Explaining Spatial Heterogeneity in Population Dynamics and Genetics from Spatial Variation in Resources for a Large Herbivore

Fine-scale spatial variation in genetic relatedness and inbreeding occur across continuous distributions of several populations of vertebrates; however, the basis of observed variation is often left untested. Here we test the hypothesis that prior observations of spatial patterns in genetics for an island population of feral horses (Sable Island, Canada) were the result of spatial variation in population dynamics, itself based in spatial heterogeneity in underlying habitat quality. In order to assess how genetic and population structuring related to habitat, we used hierarchical cluster analysis of water sources and an indicator analysis of the availability of important forage species to identify a longitudinal gradient in habitat quality along the length of Sable Island. We quantify a west-east gradient in access to fresh water and availability of two important food species to horses: sandwort, Honckenya peploides, and beach pea, Lathyrus japonicas. Accordingly, the population clusters into three groups that occupy different island segments (west, central, and east) that vary markedly in their local dynamics. Density, body condition, and survival and reproduction of adult females were highest in the west, followed by central and east areas. These results mirror a previous analysis of genetics, which showed that inbreeding levels are highest in the west (with outbreeding in the east), and that there are significant differences in fixation indices among groups of horses along the length of Sable Island. Our results suggest that inbreeding depression is not an important limiting factor to the horse population. We conclude that where habitat gradients exist, we can anticipate fine-scale heterogeneity in population dynamics and hence genetics.     

Evaluating temporal variation in Citizen Science Data against temporal variation in the environment

Citizen Science Data (CSD) is increasingly contributing to the assessment of biodiversity and ecosystems. However, there is a need to evaluate the usefulness of CSD for different purposes. Ideally, CSD from populations should be evaluated against independent population data collected using a proper sampling design, but such data are lacking for almost all species. We propose an approach for evaluating CSD against environmental data. First, an evaluation model is formulated based on knowledge of how environmental variables affect population dynamics. Second, the hypotheses of the evaluation model are tested statistically. Support for the evaluation model is interpreted as support for the CSD. We applied the approach to six longhorn beetle species using Swedish data from 1930–2000. The evaluation model assumed that early summer temperature affects larval development time. We found support for the evaluation model in two species, and some evidence in its favour in one species. This suggests that the CSD from these species reflect true inter‐annual variation. We also found statistical evidence for population trends in three to four species. In two of these, the evaluation model was supported thus providing particular support for the trend estimates. Lack of support for the evaluation model may be due to biological inaccuracy, the general characteristics of CSD, or low resolution of the environmental evaluation data. We also discuss alternative environmental data for evaluating CSD.     

Variation in DNA-ploidy Levels of Reynoutria Taxa in the Czech Republic

The genus Reynoutria is represented by four taxa in the Czech Republic: Reynoutria japonica var. japonica, R. japonica var. compacta, R. sachalinensis and R. xbohemica. By using flow cytometry, cytological variability within the genus is described based on 257 Reynoutria samples. The varieties of R. japonica are cytologically uniform, var. japonica is exclusively octoploid (2n = 8x = 88) and var. compacta occurs only as a tetraploid (2n = 4x = 44), but R. sachalinensis and R. xbohemica exhibit some variation in chromosome numbers. Reynoutria sachalinensis is predominantly tetraploid (2n = 4 x = 44), but also occurs occasionally as hexaploid and octoploid cytotypes. The most common ploidy level in R. xbohemica is hexaploid (2n = 6x = 66), but tetraploid and octoploid clones were also found. The four taxa occurring in the Czech Republic are described briefly and the possible origins of the cytotypes discussed.     

Assessing Uncertainty in High-Resolution Spatial Climate Data across the US Northeast

Local and regional-scale knowledge of climate change is needed to model ecosystem responses, assess vulnerabilities and devise effective adaptation strategies. High-resolution gridded historical climate (GHC) products address this need, but come with multiple sources of uncertainty that are typically not well understood by data users. To better understand this uncertainty in a region with a complex climatology, we conducted a ground-truthing analysis of two 4 km GHC temperature products (PRISM and NRCC) for the US Northeast using 51 Cooperative Network (COOP) weather stations utilized by both GHC products. We estimated GHC prediction error for monthly temperature means and trends (1980–2009) across the US Northeast and evaluated any landscape effects (e.g., elevation, distance from coast) on those prediction errors. Results indicated that station-based prediction errors for the two GHC products were similar in magnitude, but on average, the NRCC product predicted cooler than observed temperature means and trends, while PRISM was cooler for means and warmer for trends. We found no evidence for systematic sources of uncertainty across the US Northeast, although errors were largest at high elevations. Errors in the coarse-scale (4 km) digital elevation models used by each product were correlated with temperature prediction errors, more so for NRCC than PRISM. In summary, uncertainty in spatial climate data has many sources and we recommend that data users develop an understanding of uncertainty at the appropriate scales for their purposes. To this end, we demonstrate a simple method for utilizing weather stations to assess local GHC uncertainty and inform decisions among alternative GHC products.     

