A comparison of alternative methods to compute conditional genotype probabilities for genetic evaluation with finite locus models

An increased availability of genotypes at marker loci has prompted the development of models that include the effect of individual genes. Selection based on these models is known as marker-assisted selection (MAS). MAS is known to be efficient especially for traits that have low heritability and non-additive gene action. BLUP methodology under non-additive gene action is not feasible for large inbred or crossbred pedigrees. It is easy to incorporate non-additive gene action in a finite locus model. Under such a model, the unobservable genotypic values can be predicted using the conditional mean of the genotypic values given the data. To compute this conditional mean, conditional genotype probabilities must be computed. In this study these probabilities were computed using iterative peeling, and three Markov chain Monte Carlo (MCMC) methods – scalar Gibbs, blocking Gibbs, and a sampler that combines the Elston Stewart algorithm with iterative peeling (ESIP). The performance of these four methods was assessed using simulated data. For pedigrees with loops, iterative peeling fails to provide accurate genotype probability estimates for some pedigree members. Also, computing time is exponentially related to the number of loci in the model. For MCMC methods, a linear relationship can be maintained by sampling genotypes one locus at a time. Out of the three MCMC methods considered, ESIP, performed the best while scalar Gibbs performed the worst.     

On the Paucity of Duplicated Genes in Caenorhabditis elegans Operons

Spliced leader trans-splicing is an mRNA maturation process used by a small set of eukaryotes, including the nematode C. elegans, to cap the downstream genes of operons. We analyzed the frequency of duplication of operonic genes in C. elegans and confirmed that they are duplicated less often in the genome than monocistronic genes. Because operons account for about 15% of the genes in C. elegans, this lower duplication frequency might place a large constraint on the plasticity of the genome. Further analyses suggest that this paucity of duplicated genes results from operon organization hindering specific types of gene duplication. [Reviewing Editor: Dr. Yves van de Peer]     

An investigation of the interactions between lower-limb bone morphology,limb inertial properties and limb dynamics

Bone mass and size clearly affect the safety and survival of wild animals as well as human beings, however, little is known about the interactions between bone size and movement dynamics. A modeling approach was used to investigate the hypothesis that increased bone cortical area causes increased limb moments of inertia, decreased lower-limb movement maximum velocities, and increased energy requirements to sustain submaximum lower-limb locomotion movements. Custom software and digital data of a human leg were used to simulate femur, tibia, and fibula cortical bone area increases of 0%, 22%, 50%, and 80%. Limb segment masses, center of mass locations, and moments of inertia in the sagittal plane were calculated for each bone condition. Movement simulations of unloaded running and cycling motions were performed. Linear regression analyses were used to determine the magnitude of the effect cortical area has on limb moment of inertia, velocity, and the internal work required to move the limbs at a given velocity. The thigh and shank moment of inertia increased linearly up to 1.5% and 6.9%, respectively for an 80% increase in cortical area resulting in 1.3% and 2.0% decreases in maximum unloaded cycling and running velocities, respectively, and in 3.0% and 2.9% increases in internal work for the cycling and running motions, respectively. These results support the hypothesis and though small changes in movement speed and energy demands were observed, such changes may have played an important role in animal survival as bones evolved and became less robust.     

Evaluation of a subject-specific finite-element model of the equine metacarpophalangeal joint under physiological load

The equine metacarpophalangeal (MCP) joint is frequently injured, especially by racehorses in training. Most injuries result from repetitive loading of the subchondral bone and articular cartilage rather than from acute events. The likelihood of injury is multi-factorial but the magnitude of mechanical loading and the number of loading cycles are believed to play an important role. Therefore, an important step in understanding injury is to determine the distribution of load across the articular surface during normal locomotion. A subject-specific finite-element model of the MCP joint was developed (including deformable cartilage, elastic ligaments, muscle forces and rigid representations of bone), evaluated against measurements obtained from cadaver experiments, and then loaded using data from gait experiments. The sensitivity of the model to force inputs, cartilage stiffness, and cartilage geometry was studied. The FE model predicted MCP joint torque and sesamoid bone flexion angles within 5% of experimental measurements. Muscle–tendon forces, joint loads and cartilage stresses all increased as locomotion speed increased from walking to trotting and finally cantering. Perturbations to muscle–tendon forces resulted in small changes in articular cartilage stresses, whereas variations in joint torque, cartilage geometry and stiffness produced much larger effects. Non-subject-specific cartilage geometry changed the magnitude and distribution of pressure and the von Mises stress markedly. The mean and peak cartilage stresses generally increased with an increase in cartilage stiffness. Areas of peak stress correlated qualitatively with sites of common injury, suggesting that further modelling work may elucidate the types of loading that precede joint injury and may assist in the development of techniques for injury mitigation.     

