Hypotheses, evidence and relationships: The HypER approach for representing scientific knowledge claims

Biological knowledge is increasingly represented as a collection of (entity-relationship-entity) triplets. These are queried, mined, appended to papers, and published. However, this representation ignores the argumentation contained within a paper and the relationships between hypotheses, claims and evidence put forth in the article. In this paper, we propose an alternate view of the research article as a network of 'hypotheses and evidence'. Our knowledge representation focuses on scientific discourse as a rhetorical activity, which leads to a different direction in the development of tools and processes for modeling this discourse. We propose to extract knowledge from the article to allow the construction of a system where a specific scientific claim is connected, through trails of meaningful relationships, to experimental evidence. We discuss some current efforts and future plans in this area

European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation?

Extant populations of the European wildcat are fragmented across the continent, the likely consequence of recent extirpations due to habitat loss and over-hunting. However, their underlying phylogeographic history has never been reconstructed. For testing the hypothesis that the European wildcat survived the Ice Age fragmented in Mediterranean refuges, we assayed the genetic variation at 31 microsatellites in 668 presumptive European wildcats sampled in 15 European countries. Moreover, to evaluate the extent of subspecies/population divergence and identify eventual wild × domestic cat hybrids, we genotyped 26 African wildcats from Sardinia and North Africa and 294 random-bred domestic cats. Results of multivariate analyses and Bayesian clustering confirmed that the European wild and the domestic cats (plus the African wildcats) belong to two well-differentiated clusters (average Ф ST = 0.159, r st = 0.392, P > 0.001; Analysis of molecular variance [AMOVA]). We identified from c. 5% to 10% cryptic hybrids in southern and central European populations. In contrast, wild-living cats in Hungary and Scotland showed deep signatures of genetic admixture and introgression with domestic cats. The European wildcats are subdivided into five main genetic clusters (average Ф ST = 0.103, r st = 0.143, P > 0.001; AMOVA) corresponding to five biogeographic groups, respectively, distributed in the Iberian Peninsula, central Europe, central Germany, Italian Peninsula and the island of Sicily, and in north-eastern Italy and northern Balkan regions (Dinaric Alps). Approximate Bayesian Computation simulations supported late Pleistocene-early Holocene population splittings (from c. 60 k to 10 k years ago), contemporary to the last Ice Age climatic changes. These results provide evidences for wildcat Mediterranean refuges in southwestern Europe, but the evolution history of eastern wildcat populations remains to be clarified. Historical genetic subdivisions suggest conservation strategies aimed at enhancing gene flow through the restoration of ecological corridors within each biogeographic units. Concomitantly, the risk of hybridization with free-ranging domestic cats along corridor edges should be carefully monitored

Networked buffering: a basic mechanism for distributed robustness in complex adaptive systems

A generic mechanism - networked buffering - is proposed for the generation of robust traits in complex systems. It requires two basic conditions to be satisfied: 1) agents are versatile enough to perform more than one single functional role within a system and 2) agents are degenerate, i.e. there exists partial overlap in the functional capabilities of agents. Given these prerequisites, degenerate systems can readily produce a distributed systemic response to local perturbations. Reciprocally, excess resources related to a single function can indirectly support multiple unrelated functions within a degenerate system. In models of genome:proteome mappings for which localized decision-making and modularity of genetic functions are assumed, we verify that such distributed compensatory effects cause enhanced robustness of system traits. The conditions needed for networked buffering to occur are neither demanding nor rare, supporting the conjecture that degeneracy may fundamentally underpin distributed robustness within several biotic and abiotic systems. For instance, networked buffering offers new insights into systems engineering and planning activities that occur under high uncertainty. It may also help explain recent developments in understanding the origins of resilience within complex ecosystems. \ud \u

Gone with the currents: lack of genetic differentiation at the circum-continental scale in the Antarctic krill Euphausia superba

