scholarly journals Differentiating Footprints of Sympatric Rodents in Coastal Dune Communities: Implications for Imperiled Beach Mice

2018 ◽  
Vol 9 (2) ◽  
pp. 593-601 ◽  
Author(s):  
Daniel U. Greene ◽  
Donna M. Oddy ◽  
Jeffery A. Gore ◽  
Michael N. Gillikin ◽  
Emily Evans ◽  
...  
Keyword(s):  
Classification Tree ◽  
Animal Health ◽  
Coastal Dunes ◽  
Accurate Method ◽  
Sympatric Species ◽  
Coastal Dune ◽  
House Mice ◽  
Accurate Identification ◽  
Peromyscus Polionotus ◽  
Quantitative Classification

Abstract Identifying techniques for conducting frequent, effective, and inexpensive monitoring of small mammals can be challenging. Traditional approaches such as livetrapping can be laborious, expensive, detrimental to animal health, and ineffective. Passive approaches such as tracking (e.g., from tracks on the ground or footprints collected at a tracking station) have been shown to lessen those burdens, but a problem with tracking, particularly for rodents, is the uncertainty in identifying species from footprints. To address the need for a more accurate method of identifying small mammal tracks, we measured footprints from live-captured rodents and developed a classification tree for distinguishing between subspecies and species using footprint widths treated as having known or unknown identification. We captured rodents within or near the coastal dunes of Florida and Alabama with a focus on areas occupied by threatened and endangered beach mice Peromyscus polionotus subspp., whose populations warrant regular monitoring but whose tracks are not easily distinguished from those of some sympatric species. We measured 6,996 front and hind footprints from 540 individuals across eight species. The overall accuracy of our classification tree was 82.6% and we achieved this using only the front footprint width. Footprint width cutoffs for species identification were < 5.5 mm for house mice Mus musculus, 5.5–6.7 mm for beach mice, and 6.7–8.3 mm for cotton mice Peromyscus gossypinus. We were most successful in confirming the identity of beach mice: we correctly classified approximately 94% of beach mice, while we misclassified fewer than 6% as house mice and fewer than 1% as cotton mice. When we input a beach mouse individual into the classification tree as of an unknown species, we correctly identified 78.1% of individuals as beach mice from their tracks, and most incorrect identifications were of house mouse tracks. Our study demonstrates that researchers can identify sympatric rodent species in coastal dune communities from tracks using quantitative classification based on footprint width. Accurate identification of beach mice or other imperiled species from tracks has important management implications. Not only can wildlife managers determine the presence of a species accurately, but they can monitor populations with considerably less effort than livetrapping requires. Although our study was specific to coastal dune communities, our methods could be adapted for the creation of a classification tree for identifying tracks from suites of species in other areas.

No evidence for interspecific interactions between plants in the first stage of succession on coastal dunes in subarctic Quebec, Canada

1997 ◽  
Vol 75 (6) ◽  
pp. 902-915 ◽  
Author(s):  
Gilles Houle
Keyword(s):  
Plant Biomass ◽  
Interspecific Interactions ◽  
Regional Climate ◽  
Salt Spray ◽  
Coastal Dunes ◽  
Growing Season ◽  
Coastal Dune ◽  
Dune System ◽  
Abiotic Conditions ◽  
Herbaceous Perennials

