No evidence of inbreeding depression in fast declining herds of migratory caribou

Identifying inbreeding depression early in small and declining populations is essential for management and conservation decisions. Correlations between heterozygosity and fitness (HFCs) provide a way to identify inbreeding depression without prior knowledge of kinship among individuals. In Northern Quebec and Labrador, the size of two herds of migratory caribou (Rivière‐George, RG and Rivière‐aux‐Feuilles, RAF) has declined by one to two orders of magnitude in the last three decades. This raises the question of a possible increase in inbreeding depression originating from, and possibly contributing to, the demographic decline in those populations. Here, we tested for the association of genomic inbreeding indices (estimated with 22,073 SNPs) with body mass and survival in 400 caribou sampled in RG and RAF herds between 1996 and 2016. We found no association of individual heterozygosity or inbreeding coefficient with body mass or annual survival. Furthermore, those genomic inbreeding indices remained stable over the period monitored. These results suggest that the rapid and intense demographic decline of the herds did not cause inbreeding depression in those populations. Although we found no evidence for HFCs, if demographic decline continues, it is possible that such inbreeding depression would be triggered.     

Germination and physiological properties of Frankia spores

Spores from four Frankia strains were isolated and purified to homogeneity. The purified spores were biochemically and physiologically characterized and compared to vegetative cells. Frankia spores exhibited low levels of endogenous respiration that were at least ten-fold lower than the endogenous respiration rate of vegetative cells. The macromolecular content of purified spores and vegetative cells differed. One striking difference among the Frankia spores was their total DNA content. From DAPI staining experiments, only 9% of strain ACN1^AG spore population contained DNA. With strains DC12 and EuI1c, 92% and 67% of their spore population contained DNA. The efficiency of spore germination was correlated to the percentage of the spore population containing DNA. These results suggest that the majority of strain ACN1^AG spores were immature or nonviable. The presence of a solidifying agent inhibited the initial stages of spore germination, but had no effect once the process had been initiated. The optimal incubation temperature for spore germination was 25°C and 30°C for strains DC12 and EuI1c, respectively. A mild heat shock increased the efficiency of spore germination, while root extracts also stimulated spore germination. These results suggest that strains DC12 and EuI1c may be suitable strains for further germination and genetic studies.     

Arabidopsis XXT5 gene encodes a putative alpha-1,6-xylosyltransferase that is involved in xyloglucan biosynthesis

The function of a putative xyloglucan xylosyltransferase from Arabidopsis thaliana (At1g74380; XXT5) was studied. The XXT5 gene is expressed in all plant tissues, with higher levels of expression in roots, stems and cauline leaves. A T-DNA insertion in the XXT5 gene generates a readily visible root hair phenotype (root hairs are shorter and form bubble-like extrusions at the tip), and also causes the alteration of the main root cellular morphology. Biochemical characterization of cell wall polysaccharides isolated from xxt5 mutant seedlings demonstrated decreased xyloglucan quantity and reduced glucan backbone substitution with xylosyl residues. Immunohistochemical analyses of xxt5 plants revealed a selective decrease in some xyloglucan epitopes, whereas the distribution patterns of epitopes characteristic for other cell wall polysaccharides remained undisturbed. Transformation of xxt5 plants with a 35S::HA-XXT5 construct resulted in complementation of the morphological, biochemical and immunological phenotypes, restoring xyloglucan content and composition to wild-type levels. These data provide evidence that XXT5 is a xyloglucan alpha-1,6-xylosyltransferase, and functions in the biosynthesis of xyloglucan.     

Persistence of Dispersal-limited Species in Structured Dynamic Landscapes

Dynamic landscape models have generally assumed random distributions of habitat although real landscapes show spatial organization at many scales. To explore the role of spatial structure in determining the frequency of dispersal-limited forest species, we used a cellular landscape model divided into two zones. Zones were distributed in a random, clustered, or regular spatial pattern. Within each zone habitat cells were randomly destroyed and regenerated, and habitat density and turnover rate were systematically varied. A hypothetical habitat-limited species dispersed between adjacent habitat cells. All trials showed a reduced species frequency relative to a static landscape. Reduction was greater at low habitat density (P = 0.30) than at high density (0.90) suggesting the importance of habitat connectivity in controlling species frequency. The greatest reduction occurred when habitat was concentrated in a small, regularly distributed zone at low habitat density reflecting the enforced isolation of individual habitat cells. Very little reduction was observed when habitat cells were packed into a small clustered zone, a situation promoting connectivity between cells. Moderate–severe frequency reduction occurred when habitat turnover was concentrated in a clustered zone at high habitat density, but little was observed when turnover was widely distributed in a regular or random pattern. These results can be interpreted in terms of a source-sink function in which spatial pattern controlled the degree of contact between landscape zones and determined opportunities for dispersal between habitat cells. We conclude that clustering of forest habitat has the potential to maintain herb species frequency in sparsely forested landscapes. Conversely, clustering of forest disturbance in heavily forested regions, or regular distribution of forest stands (as often occurs in agricultural regions) creates areas which are difficult to colonize, and should be avoided.     