Incidence and Variation of Discrepancies in Recording Chronic Conditions in Australian Hospital Administrative Data

Diagnostic data routinely collected for hospital admitted patients and used for case-mix adjustment in care provider comparisons and reimbursement are prone to biases. We aim to measure discrepancies, variations and associated factors in recorded chronic morbidities for hospital admitted patients in New South Wales (NSW), Australia. Of all admissions between July 2010 and June 2014 in all NSW public and private acute hospitals, admissions with over 24 hours stay and one or more of the chronic conditions of diabetes, smoking, hepatitis, HIV, and hypertension were included. The incidence of a non-recorded chronic condition in an admission occurring after the first admission with a recorded chronic condition (index admission) was considered as a discrepancy. Poisson models were employed to (i) derive adjusted discrepancy incidence rates (IR) and rate ratios (IRR) accounting for patient, admission, comorbidity and hospital characteristics and (ii) quantify variation in rates among hospitals. The discrepancy incidence rate was highest for hypertension (51% of 262,664 admissions), followed by hepatitis (37% of 12,107), smoking (33% of 548,965), HIV (27% of 1500) and diabetes (19% of 228,687). Adjusted rates for all conditions declined over the four-year period; with the sharpest drop of over 80% for diabetes (47.7% in 2010 vs. 7.3% in 2014), and 20% to 55% for the other conditions. Discrepancies were more common in private hospitals and smaller public hospitals. Inter-hospital differences were responsible for 1% (HIV) to 9.4% (smoking) of variation in adjusted discrepancy incidences, with an increasing trend for diabetes and HIV. Chronic conditions are recorded inconsistently in hospital administrative datasets, and hospitals contribute to the discrepancies. Adjustment for patterns and stratification in risk adjustments; and furthermore longitudinal accumulation of clinical data at patient level, refinement of clinical coding systems and standardisation of comorbidity recording across hospitals would enhance accuracy of datasets and validity of case-mix adjustment.     

Deleterious Mutations of a Claw Keratin in Multiple Taxa of Reptiles

We have recently shown that homologs of mammalian hair keratins are expressed in the claws of the green anole lizard, Anolis carolinensis. To test whether reptilian hair keratin homologs are functionally associated with claws, we investigated the conservation of the prototypical reptilian hair keratin homolog, hard acidic keratin 1 (HA1), in representative species from all main clades of reptiles. A complete cDNA of HA1 was cloned from the claw-forming epidermis of the lacertid lizard Podarcis sicula, and partial HA1 gene sequences could be amplified from genomic DNA of tuatara, lizards, gekkos, turtles, and crocodiles. In contrast, the HA1 gene of the limbless slow worm, Anguis fragilis, and of two species of turtles contained at least one deleterious mutation. Moreover, an HA1 gene was undetectable in the softshell turtle, snakes, and birds. Mapping the presence and absence of HA1 onto the phylogenetic tree of sauropsids suggested that the HA1 gene has been lost independently in several lineages of reptiles. The species distribution of HA1 is compatible with the hypothesis of a primary function of HA1 in claws but also shows that the formation of reptilian claws does not strictly depend on this keratin.     

Population Genetics of the Eastern Hellbender (Cryptobranchus alleganiensis alleganiensis) across Multiple Spatial Scales

Conservation genetics is a powerful tool to assess the population structure of species and provides a framework for informing management of freshwater ecosystems. As lotic habitats become fragmented, the need to assess gene flow for species of conservation management becomes a priority. The eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is a large, fully aquatic paedamorphic salamander. Many populations are experiencing declines throughout their geographic range, yet the genetic ramifications of these declines are currently unknown. To this end, we examined levels of genetic variation and genetic structure at both range-wide and drainage (hierarchical) scales. We collected 1,203 individuals from 77 rivers throughout nine states from June 2007 to August 2011. Levels of genetic diversity were relatively high among all sampling locations. We detected significant genetic structure across populations (F_st values ranged from 0.001 between rivers within a single watershed to 0.218 between states). We identified two genetically differentiated groups at the range-wide scale: 1) the Ohio River drainage and 2) the Tennessee River drainage. An analysis of molecular variance (AMOVA) based on landscape-scale sampling of basins within the Tennessee River drainage revealed the majority of genetic variation (∼94–98%) occurs within rivers. Eastern hellbenders show a strong pattern of isolation by stream distance (IBSD) at the drainage level. Understanding levels of genetic variation and differentiation at multiple spatial and biological scales will enable natural resource managers to make more informed decisions and plan effective conservation strategies for cryptic, lotic species.     

