Validation of meter-scale surface faulting offset measurements from high-resolution topographic data

Studies of active fault zones have flourished with the availability of high-resolution topographic data, particularly where airborne light detection and ranging (lidar) and structure from motion (SfM) data sets provide a means to remotely analyze submeter-scale fault geomorphology. To determine surface offset at a point along a strike-slip earthquake rupture, geomorphic features (e.g., stream channels) are measured days to centuries after the event. Analysis of these and cumulatively offset features produces offset distributions for successive earthquakes that are used to understand earthquake rupture behavior. As researchers expand studies to more varied terrain types, climates, and vegetation regimes, there is an increasing need to standardize and uniformly validate measurements of tectonically displaced geomorphic features. A recently compiled catalog of nearly 5000 earthquake offsets across a range of measurement and reporting styles provides insight into quality rating and uncertainty trends from which we formulate best-practice and reporting recommendations for remote studies. In addition, a series of public and beginner-level studies validate the remote methodology for a number of tools and emphasize considerations to enhance measurement accuracy and precision for beginners and professionals. Our investigation revealed that (1) standardizing remote measurement methods and reporting quality rating schemes is essential for the utility and repeatability of fault-offset measurements; (2) measurement discrepancies often involve misinterpretation of the offset geomorphic feature and are a function of the investigator’s experience; (3) comparison of measurements made by a single investigator in different climatic regions reveals systematic differences in measurement uncertainties attributable to variation in feature preservation; (4) measuring more components of a displaced geomorphic landform produces more consistently repeatable estimates of offset; and (5) inadequate understanding of pre-event morphology and post-event modifications represents a greater epistemic limitation than the aleatoric limitations of the measurement process

A compendium and functional characterization of mammalian genes involved in adaptation to Arctic or Antarctic environments

Many mammals are well adapted to surviving in extremely cold environments. These species have likely accumulated genetic changes that help them efficiently cope with low temperatures. It is not known whether the same genes related to cold adaptation in one species would be under selection in another species. The aims of this study therefore were: to create a compendium of mammalian genes related to adaptations to a low temperature environment; to identify genes related to cold tolerance that have been subjected to independent positive selection in several species; to determine promising candidate genes/pathways/organs for further empirical research on cold adaptation in mammals

Applying genetic technologies to combat infectious diseases in aquaculture

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies—sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/ parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.publishedVersio

The association between genetic variants in hMLH1 and hMSH2 and the development of sporadic colorectal cancer in the Danish population

<p>Abstract</p> <p>Background</p> <p>Mutations in the mismatch repair genes <it>hMLH1 </it>and <it>hMSH2 </it>predispose to hereditary non-polyposis colorectal cancer (HNPCC). Genetic screening of more than 350 Danish patients with colorectal cancer (CRC) has led to the identification of several new genetic variants (e.g. missense, silent and non-coding) in <it>hMLH1 </it>and <it>hMSH2</it>. The aim of the present study was to investigate the frequency of these variants in <it>hMLH1 </it>and <it>hMSH2 </it>in Danish patients with sporadic colorectal cancer and in the healthy background population. The purpose was to reveal if any of the common variants lead to increased susceptibility to colorectal cancer.</p> <p>Methods</p> <p>Associations between genetic variants in <it>hMLH1 </it>and <it>hMSH2 </it>and sporadic colorectal cancer were evaluated using a case-cohort design. The genotyping was performed on DNA isolated from blood from the 380 cases with sporadic colorectal cancer and a sub-cohort of 770 individuals. The DNA samples were analyzed using Single Base Extension (SBE) Tag-arrays. A Bonferroni corrected Fisher exact test was used to test for association between the genotypes of each variant and colorectal cancer. Linkage disequilibrium (LD) was investigated using HaploView (v3.31).</p> <p>Results</p> <p>Heterozygous and homozygous changes were detected in 13 of 35 analyzed variants. Two variants showed a borderline association with colorectal cancer, whereas the remaining variants demonstrated no association. Furthermore, the genomic regions covering <it>hMLH1 </it>and <it>hMSH2 </it>displayed high linkage disequilibrium in the Danish population. Twenty-two variants were neither detected in the cases with sporadic colorectal cancer nor in the sub-cohort. Some of these rare variants have been classified either as pathogenic mutations or as neutral variants in other populations and some are unclassified Danish variants.</p> <p>Conclusion</p> <p>None of the variants in <it>hMLH1 </it>and <it>hMSH2 </it>analyzed in the present study were highly associated with colorectal cancer in the Danish population. High linkage disequilibrium in the genomic regions covering <it>hMLH1 </it>and <it>hMSH2</it>, indicate that common genetic variants in the two genes in general are not involved in the development of sporadic colorectal cancer. Nevertheless, some of the rare unclassified variants in <it>hMLH1 </it>and <it>hMSH2 </it>might be involved in the development of colorectal cancer in the families where they were originally identified.</p

Urbanisation generates multiple trait syndromes for terrestrial animal taxa worldwide

