Comparing genetic patterns in native and introduced species

Abstract: The vast majority of species are characterised by some form of special genetic structure across their ranges. These genetic patterns arise as a result of gene flow restrictions between populations due to barriers (such as geographical barriers, climate or habitat specificity). The biology, life history as well as habitat requirement of a species determines whether a barrier will be effective or not e.g. the Knersvlakte being an effective barrier to saxicolous species. Invasive species on the other hand are recently introduced species into new habitats. These species are often adaptive in nature as well as often closely associated with humans. Within this study, we aim to determine the genetic structure of two native species (a generalist species, the pouched mouse Saccostomus campestris, and a specialist species, the Eastern rock elephant shrew Elephantulus myurus) to determine how habitat connectivity influences the genetic patterns of comparable species. By using existing data, we will then analyse the genetic structure of an invasive species (the black rat, Rattus rattus) within two countries, The Democratic Republic of the Congo (DRC) (data obtained from Kaleme et al., 2011), and South Africa (data obtained from Bastos et al., 2011). Mitochondrial DNA was used to determine the genetic structure of all 3 species (the control region was used for both native species and the dataset from the DRC while cytochrome b was used for the invasives from South Africa). Bayesian trees as well as haplotype networks were constructed for all three species and an AMOVA was used to calculate standard Φ-statistics. All species were significantly structured, but the invasive species showed higher structure than the native species. Habitat connectivity was not the major driving forces behind the genetic structure observed within the native species. Instead we identified behaviour and possibly taxon-specific mutational rate as the likely factors responsible for the genetic structures observed. The dataset for the DRC consisted of two genetic groupings while the dataset for South Africa had three genetic groupings. This was the result of multiple introductions along independent introductory pathways, which mainly correspond to trade routes. Anthropogenic aided long distance dispersal is responsible for the large distances the species covers while intraspecific aggression enhances the introductory circumstance of the invasive species. The genetic structure observed in the two native species is a result of the interaction of the species with the natural habitat as well as behaviour and the taxon-specific mutational rate. In contrast, the invasive species’ genetic patterns reflect the different trade routes and introductory circumstance.M.Sc. (Zoology

BIM Implementation in the UK Residential Sector Current Barriers and Potential Solutions

Despite the interest gained throughout the construction industry to BIM and more modern methods of construction, the uptake in the UK residential sector has been slow and hampered by several barriers and misconceptions towards the concept. The unwillingness to change by house builders and residential stakeholders alike is exacerbated by the barriers encountered with costs, training and procurement, which have generated a negative perception of the BIM implementation. This study aims to identify the barriers currently faced within the UK residential sector influencing the uptake of BIM. The study examines further both the drivers and current rate of BIM implementation along with the main barriers to the progress of BIM adoption specifically to the UK residential sector. A survey across a diverse range of industry professionals was conducted to recognise the differences in opinions and views to the BIM adoption in the residential sector including BIM’s barriers and benefits, the UK government strategies, and respondents’ belief about whether BIM can be successful in the UK residential sector in the future. The results reverberated what was found in some secondary data confirming that the main barrier to the BIM adoption in the residential sector is lack of the clients’ demand. The responses illustrated a scepticism towards the UK government’s mandate and its effectiveness whilst highlighting potential solutions offering grounds for the further improvement in the residential sector

Interplay Between Magnetic Frustration and Quantum Criticality in the Unconventional Ladder Antiferromagnet C9H18N2CuBr4

Quantum fluctuation in frustrated magnets and quantum criticality at the transition between different quantum phases of matter are two of the cornerstones in condensed matter physics. Here we demonstrate the nontrivial interplay between them in the spin-1/2 coupled two-leg ladder antiferromagnet C9H18N2CuBr4. Employing the high-resolution neutron spectroscopy, we unambiguously identify a weakly first-order hydrostatic pressure-driven quantum phase transition, which arises from fluctuations enhanced by the frustrating interlayer coupling. An exotic pressure-induced quantum disordered state is evidenced by the broad spectral linewidth observed near the phase transition. Interestingly, we find that the gapped transverse excitations in the Neel-ordered phase at ambient pressure cannot be described by the conventional S=1 magnons, i.e., the spin wave quanta, associated with explicit symmetry breaking, and thus the three-dimensional magnetic order ought to emerge in an unconventional way. We further apply the quantum Fisher information to show the presence of bipartite entanglement at criticality at least up to 1.1 K in the same material.Comment: 10 pages and 6 figures. We call for theoretical understanding of the nontrivial interplay observed in this materia

Regulation of Carotenoid Composition and Shoot Branching in Arabidopsis by a Chromatin Modifying Histone Methyltransferase, SDG8

