The new sequencer on the block: comparison of Life Technology’s Proton sequencer to an Illumina HiSeq for whole-exome sequencing

We assessed the performance of the new Life Technologies Proton sequencer by comparing whole-exome sequence data in a Centre d’Etude du Polymorphisme Humain trio (family 1463) to the Illumina HiSeq instrument. To simulate a typical user’s results, we utilized the standard capture, alignment and variant calling methods specific to each platform. We restricted data analysis to include the capture region common to both methods. The Proton produced high quality data at a comparable average depth and read length, and the Ion Reporter variant caller identified 96 % of single nucleotide polymorphisms (SNPs) detected by the HiSeq and GATK pipeline. However, only 40 % of small insertion and deletion variants (indels) were identified by both methods. Usage of the trio structure and segregation of platform-specific alleles supported this result. Further comparison of the trio data with Complete Genomics sequence data and Illumina SNP microarray genotypes documented high concordance and accurate SNP genotyping of both Proton and Illumina platforms. However, our study underscored the problem of accurate detection of indels for both the Proton and HiSeq platforms.     

Breeding distribution,population size and conservation of the Greyheaded Gull Larus cirrocephalus in southern Africa

Brooke, R.K., Allan, D.G., Cooper, J., Cyrus, D.P., Dean, W.R.J., Dyer, B.M., Martin, A.P. & Taylor, R.H. 1999. Breeding distribution, population size and conservation of the Greyheaded Gull Larus cirrocephalus in southern Africa. Ostrich 70 (3&4): 157–163.

The Greyheaded Gull Larus cirrocephalus occurs throughout southern Africa, both coastally and inland, and has bred at one time or another at 67 known localities since the 1860s. Most of these sites have been occupied by small numbers of birds, even single pairs, and for only one or a few years. The two principal breeding areas are the East Rand in Gauteng and Lake St Lucia in KwaZulu-Natal, both in South Africa. The next most important sites are Walvis Bay, Namibia and Lake Ngami, Botswana. The total southern African breeding population is estimated as about 2000 pairs. The Greyheaded Gull is not a threatened species in southern Africa, with 27 breeding sites supporting more than half the breeding population within formally conserved areas.     

Male nest building but not display behaviour directly influences mating success in the polygynous Red Bishop,Euplectes orix

Previous studies of the highly polygynous and strikingly sexually dimorphic Red Bishop, Euplectes orix (Ploceinae, weaverbirds), have suggested random female settlement patterns and no correlates of male reproductive success except the number of nest frames (‘cock's nests’) built by the male. Although this confirms the central role of the nest in weaverbird courtship it also contrasts with demonstrated sexual selection on male morphology and behaviour in several closely related Euplectes species. Two major aspects of male sexual advertising have not been included in previous studies; display behaviour and territory size. In this study we use multivariate selection analysis, with the number of active nests in a territory as the fitness measure, to identify direct and indirect sexual selection on male sexual behaviour, territory size and nest building. In accor–dance with previous findings, mating success was not strongly skewed among the territorial males, and females appeared to settle randomly with respect to available nests. The number of cock𠀧s nest built was the only determinant of male breeding success, even when controlling for male display activity and territory size. We argue that, despite their conspicuous sexual dimorphism, females settle independently of both male or territory quality, and that variance in male reproductive success is a consequence of male–male competition.     

A preliminary assessment of the habitat selection of two Palaearctic migrant passerine species in West Africa

We investigated the habitat selected by two Palaearctic migrants (Pied Flycatcher, Ficedula hypoleuca, Willow Warbler, Phylloscopus trochilus) in a patchy landscape in Ivory Coast and compared it with the habitat selection of Afrotropical species in the same foraging guilds. Transect counts were used to test the hypothesis that migrants use more open and more seasonal habitats and have a broader use of habitats compared with resident species. Habitats compared were, in order of decreasing tree density, gallery forest, an isolated forest and bush/tree savanna. The isolated forest had the most pronounced seasonal changes (deciduous trees) and was the one with the most diverse vegetation structure. The habitat where both migrants were most frequent was the isolated forest, and thus occurred in the habitat with the most pronounced seasonal change. Diversity of habitats selected was highest in migrants but in the Pied Flycatcher this was possibly an artefact due to subdominant individuals being excluded from the preferred habitat by territorial birds. Potential competition for habitat with Afrotropical species was found to be low.     

Migratory Masked Shrikes,Lanius nubicus staging at the desert edge: phenology,and sex- and age-related differences in body mass

Migratory Masked Shrikes (Lanius nubicus) were mist-netted during the spring and autumn migrations at Eilat, Israel. Nearly four times more shrikes were trapped during spring than in autumn. This could be explained by either the species assorting to loop migration, or a higher capture rate owing to poor body condition after crossing the Sahara in spring. In spring, no differences in phenology were observed between the sex- and age-groups. In contrast, in autumn juvenile males arrived significantly later than the rest of the population. Significant differences in wing chord length were found between the four sex and age classes (adult male, adult female, juvenile male, juvenile female) both in spring and autumn. However, significant differences in body mass were found only in autumn. In spring, in both sexes, wing length and body mass changed significantly with date of arrival. Masked Shrike in spring were lighter than in autumn. The results suggest that migration over desert is energetically costly and Eilat is a very important staging place for migratory Masked Shrikes.     

