Clonality and Genetic Diversity Revealed by AFLPs in Schisandra glabra (Brickell) Rheder (Schisandraceae), a Rare Basal Angiosperm

Rare species with fragmented distributions often exhibit reduced levels of genetic diversity within populations. However, life history traits such as long lived perennial habit and outcrossing mating system, are associated with high levels of within species genetic variation being partitioned within populations. Schisandra glabra (Schisandraceae) is a rare basal angiosperm with a fragmented distribution across the southeastern US and in a disjunct population in cloudforest of Mexico. The species’ clonal reproduction by rhizomes, confounds the delineation of genetically distinct individuals in the field. The patterns of genetic diversity and clonality in 10 populations of S. glabra were investigated using AFLP markers. I found a surprising number of distinct genetic individuals in the two populations sampled on 3m grids, with 31 unique genotypes out of 42 samples at Wolfpen Creek, KY, and unique genotypes in all 48 samples from Panther Creek, GA. AMOVA of 237 individuals from 10 populations revealed that the largest portion of the genetic variation is found within populations (58.0%; P\u3c0.0001), and 27.7% (P\u3c0.0001) of the genetic variation is partitioned between the US and Mexico S. glabra populations. Population structure was also detected between the US and Mexico populations, but no structure was detected between the majority of the US populations. The genetic differentiation of the disjunct population in Mexico, may be the result of a Pliocene or Miocene vicariance hypothesized for many species with similar distributions. The high levels of genetic diversity found within populations are evidence of historical gene flow between the US populations, and the preservation of genetic diversity by the long lived species in its present fragmented distribution

Response to fragmentation by avian communities is mediated by species traits

Aim The hypothesis that habitat fragmentation negatively influences biodiversity stems from island biogeography and metapopulation theory which predict negative impacts of decreasing patch size on richness and distribution patterns. Empirical support of this idea is weak in terrestrial systems, though tests of fragmentation effects are typically confounded with landscape composition and potentially obscured by imperfect detection. Here, we used multispecies occupancy models and a mensurative experimental design to test competing hypotheses about how forest fragmentation influences distributions of breeding forest bird species and communities. Location Southern Indiana, USA. Methods During the breeding seasons of 2011-2013, we recorded over 80,000 bird detections in 202 forest fragments using a sampling design that isolated the effects of patch size per se from the effects of forest amount within a 2 km radius, edge distance, local vegetation and sampling area. We modelled the effects of these covariates on distributions of individual species categorized by ecological trait groups (i.e., forest, forest interior or forest edge), and evaluated how forest loss and fragmentation impact species richness. Results Though our results indicated little effect of patch size on total species richness, decreasing patch size had a negative effect on interior species, and a positive effect on edge species. The effects of total forest amount were much more variable, and surprisingly had a negative influence on many species, particularly cavity nesters. Main conclusions Our results do not support theoretical predictions that forest patch size should positively influence bird species richness. However, composition of bird communities shifted towards edge species from interior species with decreasing patch size. Maintaining large forest patches is thus critical for supporting forest interior species, which tend to be of the greatest conservation concern

The effect of the addition of resistance training to a dietary education intervention on apolipoproteins and diet quality in overweight and obese older adults

Objectives: The aim of the study was to examine the additive effect of resistance training (RT) to a dietary education (DE) intervention on emerging coronary heart disease (CHD) risk factors, concentration of apolipoproteins B (apoB) and A-I (apoA-I), and Dietary Approaches to Stop Hypertension (DASH) Diet Index scores in overweight and obese older adults. Patients and Methods: This was an ancillary study of a randomized clinical trial held in the Fall of 2008 at the University of Rhode Island. Participants were overweight or obese subjects (mean body mass index [BMI] of 31.7 kg/m2) randomized into two groups, one participating in DE only (n = 12) and the other participating in DE plus RT (DERT) (n = 15). The intervention involved all subjects participating in 30 minutes of DE per week for 10 weeks. Subjects in the DERT group participated in an additional 40 minutes of RT three times per week for 10 weeks. Measurements taken were anthropometric (height, weight, waist circumference, and body composition using the BOD POD® [Body Composition System, v 2.14; Life Measurement Instruments, Concord, CA]), clinical (blood pressure), and biochemical (lipid profile and apoB and apoA-I concentrations), and the DASH Diet Index was used to measure diet quality. Results: 27 subjects (11 males, 16 females), with a mean age of 66.6 ± 4.3 years, were included in analyses. The DERT subjects had significantly better triacylglycerol and apoB concentrations and DASH Diet Index scores than the DE subjects post-intervention. Improvements were seen within the DE group in energy intake, fat-free mass, and systolic blood pressure and within the DERT group in body weight, percentage of body fat, BMI, diastolic blood pressure, and oxidized low-density lipoprotein (all P \u3c 0.05). Conclusion: The addition of RT effectively reduced CHD risk factors, body composition, and diet quality in overweight and obese older adults; DERT was more effective than DE alone in improving DASH Diet Index scores and lowering apoB concentrations but was not more effective in increasing apoA-I concentrations. Future research is needed to determine if apolipoproteins are superior to lipoprotein cholesterol concentrations in predicting CHD risk

Genome-Scale Multilocus Microsatellite Typing of Trypanosoma cruzi Discrete Typing Unit I Reveals Phylogeographic Structure and Specific Genotypes Linked to Human Infection