Changes in Task-Related Functional Connectivity across Multiple Spatial Scales Are Related to Reading Performance

Reading requires the interaction of a distributed set of cortical areas whose distinct patterns give rise to a wide range of individual skill. However, the nature of these neural interactions and their relation to reading performance are still poorly understood. Functional connectivity analyses of fMRI data can be used to characterize the nature of interactivity of distributed brain networks, yet most previous studies have focused on connectivity during task-free (i.e., “resting state”) conditions. Here, we report new methods for assessing task-related functional connectivity using data-driven graph theoretical methods and describe how large-scale patterns of connectivity relate to individual variability in reading performance among children. We found that connectivity patterns of subjects performing a reading task could be decomposed hierarchically into multiple sub-networks, and we observed stronger long-range interaction between sub-networks in subjects with higher task accuracy. Additionally, we found a network of hub regions known to be critical to reading that displays increased short-range synchronization in higher accuracy subjects. These individual differences in task-related functional connectivity reveal that increased interaction between distant regions, coupled with selective local integration within key regions, is associated with better reading performance. Importantly, we show that task-related neuroimaging data contains far more information than usually extracted via standard univariate analyses – information that can meaningfully relate neural connectivity patterns to cognition and task.     

Spatial Variation in Fish Assemblages across small Mediterranean Drainages: Effects of Habitat and Landscape Context

Much debate about assemblage organization in stream fish may stem from analysing the effects of both local and large-scale processes on assemblage attributes over whole geographic regions. This study addresses this issue, by examining the contribution of local habitat attributes and landscape context to fish assemblage variation across small Mediterranean drainages in southern Portugal. Fish abundance and species composition was estimated in 28 sites, across 10 drainages, in both a dry year (1999) and a wet year (2001), and related to two sets of variables reflecting habitat and landscape characteristics. Fish showed responses to both sets of variables with variance partitioning indicating that landscape context had important effects on species richness whereas habitat attributes were the primary determinants of local fish abundance. In general, high species richness was associated with larger drainage area and higher rainfall variability, whereas variation in species abundances mostly reflected the influence of width, depth, conductivity, current velocity, substrate size and emergent vegetation. The relative contributions of both landscape context and habitat attributes to species richness and abundance were generally lower in 1999 than in 2001, with much less diversified species–habitat relationships being found in the former dry year. These results point to the dynamic nature of assemblage organization, emphasizing the importance of innovative, multi-scale approaches in advancing our knowledge of fish assemblage structure in Mediterranean streams.     

Variation in the mutation rate across mammalian genomes

It has been known for many years that the mutation rate varies across the genome. However, only with the advent of large genomic data sets is the full extent of this variation becoming apparent. The mutation rate varies over many different scales, from adjacent sites to whole chromosomes, with the strongest variation seen at the smallest scales. Some of these patterns have clear mechanistic bases, but much of the rate variation remains unexplained, and some of it is deeply perplexing. Variation in the mutation rate has important implications in evolutionary biology and underexplored implications for our understanding of hereditary disease and cancer.     

Diurnal Variation of Cell Proliferation in Three Bacterial Taxa from Coastal North Sea Waters

