Genome size variation in Deschampsia cespitosa sensu lato (Poaceae) in Eurasia

The grass Deschampsia cespitosa is a variable taxon out of which many varieties, subspecies and endemic species have been separated. In this paper, the variation in genome size (GS) and ploidy of this grass including several of its subspecies and two related species in Eurasia was investigated by flow cytometric (FCM) measurements. GS and ploidy data were also related to specific environments and reproduction mode. Ploidy levels found by FCM were confirmed by chromosome counts of diploid (2n = 28) and tetraploid (2n = 52) samples. Seminiferous (seed bearing) D. cespitosa was mainly diploid (GS between 3.754 and 5.438 pg/1C). GS variation in diploids showed a geographic pattern with a significant difference (H = 41,441, P < 0.001) between European (median = 4.377 pg) and Asian (median = 4.881 pg) accessions. Genome size (1C) in tetraploids ranged from 7.9426 to 9.0399 pg. Tetraploid seminiferous D. cespitosa was found mostly in disturbed habitats in western and southern Europe, while tetraploids in Asia were registered in wet Arctic habitats. Genome size (1C between 8.3278 and 8.8603 pg) of the pseudoviviparous plants (spikelets produce plantlets asexually) of wet habitats in central and northern Europe indicated tetraploidy. A putative triploid (GS 6.6817 pg) was detected in Iceland. Summing up, we found a high variation in GS on the geographic scale with significant regional differences in diploid D. cespitosa. Among the tetraploids, the asexually reproducing plants were bound to specific habitats, while the seminiferous plants showed a habitat preference similar to the diploids.

Elevated Post K-Pg Export Productivity in the Gulf of Mexico and Caribbean

The global heterogeneity in export productivity after the Cretaceous-Paleogene (K-Pg) mass extinction is well documented, with some sites showing no change on geologic timescales, some demonstrating sustained decline, and a few showing a somewhat surprising increase. However, these records come from sites so widespread that a key outstanding question is the geographic scale of changes in export productivity, and whether similar environments (open ocean gyres, western boundary currents) responded similarly or whether heterogeneity is unrelated to environment. To address this, we developed three new Ba/Ti export productivity records from sites in the Gulf of Mexico and Caribbean which, combined with published data from a fourth site in the Chicxulub Crater itself, allows us to reconstruct regional changes in post K-Pg export productivity for the first time. We find that, on a regional scale, export productivity change is homogenous, with all four sites showing a ~300 kyr period of elevated export production just after the boundary, followed by a longer period of decline. Interestingly, this interval of elevated export production appears to coincide with the post K-Pg global micrite layer, which is thought to at least partially have been produced by blooms of carbonate-producing cyanobacteria and other picophytoplankton. We note from a global comparison of sites that elevated export productivity appears to be most common in tropical waters, which suggests that changing plankton ecology evidenced by the micrite layer altered the biological pump in a way that encouraged a temporary increase in export production in the tropics.

Paranephelius (Asteraceae: Liabeae): A case study in high-elevation hybridization and taxonomic insights

Paranephelius Poepp. (Liabeae: Asteraceae) is a genus, here comprised of three species confined to high-elevation Andean habitats from 3°–25°S latitude from northern Peru to northern Argentina. In a prior investigation, sequence data was analyzed from samples throughout the range of the genus to evaluate the morphological variation used in delineating species. This detailed sampling allowed for molecular studies at a fine geographic scale. Within Paranephelius, genetic divergence is low, and not adequate to fully resolve phylogenetic relationships at the species level. Two genetically and morphologically recognizable genomes were reveled in northern Peru; these correspond to P. ovatus Wedd. and P. uniflorus Poepp., respectively. Several accessions possess sequences representing putative hybrids between these two species. These putative hybrids have caused taxonomic confusion in establishing species boundaries in Paranephelius. The molecular analysis suggested that P. asperifolius (Muschl.) H. Rob. & Brettell, distributed in Bolivia and northwestern Argentina, is related to P. ovatus, while it most closely resembles P. uniflorus. Species that have changed status include, P. ferreyrae H. Rob., here within the parameters of P. uniflorus; and P. jelskii (Hieron.) H. Rob. & Brettell, P. bullatus A. Gray ex Wedd., and P. wurdackii H. Rob. are here within parameters of P. ovatus. This study is not intended to be a monograph, but does includes a key to species, descriptions, illustrations, and citation of specimens examined.