Coastal dunes are very dynamic systems, particularly where the coast is rising as a result of isostatic rebound. In those environments, succession proceeds from plants highly tolerant to sand accumulation, salt spray, and low nutrient availability to less disturbance-tolerant and stress-tolerant, more nutrient-demanding, and supposedly more competitive species. In the subarctic, the regional climate exacerbates the stresses imposed by local abiotic conditions on the dunes. I hypothesized that facilitation would be particularly significant on the foredune of subarctic coastal dune systems because of intense stresses (local and regional) and frequent disturbance in the form of sand deposition. Belowground and aboveground plant biomass was sampled at three different periods during the 1990 growing season along transects perpendicular to the shoreline on a coastal dune system in subarctic Quebec (Canada). The three herbaceous perennials found on the foredune (Honckenya peploides, Elymus mollis, and Lathyrus japonicus) were segregated in time during the growing season and in space along the topographical gradient. The biomass of Honckenya, the first species encountered as one progresses from the upper part of the beach towards the foredune ridge, was not correlated to substrate physicochemistry. However, the biomass of Elymus and that of Lathyrus, the next two species to appear along the flank of the foredune, were related to pH, Mg, Na, and Cl (negatively), and to P and Ca (positively). These results suggest variable linkages between substrate physicochemistry and plant species along the foredune, possibly in relation to species-specific tolerance for abiotic conditions and requirements for substrate resources or to microscale influence of the plants themselves on substrate physicochemistry. Removal experiments carried out over 2 years revealed only one significant unidirectional interaction between these three species along the topographical gradient, and little plant control over abiotic variables (e.g., soil temperature, wind velocity, and photosynthetically active radiation). Early primary succession on subarctic coastal dunes (and elsewhere) appears to be under the control of strong limiting abiotic conditions. As plants slowly gain more control over the physical environment, interspecific interactions (positive and negative) may become more significant. Key words: Elymus mollis, facilitation, Honckenya peploides, inhibition, Lathyrus japonicus, removal experiment, succession, tolerance.

The “ReDune” index (Restoration of coastal Dunes Index) to assess the need and viability of coastal dune restoration

2015 ◽  
Vol 49 ◽  
pp. 178-187 ◽  
Author(s):  
Debora Lithgow ◽  
M. Luisa Martínez ◽  
Juan B. Gallego-Fernández
Keyword(s):  
Coastal Dunes ◽  
Coastal Dune ◽  
Dune Restoration

scholarly journals Urbanization and Carpobrotus edulis invasion alter the diversity and composition of soil bacterial communities in coastal areas

2020 ◽  
Vol 96 (7) ◽  
Author(s):  
Ana Novoa ◽  
Jan-Hendrik Keet ◽  
Yaiza Lechuga-Lago ◽  
Petr Pyšek ◽  
Johannes J Le Roux
Keyword(s):  
Community Composition ◽  
Bacterial Communities ◽  
Soil Bacteria ◽  
Coastal Dunes ◽  
Coastal Dune ◽  
Western Coast ◽  
Carpobrotus Edulis ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
The Impact

ABSTRACT Coastal dunes are ecosystems of high conservation value that are strongly impacted by human disturbances and biological invasions in many parts of the world. Here, we assessed how urbanization and Carpobrotus edulis invasion affect soil bacterial communities on the north-western coast of Spain, by comparing the diversity, structure and composition of soil bacterial communities in invaded and uninvaded soils from urban and natural coastal dune areas. Our results suggest that coastal dune bacterial communities contain large numbers of rare taxa, mainly belonging to the phyla Actinobacteria and Proteobacteria. We found that the presence of the invasive C. edulis increased the diversity of soil bacteria and changed community composition, while urbanization only influenced bacterial community composition. Furthermore, the effects of invasion on community composition were conditional on urbanization. These results were contrary to predictions, as both C. edulis invasion and urbanization have been shown to affect soil abiotic conditions of the studied coastal dunes in a similar manner, and therefore were expected to have similar effects on soil bacterial communities. Our results suggest that other factors (e.g. pollution) might be influencing the impact of urbanization on soil bacterial communities, preventing an increase in the diversity of soil bacteria in urban areas.

scholarly journals Deep learning and taphonomy: high accuracy in the classification of cut marks made on fleshed and defleshed bones using convolutional neural networks

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Gabriel Cifuentes-Alcobendas ◽  
Manuel Domínguez-Rodrigo
Keyword(s):  
Machine Learning ◽  
Accurate Method ◽  
High Accuracy ◽  
Machine Learning Algorithms ◽  
Accurate Identification ◽  
Cut Marks ◽  
Eating Meat ◽  
Microscopic Features ◽  
Immense Potential