The effect of rainfall on the breeding behaviour of the Red Bishop,Euplectes orix

The behaviour and activities of 6 458 raptors (Accipitridae and Falconidae) and 1 947 Corvidae in the Karoo, South Africa, were recorded during the period January 1988 to June 2000 (n = 208 surveys) over a total distance of 90 012km. A significantly larger proportion of raptors and corvids were recorded foraging in road verges, or flying along roads than foraging or flying over rangelands. About 21% of all observations of crows feeding or foraging were associated with road-kills, whereas less than 2% of observations of feeding and foraging Accipitridae and Falconidae were associated with road-kills. The most frequent Accipitridae feeding on road-kills were Pale Chanting Goshawk (Melierax canorus), Yellow-billed Kite (Milvus migrans parasitus) and Jackal Buzzard (Buteo rufofuscus). There was no seasonal pattern in the number of crows feeding on roadkills, although there was a trend for more mammals to be killed on the roads, and thus more available food, in winter (June). It is likely that Accipitridae and Falconidae are attracted to roads by the availability of perches and the relatively productive road verges rather than the availability of road-killed animals, whereas crows may be attracted by road-kills as well.     

Evidence for Transaldolase Activity in the Isolated Heart Supplied with [U-13C3]Glycerol

Studies of glycerol metabolism in the heart have largely emphasized its role in triglyceride synthesis. However, glycerol may also be oxidized in the citric acid cycle, and glycogen synthesis from glycerol has been reported in the nonmammalian myocardium. The intent of this study was to test the hypothesis that glycerol may be metabolized to glycogen in mammalian heart. Isolated rat hearts were supplied with a mixture of substrates including glucose, lactate, pyruvate, octanoate, [U-¹³C₃]glycerol, and ²H₂O to probe various metabolic pathways including glycerol oxidation, glycolysis, the pentose phosphate pathway, and carbon sources of stored glycogen. NMR analysis confirmed that glycogen production from the level of the citric acid cycle did not occur and that the glycerol contribution to oxidation in the citric acid cycle was negligible in the presence of alternative substrates. Quite unexpectedly, ¹³C from [U-¹³C₃]glycerol appeared in glycogen in carbon positions 4–6 of glucosyl units but none in positions 1–3. The extent of [4,5,6-¹³C₃]glucosyl unit enrichment in glycogen was enhanced by insulin but decreased by H₂O₂. Given that triose phosphate isomerase is generally assumed to fully equilibrate carbon tracers in the triose pool, the marked ¹³C asymmetry in glycogen can only be attributed to conversion of [U-¹³C₃]glycerol to [U-¹³C₃]dihydroxyacetone phosphate and [U-¹³C₃]glyceraldehyde 3-phosphate followed by rearrangements in the nonoxidative branch of the pentose phosphate pathway involving transaldolase that places this ¹³C-enriched 3-carbon unit only in the bottom half of hexose phosphate molecules contributing to glycogen.     

Disruption of Ttll5/Stamp Gene (Tubulin Tyrosine Ligase-like Protein 5/SRC-1 and TIF2-associated Modulatory Protein Gene) in Male Mice Causes Sperm Malformation and Infertility

TTLL5/STAMP (tubulin tyrosine ligase-like family member 5) has multiple activities in cells. TTLL5 is one of 13 TTLLs, has polyglutamylation activity, augments the activity of p160 coactivators (SRC-1 and TIF2) in glucocorticoid receptor-regulated gene induction and repression, and displays steroid-independent growth activity with several cell types. To examine TTLL5/STAMP functions in whole animals, mice were prepared with an internal deletion that eliminated several activities of the Stamp gene. This mutation causes both reduced levels of STAMP mRNA and C-terminal truncation of STAMP protein. Homozygous targeted mutant (Stamp^tm/tm) mice appear normal except for marked decreases in male fertility associated with defects in progressive sperm motility. Abnormal axonemal structures with loss of tubulin doublets occur in most Stamp^tm/tm sperm tails in conjunction with substantial reduction in α-tubulin polyglutamylation, which closely correlates with the reduction in mutant STAMP mRNA. The axonemes in other structures appear unaffected. There is no obvious change in the organs for sperm development of WT versus Stamp^tm/tm males despite the levels of WT STAMP mRNA in testes being 20-fold higher than in any other organ examined. This defect in male fertility is unrelated to other Ttll genes or 24 genes previously identified as important for sperm function. Thus, STAMP appears to participate in a unique, tissue-selective TTLL-mediated pathway for α-tubulin polyglutamylation that is required for sperm maturation and motility and may be relevant for male fertility.