The opening and closure of oceanic seaways during the Cenozoic: pacemaker of global climate change?

The opening and constriction of oceanic gateways played an essential role in shaping global climate throughout Earth's history. In this review we provide an overview of the best documented feedbacks between gateway dynamics and climate change throughout the Cenozoic. The discussed tectonically induced events comprise (i) the opening of the Tasmanian Gateway and the glaciation of Antarctica during the Eocene/Oligocene, (ii) the water mass exchange between Atlantic and Mediterranean via the Strait of Gibraltar since the Miocene, (iii) the closure of the American Seaway, as well as (iv) the constriction of the Indonesian Throughflow, both argued to have been instrumental for intensification of the Northern Hemisphere Glaciation during the late Pliocene and early Pleistocene. Lastly, we look at (v) the climatic impact of the flooding and submergence of the Bering Strait during the Plio-Pleistocene and its influence on the Atlantic Meridional Overturning Circulation. While different in underlying mechanisms, geographic scale and temporal evolution, these case studies demonstrate that even seemingly small-scale changes in the configuration of ocean seaways fundamentally altered the global climate system via their impact on oceanic currents, global heat transfer, and carbon storage.

Bayesian spatio-temporal distributed lag modeling for delayed climatic effects on sparse malaria incidence data

Background In many areas of the Greater Mekong Subregion (GMS), malaria endemic regions have shrunk to patches of predominantly low-transmission. With a regional goal of elimination by 2030, it is important to use appropriate methods to analyze and predict trends in incidence in these remaining transmission foci to inform planning efforts. Climatic variables have been associated with malaria incidence to varying degrees across the globe but the relationship is less clear in the GMS and standard methodologies may not be appropriate to account for the lag between climate and incidence and for locations with low numbers of cases. Methods In this study, a methodology was developed to estimate the spatio-temporal lag effect of climatic factors on malaria incidence in Thailand within a Bayesian framework. A simulation was conducted based on ground truth of lagged effect curves representing the delayed relation with sparse malaria cases as seen in our study population. A case study to estimate the delayed effect of environmental variables was used with malaria incidence at a fine geographic scale of sub-districts in a western province of Thailand. Results From the simulation study, the model assumptions which accommodated both delayed effects and excessive zeros appeared to have the best overall performance across evaluation metrics and scenarios. The case study demonstrated lagged climatic effect estimation of the proposed modeling with real data. The models appeared to be useful to estimate the shape of association with malaria incidence. Conclusions A new method to estimate the spatiotemporal effect of climate on malaria trends in low transmission settings is presented. The developed methodology has potential to improve understanding and estimation of past and future trends in malaria incidence. With further development, this could assist policy makers with decisions on how to more effectively distribute resources and plan strategies for malaria elimination.

Plant Nutrients Appears Decoupled from Soil: Increasing Influences from Changing Climate in the Grassland’s of Inner Mongolia, China

Extremes in weather episodes seem to be the new normal. We need to better understand how changing climatic conditions alter plant growth in grasslands, especially macro nutrient uptake and stoichiometry. However, few studies have examined how warmer/colder or wetter/drier climates influence the nutrient decoupling between plants and soils at the ecosystem level. Here, we investigated the changes in carbon (C), nitrogen (N), and phosphorus (P) concentrations and their stoichiometric ratios in plants and soils from 65 grassland sites along a geographic gradient of temperature and aridity in northern China. Often, we saw inverse responses between plant and soil nutrients with respect to temperature and aridity. Soil C and N were negatively correlated with temperature and aridity. Soil P was negatively correlated with aridity. Plant N was positively correlated with aridity and plant P was negatively correlated with temperature, while plant C had no relationship with either. Temperature and aridity were positively correlated with C:N and negatively correlated with C:P and N:P ratios in soils. However, aridity was negatively correlated with plant C:N ratios. Plant N:P ratios were positively correlated with temperature and aridity, whereas plant C:P ratios had no relationship with either. Our findings suggest at a broad geographic scale, plant nutrients do not always reflect soil nutrient availability. It is conceivable that rapid climate shifts and the resulting changes in element availability, turnover rates, absorption, and use efficiency might cause decoupling of C, N, and P cycles between plants and soils.

