Fine-scale phylogeographic congruence despite demographic incongruence in two low-mobility saproxylic springtails

Evolutionary trajectories of codistributed taxa with comparable ecological preferences and dispersal abilities may be similarly impacted by historical landscape-level processes. Species' responses to changes in a shared biogeographic landscape may be purely concerted, completely independent, or classified as falling within an intermediate part of the continuum bounded by these two extremes. With sufficient molecular data, temporal contrasts of congruence among taxa with respect to these responses can be made. Such contrasts provide insights into the relative influence of ancient versus more recent climatic (and other) impacts on genetic structuring. Using phylogenetic, allele frequency, and genotypic data from two low-mobility, rotting-log-adapted (saproxylic) springtail species (Collembola) from an isolated 100-km-long section of the Great Dividing Range in southeastern Australia, we tested the concerted-response hypothesis over three timescales. Tests of phylogeographic, demographic, and contemporary population-genetic congruence were performed using an integrative approach that draws on both direct (pattern-based) and indirect (scenario-based) analyses. Our data revealed a general pattern of broad-scale similarities in species' responses to the interaction between Pleistocene climatic cycles and landscape setting, overlaid with some species-specific differences on local geographic and more recent temporal scales. This general pattern of phylogeographic congruence was accompanied by evidence for contemporaneous demographic incongruence indicating that, even at relatively small spatial scales, biogeographic context can exert an overarching influence on genetic structuring.     

Endothelial cell permeability to water

We have calculated diffusional permeability coefficients for tracer water and for [14C]antipyrine in endothelial cells. With these values and those from studies in whole lungs we set a range for diffusional water permeability coefficients of the intact endothelium.     

Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

Background

Residual feed intake (RFI), a measure of feed efficiency, is the difference between observed feed intake and the expected feed requirement predicted from growth and maintenance. Pigs with low RFI have reduced feed costs without compromising their growth. Identification of genes or genetic markers associated with RFI will be useful for marker-assisted selection at an early age of animals with improved feed efficiency.

Methodology/Principal findings

Whole genome association studies (WGAS) for RFI, average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA) were performed on 1,400 pigs from the divergently selected ISU-RFI lines, using the Illumina PorcineSNP60 BeadChip. Various statistical methods were applied to find SNPs and genomic regions associated with the traits, including a Bayesian approach using GenSel software, and frequentist approaches such as allele frequency differences between lines, single SNP and haplotype analyses using PLINK software. Single SNP and haplotype analyses showed no significant associations (except for LMA) after genomic control and FDR. Bayesian analyses found at least 2 associations for each trait at a false positive probability of 0.5. At generation 8, the RFI selection lines mainly differed in allele frequencies for SNPs near (<0.05 Mb) genes that regulate insulin release and leptin functions. The Bayesian approach identified associations of genomic regions containing insulin release genes (e.g., GLP1R, CDKAL, SGMS1) with RFI and ADFI, of regions with energy homeostasis (e.g., MC4R, PGM1, GPR81) and muscle growth related genes (e.g., TGFB1) with ADG, and of fat metabolism genes (e.g., ACOXL, AEBP1) with BF. Specifically, a very highly significantly associated QTL for LMA on SSC7 with skeletal myogenesis genes (e.g., KLHL31) was identified for subsequent fine mapping.

Conclusions/significance

Important genomic regions associated with RFI related traits were identified for future validation studies prior to their incorporation in marker-assisted selection programs.     

Environmental Complexity and Biodiversity: The Multi-Layered Evolutionary History of a Log-Dwelling Velvet Worm in Montane Temperate Australia

Phylogeographic studies provide a framework for understanding the importance of intrinsic versus extrinsic factors in shaping patterns of biodiversity through identifying past and present microevolutionary processes that contributed to lineage divergence. Here we investigate population structure and diversity of the Onychophoran (velvet worm) Euperipatoides rowelli in southeastern Australian montane forests that were not subject to Pleistocene glaciations, and thus likely retained more forest cover than systems under glaciation. Over a ~100 km transect of structurally-connected forest, we found marked nuclear and mitochondrial (mt) DNA genetic structuring, with spatially-localised groups. Patterns from mtDNA and nuclear data broadly corresponded with previously defined geographic regions, consistent with repeated isolation in refuges during Pleistocene climatic cycling. Nevertheless, some E. rowelli genetic contact zones were displaced relative to hypothesized influential landscape structures, implying more recent processes overlying impacts of past environmental history. Major impacts at different timescales were seen in the phylogenetic relationships among mtDNA sequences, which matched geographic relationships and nuclear data only at recent timescales, indicating historical gene flow and/or incomplete lineage sorting. Five major E. rowelli phylogeographic groups were identified, showing substantial but incomplete reproductive isolation despite continuous habitat. Regional distinctiveness, in the face of lineages abutting within forest habitat, could indicate pre- and/or postzygotic gene flow limitation. A potentially functional phenotypic character, colour pattern variation, reflected the geographic patterns in the molecular data. Spatial-genetic patterns broadly match those in previously-studied, co-occurring low-mobility organisms, despite a variety of life histories. We suggest that for E. rowelli, the complex topography and history of the region has led to interplay among limited dispersal ability, historical responses to environmental change, local adaptation, and some resistance to free admixture at geographic secondary contact, leading to strong genetic structuring at fine spatial scale.     

