Extending phylogeography to account for lineage fusion

Secondary contact between long isolated populations has several possible outcomes. These include the strengthening of preexisting reproductive isolating mechanisms via reinforcement, the emergence of a hybrid lineage that is distinct from its extant parental lineages and which occupies a spatially restricted zone between them, or complete merging of two populations such that parental lineages are no longer extant (“lineage fusion” herein). The latter scenario has rarely been explicitly considered in single‐species and comparative phylogeographic studies, yet it has the potential to impact inferences about population history and levels of congruence. In this paper, we explore the idea that insights into past lineage fusion may now be possible, owing to the advent of next‐generation sequencing. Using simulated DNA sequence haplotype datasets (i.e., loci with alleles comprised of a set of linked nucleotide polymorphisms), we examined basic requirements (number of loci and individuals sampled) for identifying cases when a present‐day panmictic population is the product of lineage fusion, using an exemplar statistical framework—approximate Bayesian computation. We found that with approximately 100 phased haplotype loci (each 400 bp long) and modest sample sizes of individuals (10 per population), lineage fusion can be detected under rather challenging scenarios. This included some scenarios where reticulation was fully contained within a Last Glacial Maximum timeframe, provided that mixing was symmetrical, ancestral gene pools were moderately to deeply diverged, and the lag time between the fusion event and gene pool sampling was relatively short. However, the more realistic case of asymmetrical mixing is not prohibitive if additional genetic data (e.g., 400 loci) are available. Notwithstanding some simplifying assumptions of our simulations and the knowledge gaps that remain about the circumstances under which lineage fusion is potentially detectable, we suggest that the recent release from data limitation allows phylogeographers to expand the scope of inferences about long‐term population history.     

Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences

We derive an analytic expression for site-specific stationary distributions of amino acids from the structurally constrained neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that we obtain have a Boltzmann-like shape, and their effective temperature parameter, measuring the limit of divergent evolutionary changes at a given site, can be predicted from a site-specific topological property, the principal eigenvector of the contact matrix of the native conformation of the protein. These analytic results, obtained without free parameters, are compared with simulations of the SCN model and with the site-specific amino acid distributions obtained from the Protein Data Bank. These results also provide new insights into how the topology of a protein fold influences its designability, i.e., the number of sequences compatible with that fold. The dependence of the effective temperature on the principal eigenvector decreases for longer proteins, as a possible consequence of the fact that selection for thermodynamic stability becomes weaker in this case.     

Sac1, a lipid phosphatase at the interface of vesicular and nonvesicular transport

The lipid phosphatase Sac1 dephosphorylates phosphatidylinositol 4‐phosphate (PI4P), thereby holding levels of this crucial membrane signaling molecule in check. Sac1 regulates multiple cellular processes, including cytoskeletal organization, membrane trafficking and cell signaling. Here, we review the structure and regulation of Sac1, its roles in cell signaling and development and its links to health and disease. Remarkably, many of the diverse roles attributed to Sac1 can be explained by the recent discovery of its requirement at membrane contact sites, where its consumption of PI4P is proposed to drive interorganelle transfer of other cellular lipids, thereby promoting normal lipid homeostasis within cells.      

The distribution and abundance of wheat roots in a dense,structured subsoil – implications for water uptake

We analysed the abundance, spatial distribution and soil contact of wheat roots in dense, structured subsoil to determine whether incomplete extraction of subsoil water was due to root system limitations. Intact soil cores were collected to 1.6 m below wheat crops at maturity on a red Kandosol in southern Australia. Wheat roots, remnant roots, soil pores and root–soil contact were quantified at fresh breaks in the soil cores. In surface soil layers (<0.6 m) 30–40% of roots were clumped within pores and cracks in the soil, increasing to 85–100% in the subsoil (>0.6 m), where 44% of roots were in pores with at least three other roots. Most pores contained no roots, with occupancy declining from 20% in surface layers to 5% in subsoil. Wheat roots clumped into pores contacted the surrounding soil via numerous root hairs, whereas roots in cracks were appressed to the soil surface and had very few root hairs. Calculations assuming good root–soil contact indicated that root density was sufficient to extract available subsoil water, suggesting that uptake is constrained at the root–soil interface. To increase extraction of subsoil water, genetic targets could include increasing root–soil contact with denser root hairs, and increasing root proliferation to utilize existing soil pores.     