<p>Abstract</p> <p>Background</p> <p>Southern Ocean fauna represent a significant amount of global biodiversity, whose origin may be linked to glacial cycles determining local extinction/eradication with ice advance, survival of refugee populations and post-glacial re-colonization. This pattern implies high potential for differentiation in benthic shelf species with limited dispersal, yet consequences for pelagic organisms are less clear. The present study investigates levels of genetic variation and population structure of the Antarctic krill <it>Euphausia superba </it>using mitochondrial DNA and EST-linked microsatellite markers for an unprecedentedly comprehensive sampling of its populations over a circum-Antarctic range.</p> <p>Results</p> <p>MtDNA (ND1) sequences and EST-linked microsatellite markers indicated no clear sign of genetic structure among populations over large geographic scales, despite considerable power to detect differences inferred from forward-time simulations. Based on ND1, few instances of genetic heterogeneity, not significant after correction for multiple tests, were detected between geographic or temporal samples. Neutrality tests and mismatch distribution based on mtDNA sequences revealed strong evidence of past population expansion. Significant positive values of the parameter <it>g </it>(a measure of population growth) were obtained from microsatellite markers using a coalescent-based genealogical method and suggested a recent start (60 000 - 40 000 years ago) for the expansion.</p> <p>Conclusions</p> <p>The results provide evidence of lack of genetic heterogeneity of Antarctic krill at large geographic scales and unequivocal support for recent population expansion. Lack of genetic structuring likely reflects the tight link between krill and circum-Antarctic ocean currents and is consistent with the hypothesis that differentiation processes in Antarctic species are largely influenced by dispersal potential, whereas small-scale spatial and temporal differentiation might be due to local conditions leading to genetic patchiness. The signal of recent population growth suggests differential impact of glacial cycles on pelagic Antarctic species, which experienced population expansion during glaciations with increased available habitat, <it>versus </it>sedentary benthic shelf species.</p> <p>EST-linked microsatellites provide new perspectives to complement the results based on mtDNA and suggest that data-mining of EST libraries will be a useful approach to facilitate use of microsatellites for additional species.</p

Next generation sequencing analyses on Norwegian isolates of the tick Ixodes ricinus

Masteroppgave i marin økologi - Nord universitet, 2016Sperra for utlån til 2019-11-0

A Phylogenetic Study of Vulnerable Batoid Species from the North Atlantic

Successful resolution of the nomenclature and taxonomy of batoid fish complicated by the high degree of morphological and ecological conservatism in this group. However, both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) phylogenies have been utilised to resolve batoid phylogenies and even to identify cryptic species. As a result, the number of ray species described in recent decades has dramatically increased- although questions still remain regarding the taxonomic status of many batoid species. In chapter one of this thesis, the importance of taxonomy in skate conservation and management is reviewed. In chapter two, control region (CR) and cytochrome oxidase I (COI) sequencing of the blue skate (Dipturus batis) and the flapper skate (Dipturus intermedius) from across the Northeast Atlantic was performed, in order to clarify their geographical distribution. Although now formally recognised as distinct species, before 2010 these two taxa were classified together as the critically endangered ‘common skate’, D. batis. Although this has important conservation implications, their protection is currently being hindered by a lack of spatiotemporal data. In the present study, the blue skate generally appears to be more common than the flapper skate, with a distribution extending from Rockall and Iceland to the Western Approaches and the Celtic Sea. Whilst the flapper skate appears most frequent around northern Scotland, the North Sea and Ireland, novel data also suggests that it may have once had a much wider distribution. For the first time, this species was identified in the Azores, where unique haplotypes were also isolated, potentially highlighting the genetic distinctiveness of the population in this region. In chapter three, nextRAD and mtDNA (concatenated CR and COI) sequencing were utilised to explore the phylogenetics of several vulnerable species of European skate. Whilst the current designation of the Madeiran skate (Raja maderensis) and the thornback ray (Raja clavata) as distinct species wasn’t fully supported, genetically distinct populations were identified in the Azores and surrounding seamounts. The presence of a cryptic Dipturus species in the Azores wasn’t supported, as suggested by previous work on the longnosed skate (Dipturus oxyrinchus). However, Azorean longnosed skate and flapper skate were distinct from their geographically proximate counterparts, and may represent distinct populations. The uniqueness of the Azores highlights the importance of seamounts as ‘hotspots’ of biodiversity, which has important implications for marine protected areas that include these batoid species as a protected feature. In addition to resolving these phylogenies, this thesis also offered an opportunity to comment on the utility of mtDNA and nextRAD sequencing for batoid phylogenetics, the latter of which has never been applied to skates and rays before