AbstractAccurate identification of bone surface modifications (BSM) is crucial for the taphonomic understanding of archaeological and paleontological sites. Critical interpretations of when humans started eating meat and animal fat or when they started using stone tools, or when they occupied new continents or interacted with predatory guilds impinge on accurate identifications of BSM. Until now, interpretations of Plio-Pleistocene BSM have been contentious because of the high uncertainty in discriminating among taphonomic agents. Recently, the use of machine learning algorithms has yielded high accuracy in the identification of BSM. A branch of machine learning methods based on imaging, computer vision (CV), has opened the door to a more objective and accurate method of BSM identification. The present work has selected two extremely similar types of BSM (cut marks made on fleshed an defleshed bones) to test the immense potential of artificial intelligence methods. This CV approach not only produced the highest accuracy in the classification of these types of BSM until present (95% on complete images of BSM and 88.89% of images of only internal mark features), but it also has enabled a method for determining which inconspicuous microscopic features determine successful BSM discrimination. The potential of this method in other areas of taphonomy and paleobiology is enormous.

Coastal dune mobility over the past century: A global review

2020 ◽  
Vol 44 (6) ◽  
pp. 814-836 ◽  
Author(s):  
Jinjuan Gao ◽  
David M Kennedy ◽  
Teresa M Konlechner
Keyword(s):  
Human Activities ◽  
Vegetation Cover ◽  
Dominant Role ◽  
Coastal Dunes ◽  
Mediterranean Area ◽  
Global Scale ◽  
Coastal Dune ◽  
Sediment Supply ◽  
Past Century ◽  
The Past

The mobility of coastal dunes is characterised by bio-geomorphological responses related to change in boundary conditions, particularly sediment supply, wind and vegetation cover, as well as human activities. There remains uncertainty regarding the relative importance of these drivers on dune mobility at a global scale. In this study, trends and dominant drivers of coastal dune mobility are synthesised through the literature review focusing on shifts in dune mobility over the last century (1870–2018). In total, 176 individual dunes, with 55 dunes from the Europe-Mediterranean area, 23 from Africa, 30 from North America, 23 from South America, 20 from Oceania and 23 from Asia, are reviewed in this work. The results show that there is a worldwide trend of dune stabilisation, with 93% (164 out of 176) of the reviewed sites showing a loss of bare sand area due to an increase in vegetation cover and urbanisation expansion. Multiple factors have contributed to the stabilisation process, including (a) land-use change such as the change of traditional farming practises, coastal urbanisation and tourism development; (b) dune stabilisation projects; (c) sediment decline caused by the riverine and coastal constructions; and (d) change in climate (i.e. the decrease in windiness, and the increase in temperature and rainfall) and storms. Our results suggest human intervention played a dominant role in altering dune mobility for most dunes during the past century, while climate and storms are also important drivers, especially for dune sites with limited human activities.

Records of climate changes and anthropogenic actions over dune fields in historical times

2020 ◽  
Author(s):  
Mihaela Tudor ◽  
Ana Ramos-Pereira ◽  
Joana Gaspar de Freitas
Keyword(s):  
Climatic Variability ◽  
Coastal Dunes ◽  
Coastal Dune ◽  
Environmental Data ◽  
Dune System ◽  
Climatic Fluctuations ◽  
Dune Systems ◽  
Sand Drift ◽  
Aeolian Activity ◽  
Historical Times