The Balearic Islands: a reservoir of cpDNA genetic variation for evergreen oaks

Aim To analyse the role of the Balearic Islands as a refuge area for evergreen Quercus (cork oak: Quercus suber L., holm oak: Q. ilex L., kermes oak: Q. coccifera L.), by using molecular, historical and palaeobotanical data. Location The Western Mediterranean Basin (Balearic Islands, eastern Iberia, Provence, Sardinia, Corsica, Sicily, Malta, Italy, Northern Africa). Methods We sampled 108 populations and used the PCR‐RFLP technique with five universal cpDNA primers to define haplotypes in the sampled populations. Diversity, differentiation parameters and spatial analysis of the populations, using a spatial version of amova , were linked to the geological history of the Western Mediterranean Basin in order to explain the present spatial pattern of the evergreen Quercus populations in the Balearics. Results Evergreen Quercus cpDNA shows a complex structure, with remnants of ancient diversity in the Balearics. Balearic populations of holm oak are related to Iberian populations, while for cork and kermes oaks, we found both Tyrrhenian and Iberian haplotypes. Main conclusions The complex spatial patterns of cpDNA in Balearic evergreen Quercus appears explicable in terms of a combination of physical (vicariance and long distance dispersal) and biological (introgressive hybridization) factors. The Balearics constitute a glacial refuge area and a reservoir of genetic variation with traces of ancient diversity from Messinian–Pliocene stages.     

Using differential introgression in hybrid zones to identify genomic regions involved in speciation

Hybrids between species provide information about the evolutionary processes involved in divergence. In addition to creating hybrids in the laboratory, biologists can take advantage of natural hybrid zones to understand the factors that shape gene flow between divergent lineages. In the early stages of speciation, most regions of the genome continue to flow freely between populations. Alternatively, the subset of the genome that confers reproductive barriers between nascent species is expected to reject introgression. Now enabled by advances in genomics, this perspective is motivating detailed comparisons of gene flow across genomic regions in hybrid zones. Here, I review methods for measuring and interpreting introgression at multiple loci in hybrid zones, focusing on the problem of identifying loci that contribute to reproductive isolation. Emerging patterns from multi-locus studies of hybrid zones are highlighted, including remarkable variance in introgression across the genome. Although existing methods have been useful, there is scope for development of new analytical approaches that better connect differential patterns of gene flow in hybrid zones with current knowledge of speciation mechanisms. I outline future prospects for differential introgression studies on a genomic scale.     

Characterization of AT2 Receptor Expression in NIH 3T3 Fibroblasts

1. A high expression of angiotensin II receptors and of angiotensin-converting enzyme (ACE) activity was detected in confluent NIH 3T3 fibroblasts.2. Characterization with selective ligands, dithiothreitol, and GTPS, indicated that only the AT₂ subtype was expressed.3. AT₂ receptors and ACE expression were strictly dependent on the cell density and growth phase of the cells, with AT₂ receptors being expressed earlier than ACE. In contrast, high expression of AT₂ receptors irrespective of their growth state was observed in NIH 3T3 cells lacking contact inhibition upon neoplastic transformation with ras.4. Our results imply a possible relation of AT₂ receptors to cell growth and cell–cell contact.     

Defective dendritic cell migration and activation of adaptive immunity in PI3Kgamma-deficient mice

Gene-targeted mice were used to evaluate the role of the gamma isoform of phosphoinositide 3-kinase (PI3Kgamma) in dendritic cell (DC) migration and induction of specific T-cell-mediated immune responses. DC obtained from PI3Kgamma-/- mice showed a reduced ability to respond to chemokines in vitro and ex vivo and to travel to draining lymph nodes under inflammatory conditions. PI3Kgamma-/- mice had a selective defect in the number of skin Langerhans cells and in lymph node CD8alpha- DC. Furthermore, PI3Kgamma-/- mice showed a defective capacity to mount contact hypersensitivity and delayed-type hypersensitivity reactions. This defect was directly related to the reduced ability of antigen-loaded DC to migrate from the periphery to draining lymph nodes. Thus, PI3Kgamma plays a nonredundant role in DC trafficking and in the activation of specific immunity. Therefore, PI3Kgamma may be considered a new target to control exaggerated immune reactions.     

Hepatitis A virus attachment to agri-food surfaces using immunological, virological and thermodynamic assays

AIMS: This study was designed to investigate the ability of hepatitis A virus (HAV) to attach to various food contact surfaces. METHODS AND RESULTS: HAV attachment was demonstrated after elution of attached viruses from solid surfaces by an immunofluorescent method using anti-HAV-specific antibodies and confocal microscopy. Attachment and survival of HAV on stainless steel, copper, polythene and polyvinyl chloride (PVC) at 20 and 4 degrees C after 2 and 4 h were quantified by plaque assay. HAV was shown to attach almost instantaneously to all four surfaces tested. Attachment of HAV depended on initial viral concentration and was slightly greater at 4 degrees C. The total surface energy (gammaTOT), nonpolar Lifshitz-Van der Waals (gammaLW) and polar short range (gammaSR) hydrogen-bonding components for HAV and each surface as well as total free energy of the system were determined by contact angle measurements using an extended Young equation [Young (1805) Philosophical Transactions of The Royal Society (London) 95, 65-87). The calculation of these parameters predicted the favourable conditions for attachment of HAV to all four surfaces tested. CONCLUSION: HAV particles attach to stainless steel, copper, polythene and PVC at 20 and 4 degrees C and the total free energy of the interaction is optimal for this attachment. SIGNIFICANCE AND IMPACT OF THE STUDY: Comprehension of viral attachment to the solid surfaces will permit to successfully disinfect these surfaces and to establish a better surveillance programme for control of viral food-borne illnesses.