A simple procedure for directly obtaining haplotype sequences of diploid genomes.

BACKGROUND: Almost all genome sequencing projects neglect the fact that diploid organisms contain two genome copies and consequently what is published is a composite of the two. This means that the relationship between alternate alleles at two or more linked loci is lost. We have developed a simplified method of directly obtaining the haploid sequences of each genome copy from an individual organism. RESULTS: The diploid sequences of three groups of cattle samples were obtained using a simple sample preparation procedure requiring only a microscope and a haemocytometer. Samples were: 1) lymphocytes from a single Angus steer; 2) sperm cells from an Angus bull; 3) lymphocytes from East African Zebu (EAZ) cattle collected and processed in a field laboratory in Eastern Kenya. Haploid sequence from a fosmid library prepared from lymphocytes of an EAZ cow was used for comparison. Cells were serially diluted to a concentration of one cell per microlitre by counting with a haemocytometer at each dilution. One microlitre samples, each potentially containing a single cell, were lysed and divided into six aliquots (except for the sperm samples which were not divided into aliquots). Each aliquot was amplified with phi29 polymerase and sequenced. Contigs were obtained by mapping to the bovine UMD3.1 reference genome assembly and scaffolds were assembled by joining adjacent contigs that were within a threshold distance of each other. Scaffolds that appeared to contain artefacts of CNV or repeats were filtered out leaving scaffolds with an N50 length of 27-133 kb and a 88-98 % genome coverage. SNP haplotypes were assembled with the Single Individual Haplotyper program to generate an N50 size of 97-201 kb but only ~27-68 % genome coverage. This method can be used in any laboratory with no special equipment at only slightly higher costs than conventional diploid genome sequencing. A substantial body of software for analysis and workflow management was written and is available as supplementary data. CONCLUSIONS: We have developed a set of laboratory protocols and software tools that will enable any laboratory to obtain haplotype sequences at only modestly greater cost than traditional mixed diploid sequences.

Density-dependent investment in costly anti-predator defences: an explanation for the weak survival benefit of group living.

A central explanation for group living across animal taxa is the reduced rate of attack by predators. However, many field observations show a weak or non-existent effect of group size on per capita mortality rates. Herein we resolve this apparent paradox. We found that Pieris brassicae larvae defended themselves less readily when in groups than when alone, in that they were more reluctant to regurgitate in response to simulated attacks and produced less regurgitant. Furthermore, a simple model demonstrates that this reluctance was sufficient to cancel out the benefit from being in a group. This conditional strategy can be understood in terms of the costs and benefits of defences. For grouped individuals, defence is less often required because attack rates are lower and the costs of defence may be higher due to competition for resources. These phenomena are likely to be widespread in facultatively gregarious species that utilise anti-predator defences.

Spatio-Environmental Analysis of Vespula germanica Nest Records Explains Slow Invasion in South Africa.

Investigating the distributions of invasive species in marginal habitats can give clues to the factors constraining invasive spread. Vespula germanica is the most widely distributed of all the invasive Vespids, which in the Southern Hemisphere typically have large extensive invasive populations. In contrast, the invasion into South Africa has been slow and is still confined to a small geographic area. Here we analyse the distribution of all recent nest records in South Africa (n = 405). The distance to main rivers, mean annual rainfall, summer normalised difference moisture index (NDMI) values, and mean annual temperatures (average, minimum, maximum, and summer maximum temperature) was measured for every nest. We find that value ranges of these variables are different between the value ranges recorded for nests, the general distribution area of the wasp, and the area of absence. Optimised Hot Spot Analysis was used to quantify spatial structure in the measured climatic variables. Generally, factors related to moisture stress set the environmental limits of V. germanica's landscape distribution. Due to the strong preference of nesting sites close to river courses, for higher rainfall conditions, medium to medium-high NDMI values, and lower mean annual temperatures, it is unlikely that V. germanica will be able to spread uniformly where it is currently found in South Africa.