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Fossil sequences provide observations of phenotypes within a lineage over time and represent essential data for increasing our understanding of phyletic evolution beyond microevolutionary timescales. I investigate if fossil times-series of the diatom Stephanodiscus niagarae/yellowstonensis follow evolutionary dynamics compatible with hypotheses for how the adaptive landscape changes when a population enters a new environment. The lineage – which has a remarkably detailed stratigraphic record – invaded Yellowstone Lake immediately after recession of ice from the basin 14,000 years ago. Several phyletic models portraying different types of evolutionary dynamics – both compatible and not compatible with changes in the adaptive landscape following ecological opportunity – were fitted to the fossil times-series of S. niagarae/yellowstonensis. Different models best describe the three analyzed traits. Two of the models (a new model of decelerated evolution and an Ornstein-Uhlenbeck model) capture trait dynamics compatible with an event of ecological opportunity, while the third model (random walk) does not. Entering a new environment may accordingly affect trait dynamics for thousands of years, but the effects can vary across phenotypes. However, tests of model adequacy reveal shortcomings in all three models explaining the trait dynamics, suggesting model development is needed to more fully understand the phyletic evolution in Stephanodiscus niagarae/yellowstonensis.
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Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards and snakes, amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. Here, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites, phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of parsimony informative sites), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; and between the three toxiferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).
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Objectives: Preemptive conversations (PCs) about end-of-life (EOL) preferences are beneficial for both elderly people and their families to understand and share the preferences. However, the factors which promote/inhibit PCs have yet to be clarified. We therefore aimed to determine the factors related to having PCs with hypothesis that age, subjective economic status and subjective health status are associated with having PC experience. Design: A cross-sectional study administering a questionnaire and using stratified random sampling by gender and region. Setting: Residents aged 65 years or older who were not receiving nursing care as of November 1, 2016, were extracted from the Japanese long-term care insurance system registry in Koriyama City, Fukushima Prefecture, Japan. Participants: 1,575 participants (717 males and 858 females). Outcome: Presence or absence of PC experience with family or friends (yes/no). Results: The mean age of the participants was 74.0 years. A multivariable logistic-regression analysis revealed that having PC experience was significantly associated with gender (OR = 1.907; 95% CI = 1.556, 2.337; p < 0.001), subjective economic status (OR = 0.832; 95% CI = 0.716, 0.966; p=0.016), and subjective happiness (OR = 0.926; 95% CI = 0.880, 0.973; p=0.003). Conclusions: Poor subjective economic status of elderly people may result in absence of EOL conversation experience with their families and friends, hindering the elderly from sharing and understanding the EOL preferences. To promote PCs about EOL, gerontology and public health professionals should give special consideration to the subjective economic status of elderly people.
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Women in STEM are not equally represented across tenure-track career stages, and this extends to grant funding, where women applicants often have lower success rates compared to men. While gender bias in reviewers has been documented, it is currently unknown whether written language in grant applications varies predictably with gender to elicit bias against women. Here we analyse the text of ~2000 public research summaries from the 2016 Natural Sciences and Engineering Research Council (NSERC) individual Discovery Grant (DG) program. We explore the relationship between language variables, inferred gender and career stage, and funding levels. We also analyse aggregated data from the 2012-2018 NSERC DG competitions to determine whether gender impacted the probability of receiving a grant for early-career researchers. We document a marginally significant gender difference in funding levels for successful grants, with women receiving $1756 less than men, and a large and significant difference in rejection rates among early-career applicants (women: 40.4% rejection; men: 33.0% rejection rate). Language variables had little ability to predict gender or funding level using predictive modelling. Our results indicate that NSERC funding levels and success rates differ between men and women, but we find no evidence that gendered language use affected funding outcomes.
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In an attempt to control the mosquito-borne diseases yellow fever, dengue, chikungunya, and Zika fevers, a strain of transgenically modified Aedes aegypti mosquitoes containing a dominant lethal gene has been developed by a commercial company, Oxitec Ltd. If lethality is complete, releasing this strain should only reduce population size and not affect the genetics of the target populations. Approximately 450 thousand males of this strain were released each week for 27 months in Jacobina, Bahia, Brazil. We genotyped the release strain and the target Jacobina population before releases began for >21,000 single nucleotide polymorphisms (SNPs). Genetic sampling from the target population six, 12, and 27–30 months after releases commenced provides clear evidence that portions of the transgenic strain genome have been incorporated into the target population. Evidently, rare viable hybrid offspring between the release strain and the Jacobina population are sufficiently robust to be able to reproduce in nature. The release strain was developed using a strain originally from Cuba, then outcrossed to a Mexican population. Thus, Jacobina Ae. aegypti are now a mix of three populations. It is unclear how this may affect disease transmission or affect other efforts to control these dangerous vectors. These results highlight the importance of having in place a genetic monitoring program during such releases to detect un-anticipated outcomes.
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Background and Aims Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution. Methods We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of individually analysed 48 tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness. Key results Brassicaceae diverged 29.9 Mya during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes. Conclusions The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant "pump" for continuous and high species diversification.
