| 1. |
- Hillier, Ladeana W, et al.
(author)
-
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
-
In: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
-
Journal article (peer-reviewed)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
|
|
| 2. |
|
|
| 3. |
- Jenkins, S. R., et al.
(author)
-
Population dynamics of the intertidal barnacle Semibalanus balanoides at three European locations: spatial scales of variability
- 2001
-
In: Marine Ecology Progress Series. - : Inter-Research Science Center. - 0171-8630 .- 1616-1599. ; 217, s. 207-217
-
Journal article (peer-reviewed)abstract
- Spatial variability in the population dynamics of the intertidal acorn barnacle Semibalanus balanoides was investigated using a hierarchical sampling programme. Variability in a number of population parameters (size distribution, density, % cover, absolute growth and instantaneous mortality) was determined separately for new recruits and adults over 3 spatial scales. Three locations, SW Ireland, the Isle of Man and the west coast of Sweden, which cover a large part of the European range of this species, were selected to investigate variability over a large spatial scale (100s of kilometres). Two smaller scales, shore (1000s of metres) and site (10s of metres) nested within each location were also used. In addition, temporal variation over two 6 mo periods was also examined in the Isle of Man and Ireland. Most variability for all population parameters occurred over the largest spatial scale (location). This was a direct result of differences between Sweden and the other 2 locations, the Isle of Man and Ireland, which showed highly similar levels of all population parameters. The population of S, balanoides at the Swedish location was characterised by high growth rates, large size, high levels of mortality and a large turnover of bare space. At the spatial scale 'shore', only 1 population parameter, the growth rate of recruits, showed variability. At the smallest scale of 'site', all parameters showed significant variability except growth rate of adults. Calculation of variance components showed that differences between replicates (spatial scale: <0.5 m) accounted for little of the overall variability, in general less than the scales of site and shore. Examination of temporal variability over two 6 mo periods revealed no difference between time periods and no significant interaction between temporal and spatial scales, Thus, there was consistency of spatial variability over time. The potential causes of variability in population parameters of S, balanoides at different spatial scales and the implications for future studies are discussed.
|
|
| 4. |
- Jenkins, S. R., et al.
(author)
-
Spatial and temporal variation in settlement and recruitment of the intertidal barnacle Semibalanus balanoides (L.) (Crustacea : Cirripedia) over a European scale
- 2000
-
In: Journal of Experimental Marine Biology and Ecology. - 0022-0981. ; 243:2, s. 209-225
-
Journal article (peer-reviewed)abstract
- Variation in the level of settlement and recruitment in the intertidal barnacle Semibalanus balanoides was studied using a hierarchical sampling programme. The effect of three spatial scales, 10s of metres (sites), 1000s of metres (shores) and 100s of kilometres (locations), was determined. The largest spatial scale represented the distance between four widely separated locations, Sweden, the Isle of Man, SW Ireland and SW England, covering a. large part of the range of S. balanoides in Europe. Temporal variation was determined by comparison between two years, 1997 and 1998. The settlement period of S. balanoides varied in length and timing, being earlier and shorter at the most northerly location, Sweden. The duration of settlement showed little difference among shores within locations, but the pattern of settlement did vary. Estimates of total settlement throughout the settlement period and of recruitment at the end of this period both showed substantial variation among locations which was dependent on the year of study. There was little consistency in the ranking of locations between the two years. Recruitment showed significant variation I the lower spatial scales of shore and site. In addition, examination of variance components showed a high degree of variation between replicates within sites in 1997. There was a significant relationship between settlement and recruitment at three of the four locations. Across all locations variation in settlement explained between 29 and 99% of variation in recruitment. However, locations showed distinct differences in the level of post-settlement survival. (C) 2000 Elsevier Science B.V. All rights reserved.
|
|
| 5. |
|
|
| 6. |
- Sundelöf, Andreas, 1974, et al.