Community violence and academic achievement: High-crime neighborhoods, hotspot streets, and the geographic scale of “community”

Numerous studies have demonstrated a negative relationship between community violence and youth academic achievement, but they have varied in their geographic definition of “community,” especially as it relates to proximity to students’ residences. We extend this by considering the independent relationships between academic achievement and violent events (from 911 dispatches; e.g., gun shots) at the neighborhood (i.e., census tract) and street-block levels. We use data from standardized Math and English Language Arts (ELA) tests from Boston, MA for 2011–2013. Exposure to community violence was partially independent between streets and tracts, with some students living on low-crime streets in high-crime neighborhoods or high-crime streets in low-crime neighborhoods. Initial regression models found that differences in a neighborhood’s violent crime predicted up to a 3% difference in test scores on both Math and ELA tests. Students living on high-crime streets scored an additional 1% lower than neighbors on safer streets. Subsequent models with student-level fixed effects, however, eliminated these relationships, except for the effect of neighborhood-level violence on Math scores. These findings suggest that future work should consider community violence at both geographic scales, but that in this case the impacts were only consistent at the neighborhood level and associations at the street level were seemingly due to spatial segregation of households.

Genomic analysis reveals geography rather than culture as the predominant factor shaping genetic variation in northern Kenyan human populations

Objectives: The aim of this study was to characterize the genetic relationships within and among four neighboring populations in northern Kenya in light of cultural relationships to understand the extent to which geography and culture shape patterns of genetic variation. Materials and Methods: We collected DNA and demographic information pertaining to aspects of social identity and heritage from 572 individuals across the Turkana, Samburu, Waso Borana, and Rendille of northern Kenya. We sampled individuals across a total of nine clans from these four groups and, additionally, three territorial sections within the Turkana and successfully genotyped 376 individuals. Results: Here we report that geography predominately shapes genetic variation within and among human groups in northern Kenya. We observed a clinal pattern of genetic variation that mirrors the overall geographic distribution of the individuals we sampled. We also found relatively higher rates of intermarriage between the Rendille and Samburu and evidence of gene flow between them that reflect these higher rates of intermarriage. Among the Turkana, we observed strong recent genetic substructuring based on territorial section affiliation. Within ethnolinguistic groups, we found that Y chromosome haplotypes do not consistently cluster by natal clan affiliation. Finally, we found that sampled populations that are geographically closer have lower genetic differentiation, and that cultural similarity does not predict genetic similarity as a whole across these northern Kenyan populations. Discussion: Overall, the results from this study highlight the importance of geography, even on a local geographic scale, in shaping observed patterns of genetic variation in human populations.

A highly endemic area of Echinococcus multilocula is identified through a comparative re-assessment of prevalence in red fox (Vulpes vulpes), Alto Adige (Italy: 2019-2020)

Background: Surveillance of E. multilocularis at the edge of its range is hindered by fragmented distributional patterns and low prevalence and burden in definitive hosts. Thus, tests with adequate levels of sensitivity are especially important for discriminating between infected and non-infected areas. Aim: We reassessed the prevalence of E. multilocularis at the southern border of its distribution in Alto Adige (Italy), to improve surveillance in wildlife and provide more accurate estimates of exposure risk. Methods: We compared results from the diagnostic test currently implemented for surveillance (based on Coproscopy+Multiplex PCR - CMPCR), against a real-time quantitative PCR (qPCR) for 235 fox faeces collected in 2019-2020. The performances of the two tests were estimated using a scraping technique (SFCT) as the gold standard applied to the small intestines of a subsample (n=123) of the same hosts. True prevalence was calculated and sample size required by each faecal test for the detection of the parasite was then estimated. Results: True prevalence of E. multilocularis in foxes (14.3%) was definitely higher than reported in the last decade (never >5% from 2012 to 2018). The qPCR also had a higher sensitivity (83%) compared to CMPCR (21%). Agreement with the gold standard was far higher for qPCR (0.816) than CMPCR (0.298) as well, determining a smaller sample size required to detect the disease. Conclusions: Alto Adige should be considered a highly endemic area. Surveillance at the edges of E. multilocularis distribution should adopt qPCR diagnostics on definitive hosts on a small geographic scale.