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A laborious and difficult task in current tree of life reconstruction is to resolve evolutionary relationships of closely related congeneric species that originated from recent radiations. This is particularly difficult for forest species with long generation times and large effective population sizes such as conifers. As the species diversity center of Picea, the Qinghai-Tibetan Plateau (QTP) and its adjacent areas harbor 11 species (including 5 varieties) of this genus, but evolutionary relationships of these species are far from being resolved due to recent radiation, morphological convergence, and frequent interspecific gene flow. In this study, we use these spruce species to test whether phylotranscriptomic analysis, combined with population genetic analysis, can disentangle their evolutionary relationships, and to explore whether reticulate evolution has occurred among them. Phylogenomic analyses indicate that all spruce species in the QTP and neighboring areas, except P. asperata and P. crassifolia, cluster together, and in particular, nearly all taxa (including varieties) form their own monophyletic groups, although the two species P. likiangensis and P. brachytyla are not monophyletic. We found that, compared to herbaceous plants, many more genes (a minimum of 600 OGs for Picea) are required to resolve interspecific relationships of conifers. Our study does not support a hybrid origin of P. purpurea reported in previous studies, but suggests a hybrid origin for P. brachytyla var. brachytyla and P. likiangensis var. rubescens. Moreover, we emphasize that population genetic and phylogeographical studies should sample a monophyletic group if more than one species are involved.
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Context: Familial hyperaldosteronism type I or glucocorticoid-remediable aldosteronism (FH-I; GRA) is caused by unequal crossing-over of the steroid 11β-hydroxylase (CYP11B1) and aldosterone synthase (CYP11B2) genes. Somatic KCNJ5 mutations have not been reported in patients with GRA; therefore, the appropriate treatment and prognosis of such concurrent cases remain unknown. Case description: Two siblings of a Taiwanese family with GRA were found to have adrenal adenomas and somatic KCNJ5 mutations. Complete clinical cure was achieved after unilateral adrenalectomy. Furthermore, the conversion site of the chimeric gene was identified by direct sequencing. Conclusions: We report for the first time the coexistence of a somatic KCNJ5 mutation and GRA. GRA patients whose blood pressure management develops resistance to glucocorticoid treatment could therefore benefit from a lateralization test. The promising outcomes after unilateral adrenalectomy presented in this report offer new perspectives for further research into various PA subtypes.
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(1) Camera trapping allows scientists to study activity patterns of animals under natural conditions. However, comparisons of activity patterns across seasons or latitudes can be biased, because activity is often attuned to sunrise and sunset, the timing of which varies with latitude and season. Existing transformation methods to solve this problem have limitations. (2) Here, we explore whether and how activity patterns can be transformed more accurately using two alternative ‘double anchoring’ transformations – equinoctial and average anchoring – that anchor activity time to two chosen anchor points during the study period. (3) Using simulated noisy datasets mimicking species with either crepuscular, diurnal or cathemeral activity patterns, we compared the ability of different transformation methods to extract the latent pattern and activity levels under different study conditions. We found that average anchoring best retrieved the original diel activity pattern and yielded accurate estimates of activity level. Two alternative transformation methods – single anchoring and equinoctial anchoring – performed less well. Bias in estimates from using untransformed clock times was most marked (up to 2.5-fold over-estimation) for longer studies covering 4-5 months either side of an equinox at high latitude, and focusing on crepuscular species. (4) We applied the average anchoring method to 9 months of data on Red deer (Cervus elaphus), Wild boar (Sus scrofa) and Mouflon (Ovis amon musimon) activity as captured by camera traps in National Park Hoge Veluwe, the Netherlands. Average anchoring revealed more pronounced peaks of activity after sunset than was apparent from untransformed data in red deer and wild boar, but not for mouflon, a cathemeral species. Similarly, activity level was lower when calculated using average-anchored time for red deer and wild boar, but no difference was observed for mouflon. (5) We conclude that transformation of time might not be necessary at latitudes below 20°, or in studies with a duration of less than a month (below 40° latitude). For longer study periods and/or higher latitudes, average-anchoring resolves the problem of variable day length. Code is provided. The transformation functions are incorporated in the R-package ‘activity’.
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Premature senescence in annual crops reduces yield while delayed senescence, termed stay-green, is known to impose both positive and negative impact on yield and nutrition quality. Despite the importance, scant information is available on the genetic architecture of senescence in maize (Zea mays L.) and other cereals. We combined a systematic characterization of natural diversity for senescence in maize and co-expression networks derived from transcriptome analysis of normally senescing and stay-green lines. Sixty-four candidate genes were identified by GWAS, and 14 of these are supported by additional evidence for involvement in senescence-related processes including proteolysis, sugar transport and signaling, and sink activity. Eight of the GWAS candidates, independently supported by a co-expression network underlying stay-green, include a trehalose-6-phosphate synthase, a NAC transcription factor, and two xylan biosynthetic enzymes. Source-sink communication and the activity of cell walls as a secondary sink emerge as key determinants of stay-green. Mutant analysis supports the role of a candidate encoding cysteine protease in stay-green in Arabidopsis (Arabidopsis thaliana), and analysis of natural alleles suggest a similar role in maize. This study provides a foundation for enhanced understanding and manipulation of senescence for increasing carbon yield, nutritional quality, and stress tolerance of maize and other cereals.
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