Academic journal article Genetics

Molecular Population Genetics of Drosophila Subtelomeric DNA

Academic journal article Genetics

Molecular Population Genetics of Drosophila Subtelomeric DNA

Article excerpt

ABSTRACT

DNA sequence surveys in yeast and humans suggest that the forces shaping telomeric polymorphism and divergence are distinctly more dynamic than those in the euchromatic, gene-rich regions of the chromosomes. However, the generality of this pattern across outbreeding, multicellular eukaryotes has not been determined. To characterize the structure and evolution of Drosophila telomeres, we collected and analyzed molecular population genetics data from the X chromosome subtelomere in 58 lines of North American Drosophila melanogaster and 29 lines of African D. melanogaster. We found that Drosophila subtelomeres exhibit high levels of both structural and substitutional polymorphism relative to linked euchromatic regions. We also observed strikingly different patterns of variation in the North American and African samples. Moreover, our analyses of the polymorphism data identify a localized hotspot of recombination in the most-distal portion of the X subtelomere. While the levels of polymorphism decline sharply and in parallel with rates of crossing over per physical length over the distal first euchromatic megabase pairs of the X chromosome, our data suggest that they rise again sharply in the subtelomeric region ([asymptotically =]80 kbp). These patterns of historical recombination and geographic differentiation indicate that, similar to yeast and humans, Drosophila subtelomeric DNA is evolving very differently from euchromatic DNA.

POPULATION geneticists aspire to understand the evolutionary forces shaping patterns of molecular polymorphism and divergence. The recent increase in the quantity of DNA sequence data from proteincoding regions has led to considerable advances in our understanding of the forces governing the evolution of such regions. For example, genomic surveys have revealed functional variants as well as classes of genes enriched for the signature of natural selection (e.g., Bustamante et al. 2005; Nielsen et al. 2005; Begun et al. 2007). In contrast, regions of the genome containing fewer genes but an increased density of repetitive sequences have been less amenable to population and molecular evolutionary analysis. These regions, typically found adjacent to telomeres and centromeres, are collectively referred to as the heterochromatin. Because heterochromatic DNA is difficult to clone, sequence, and assemble, much less is known about the structure of these regions. Thus, there is almost no foundation for effective population or comparative genomic analyses. Indeed, only recently have researchers begun to identify the sparsely distributed protein-coding sequences embedded in heterochromatin (reviewed in Yasuhara and Wakimoto 2006).

Most population and molecular evolutionary surveys from telomeric regions come from yeast and primates (but see recent work on Arabidopsis in Kuo et al. 2006). These studies show that telomeric DNA is evolving very differently from the gene-rich euchromatin. For example, the telomeric regions of several human chromosomes are dramatically different fromthe corresponding regions in chimpanzees (e.g., Trasket al. 1998), showing large-scale rearrangements, as well as extensive differentiation of highly repeated elements. In addition, the telomeric regions of the human and yeast genomes exhibit unusually high levels of within-species structural and nucleotide polymorphism (see Pryde et al. 1997 and Mefford and Trask 2002 for reviews).

Although data from other organisms are scarce, we have recently found that the most-distal regions of Drosophila subtelomeres are evolving quite rapidly between Drosophila melanogaster and its close relatives, D. simulans and D. yakuba, which is consistent with observations of primates ( J. A. Anderson, S. E. Celniker and C. H. Langley, unpublished results). Figure 1 depicts a typical telomeric region of D. melanogaster; at a large scale, the structure of this genomic region resembles the structure typical of other eukaryotes. …

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