contribution to phenotypic evolution.
Project description:Over the past few years, studies of DNA isolated from human fossils and archaeological remains have generated considerable novel insight into the history of our species. Several landmark papers have described the genomes of ancient human ancestors and have demonstrated that contemporary humans harbour genetic material from ancient close relatives, the Neanderthals and Denisovans, and that ancient human individuals are often genetically distinct from nearby extant populations whilst also showing affinities with populations from further afield. Across West Eurasia, there is growing genetic evidence of large-scale, dynamic population movements over the period between 10,000 to 2,000 years ago, such that the ancestry across present-day populations is likely to be a mixture of several ancient groups. Whilst these efforts are bringing the details of West Eurasian prehistory into increasing focus, studies aimed at understanding the processes behind the generation of the current West Eurasian genetic landscape have been limited by the number of populations sampled, or have been either too regional or global in their outlook. Here, using recently described haplotype-based techniques, we present the results of a systematic survey of recent admixture history across Western Eurasia and show that admixture is a universal property across almost all groups. Admixture in all regions except North Western Europe involved the influx of genetic material from outside of West Eurasia, which we date to specific time periods. Within Northern, Western, and Central Europe, admixture tended to occur between local groups during the period 300 to 1200CE. Comparisons of the genetic profiles of West Eurasians before and after admixture show that population movements within the last 1500 years are likely to have maintained differentiation amongst groups. Our analysis provides a timeline of the gene flow events that have generated the contemporary genetic landscape of West Eurasia. 20 individuals from Croatia included as part of an analysis of admixture in West Eurasia