Drosophila melanogaster, an ancestrally African species, has recently spread throughout the world, associated with human activity. The species has served as the focus of many studies investigating local adaptation relating to latitudinal variation in non-African populations, especially those from the United States and Australia. These studies have documented the existence of shared, genetically determined phenotypic clines for several life history and morphological traits. However, there are no studies designed to formally address the degree of shared latitudinal differentiation at the genomic level. Here we present our comparative analysis of such differentiation. Not surprisingly, we find evidence of substantial, shared selection responses on the two continents, probably resulting from selection on standing ancestral variation. The polymorphic inversion In(3R)P has an important effect on this pattern, but considerable parallelism is also observed across the genome in regions not associated with inversion polymorphism. Interestingly, parallel latitudinal differentiation is observed even for variants that are not particularly strongly differentiated, which suggests that very large numbers of polymorphisms are targets of spatially varying selection in this species. HOW organisms adapt to the ecological challenges of a new environment remains poorly understood. Indeed, while observations from comparative biology show that organisms often evolve convergent phenotypes when faced with similar selection pressures, we have little insight into how underlying historical and population genetic processes determine the degree of shared or divergent selection responses across populations or species. The latitudinal clines of Drosophila melanogaster provide a rich system for exploring these questions.While there is general agreement that D. melanogaster evolved in Africa, spread through Eurasia several thousand years ago, and only recently colonized the Americas and Australia (David and Capy 1988;Lachaise et al. 1988;Begun and Aquadro 1993;Keller 2007;Stephan and Li 2007;Duchen et al. 2013), our understanding of the species' historical biogeography is incomplete. There are at least two potential clines that have received much attention-one in Australia and one in North America-that likely represent independent samplings of shared ancestral variation (Knibb 1982;Hoffmann and Weeks 2007).Decades of research on D. melanogaster clines have revealed broad shared patterns of adaptive phenotypic divergence along latitudinal transects in the Americas and Australia. For example, several phenotypes including body size, multiple physiological traits, and multiple allozyme variants show parallel clines on these continents (Singh and Long 1992). Paracentric chromosome inversion polymorphism is also well documented as showing similar patterns of clinal variation on the two continents (Voelker et al. 1978;Knibb 1982). Genomic description of the two clines is minimal. The most comprehensive data bearing on the issue of shared clinal...

http://152.2.15.114/~labweb/VCAKE

How non-coding DNA gives rise to new protein-coding genes (de novo genes) is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs), while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important.

Exceptionally long-lived species, including many bats, rarely show overt signs of aging, making it difficult to determine why species differ in lifespan. Here, we use DNA methylation (DNAm) profiles from 712 known-age bats, representing 26 species, to identify epigenetic changes associated with age and longevity. We demonstrate that DNAm accurately predicts chronological age. Across species, longevity is negatively associated with the rate of DNAm change at age-associated sites. Furthermore, analysis of several bat genomes reveals that hypermethylated age- and longevity-associated sites are disproportionately located in promoter regions of key transcription factors (TF) and enriched for histone and chromatin features associated with transcriptional regulation. Predicted TF binding site motifs and enrichment analyses indicate that age-related methylation change is influenced by developmental processes, while longevity-related DNAm change is associated with innate immunity or tumorigenesis genes, suggesting that bat longevity results from augmented immune response and cancer suppression.