Genome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster.

Experimental evolutionary genomics now allows biologists to test fundamental theories concerning the genetic basis of adaptation. We have conducted one of the longest laboratory evolution experiments with any sexually-reproducing metazoan, Drosophila melanogaster. We used next-generation resequencing data from this experiment to examine genome-wide patterns of genetic variation over an evolutionary time-scale that approaches 1,000 generations. We also compared measures of variation within and differentiation between our populations to simulations based on a variety of evolutionary scenarios. Our analysis yielded no clear evidence of hard selective sweeps, whereby natural selection acts to increase the frequency of a newly-arising mutation in a population until it becomes fixed. We do find evidence for selection acting on standing genetic variation, as independent replicate populations exhibit similar population-genetic dynamics, without obvious fixation of candidate alleles under selection. A hidden-Markov model test for selection also found widespread evidence for selection. We found more genetic variation genome-wide, and less differentiation between replicate populations genome-wide, than arose in any of our simulated evolutionary scenarios.

The great evolutionary divide: two genomic systems biologies of aging.

There is not one systems biology of aging, but two. Though aging can evolve in either sexual or asexual species when there is asymmetric reproduction, the evolutionary genetics of aging in species with frequent sexual recombination are quite different from those arising when sex is rare or absent. When recombination is rare, selection is expected to act chiefly on rare large-effect mutations, which purge genetic variation due to genome-wide hitchhiking. In such species, the systems biology of aging can focus on the effects of large-effect mutants, transgenics, and combinations of such genetic manipulations. By contrast, sexually outbreeding species maintain abundant genetic polymorphism within populations. In such species, the systems biology of aging can examine the genome-wide effects of selection and genetic drift on the numerous polymorphic loci that respond to laboratory selection for different patterns of aging. An important question of medical relevance is to what extent insights derived from the systems biology of aging in model species can be applied to human aging.

An evolutionary and genomic approach to challenges and opportunities for eliminating aging.

While solutions to major scientific and medical problems are never perfect or complete, it is still reasonable to delineate cases where both have been essentially solved. For example, Darwin's theory of natural selection provides a successful solution to the problem of biological adaptation, while the germ theory of infection solved the scientific problem of contagious disease. Likewise in the context of medicine, we have effectively solved the problem of contagious disease, reducing it to a minor cause of death and disability for almost everyone in countries with advanced medicine and adequate resources. Evolutionary biologists claim to have solved the scientific problem of aging: we explain it theoretically using Hamilton's forces of natural selection; in experimental evolution we readily manipulate the onset, rate, and eventual cessation of aging by manipulating these forces. In this article, we turn to the technological challenge of solving the medical problem of aging. While we feel that the broad outlines of such a solution are clear enough starting from the evolutionary solution to the scientific problem of aging, we do not claim that we can give a complete or exhaustive plan for medically solving the problem of aging. But we are confident that biology and medicine will effectively solve the problem of aging within the next 50 years, providing Hamiltonian lifestyle changes, tissue repair, and genomic technological opportunities are fully exploited in public health practices, in medical practice, and in medical research, respectively.

Cryptic speciation within Asthenodipsas vertebralis (Boulenger, 1900) (Squamata: Pareatidae), the description of a new species from Peninsular Malaysia, and the resurrection of A. tropidonotus (Lidth de Jude, 1923) from Sumatra: an integrative taxonomic analysis.

A review of the taxonomic status of the Asian Slug Snake, Asthenodipsas vertebralis (Boulenger, 1900) based on an integrative taxonomic approach using molecular, morphological, color pattern, and ecological data indicate it is composed of three well supported monophyletic lineages: (1) Pulau Tioman and Fraser's Hill, Pahang and Bukit Larut, Perak; Peninsular Malaysia; (2) its sister lineage from Northern Sumatra; and (3) the remaining basal lineage from Peninsular Malaysia. Furthermore, we consider the high sequence divergence (6.3%-10.2%) between these lineages (especially in areas of sympatry) and discrete differences in their morphology, color pattern, and microhabitat preference as evidence they are not conspecific. As such, we resurrect the name A. tropidonotus (Lidth de Jeude, 1923) for the Sumatra populations, restrict the name A. vertebralis to the populations from Pulau Tioman, Genting Highlands, Fraser's Hill, Gunung Benom, and Bukit Larut that contain terrestrial, banded adults; and consider A. lasgalenensis sp. nov. to be restricted to the populations from Fraser's Hill, Cameron Highlands, and Bukit Larut that contain arboreal, unbanded adults.

Imaging of light emission from the expression of luciferases in living cells and organisms: a review.

Luciferases are enzymes that emit light in the presence of oxygen and a substrate (luciferin) and which have been used for real-time, low-light imaging of gene expression in cell cultures, individual cells, whole organisms, and transgenic organisms. Such luciferin-luciferase systems include, among others, the bacterial lux genes of terrestrial Photorhabdus luminescens and marine Vibrio harveyi bacteria, as well as eukaryotic luciferase luc and ruc genes from firefly species (Photinus) and the sea pansy (Renilla reniformis), respectively. In various vectors and in fusion constructs with other gene products such as green fluorescence protein (GFP; from the jellyfish Aequorea), luciferases have served as reporters in a number of promoter search and targeted gene expression experiments over the last two decades. Luciferase imaging has also been used to trace bacterial and viral infection in vivo and to visualize the proliferation of tumour cells in animal models.