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theologians for centuries have delved into nature’s workings through field observations and phenotypic investigations. Yet before the advent and widespread use of molecular markers, many of nature’s incredible operations remained hidden from view. Nature can now be revealed at and through this new window of molecular-level observation, and the results are often far more engrossing than might ever have been predicted.

First are the astounding findings about genomes. Even a few years ago, few scientists could have imagined that genes encoding functional RNA and protein molecules of obvious benefit to the organism would prove to constitute only a small fraction of the eukaryotic genome, and that the rest of the composite DNA sequence includes an astonishing collection of noncoding regions, regulatory modules, pseudogenes, and legions of repetitive elements, many of which are descended from selfish virus-like elements that have proliferated and jumped around the genome often at the immediate fitness expense of their hosts. A new metaphor is emerging in which each eukaryotic genome can be viewed, in effect, as a miniature ecological community whose quasi-independent members (unlinked DNA sequences) all struggle for representation in the next generation of sexual reproducers and thereby become involved in elaborate coevolutionary games that can be quite analogous to the parasitisms, commensalisms, and mutualisms routinely observed among species in natural ecosystems (Avise, 2001). This metaphor of the genome as a submicroscopic community of genes constantly undergoing evolutionary adjustments is far from perfect, but it does promote a perspective on genomic operations that today may be much more useful and research-stimulating than earlier genomic metaphors (such as the “beads on a string” image of functional and fully collaborative genes packed tightly along chromosomes).

A second arena in which molecular genetic markers are having a huge scientific impact is in uncovering heretofore hidden secrets about the ecologies, behaviors, natural histories, and evolution of organisms in nature. An adequate discussion of this topic is far beyond the scope of this chapter, so what follow are merely a few examples of the many types of questions that scientists have answered using molecular markers, but that for one logistical reason or another had been inadequately addressed by earlier field observations or phenotypic assessments. For fuller answers to the following questions and many others like them, all in layperson language, see Avise (2002, 2006).

How big and old can natural clones of mushrooms become? (Living members of one clone were estimated to weigh a collective 100 tons, occupy 40 acres, and derive from a single zygote that formed ≈1,500 years ago.) Does each female green turtle (a highly migratory marine species) return to her natal beach to nest? (Yes, normally.) Why do female roly-poly pill bugs often greatly outnumber males? (Because many strains are

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