Carotenoid pigments are critical for plant survival, and carotenoid composition is tuned to the developmental stage, tissue, and to environmental stimuli. We report the cloning of the CAROTENOID CHLOROPLAST REGULATORY1 (CCR1) gene. The ccr1 mutant has increased shoot branching and altered carotenoid composition, namely, reduced lutein in leaves and accumulation of cis-carotenes in dark-grown seedlings. The CCR1 gene was previously isolated as EARLY FLOWERING IN SHORT DAYS and encodes a histone methyltransferase (SET DOMAIN GROUP 8) that methylates histone H3 on Lys 4 and/or 36 (H3K4 and H3K36). ccr1 plants show reduced trimethyl-H3K4 and increased dimethyl-H3K4 surrounding the CAROTENOID ISOMERASE (CRTISO) translation start site, which correlates with low levels of CRTISO mRNA. Microarrays of ccr1 revealed the downregulation of 85 genes, including CRTISO and genes associated with signaling and development, and upregulation of just 28 genes. The reduction in CRTISO transcript abundance explains the altered carotenoid profile. The changes in shoot branching are additive with more axillary branching mutants, but the altered carotenoid profile may partially affect shoot branching, potentially by perturbed biosynthesis of the carotenoid substrates of strigolactones. These results are consistent with SDG8 regulating shoot meristem activity and carotenoid biosynthesis by modifying the chromatin surrounding key genes, including CRTISO. Thus, the level of lutein, the most abundant carotenoid in higher plants that is critical for photosynthesis and photoprotection, appears to be regulated by a chromatin modifying enzyme in Arabidopsis thaliana

Prognostic value of upper respiratory tract microbes in children presenting to primary care with respiratory infections:a prospective cohort study

BACKGROUND: The association between upper respiratory tract microbial positivity and illness prognosis in children is unclear. This impedes clinical decision-making and means the utility of upper respiratory tract microbial point-of-care tests remains unknown. We investigated for relationships between pharyngeal microbes and symptom severity in children with suspected respiratory tract infection (RTI). METHODS: Baseline characteristics and pharyngeal swabs were collected from 2,296 children presenting to 58 general practices in Bristol, UK with acute cough and suspected RTI between 2011–2013. Post-consultation, parents recorded the severity of six RTI symptoms on a 0–6 scale daily for ≤28 days. We used multivariable hurdle regression, adjusting for clinical characteristics, antibiotics and other microbes, to investigate associations between respiratory microbes and mean symptom severity on days 2–4 post-presentation. RESULTS: Overall, 1,317 (57%) children with complete baseline, microbiological and symptom data were included. Baseline characteristics were similar in included participants and those lacking microbiological data. At least one virus was detected in 869 (66%) children, and at least one bacterium in 783 (60%). Compared to children with no virus detected (mean symptom severity score 1.52), adjusted mean symptom severity was 0.26 points higher in those testing positive for at least one virus (95% CI 0.15 to 0.38, p<0.001); and was also higher in those with detected Influenza B (0.44, 0.15 to 0.72, p = 0.003); RSV (0.41, 0.20 to 0.60, p<0.001); and Influenza A (0.25, -0.01 to 0.51, p = 0.059). Children positive for Enterovirus had a lower adjusted mean symptom severity (-0.24, -0.43 to -0.05, p = 0.013). Children with detected Bordetella pertussis (0.40, 0.00 to 0.79, p = 0.049) and those with detected Moraxella catarrhalis (-0.76, -1.06 to -0.45, p<0.001) respectively had higher and lower mean symptom severity compared to children without these bacteria. CONCLUSIONS: There is a potential role for upper respiratory tract microbiological point-of-care tests in determining the prognosis of childhood RTIs

Fecal DNA versus Fecal Occult Blood for Colorectal-Cancer Screening in an Average-Risk Population

BACKGROUND Although fecal occult-blood testing is the only available noninvasive screening method that reduces the risk of death from colorectal cancer, it has limited sensitivity. We compared an approach that identifies abnormal DNA in stool samples with the Hemoccult II fecal occult-blood test in average-risk, asymptomatic persons 50 years of age or older. METHODS Eligible subjects submitted one stool specimen for DNA analysis, underwent standard Hemoccult II testing, and then underwent colonoscopy. Of 5486 subjects enrolled, 4404 completed all aspects ofthe study. A subgroup of 2507 subjects was analyzed, including all those with a diagnosis of invasive adenocarcinoma or advanced adenoma plus randomly chosen subjects with no polyps or minor polyps. The fecal DNA panel consisted of 21 mutations. RESULTS The fecal DNA panel detected 16 of 31 invasive cancers, whereas Hemoccult II identified 4 of 31 (51.6 percent vs. 12.9 percent, P=0.003). The DNA panel detected 29 of 71 invasive cancers plus adenomas with high-grade dysplasia, whereas Hemoccult II identified 10 of 71 (40.8 percent vs. 14.1 percent, P<0.001). Among 418 subjects with advanced neoplasia (defined as a tubular adenoma at least 1 cm in diameter, a polyp with a villous histologic appearance, a polyp with high-grade dysplasia, or cancer), the DNA panel was positive in 76 (18.2 percent), whereas Hemoccult II was positive in 45 (10.8 percent). Specificity in subjects with negative findings on colonoscopy was 94.4 percent for the fecal DNA panel and 95.2 percent for Hemoccult II. CONCLUSIONS Although the majority of neoplastic lesions identified by colonoscopy were not detected by either noninvasive test, the multitarget analysis of fecal DNA detected a greater proportion of important colorectal neoplasia than did Hemoccult II without compromising specificity

