Mitochondrial D-loop phylogeny signals two native Iberian red deer (Cervus elaphus) Lineages genetically different to Western and Eastern European red deer and infers human-mediated translocations

Native red deer (Cervus elaphus) in Western Europe might at least partially derive from refugial populations which survived in the Iberian Peninsula during the last glacial maximum, and that expanded northwards at the onset of the Holocene. However, the phylogeny and genetic structure of red deer populations in the Iberian Peninsula are still poorly known. This study was planned, in a first step, to reconstruct the phylogenetic relationship of the main red deer populations extant in Spain by the analyses of an extensive sample of mitochondrial DNA sequences. Results indicate that sequences from these populations can be assigned to one of two deeply divergent mtDNA lineages (South-Western and Central-Eastern) with molecular divergence nearby the 2 %. In each lineage were respectively found sixteen and thirteen different haplotypes. It was evidenced that they may be allopatrically distributed in Spain with 86.6 % sequences of the South-Western lineage at the South-Western side and the 65 % sequences of Central-Eastern lineage in the Central-Eastern side. These mitochondrial lineages might have originated in two distinct refugial populations during the last glacial maximum. Genetic data also reveal instances of admixture between native populations and translocated European red deer, which belong to at least three distinct subspecies. Gene introgression was mainly due to red deer from Western European populations. The genetic contribution of red deer translocated from Eastern Europe (C. e. hippelaphus) or North Africa (C. e. corsicanus, C. e. barbarus) was apparently less deep. The extant phylogenetic relationship and evidences of genetic admixture suggest that sound conservation actions for the native Iberian red deer should severely restrict the introduction of alien red deer and, when possible, avoid admixture between the South-Western and Central-Eastern mtDNA lineages.     

Identification of surface proteins of group B streptococci: Serotyping versus genotyping

We compared serotyping to genotyping of group B streptococcal (GBS) surface proteins in 147 Australasian isolates. Results were concordant for the two methods in 73.8% of 122 isolates, discordant for three and partially discordant for 29 isolates. For the purpose of epidemiological typing of GBS, genotyping is superior to serotyping.     

Vacancy Chains Provide Aggregate Benefits To Coenobita clypeatus Hermit Crabs

Vacancy chain theory describes a unique mechanism for the sequential distribution of animal resources across multiple individuals. This theory applies to any resources, such as shelters or nest sites, that are discrete, reusable, and limited in use to single individuals or groups at one time. Hermit crabs rely on gastropod shells for shelter, and a single vacant shell can initiate a chain of sequential shell switches that distributes new resources across many individuals. Using the terrestrial hermit crab Coenobita clypeatus , we examined the previously untested theoretical prediction that this process will yield trickle-down resource benefits to vacancy chain participants (aggregate benefits). In laboratory experiments, we measured improvements in shell quality when a single vacant shell was provided to groups of eight crabs. We found that crabs participating in vacancy chains (averaging 3.2 individuals) gained significant reductions in their shell crowding. In addition, vacancy chains terminated early when experimental groups included a single crab occupying a damaged shell, because damaged vacancies always remained unoccupied. Hermit crabs in damaged shells were more likely to win resource contests for high quality shells against size-matched hermit crabs in crowded shells. Finally, field additions of many new shells to an island population of C. clypeatus hermit crabs reduced average shell crowding for crabs of all sizes, possibly from propagation of benefits through vacancy chains. These results provide empirical support for the theoretical prediction that vacancy chains should provide benefits distributed across many vacancy chain participants. Since shelter-based vacancy chains likely occur in other animals, additional studies of vacancy chain processes should provide new insights into resource acquisition behaviors in diverse animal groups.     

Solitary epileptic seizure--the risk of recurrence

Patients experiencing solitary unprovoked epileptic seizure have different risks of recurrence. The possible risk factors include in particular: structural cerebral lesion and its cause, history of febrile seizures, family history of epilepsy, the type of seizure, epileptiform EEG discharges and the problem of initiation or (or not initiation) of antiepileptic treatment after the first paroxysm. The factors shown above were evaluated in a group of 30 patients with solitary unprovoked epileptic seizure. Regarding recurrence of epileptic seizure, the only significant factor appeared to be initiation of treatment after the first unprovoked paroxysm (p<0.001). We observed a 30% and 33.33% risk of recurrence following the initial epileptic seizure in patients after the first unprovoked seizure in less than 1 and 3 years, respectively.     