Consequences of Dispersal Heterogeneity for Population Spread and Persistence

Dispersal heterogeneity is increasingly being observed in ecological populations and has long been suspected as an explanation for observations of non-Gaussian dispersal. Recent empirical and theoretical studies have begun to confirm this. Using an integro-difference model, we allow an individual’s diffusivity to be drawn from a trait distribution and derive a general relationship between the dispersal kernel’s moments and those of the underlying heterogeneous trait distribution. We show that dispersal heterogeneity causes dispersal kernels to appear leptokurtic, increases the population’s spread rate, and lowers the critical reproductive rate required for persistence in the face of advection. Wavespeed has been shown previously to be determined largely by the form of the dispersal kernel tail. We qualify this by showing that when reproduction is low, the precise shape of the tail is less important than the first few dispersal moments such as variance and kurtosis. If the reproductive rate is large, a dispersal kernel’s asymptotic tail has a greater influence over wavespeed, implying that estimating the prevalence of traits which correlate with long-range dispersal is critical. The presence of multiple dispersal behaviors has previously been characterized in terms of long-range versus short-range dispersal, and it has been found that rare long-range dispersal essentially determines wavespeed. We discuss this finding and place it within a general context of dispersal heterogeneity showing that the dispersal behavior with the highest average dispersal distance does not always determine wavespeed.     

The ancestor of the <Emphasis Type="Italic">Paulinella</Emphasis> chromatophore obtained a carboxysomal operon by horizontal gene transfer from a <Emphasis Type="Italic">Nitrococcus</Emphasis>-like γ-proteobacterium

Background  

Paulinella chromatophora is a freshwater filose amoeba with photosynthetic endosymbionts (chromatophores) of cyanobacterial origin that are closely related to free-living Prochlorococcus and Synechococcus species (PS-clade). Members of the PS-clade of cyanobacteria contain a proteobacterial form 1A RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) that was acquired by horizontal gene transfer (HGT) of a carboxysomal operon. In rDNA-phylogenies, the Paulinella chromatophore diverged basal to the PS-clade, raising the question whether the HGT occurred before or after the split of the chromatophore ancestor.     

The rat and mouse homologues of MASP-2 and MAp19, components of the lectin activation pathway of complement

Recently, we described two novel constituents of the multimolecular initiation complex of the mannan-binding lectin (MBL) pathway of complement activation, a serine protease of 76 kDa, termed MASP-2, and a MASP-2 related plasma protein of 19 kDa, termed MAp19. Upon activation of the MBL/MASPs/MAp19 complex, MASP-2 cleaves the fourth complement component C4, while the role of MAp19 within the MBL/MASP-1/MASP-2/MAp19 complex remains to be clarified. In humans, the mRNA species encoding MASP-2 (2.6 kb) and MAp19 (1.0 kb) arise by an alternative polyadenylation/splicing mechanism from a single structural MASP-2 gene. Here, we report the complete primary structures of the rat homologue of MASP-2 and of rat and mouse MAp19. We show that both MASP-2 and MAp19 are part of the rat MBL pathway activation complex and demonstrate their exclusively hepatic biosynthesis. Southern blot and PCR analyses of rat genomic DNA indicate that as in humans, rat MASP-2 and MAp19 are encoded by a single structural gene.     

Association between pygmy right whales (Caperea marginata) and areas of high marine productivity off Australia and New Zealand

Abstract

Opportunistic sightings and strandings of Caperea marginata (n=196) from the vicinity of Australia and New Zealand (1884 to early 2007) were used to relate geographic and temporal patterns to oceanographic and broad-scale climatic variability. Records were not uniformly distributed along the coast and more (69%) were from Australia than New Zealand. Seven coastal whale ‘hotspots’ were identified which accounted for 61% of records with locality data. Half of the hotspot records were from southeast (37) and northwest (20) Tasmania—others each had 9–15 events. Upwelling and/or high zooplankton abundance has been documented near all whale hotspots. Records of C. marginata occurred in all months, with 75% in spring and summer. Inter-annual variability showed broad agreement between increased whale records (usually in spring/summer) and strongly positive ‘Niño 3.4’ during 1980–1995 but not thereafter. Coastal upwelling and productivity increase during climatic phenomena such as El Niño and are likely to be quickly beneficial to plankton-feeding whales such as C. marginata.