Cities can host significant biological diversity. Yet, urbanisation leads to the loss of habitats, species, and functional groups. Understanding how multiple taxa respond to urbanisation globally is essential to promote and conserve biodiversity in cities. Using a dataset encompassing six terrestrial faunal taxa (amphibians, bats, bees, birds, carabid beetles and reptiles) across 379 cities on 6 continents, we show that urbanisation produces taxon-specific changes in trait composition, with traits related to reproductive strategy showing the strongest response. Our findings suggest that urbanisation results in four trait syndromes (mobile generalists, site specialists, central place foragers, and mobile specialists), with resources associated with reproduction and diet likely driving patterns in traits associated with mobility and body size. Functional diversity measures showed varied responses, leading to shifts in trait space likely driven by critical resource distribution and abundance, and taxon-specific trait syndromes. Maximising opportunities to support taxa with different urban trait syndromes should be pivotal in conservation and management programmes within and among cities. This will reduce the likelihood of biotic homogenisation and helps ensure that urban environments have the capacity to respond to future challenges. These actions are critical to reframe the role of cities in global biodiversity loss.info:eu-repo/semantics/publishedVersio

Theropod Fauna from Southern Australia Indicates High Polar Diversity and Climate-Driven Dinosaur Provinciality

The Early Cretaceous fauna of Victoria, Australia, provides unique data on the composition of high latitude southern hemisphere dinosaurs. We describe and review theropod dinosaur postcranial remains from the Aptian–Albian Otway and Strzelecki groups, based on at least 37 isolated bones, and more than 90 teeth from the Flat Rocks locality. Several specimens of medium- and large-bodied individuals (estimated up to ∼8.5 metres long) represent allosauroids. Tyrannosauroids are represented by elements indicating medium body sizes (∼3 metres long), likely including the holotype femur of Timimus hermani, and a single cervical vertebra represents a juvenile spinosaurid. Single specimens representing medium- and small-bodied theropods may be referrable to Ceratosauria, Ornithomimosauria, a basal coelurosaur, and at least three taxa within Maniraptora. Thus, nine theropod taxa may have been present. Alternatively, four distinct dorsal vertebrae indicate a minimum of four taxa. However, because most taxa are known from single bones, it is likely that small-bodied theropod diversity remains underestimated. The high abundance of allosauroids and basal coelurosaurs (including tyrannosauroids and possibly ornithomimosaurs), and the relative rarity of ceratosaurs, is strikingly dissimilar to penecontemporaneous dinosaur faunas of Africa and South America, which represent an arid, lower-latitude biome. Similarities between dinosaur faunas of Victoria and the northern continents concern the proportional representatation of higher clades, and may result from the prevailing temperate–polar climate of Australia, especially at high latitudes in Victoria, which is similar to the predominant warm–temperate climate of Laurasia, but distinct from the arid climate zone that covered extensive areas of Gondwana. Most dinosaur groups probably attained a near-cosmopolitan distribution in the Jurassic, prior to fragmentation of the Pangaean supercontinent, and some aspects of the hallmark ‘Gondwanan’ fauna of South America and Africa may therefore reflect climate-driven provinciality, not vicariant evolution driven by continental fragmentation. However, vicariance may still be detected at lower phylogenetic levels

Ochre, ground stone and wrapping the dead in the Late Epipalaeolithic (Natufian) Levant: revealing the funerary practices at Shubayqa 1, Jordan

The appearance of rich and diverse funerary practices is one of the hallmarks of the Late Epipalaeolithic Natufian in the Levant. Numerous burials at a number of sites excavated mostly in the Mediterranean zone of the southern Levant have fed into the interpretation of the Natufian as a sedentary society of complex hunter-gatherers. Here, we report on the human remains recovered from Shubayqa 1, a well-dated early to late Natufian site in northeast Jordan. The majority of the minimum of 23 individuals that are represented are perinates and infants, which represents an atypical population profile. Ground stone artifacts and traces of colourants are associated with some of these individuals, providing a rare insight into funerary treatment of subadults in Natufian contexts. We interpret the Shubayqa 1 evidence in the light of current and ongoing debates concerning Natufian burial practices and the issue of social complexity

Accretion, structure and hydrology of intermediate spreading-rate oceanic crust from drillhole experiments and seafloor observations

Downhole measurements recorded in the context of the Ocean Drilling Program in Hole 504B, the deepest hole drilled yet into the oceanic crust, are analyzed in terms of accretion processes of the upper oceanic crust at intermediate spreading-rate. The upper part of the crust is found to support the non steady-state models of crustal accretion developed from seafloor observations (Kappel and Ryan, 1986; Gente, 1987). The continuous and vertical nature of borehole measurements provides stratigraphic and structural data that cannot be obtained solely from seafloor studies and, in turn, these models define a framework to analyze the structural, hydrological, and mineralogical observations made in the hole over the past decade.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43190/1/11001_2005_Article_BF01204282.pd