Chemical Evidence for the Separation of Gy and AY Globin Chains by Polyacrylamide Gel Electrophoresis in Urea and Triton X-100

Polyacrylamide gel electrophoresis in urea and Triton X-100 of a hemolysate from human fetal red blood cells produces four major protein bands: α, β, and 2 γ globin chains. We have verified that the latter two are the ^Gγ and ^Aγ globin chains which have respectively glycine or alanine at position 136. After incorporation of either [³H] alanine or [³H] glycine into newly synthesized globin each y chain was isolated by preparative electrophoresis. The chains were cleaved with cyanogen bromide at methionines 55 and 133, then subjected to automated sequencing, and the residues from each sequencer turn counted. Glycine incor-poration was detected for the third turn (position 136) of the ^Gγ chain and alanine for the ^Aγ. Substantial metabolic conversion of [³H] glycine to serine and proline was also noted.     

Comparison of breeding value prediction for two traits in a Nellore-Angus crossbred population using different Bayesian modeling methodologies

The objectives of this study were to 1) compare four models for breeding value prediction using genomic or pedigree information and 2) evaluate the impact of fixed effects that account for family structure. Comparisons were made in a Nellore-Angus population comprising F₂, F₃ and half-siblings to embryo transfer F₂ calves with records for overall temperament at weaning (TEMP; n = 769) and Warner-Bratzler shear force (WBSF; n = 387). After quality control, there were 34,913 whole genome SNP markers remaining. Bayesian methods employed were BayesB ($\tilde{\pi }$ = 0.995 or 0.997 for WBSF or TEMP, respectively) and BayesC (π = 0 and $\tilde{\pi }$), where $\tilde{\pi }$ is the ideal proportion of markers not included. Direct genomic values (DGV) from single trait Bayesian analyses were compared to conventional pedigree-based animal model breeding values. Numerically, BayesC procedures (using $\tilde{\pi }$) had the highest accuracy of all models for WBSF and TEMP ($\widehat{\rho }$_gĝ = 0.843 and 0.923, respectively), but BayesB had the least bias (regression of performance on prediction closest to 1, $\widehat{\beta }$_y,x = 2.886 and 1.755, respectively). Accounting for family structure decreased accuracy and increased bias in prediction of DGV indicating a detrimental impact when used in these prediction methods that simultaneously fit many markers.     

The evolution of phylogeographic data sets

Empirical phylogeographic studies have progressively sampled greater numbers of loci over time, in part motivated by theoretical papers showing that estimates of key demographic parameters improve as the number of loci increases. Recently, next‐generation sequencing has been applied to questions about organismal history, with the promise of revolutionizing the field. However, no systematic assessment of how phylogeographic data sets have changed over time with respect to overall size and information content has been performed. Here, we quantify the changing nature of these genetic data sets over the past 20 years, focusing on papers published in Molecular Ecology. We found that the number of independent loci, the total number of alleles sampled and the total number of single nucleotide polymorphisms (SNPs) per data set has improved over time, with particularly dramatic increases within the past 5 years. Interestingly, uniparentally inherited organellar markers (e.g. animal mitochondrial and plant chloroplast DNA) continue to represent an important component of phylogeographic data. Single‐species studies (cf. comparative studies) that focus on vertebrates (particularly fish and to some extent, birds) represent the gold standard of phylogeographic data collection. Based on the current trajectory seen in our survey data, forecast modelling indicates that the median number of SNPs per data set for studies published by the end of the year 2016 may approach ~20 000. This survey provides baseline information for understanding the evolution of phylogeographic data sets and underscores the fact that development of analytical methods for handling very large genetic data sets will be critical for facilitating growth of the field.