The function-dominance correlation drives the direction and strength of biodiversity-ecosystem functioning relationships

Community composition is a primary determinant of how biodiversity change influences ecosystem functioning and, therefore, the relationship between biodiversity and ecosystem functioning (BEF). We examine the consequences of community composition across six structurally realistic plant community models. We find that a positive correlation between species' functioning in monoculture versus their dominance in mixture with regard to a specific function (the "function-dominance correlation") generates a positive relationship between realised diversity and ecosystem functioning across species richness treatments. However, because realised diversity declines when few species dominate, a positive function-dominance correlation generates a negative relationship between realised diversity and ecosystem functioning within species richness treatments. Removing seed inflow strengthens the link between the function-dominance correlation and BEF relationships across species richness treatments but weakens it within them. These results suggest that changes in species' identities in a local species pool may more strongly affect ecosystem functioning than changes in species richness

Morphological evolution of the mammalian jaw adductor complex

The evolution of the mammalian jaw during the transition from non-mammalian synapsids to crown mammals is a key event in vertebrate history and characterised by the gradual reduction of its individual bones into a single element and the concomitant transformation of the jaw joint and its incorporation into the middle ear complex. This osteological transformation is accompanied by a rearrangement and modification of the jaw adductor musculature, which is thought to have allowed the evolution of a more-efficient masticatory system in comparison to the plesiomorphic synapsid condition. While osteological characters relating to this transition are well documented in the fossil record, the exact arrangement and modifications of the individual adductor muscles during the cynodont–mammaliaform transition have been debated for nearly a century. We review the existing knowledge about the musculoskeletal evolution of the mammalian jaw adductor complex and evaluate previous hypotheses in the light of recently documented fossils that represent new specimens of existing species, which are of central importance to the mammalian origins debate. By employing computed tomography (CT) and digital reconstruction techniques to create three-dimensional models of the jaw adductor musculature in a number of representative non-mammalian cynodonts and mammaliaforms, we provide an updated perspective on mammalian jaw muscle evolution. As an emerging consensus, current evidence suggests that the mammal-like division of the jaw adductor musculature (into deep and superficial components of the m. masseter, the m. temporalis and the m. pterygoideus) was completed in Eucynodontia. The arrangement of the jaw adductor musculature in a mammalian fashion, with the m. pterygoideus group inserting on the dentary was completed in basal Mammaliaformes as suggested by the muscle reconstruction of Morganucodon oehleri. Consequently, transformation of the jaw adductor musculature from the ancestral (‘reptilian’) to the mammalian condition must have preceded the emergence of Mammalia and the full formation of the mammalian jaw joint. This suggests that the modification of the jaw adductor system played a pivotal role in the functional morphology and biomechanical stability of the jaw joint

Prioritisation by FIT to mitigate the impact of delays in the 2-week wait colorectal cancer referral pathway during the COVID-19 pandemic: a UK modelling study

OBJECTIVE: To evaluate the impact of faecal immunochemical testing (FIT) prioritisation to mitigate the impact of delays in the colorectal cancer (CRC) urgent diagnostic (2-week-wait (2WW)) pathway consequent from the COVID-19 pandemic. DESIGN: We modelled the reduction in CRC survival and life years lost resultant from per-patient delays of 2-6 months in the 2WW pathway. We stratified by age group, individual-level benefit in CRC survival versus age-specific nosocomial COVID-19-related fatality per referred patient undergoing colonoscopy. We modelled mitigation strategies using thresholds of FIT triage of 2, 10 and 150 µg Hb/g to prioritise 2WW referrals for colonoscopy. To construct the underlying models, we employed 10-year net CRC survival for England 2008-2017, 2WW pathway CRC case and referral volumes and per-day-delay HRs generated from observational studies of diagnosis-to-treatment interval. RESULTS: Delay of 2/4/6 months across all 11 266 patients with CRC diagnosed per typical year via the 2WW pathway were estimated to result in 653/1419/2250 attributable deaths and loss of 9214/20 315/32 799 life years. Risk-benefit from urgent investigatory referral is particularly sensitive to nosocomial COVID-19 rates for patients aged >60. Prioritisation out of delay for the 18% of symptomatic referrals with FIT >10 µg Hb/g would avoid 89% of these deaths attributable to presentational/diagnostic delay while reducing immediate requirement for colonoscopy by >80%. CONCLUSIONS: Delays in the pathway to CRC diagnosis and treatment have potential to cause significant mortality and loss of life years. FIT triage of symptomatic patients in primary care could streamline access to colonoscopy, reduce delays for true-positive CRC cases and reduce nosocomial COVID-19 mortality in older true-negative 2WW referrals. However, this strategy offers benefit only in short-term rationalisation of limited endoscopy services: the appreciable false-negative rate of FIT in symptomatic patients means most colonoscopies will still be required