Supporting cognition in systems biology analysis: findings on users' processes and design implications

Abstract Background Current usability studies of bioinformatics tools suggest that tools for exploratory analysis support some tasks related to finding relationships of interest but not the deep causal insights necessary for formulating plausible and credible hypotheses. To better understand design requirements for gaining these causal insights in systems biology analyses a longitudinal field study of 15 biomedical researchers was conducted. Researchers interacted with the same protein-protein interaction tools to discover possible disease mechanisms for further experimentation. Results Findings reveal patterns in scientists' exploratory and explanatory analysis and reveal that tools positively supported a number of well-structured query and analysis tasks. But for several of scientists' more complex, higher order ways of knowing and reasoning the tools did not offer adequate support. Results show that for a better fit with scientists' cognition for exploratory analysis systems biology tools need to better match scientists' processes for validating, for making a transition from classification to model-based reasoning, and for engaging in causal mental modelling. Conclusion As the next great frontier in bioinformatics usability, tool designs for exploratory systems biology analysis need to move beyond the successes already achieved in supporting formulaic query and analysis tasks and now reduce current mismatches with several of scientists' higher order analytical practices. The implications of results for tool designs are discussed.http://deepblue.lib.umich.edu/bitstream/2027.42/134554/1/13009_2008_Article_29.pd

The role of glacial-interglacial climate change in shaping the genetic structure of eastern subterranean termites in the southern Appalachian Mountains, USA

Abstract: The eastern subterranean termite, Reticulitermes flavipes, currently inhabits previously glaciated regions of the northeastern U.S., as well as the unglaciated southern Appalachian Mountains and surrounding areas. We hypothesized that Pleistocene climatic fluctuations have influenced the distribution of R. flavipes, and thus the evolutionary history of the species. We estimated contemporary and historical geographic distributions of R. flavipes by constructing Species Distribution Models (SDM). We also inferred the evolutionary and demographic history of the species using mitochondrial (cytochrome oxidase I and II) and nuclear (endo-beta-1,4-glucanase) DNA sequence data. To do this, genetic populations were delineated using Bayesian spatial-genetic clustering, competing hypotheses about population divergence were assessed using approximate Bayesian computation (ABC), and changes in population size were estimated using Bayesian skyline plots. SDMs identified areas in the north with suitable habitat during the transition from the Last Interglacial to the Last Glacial Maximum, as well as an expanding distribution from the mid-Holocene to the present. Genetic analyses identified three geographically cohesive populations, corresponding with northern, central, and southern portions of the study region. Based on ABC analyses, divergence between the Northern and Southern populations was the oldest, estimated to have occurred 64.80 thousand years ago (kya), which corresponds with the timing of available habitat in the north. The Central and Northern populations diverged in the mid-Holocene, 8.63 kya, after which the Central population continued to expand. Accordingly, phylogeographic patterns of R. flavipes in the southern Appalachians appear to have been strongly influenced by glacial-interglacial climate change. OPEN RESEARCH BADGES This article has been awarded Open Materials, Open Data Badges. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.5061/dryad.5hr7f31

Population genomics meet Lagrangian simulations: Oceanographic patterns and long larval duration ensure connectivity among Paracentrotus lividus populations in the Adriatic and Ionian seas

Connectivity between populations influences both their dynamics and the genetic structuring of species. In this study, we explored connectivity patterns of a marine species with long-distance dispersal, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic-Ionian basins (Central Mediterranean). We applied a multidisciplinary approach integrating population genomics, based on 1,122 single nucleotide polymorphisms (SNPs) obtained from 2b-RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples collected in the focal Adriatic-Ionian area, whereas weak but significant differentiation was found with respect to two samples from the Western Mediterranean (France and Tunisia). This result was not affected by the few putative outlier loci identified in our dataset. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic-Ionian locations, supporting the hypothesis of connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, the latter revealing genetic differentiation in the same geographic area despite a smaller sample size and a lower power to detect differences. The comparison with studies conducted using nuclear markers on other species with similar pelagic larval durations in the same Adriatic-Ionian locations indicates species-specific differences in genetic connectivity patterns and warns against generalizing single-species results to the entire community of rocky shore habitats