A direct observation of bacterial coverage and biofilm formation by Acidithiobacillus ferrooxidans on chalcopyrite and pyrite surfaces

To obtain a fundamental understanding of the population behaviour of Acidithiobacillus ferrooxidans at chalcopyrite and pyrite surfaces, the early stage attachment behaviour and biofilm formation by this bacterium on chalcopyrite (CuFeS₂) and pyrite (FeS₂) were studied by optical microscopy, Raman spectroscopy, time-of-flight secondary ion mass spectrometry (ToF-SIMS) and electron backscatter diffraction (EBSD). The results indicate there was no significant difference in selectivity of bacterial attachment between chalcopyrite and pyrite. However, the result of ToF-SIMS analysis suggests that the surface of the pyrite was covered more extensively by biofilm than that of the chalcopyrite, which may indicate more extracellular polymeric substances (EPS) formation by bacterial cells growing on pyrite. EBSD and optical image analysis indicated that selectivity of bacterial attachment to chalcopyrite was not significantly affected by crystal orientation. The results also suggest that the bacterial population in defective areas of chalcopyrite was significantly higher than on the polished surfaces.     

Oxygen-binding and immunological properties of complexes between dextran and animal haemoglobins.

Complexes of dextran 20 000 with haemoglobins of sheep, rabbit, dog, bovine and human origin were prepared through alkylation of haemoglobin by N-bromoacetylaminoethylamino-dextran. The yields were uniformly high. Complex-formation in each case was accompanied by the disappearance of reactive thiol groups on the haemoglobin, and by an increase in the affinity of the haemoglobin for oxygen. The immunological properties of dog, rabbit and sheep dextran-haemoglobin were investigated in both homologous and heterologous species. The complexes were found to be non-immunogenic in the homologous species. In heterologous species the anti-haemoglobin response induced by each complex was generally of a similar level to that induced by the haemoglobin alone.     

Evolution by Squinches

Evolution: The Story of Life on Earth provides a lively, accurate, and delightful explanation of evolution in the form of a graphic novel.     

QTL mapping in autotetraploids using SNP dosage information

Key message

Dense linkage maps derived by analysing SNP dosage in autotetraploids provide detailed information about the location of, and genetic model at, quantitative trait loci.

Abstract

Recent developments in sequencing and genotyping technologies enable researchers to generate high-density single nucleotide polymorphism (SNP) genotype data for mapping studies. For polyploid species, the SNP genotypes are informative about allele dosage, and Hackett et al. (PLoS ONE 8:e63939, 2013) presented theory about how dosage information can be used in linkage map construction and quantitative trait locus (QTL) mapping for an F₁ population in an autotetraploid species. Here, QTL mapping using dosage information is explored for simulated phenotypic traits of moderate heritability and possibly non-additive effects. Different mapping strategies are compared, looking at additive and more complicated models, and model fitting as a single step or by iteratively re-weighted modelling. We recommend fitting an additive model without iterative re-weighting, and then exploring non-additive models for the genotype means estimated at the most likely position. We apply this strategy to re-analyse traits of high heritability from a potato population of 190 F₁ individuals: flower colour, maturity, height and resistance to late blight (Phytophthora infestans (Mont.) de Bary) and potato cyst nematode (Globodera pallida), using a map of 3839 SNPs. The approximate confidence intervals for QTL locations have been improved by the detailed linkage map, and more information about the genetic model at each QTL has been revealed. For several of the reported QTLs, candidate SNPs can be identified, and used to propose candidate trait genes. We conclude that the high marker density is informative about the genetic model at loci of large effects, but that larger populations are needed to detect smaller QTLs.     

Isolation and characterization of 23 polymorphic microsatellite loci for a West Indian iguana (Cyclura pinguis) from the British Virgin Islands

Twenty-three polymorphic microsatellite markers were identified and characterized for Cyclura pinguis, a critically endangered species of lizard (Sauria: Iguanidae) native to Anegada Island in the British Virgin Islands. We examined variation at these loci for 39 C. pinguis, finding up to five alleles per locus and an average expected heterozygosity of 0.55. Allele frequency estimates for these microsatellite loci will be used to characterize genetic diversity of captive and wild C. pinguis populations and to estimate relatedness among adult iguanas at the San Diego Zoo that form the nucleus of a captive breeding programme for this critically endangered species.