Trypanosoma cruzi is the most important parasitic infection in Latin America and is also genetically highly diverse, with at least six discrete typing units (DTUs) reported: Tc I, IIa, IIb, IIc, IId, and IIe. However, the current six-genotype classification is likely to be a poor reflection of the total genetic diversity present in this undeniably ancient parasite. To determine whether epidemiologically important information is “hidden” at the sub-DTU level, we developed a 48-marker panel of polymorphic microsatellite loci to investigate population structure among 135 samples from across the geographic distribution of TcI. This DTU is the major cause of resurgent human disease in northern South America but also occurs in silvatic triatomine vectors and mammalian reservoir hosts throughout the continent. Based on a total dataset of 12,329 alleles, we demonstrate that silvatic TcI populations are extraordinarily genetically diverse, show spatial structuring on a continental scale, and have undergone recent biogeographic expansion into the southern United States of America. Conversely, the majority of human strains sampled are restricted to two distinct groups characterised by a considerable reduction in genetic diversity with respect to isolates from silvatic sources. In Venezuela, most human isolates showed little identity with known local silvatic strains, despite frequent invasion of the domestic setting by infected adult vectors. Multilocus linkage indices indicate predominantly clonal parasite propagation among all populations. However, excess homozygosity among silvatic strains and raised heterozygosity among domestic populations suggest that some level of genetic recombination cannot be ruled out. The epidemiological significance of these findings is discussed

Hexacoordinate Ru-based olefin metathesis catalysts with pH-responsive N-heterocyclic carbene (NHC) and N-donor ligands for ROMP reactions in non-aqueous, aqueous and emulsion conditions

Three new ruthenium alkylidene complexes (PCy3)Cl2(H2ITap)Ru=CHSPh (9), (DMAP)2Cl2(H2ITap)Ru=CHPh (11) and (DMAP)2Cl2(H2ITap)Ru=CHSPh (12) have been synthesized bearing the pH-responsive H2ITap ligand (H2ITap = 1,3-bis(2’,6’- dimethyl-4’-dimethylaminophenyl)-4,5-dihydroimidazol-2-ylidene). Catalysts 11 and 12 are additionally ligated by two pH-responsive DMAP ligands. The crystal structure was solved for complex 12 by X-ray diffraction. In organic, neutral solution, the catalysts are capable of performing standard ring-opening metathesis polymerization (ROMP) and ring closing metathesis (RCM) reactions with standard substrates. The ROMP with complex 11 is accelerated in the presence of two equiv of H3PO4, but is reduced as soon as the acid amount increased. The metathesis of phenylthiomethylidene catalysts 9 and 12 is sluggish at room temperature, but their ROMP can be dramatically accelerated at 60 °C. Complexes 11 and 12 are soluble in aqueous acid. They display the ability to perform RCM of diallylmalonic acid (DAMA), however, their conversions are very low amounting only to few turnovers before decomposition. However, both catalysts exhibit outstanding performance in the ROMP of dicyclopentadiene (DCPD) and mixtures of DCPD with cyclooctene (COE) in acidic aqueous microemulsion. With loadings as low as 180 ppm, the catalysts afforded mostly quantitative conversions of these monomers while maintaining the size and shape of the droplets throughout the polymerization process. Furthermore, the coagulate content for all experiments staye

Diversification in evolutionary arenas : Assessment and synthesis

Understanding how and why rates of evolutionary diversification vary is a central issue in evolutionary biology and ecology. The concept of adaptive radiation has attracted much interest, but is metaphorical and verbal in nature, making it difficult to quantitatively compare different evolutionary lineages or geographic regions. In addition, the causes of evolutionary stasis are relatively neglected. Here we review the central concepts in the evolutionary diversification literature and bring these together by proposing a general framework for estimating rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b) and clade-specific phenotypes or traits (c); thus d~a,b,c. We refer to the four components (a-d) and their interactions collectively as the 'Evolutionary Arena'. We outline analytical approaches to this conceptual model that open up new avenues for research, and present a case study on conifers, for which we parameterise the general model. We also discuss three conceptual examples based on existing literature: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating fragmentation due to climatic oscillation; oceanic island radiations in the context of archipelago isolation and island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys. The results of the conifer case study are consistent with the long-standing scenario that large niches, lack of competition, and high-rates of niche evolution differentially promote diversification, but these results go further by quantifying the statistical interactions between variables representing these three drivers. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework results in highlighting gaps in current knowledge, and thus help to identify future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Dark sectors 2016 Workshop: community report

This report, based on the Dark Sectors workshop at SLAC in April 2016, summarizes the scientific importance of searches for dark sector dark matter and forces at masses beneath the weak-scale, the status of this broad international field, the important milestones motivating future exploration, and promising experimental opportunities to reach these milestones over the next 5-10 years

Clinical impact of genomic testing in patients with suspected monogenic kidney disease

Purpose: To determine the diagnostic yield and clinical impact of exome sequencing (ES) in patients with suspected monogenic kidney disease. Methods: We performed clinically accredited singleton ES in a prospectively ascertained cohort of 204 patients assessed in multidisciplinary renal genetics clinics at four tertiary hospitals in Melbourne, Australia. Results: ES identified a molecular diagnosis in 80 (39%) patients, encompassing 35 distinct genetic disorders. Younger age at presentation was independently associated with an ES diagnosis (p < 0.001). Of those diagnosed, 31/80 (39%) had a change in their clinical diagnosis. ES diagnosis was considered to have contributed to management in 47/80 (59%), including negating the need for diagnostic renal biopsy in 10/80 (13%), changing surveillance in 35/80 (44%), and changing the treatment plan in 16/80 (20%). In cases with no change to management in the proband, the ES result had implications for the management of family members in 26/33 (79%). Cascade testing was subsequently offered to 40/80 families (50%). Conclusion: In this pragmatic pediatric and adult cohort with suspected monogenic kidney disease, ES had high diagnostic and clinical utility. Our findings, including predictors of positive diagnosis, can be used to guide clinical practice and health service design