How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances.
Cytosine methylation is an epigenetic mechanism in eukaryotes that is often associated with stable transcriptional silencing, such as in X-chromosome inactivation and genomic imprinting. Aberrant methylation patterns occur in several inherited human diseases and in many cancers. To understand how methylated and unmethylated states of cytosine residues are transmitted during DNA replication, we develop a population-epigenetic model of DNA methylation dynamics. The model is informed by our observation that de novo methylation can occur on the daughter strand while leaving the opposing cytosine unmethylated, as revealed by the patterns of methylation on the two complementary strands of individual DNA molecules. Under our model, we can infer sitespecific rates of both maintenance and de novo methylation, values that determine the fidelity of methylation inheritance, from double-stranded methylation data. This approach can be used for populations of cells obtained from individuals without the need for cell culture. We use our method to infer cytosine methylation rates at several sites within the promoter of the human gene FMR1.bisulfite genomic sequencing ͉ epigenetic fidelity ͉ fragile X syndrome ͉ mathematical modeling ͉ population epigenetics D NA methylation is an important epigenetic mechanism in eukaryotes, where it occurs primarily in the form of 5-methylcytosine (1, 2). Cytosine methylation often is involved in stable transcriptional inactivation, such as in X-chromosome inactivation and genomic imprinting, and sometimes is transmitted through sexual reproduction, producing phenotypic variation (3). In addition, aberrant cytosine methylation patterns are associated with several inherited human diseases, including fragile X (4-6) and ICF (immune deficiency, centrometric heterochromatin, and facial abnormalities) syndromes (7,8), and many cancers (9). Understanding how methylated and unmethylated states of cytosine residues are preserved through cell division, therefore, will lend crucial insight into numerous biological processes.CpG͞CpG dyads are the principal units of cytosine methylation in vertebrates; these dyads consist of the dinucleotide CpG on one strand and the complementary CpG dinucleotide on the opposing DNA strand. The symmetry of this arrangement provides a means whereby cytosine methylation patterns can be maintained from parent to daughter strands of DNA (10-12). Methyl groups are incorporated into DNA by two types of methylation events. Maintenance methylation occurs when the pattern of methylation on the parent DNA strand serves as the signal for methylation on the newly synthesized daughter DNA strand (13); de novo methylation is defined as the addition of methylation at unmethylated dyads that occurs without regard to template pattern (14). These methylation processes are mediated by a class of enzymes known as DNA methyltransferases. Maintenance methyltransferase exhibits a preference for hemimethylated CpG͞CpG dyads (methylated on one strand only), is thought to operate principally durin...
PCR amplification of limited amounts of DNA template carries an increased risk of product redundancy and contamination. We use molecular barcoding to label each genomic DNA template with an individual sequence tag prior to PCR amplification. In addition, we include molecular 'batch-stamps' that effectively label each genomic template with a sample ID and analysis date. This highly sensitive method identifies redundant and contaminant sequences and serves as a reliable method for positive identification of desired sequences; we can therefore capture accurately the genomic template diversity in the sample analyzed. Although our application described here involves the use of hairpin-bisulfite PCR for amplification of double-stranded DNA, the method can readily be adapted to single-strand PCR. Useful applications will include analyses of limited template DNA for biomedical, ancient DNA and forensic purposes.
Recent studies have increasingly recognized evolutionary rescue (adaptive evolution that prevents extinction following environmental change) as an important process in evolutionary biology and conservation science. Researchers have concentrated on single species living in isolation, but populations in nature exist within communities of interacting species, so evolutionary rescue should also be investigated in a multispecies context. We argue that the persistence or extinction of a focal species can be determined solely by evolutionary change in an interacting species. We demonstrate that prey adaptive evolution can prevent predator extinction in two-species predator–prey models, and we derive the conditions under which this indirect evolutionary interaction is essential to prevent extinction following environmental change. A nonevolving predator can be rescued from extinction by adaptive evolution of its prey due to a trade-off for the prey between defense against predation and population growth rate. As prey typically have larger populations and shorter generations than their predators, prey evolution can be rapid and have profound effects on predator population dynamics. We suggest that this process, which we term ‘indirect evolutionary rescue’, has the potential to be critically important to the ecological and evolutionary responses of populations and communities to dramatic environmental change.
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