(author)
-
Determinants of reproductive potential and population size in open populations of Patella vulgata
- 2010
-
In: Marine Biology. - : Springer Science and Business Media LLC. - 0025-3162 .- 1432-1793. ; 157:4, s. 779-789
-
Journal article (peer-reviewed)abstract
- The importance of external and internal population processes in determining variation in reproductive output and variation in population size were quantified with model simulations for open populations of the sequentially hermaphroditic limpet Patella vulgata using field data from the Isle of Man and South West Ireland. Cross-correlation analyses of model outputs and elasticity analyses show that population dynamics are dominated by the effects of large females, and that recruitment adds little to reproductive output. However, populations experiencing low but highly variable recruitment appear male limited and recruitment pulses carrying young males into the population are correlated to reproductive output with a 2-5-year lag. We conclude that pulses in recruitment can be a major structuring force in these limpet populations, but site-specific post-recruitment processes will determine the relative importance of recruitment to population dynamics and the lag between recruitment and reproductive output.
|
|
| 7. |
|
|
| 8. |
|
|
| 9. |
- Moore, Tadhg N, et al.
(author)
-
LakeEnsemblR : An R package that facilitates ensemble modelling of lakes
- 2021
-
In: Environmental Modelling & Software. - : Elsevier. - 1364-8152 .- 1873-6726. ; 143
-
Journal article (peer-reviewed)abstract
- Model ensembles have several benefits compared to single-model applications but are not frequently used within the lake modelling community. Setting up and running multiple lake models can be challenging and time consuming, despite the many similarities between the existing models (forcing data, hypsograph, etc.). Here we present an R package, LakeEnsemblR, that facilitates running ensembles of five different vertical one-dimensional hydrodynamic lake models (FLake, GLM, GOTM, Simstrat, MyLake). The package requires input in a standardised format and a single configuration file. LakeEnsemblR formats these files to the input required by each model, and provides functions to run and calibrate the models. The outputs of the different models are compiled into a single file, and several post-processing operations are supported. LakeEnsemblR's workflow standardisation can simplify model benchmarking and uncertainty quantification, and improve collaborations between scientists. We showcase the successful application of LakeEnsemblR for two different lakes.
|
|
| 10. |
- Ranganathan, Meghna, et al.
(author)
-
Transactional sex among young women in rural South Africa : prevalence, mediators and association with HIV infection
- 2016
-
In: Journal of the International AIDS Society. - 1758-2652. ; 19
-
Journal article (peer-reviewed)abstract
- Introduction: Young adolescent women in sub-Saharan Africa are three to four times more likely to be HIV-positive than boys or men. One of the relationship dynamics that is likely to be associated with young women's increased vulnerability to HIV is transactional sex. There are a range of HIV-related risk behaviours that may drive this vulnerability. However, to date, limited epidemiological data exist on the role of transactional sex in increasing HIV acquisition, especially among young women in subSaharan Africa. Our paper presents data on the prevalence of self-reported engagement in transactional sex and explores whether transactional sex is associated with increased risk of HIV infection among a cohort of young, rural, sexually active South African women. We also explore whether this relationship is mediated through certain HIV-related risk behaviours.Methods: We analyzed baseline data from a phase III trial of conditional cash transfers for HIV prevention of 693 sexually active, school-going young women aged 13-20 years in rural South Africa. We examined the association between young women's engagement in transactional sex and HIV infection. Transactional sex is defined as a non-commercial, non-marital sexual relationship whereby sex is exchanged for money and/or gifts. We explored whether this relationship is mediated by certain HIVrelated risk behaviours. We used logistic and multinomial regression and report unadjusted and adjusted odds ratios with 95% CI.Results: Overall, 14% (n = 97) of sexually active young women reported engaging in transactional sex. Engagement in transactional sex was associated with an increased risk of being HIV-positive (aOR: 2.5, CI: 95% 1.19-5.25, p = 0.01). The effect size of this association remained nearly unchanged when adjusted for certain other dimensions of HIV risk that might help explain the underlying pathways for this relationship.Conclusions: This study provides quantitative support demonstrating that transactional sex is associated with HIV infection in young women. Even though the specific variables tested do not mediate the relationship, a potential explanation for this association may be that the men with whom young women are having sex belong to networks of sexually connected individuals who are at a "high risk" for HIV infection. The results highlight the importance of structural intervention approaches that can alter the context of young women's HIV risk.
|
|
