The joint allele-frequency spectrum in closely related species, pp. 387–398
Hua Chen, Richard E. Green, Svante Pääbo and Montgomery Slatkin
Population genetic theory is developed for computing the joint frequency spectra of alleles in two closely related species, including the special case of sampling one chromosome from one of the species. The joint-site frequency spectrum can be remarkably invariant over different demographic histories of the populations, providing that the chromosome from one of the descendant species carries the derived allele. Recent data on Neanderthal DNA sequence are used to illustrate the approach.
Genetic exchange across a species boundary in the archaeal genus Ferroplasma, pp. 407–416
John M. Eppley, Gene W. Tyson, Wayne M. Getz and Jillian F. Banfield
Exchange of DNA in bacteria, which can occur across deep taxonomic divides, may render the concept of microbial species meaningless. However, DNA sequence obtained by these authors from a natural microbial community reveals two closely related archaeal species that are genetically distinct over >97% of their genomes. Rates of recombination in these organisms decrease exponentially with increasing genetic difference and are much lower across than within populations. This probably contributes to the preservation of population clusters in a manner consistent with the biological species concept.
Distinctly different sex ratios in African and European populations of Drosophila melanogaster inferred from chromosomewide single nucleotide polymorphism data, pp. 469–480
Stephan Hutter, Haipeng Li, Steffen Beisswanger, David De Lorenzo and Wolfgang Stephan
The ratio of X-linked and autosomal DNA diversity is generally much lower than the neutral equilibrium expectations in derived populations of Drosophila melanogaster. In this article the authors create a large unbiased single nucleotide polymorphism data set from noncoding regions and use a powerful coalescent-based maximum-likelihood method to obtain unbiased estimates of the sex ratio and demography in an ancestral and a derived population. They find that unequal sex ratios and demographic events can explain the observed disparities in the ancestral population. However, in the derived population additionally positive selection seems to have taken place.
Misregulation of the kinesin-like protein Subito induces meiotic spindle formation in the absence of chromosomes and centrosomes, pp. 267–280
Janet K. Jang, Taslima Rahman, Vanessa S. Kober, Jeffry Cesario and Kim S. McKim
The segregation of chromosomes during meiosis I requires a bipolar spindle at metaphase. In many species these meiotic spindles are organized in the absence of centrosomes, which typically define the mitotic poles. Models for this process have suggested that the chromosomes recruit microtubules and then minus end-directed motors bundle them to form the tapered poles, but this article describes evidence that suggests the role of chromosomes in recruiting microtubules is indirect, possibly involving a generation of a diffusible signal to promote the bundling of microtubules. There is also evidence for similar mechanisms in mouse oocytes.
Single nucleotide polymorphisms and linkage disequilibrium in sunflower, pp. 457–468
Judith M. Kolkman, Simon T. Berry, Alberto J. Leon, Mary B. Slabaugh, Shunxue Tang, Wenxiang Gao, David K. Shintani, John M. Burke and Steven J. Knapp
Sunflower was domesticated by Native Americans >4000 years ago and has been intensely bred for oilseed production traits for more than a half century. Genetic diversity is usually narrowed by domestication and breeding, but this article reports that nucleotide diversity in sunflower cultivars is on par with that of corn, one of the most polymorphic crop species. The results suggest that the sunflower genome harbors at least 76 million common single nucleotide polymorphisms.
The dynamics of the roo transposable element in mutation-accumulation lines and segregating populations of Drosophila melanogaster, pp. 511–522
Montserrat Papaceit, Victoria Ávila, Montserrat Aguadé and Aurora García-Dorado
Large populations can successfully contain transposable element copy numbers despite the usually weak deleterious effects of new inserts. In general, natural selection becomes less effective in smaller populations, and this study shows that the roo family of transposable elements increases exponentially in copy number in small inbred populations but is contained in populations of moderate size. This storm of transposition is amplified by the increase in autonomous elements that occurs when active elements multiply.
Age specificity of inbreeding load in Drosophila melanogaster and implications for the evolution of late-life mortality plateaus, pp. 587–595
Rose M. Reynolds, Sara Temiyasathit, Melissa M. Reedy, Elizabeth A. Ruedi, Jenny M. Drnevich, Jeff Leips and Kimberly A. Hughes
Once one makes it to a certain age, chances for a long life increase significantly: mortality rates stop increasing at late ages. This flies in the face of traditional evolutionary theory on aging, which predicts increasing rates of mortality until a cohort is extinct. However, a minor alteration to the theory—including alleles affecting fitness that are moderately age specific—accounts for mortality plateaus. The authors provide compelling evidence for this modified theory in Drosophila melanogaster.
Inferring somatic mutation rates using the stop-enhanced green fluorescent protein mouse, pp. 9–16
Simon Ro and Bruce Rannala
The Ames test for mutagens, which uses bacteria, has been in use for 3 decades to screen chemicals for safety. These authors develop a system to do this in mice, which provides a mammalian system for identifying substances that are a threat to human health. They also provide a novel statistical model for estimating the rate of somatic mutation.
The DrosDel deletion collection: A Drosophila genomewide chromosomal deficiency resource, pp. 615–629
Edward Ryder, Michael Ashburner, Rosa Bautista-Llacer, Jenny Drummond, Jane Webster, Glynnis Johnson, Terri Morley, Yuk Sang Chan, Fiona Blows, Darin Coulson, Gunter Reuter, Heiko Baisch, Christian Apelt, Andreas Kauk, Thomas Rudolph, Maria Kube, Melanie Klimm, Claudia Nickel, Janos Szidonya, Peter Maróy, Margit Pal, Åsa Rasmuson-Lestander, Karin Ekström, Hugo Stocker, Christoph Hugentobler, Ernst Hafen, David Gubb, Gert Pflugfelder, Christian Dorner, Bernard Mechler, Heide Schenkel, Joachim Marhold, Florenci Serras, Montserrat Corominas, Adrià Punset, John Roote and Steven Russell
Genomewide resources—mutant and clone collections in particular—accelerate genetic analysis. This group develops a collection of P-element insertions that promises to facilitate chromosome engineering. They use it to generate a genomewide chromosomal deletion kit, also showing how custom inversions and duplications can enhance the toolbox for manipulating the Drosophila genome.
Bird and mammal sex-chromosome orthologs map to the same autosomal region in a salamander (Ambystoma), pp. 607–613
Jeramiah J. Smith and S. Randal Voss
Amphibians represent the most proximate outgroup to the amniote clade and therefore provide a key outgroup for analysis of evolution of amniote genomes. Comparisons between the salamander (Ambystoma) genome and the genomes of human and chicken reveal that bird and mammal sex chromosome orthologs map to the same autosomal region in a salamander. Results of these outgroup comparisons bring into question the widely accepted theory that the sex chromosomes of birds and mammals evolved from different ancestral chromosomes.
E(var)3-9 of Drosophila melanogaster encodes a zinc finger protein, pp. 167–178
Karen S. Weiler
If Su(var) genes, which encode heterochromatin proteins that promote silencing of genes, are the yin of chromatin, then the E(var)s, which fight the good fight to promote a euchromatic, gene-friendly environment, are the yang. One of these genes, E(var)3-9, has been cloned and found to encode a protein with multiple zinc fingers but no significant homology to other proteins. Learning why embryos devoid of E(var)3-9 fail to complete development will be necessary for understanding this interesting dialectic of chromatin.