Identification of functional domains in sarcoglycans essential for their interaction and plasma membrane targeting

Mutations in sarcoglycans have been reported to cause autosomal-recessive limb-girdle muscular dystrophies. In skeletal and cardiac muscle, sarcoglycans are assembled into a complex on the sarcolemma from four subunits (alpha, beta, gamma, delta). In this report, we present a detailed structural analysis of sarcoglycans using deletion study, limited proteolysis and co-immunoprecipitation. Our results indicate that the extracellular regions of sarcoglycans consist of distinctive functional domains connected by proteinase K-sensitive sites. The N-terminal half domains are required for sarcoglycan interaction. The C-terminal half domains of beta-, gamma- and delta-sarcoglycan consist of a cysteine-rich motif and a previously unrecognized conserved sequence, both of which are essential for plasma membrane localization. Using a heterologous expression system, we demonstrate that missense sarcoglycan mutations affect sarcoglycan complex assembly and/or localization to the cell surface. Our data suggest that the formation of a stable complex is necessary but not sufficient for plasma membrane targeting. Finally, we provide evidence that the beta/delta-sarcoglycan core can associate with the C-terminus of dystrophin. Our results therefore generate important information on the structure of the sarcoglycan complex and the molecular mechanisms underlying the effects of various sarcoglycan mutations in muscular dystrophies.     

Cutting edge: impaired glycosphingolipid trafficking and NKT cell development in mice lacking Niemann-Pick type C1 protein

Niemann-Pick type C1 (NPC1) is a late endosomal/lysosomal transmembrane protein involved in the cellular transport of glycosphingolipids and cholesterol that is mutated in a majority of patients with Niemann-Pick C neurodegenerative disease. We found that NPC1-deficient mice lacked Valpha14-Jalpha18 NKT cells, a major population of CD1d-restricted T cells that is conserved in humans. NPC1-deficient mice also exhibited marked defects in the presentation of Sphingomonas cell wall Ags to NKT cells and in bacterial clearance in vivo. A synthetic fluorescent alpha-glycosylceramide analog of the Sphingomonas Ag trafficked to the lysosome of wild-type cells but accumulated in the late endosome of NPC1-deficient cells. These findings reveal a blockade of lipid trafficking between endosome and lysosome as a consequence of NPC1 deficiency and suggest a common mechanism for the defects in lipid presentation and development of Valpha14-Jalpha18 NKT cells.     

Parrotfish abundance and selective corallivory on a Belizean coral reef

Parrotfish are important members of coral reef communities because they consume macroalgae that would otherwise outcompete reef-building corals for space. However, some Caribbean parrotfish species also feed directly on live corals, and thus have the potential to negatively impact coral fitness and survival. This study investigates selective grazing by parrotfish on particular coral species, differences in grazing incidence among reef habitats and intraspecific discrimination among colonies of several coral species. We also investigate spatial and temporal patterns of parrotfish species abundance across habitats on the Belize barrier reef, and examine correlations between parrotfish abundance and grazing intensity across reef habitats. We found that members of the Montastraea annularis species complex, major builders of Caribbean reefs, were preferred targets of parrotfish grazing across all reef habitats, while M. cavernosa, Agaricia agaricites, Diploria strigosa, Porites astreoides and Porites porites were not preferred; Siderastrea siderea was preferentially grazed only in the spur and groove habitats. Parrotfish grazing preferences varied across habitats; M. annularis was grazed most often in shallow habitats, whereas M. franksi was consumed more at depth. Although it was not possible to directly observe parrotfish grazing on corals, we did find a positive correlation between Sparisoma aurofrenatum abundance and M. franksi grazing incidence across habitats. Finally, when we compared our results to parrotfish abundances measured by a previous study, we found that Sparisoma viride and Sp. aurofrenatum, two species known to be corallivorous, had increased abundances between 1982 and 2004. In light of escalating threats on Caribbean reef corals, it would be important for future studies to evaluate the impact of parrotfish corallivory on coral survival.     

Reproductive Performance,Udder Health,and Antibiotic Resistance in Mastitis Bacteria isolated from Norwegian Red cows in Conventional and Organic Farming

Background  

The objectives of this study were to investigate whether there were differences between Norwegian Red cows in conventional and organic farming with respect to reproductive performance, udder health, and antibiotic resistance in udder pathogens.     

Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels

The genomic era has led to an unprecedented increase in the availability of genome‐wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.     

Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry

Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (Fragaria chiloensis and Fragaria virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease in heterozygosity among domesticated descendants of those hybrids. Selective sweeps were found across the genome in early and modern phases of domestication—59–76% of the selectively swept genes originated in the three less dominant ancestral subgenomes. Contrary to the tenet that genetic diversity is limited in cultivated strawberry, we found that the octoploid species harbor massive allelic diversity and that F. × ananassa harbors as much allelic diversity as either wild founder. We identified 41.8 M subgenome-specific DNA variants among resequenced wild and domesticated individuals. Strikingly, 98% of common alleles and 73% of total alleles were shared between wild and domesticated populations. Moreover, genome-wide estimates of nucleotide diversity were virtually identical in F. chiloensis,F. virginiana, and F. × ananassa (π = 0.0059–0.0060). We found, however, that nucleotide diversity and heterozygosity were significantly lower in modern F. × ananassa populations that have experienced significant genetic gains and have produced numerous agriculturally important cultivars.