Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing

The ratio of genetic diversity on chromosome X to that on the autosomes is sensitive to both natural selection and demography. On the basis of whole-genome sequences of 69 females, we report that whereas this ratio increases with genetic distance from genes across populations, it is lower in Europeans than in West Africans independent of proximity to genes. This relative reduction is most parsimoniously explained by differences in demographic history without the need to invoke natural selection.     

Prairie dog colony attributes and associated vertebrate species

A survey of colony attributes and associated vertebrates on black - tail ( Cynomys ludovicianus ), Gunnison's ( C. gunnisoni ), and white - tail ( C. leucurus ) prairie dogs was made. A belt transect 1.6 km wide and 13,334 km long from Hobbs, New Mexico, to the Utah - Wyoming state line was surveyed. There were 47 colonies located (4760 ha comprising 2.2 percent) in the belt. Intercolony distances varied significantly. Three black - tail towns averaged 33 ha in area (SD = 26, range 10 – 61), II Gunnison's averaged 46 ha (SD = 43, range 16 – 150), and 33 white - tail towns averaged 125 ha (SD = 200, range 0.2 – 958). Badger activity was positively and significantly correlated to colony size and number of burrow openings on Gunnison's and white - tail towns. There were 107 vertebrate species and subspecies (one amphibian, 25 reptiles, 51 birds, 30 mammals) observed on prairie dog colonies. Results of our surveys are compared with prairie dog studies elsewhere. The role of prairie dogs and relationships to some vertebrates species are discussed.     

Spectrin mutations cause spinocerebellar ataxia type 5

We have discovered that beta-III spectrin (SPTBN2) mutations cause spinocerebellar ataxia type 5 (SCA5) in an 11-generation American kindred descended from President Lincoln's grandparents and two additional families. Two families have separate in-frame deletions of 39 and 15 bp, and a third family has a mutation in the actin/ARP1 binding region. Beta-III spectrin is highly expressed in Purkinje cells and has been shown to stabilize the glutamate transporter EAAT4 at the surface of the plasma membrane. We found marked differences in EAAT4 and GluRdelta2 by protein blot and cell fractionation in SCA5 autopsy tissue. Cell culture studies demonstrate that wild-type but not mutant beta-III spectrin stabilizes EAAT4 at the plasma membrane. Spectrin mutations are a previously unknown cause of ataxia and neurodegenerative disease that affect membrane proteins involved in glutamate signaling.     

The rodent hippocampus and spatial memory: from synapses to systems

Although its operations are not limited to the spatial domain, there is a near consensus that the hippocampus plays a critical role in memory for place. This review aims to explore this role, with a particular emphasis on the functions performed by distinct hippocampal subregions. The use of innovative lesioning techniques, localized pharmacological treatments, and molecular genetic interventions is offering increasingly precise brain-regional specificity and temporal control. Together with the electrophysiological recording of neuronal activity, these techniques are beginning to shed light on the functioning of specific components of the hippocampal circuitry in the different phases of memory – encoding, storage, consolidation, and retrieval. In view of these developments, we examine the involvement of the hippocampus in the encoding versus retrieval of spatial memory, before turning to the issue of long-term information storage and the role of ‘cellular’ and ‘systems’ consolidation processes in the formation of lasting memories. Received 17 July 2006; received after revision 24 October 2006; accepted 16 November 2006     

Dynamic evolution of the innate immune system in Drosophila

The availability of complete genome sequence from 12 Drosophila species presents the opportunity to examine how natural selection has affected patterns of gene family evolution and sequence divergence among different components of the innate immune system. We have identified orthologs and paralogs of 245 Drosophila melanogaster immune-related genes in these recently sequenced genomes. Genes encoding effector proteins, and to a lesser extent genes encoding recognition proteins, are much more likely to vary in copy number across species than genes encoding signaling proteins. Furthermore, we can trace the apparent recent origination of several evolutionarily novel immune-related genes and gene families. Using codon-based likelihood methods, we show that immune-system genes, and especially those encoding recognition proteins, evolve under positive darwinian selection. Positively selected sites within recognition proteins cluster in domains involved in recognition of microorganisms, suggesting that molecular interactions between hosts and pathogens may drive adaptive evolution in the Drosophila immune system.