Pulse-labeling with bromodeoxyuridine (BrdU) in combination with fluorescence in situ hybridization was applied to quantify the percentage of proliferating cells in coastal North Sea waters. In order to assess diurnal variability, we sampled eight or nine times, respectively, within 3 consecutive days at two seasons. Bacteria affiliated with the Roseobacter, SAR86, and NOR5 lineages constituted on average 19% ± 3%, 8% ± 2%, and 6% ± 1% of all cells in May 2002 and 17% ± 3%, 10% ± 2%, and 11% ± 3% in August. The relative abundances of the three populations either remained stable, or they changed very gradually during the observation periods. On average, 38 and 39% of all Bacteria exhibited DNA de novo synthesis in May and August, respectively. The fractions of proliferating cells in bacteria of the SAR86 (May, 59%; August, 72%) and the Roseobacter (48 and 53%) lineages were significantly above the community average. A substantial cell proliferation of population NOR5 (34%) was only encountered in August, concomitant with a dinoflagellate bloom. Significant short-term fluctuations of DNA-synthesizing cells were observed in Roseobacter during May and in NOR5 during August, hinting at a pronounced (temporal or spatial) mesoscale patchiness of growth rates in these populations. Since the BrdU proliferation assay is susceptible to misinterpretation, we also modeled the expected number of labeled cells at increasing BrdU incubation times in a slowly growing bacterial population. We suggest that the absence of visible DNA synthesis in marine bacterioplankton cells after DNA pulse-labeling must not be interpreted as an indication of cell “inactivity.”     

Using Citizen Science Data to Model the Distributions of Common Songbirds of Turkey Under Different Global Climatic Change Scenarios

In this study, we evaluated the potential impact of climate change on the distributions of Turkey’s songbirds in the 21st century by modelling future distributions of 20 resident and nine migratory species under two global climate change scenarios. We combined verified data from an ornithological citizen science initiative (www.kusbank.org) with maximum entropy modeling and eight bioclimatic variables to estimate species distributions and projections for future time periods. Model predictions for resident and migratory species showed high variability, with some species projected to lose and others projected to gain suitable habitat. Our study helps improve the understanding of the current and potential future distributions of Turkey’s songbirds and their responses to climate change, highlights effective strategies to maximize avian conservation efforts in the study region, and provides a model for using citizen science data for biodiversity research in a large developing country with few professional field biologists. Our results demonstrate that climate change will not affect every species equally in Turkey. Expected range reductions in some breeding species will increase the risk of local extinction, whereas others are likely to expand their ranges.     

A Method of Trigonometric Modelling of Seasonal Variation Demonstrated with Multiple Sclerosis Relapse Data

This report describes a novel Stata-based application of trigonometric regression modelling to 55 years of multiple sclerosis relapse data from 46 clinical centers across 20 countries located in both hemispheres. Central to the success of this method was the strategic use of plot analysis to guide and corroborate the statistical regression modelling. Initial plot analysis was necessary for establishing realistic hypotheses regarding the presence and structural form of seasonal and latitudinal influences on relapse probability and then testing the performance of the resultant models. Trigonometric regression was then necessary to quantify these relationships, adjust for important confounders and provide a measure of certainty as to how plausible these associations were. Synchronization of graphing techniques with regression modelling permitted a systematic refinement of models until best-fit convergence was achieved, enabling novel inferences to be made regarding the independent influence of both season and latitude in predicting relapse onset timing in MS. These methods have the potential for application across other complex disease and epidemiological phenomena suspected or known to vary systematically with season and/or geographic location.     

Evolutionary Relationships Among the Eukaryotic Crown Taxa Taking into Account Site-to-Site Rate Variation in 18S rRNA

In this study we constructed a bootstrapped distance tree of 500 small subunit ribosomal RNA sequences from organisms belonging to the so-called crown of eukaryote evolution. Taking into account the substitution rate of the individual nucleotides of the rRNA sequence alignment, our results suggest that (1) animals, true fungi, and choanoflagellates share a common origin: The branch joining these taxa is highly supported by bootstrap analysis (bootstrap support [BS] > 90%), (2) stramenopiles and alveolates are sister groups (BS = 75%), (3) within the alveolates, dinoflagellates and apicomplexans share a common ancestor BS > 95%), while in turn they both share a common origin with the ciliates (BS > 80%), and (4) within the stramenopiles, heterokont algae, hyphochytriomycetes, and oomycetes form a monophyletic grouping well supported by bootstrap analysis (BS > 85%), preceded by the well-supported successive divergence of labyrinthulomycetes and bicosoecids. On the other hand, many evolutionary relationships between crown taxa are still obscure on the basis of 18S rRNA. The branching order between the animal-fungal-choanoflagellates clade and the chlorobionts, the alveolates and stramenopiles, red algae, and several smaller groups of organisms remains largely unresolved. When among-site rate variation is not considered, the inferred tree topologies are inferior to those where the substitution rate spectrum for the 18S rRNA is taken into account. This is primarily indicated by the erroneous branching of fast-evolving sequences. Moreover, when different substitution rates among sites are not considered, the animals no longer appear as a monophyletic grouping in most distance trees. Received: 11 June 1997 / Accepted: 21 July 1997     

