Genome sequence, comparative analysis and haplotype structure of the domestic dog

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.     

Molecular evidence for genetic mixing of Arctic and Antarctic subpolar populations of planktonic foraminifers

Bipolarity, the presence of a species in the high latitudes separated by a gap in distribution across the tropics, is a well-known pattern of global species distribution. But the question of whether bipolar species have evolved independently at the poles since the establishment of the cold-water provinces 16-8 million years ago, or if genes have been transferred across the tropics since that time, has not been addressed. Here we examine genetic variation in the small subunit ribosomal RNA gene of three bipolar planktonic foraminiferal morphospecies. We identify at least one identical genotype in all three morphospecies in both the Arctic and Antarctic subpolar provinces, indicating that trans-tropical gene flow must have occurred. Our genetic analysis also reveals that foraminiferal morphospecies can consist of a complex of genetic types. Such occurrences of genetically distinct populations within one morphospecies may affect the use of planktonic foraminifers as a palaeoceanographic proxy for climate change and necessitate a reassessment of the species concept for the group.     

The mosaic structure of variation in the laboratory mouse genome

Most inbred laboratory mouse strains are known to have originated from a mixed but limited founder population in a few laboratories. However, the effect of this breeding history on patterns of genetic variation among these strains and the implications for their use are not well understood. Here we present an analysis of the fine structure of variation in the mouse genome, using single nucleotide polymorphisms (SNPs). When the recently assembled genome sequence from the C57BL/6J strain is aligned with sample sequence from other strains, we observe long segments of either extremely high (approximately 40 SNPs per 10 kb) or extremely low (approximately 0.5 SNPs per 10 kb) polymorphism rates. In all strain-to-strain comparisons examined, only one-third of the genome falls into long regions (averaging >1 Mb) of a high SNP rate, consistent with estimated divergence rates between Mus musculus domesticus and either M. m. musculus or M. m. castaneus. These data suggest that the genomes of these inbred strains are mosaics with the vast majority of segments derived from domesticus and musculus sources. These observations have important implications for the design and interpretation of positional cloning experiments.     

Survival variability and population density in fish populations

To understand the processes that regulate the abundance and persistence of wild populations is a fundamental goal of ecology and a prerequisite for the management of living resources. Variable abundance data, however, make the demonstration of regulation processes challenging. A previously overlooked aspect in understanding how populations are regulated is the possibility that the pattern of variability--its strength as a function of population size--may be more than 'noise', thus revealing much about the characteristics of population regulation. Here we show that patterns in survival variability do provide evidence of regulation through density. Using a large, global compilation of marine, anadromous and freshwater fisheries data, we examine the relationship between the variability of survival and population abundance. The interannual variability in progeny survival increases at low adult abundance in an inversely density-dependent fashion. This pattern is consistent with models in which density dependence enters after the larval stage. The findings are compatible with very simple forms of density dependence: even a linear increase of juvenile mortality with adult density adequately explains the results. The model predictions explain why populations with strong regulation may experience large increases in variability at low densities. Furthermore, the inverse relationship between survival variability and the strength of density dependence has important consequences for fisheries management and recovery, and population persistence or extinction.     

Topology Adaptation for Robust Ad Hoc Cyberphysical Networks under Puncture-Style Attacks

Many cyber physical networks will involve ad hoc deployments utilizing peer-to-peer communications.Examples include transportation systems where a group of moving cars communicate in order to avoid collisions,teams of robotic agents that work together in support of disaster recovery, and sensor networks deployed for health-care monitoring, monitoring the operation of a factory plant or to coordinate and actuate mechanisms for energy conservation in a building. These networks may face a variety of threats that puncture their connectivity and, should their performance degrade, the result could be catastrophic. Consider, for example, a vehicular ad hoc network where communication assists collision avoidance. In such a case, degradation could lead to vehicle accidents. Therefore, in order to overcome network performance degradations and the puncture of a network(such as blackhole or jamming) which is under attack, we propose an algorithm called the Fiedler Value Power Adjustment Topology Adaption(FVPATA). FVPATA aims to dynamically adapt an ad hoc network's topology, even if the attacker varies its location and in the case of an interference-style attack by increasing the interference power. The algorithm utilizes the formulation from the graph theory which works with the Fiedler value to guide each node in wireless ad hoc network utilizing power adjustments to enhance the network's overall robustness. The advantage of the proposed mechanism is that it is a light-weight approach which is totally distributed, based on topology updates inherent in the Optimized Link State Routing(OLSR) protocol and, hence, it is unnecessary to introduce additional messages. Additionally, an algorithm was developed to resolve problems involving asymmetric links that arise in ad hoc networks by eliminating unnecessary energy consumption of Fiedler nodes. Simulation results using NS3 show that the proposed mechanism successfully decreases the average amount of hops used by 50% and the delay of flows when nodes are migrating at a modest rate below 60 m/min.