中国桫椤科植物新分类群

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Electrophoretic Variation in Esterases, Peroxidases and Acid Phosphatases in Some Native Greek Taxa of the Genera Hordeum and Taeniatherum

Horizontal starch gel electrophoresis has been applied to thestudy of esterase, peroxidase and acid phosphatase patternsin seven taxa, namely Hordeum diploids (2n=14) (H. marinum,H. marinum I and H. hystrix), tetraploids (2n=28) (H. bulbosumand H. murinum subsp. leporinum) and Taeniatherum (2n=14) (T.caput-medusae and T. caput-medusae I) in order to elucidatetheir phylogenetic relationships. On the basis of our experimentalresults the seven taxa may be placed in the following threegroups; (1) diploid Hordeum (H. marinum, H. marinum I, H. hystrix);(2) tetraploid Hordeum (H. bulbosum, H. murinum subsp. leporinum);(3) Taeniatherum (T. caput-medusae, T. caput-medusae I). Esterase, peroxidase and acid phosphatase patterns of the twoHordeum diploid taxa (H. marinum and H. marinum I) are verysimilar suggesting their close phylogenetic relationship; thesame is true for both the taxa of the genus Taeniatherum (T.caput-medusae and T. caput-medusae I). The taxa of the Taeniatherumgroup compared with the diploid Hordeum (H. marinum, H. marinumI, H. hystrix) and the tetraploid Hordeum (H. bulbosum, H. murinumsubsp. leporinum) show a lower degree of phylogenetic relationshipand seem to be equally distant from them. The tetraploid Hordeumgroup shows a higher phylogenetic relationship with diploidHordeum group than with the Taeniatherum group. These results confirm that the genus Taeniatherum, previouslyconsidered as part of the genus Hordeum, should be regardedas a separate genus. Gramineae (Poaceae), Hordeum L., Taeniatherum Nevski., esterase, peroxidase and acid phosphatase patterns, phylogenetic relationships     

Variation in recombination rate across the genome: evidence and implications

Recent data from humans and other species provide convincing evidence of variation in recombination rate in different genomic regions. Comparison of physical and genetic maps reveals variation on a scale of megabases, with substantial differences between sexes. Recombination is often suppressed near centromeres and elevated near telomeres, but neither of these observations is true for all chromosomes. In humans, patterns of linkage disequilibrium and experimental measures of recombination from sperm-typing reveal dramatic hotspots of recombination on a scale of kilobases. Genome-wide variation in the amount of crossing-over may be due to variation in the density of hotspots, the intensity of hotspots, or both. Theoretical models of selection and linkage predict that genetic variation will be reduced in regions of low recombination, and this prediction is supported by data from several species. Heterogeneity in rates of crossing-over provides both an opportunity and a challenge for identifying disease genes: as associations occur in blocks, genomic regions containing disease loci may be identified with relatively few markers, yet identifying the causal mutations is unlikely to be achieved through associations alone.     

Citizen Science Reveals an Extensive Shift in the Winter Distribution of Migratory Western Grebes

Marine waterbirds have shown variable trends in abundance over the past four decades with some species displaying steep declines along the Pacific coast from British Columbia through California. One of the most dramatic changes has been that of western grebes (Aechmophorus occidentalis) in the Salish Sea. This region was a former core of the species wintering distribution but they have become increasingly rare prompting calls for conservation action. A more thorough understanding of this situation requires the analysis of trends at broader geographic scales as well as a consideration of mechanisms that might have led to a change in abundance. We used hierarchical modeling with a Bayesian framework applied to 36 years of Audubon Christmas Bird Count data to assess continent-wide and regional population trends in western and Clark’s grebes (A. clarkii) from 1975 to 2010. Our results show that the North American wintering population of Aechmophorus grebes decreased by ∼52% after 1975, but also that western grebes displayed strongly opposing regional patterns. Abundance decreased by about 95% over 36 years in the Salish Sea but increased by over 300% along coastal California. As a result, the mean centre of the species distribution shifted south by an estimated 895 km between 1980 and 2010. Mechanisms underlying this shift require further study but we hypothesize that it may be related to a change in the abundance and availability of their forage fish prey base. Since the mid-1980s, the Pacific sardine stock off the California coast increased from a few thousand metric tonnes to over two million. At the same time both the abundance and availability of Pacific herring declined in the Salish Sea. Studies are needed to examine this hypothesis further and additional consideration should be directed at other changes in the marine environment that may have contributed to a range shift.