<p>Coastal dunes are very complex systems and very sensitive to climatic variability and human actions. In Portugal, coastal dune fields have undergone major changes over historical times. The aim of the paper is focused on the coastal dune systems evolution over the last five centuries, natural and man induced (namely by deforestation and afforestation) and their transformation under the present global changes (sea level rise and coastal storms). The analysis of historical records and environmental data using a set of proxies recorded over the last 1,000 yrs, show intense aeolian activity and sand drift episodes during Little Age Period, causing serious problems for human settlements and agriculture. Coastal society have responded to the wind-blown sands fixing the dunes through afforestation. The process is well documented in the historical sources and many management measures, including abundant legislation, projects and reports were carried out by Portuguese authorities to avoid sand incursion inland.  According to the main report of the General Forest Administration, in the final of 18th century, was estimated an area of about 72 000 ha of free aeolian sands in need of afforestation. Thus, along Portuguese coastline, the dunes experienced a period of stability during the 20th century, due to planting of grasses and pine forest. This paper examines the pathways of the transgressive dune fields of the Central Western Portuguese coast, over various stages of coastal evolution. Mapping the morphological features between Mondego river mouth and Nazaré, using a combination of satellite images, aerial photographs and Lidar data we identified distinct phases of aeolian activity and landforms modification that were associated to climatic fluctuations. This coastal dune system is composed by a succession of different aeolian phases, including a littoral foredune, which lies inland with a complexity of morphologies with transverse and crescentic ridges, and also parabolic dunes. The results show that the dunes building and sand migration inland appears to be linked to the conditions of predominantly negative winter North Atlantic Oscillation index (NAOi), driven by climatic variability during Holocene/Antrhopocene. The consistency of intense sand drift episodes with abrupt cold events during Little Age Period, drastically reduced the area occupied by vegetation, causing changes in aeolian sedimentary processes. Thus, it seems that coastal dunes evolution over the past centuries have been controlled by the two-way interactions between natural conditions and human activities, shaping the Portuguese coastline. Placing historical evidence in a geographical perspective, we hope to fill the gaps in coastal zone dynamics, providing new insights of the human-landscape relationships to predict the future response of the coastal dune systems to human pressure and climate change.<br>Key-words: coastal dunes evolution, geomorphological features, sand drift, anthropogenic impacts, climatic fluctuation, Western Portugal.</p>

scholarly journals DNA barcode data accurately identify higher taxa

2016 ◽  
Author(s):  
Jonathan A Coddington ◽  
Ingi Agnarsson ◽  
Ren-Chung Cheng ◽  
Klemen Čandek ◽  
Amy Driskell ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Accurate Method ◽  
Reference Database ◽  
Accurate Identification ◽  
Sequencing Errors ◽  
Sequence Identity ◽  
Percent Sequence Identity ◽  
Near Term ◽  
Accuracy Of Results

The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level identifications. We used BLAST queries of each sequence against the entire library and got the top ten hits resulting in 8160 hits. The percent sequence identity was reported from these hits (PIdent, range 75-100%). Accurate identification (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values > 95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all identifications were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of life could provide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades.

Landscape drivers of coastal dune mobility

2020 ◽  
Author(s):  
Thomas Smyth ◽  
Ryan Wilson ◽  
Paul Rooney ◽  
Katherine Yates
Keyword(s):  
Sand Dunes ◽  
Coastal Dunes ◽  
Coastal Dune ◽  
Environmental Drivers ◽  
Coastal Sand Dunes ◽  
Dune Vegetation ◽  
Near Surface ◽  
Coastal Conservation ◽  
Coastal Sand ◽  
Mobile Dunes

<p>Coastal dunes are dynamic landforms whose morphology is governed primarily by climate and vegetation dynamics. Over the last 50 years, coastal sand dunes across the globe have dramatically ‘greened’ and wind speeds fallen (Pye et al., 2014; Delgado-Fernandez et al., 2019; Jackson et al., 2019), reducing aeolian transport of sediment and minimising dune reshaping by near-surface winds.  This rapid vegetation has also been attributed to a dramatic decline of several rare species of plants and invertebrates in several coastal dune systems (Howe et al., 2010; Pye et al., 2014). In an effort to increase habitat diversity, large-scale vegetation removal and dune re-profiling are becoming increasingly common interventions. However sustained aeolian activity following intervention appears to be rare (Arens et al., 2013).</p><p>In order to better understand the environmental drivers of long-term dune mobility, this work explores the landscape scale physical factors related to self-sustaining ‘natural’ mobile dunes across the United Kingdom. The analysis presented includes the use of geographically weighted regression, a spatial analysis technique that models the local relationships between predictors (e.g. wind speed, slope, elevation, aspect, surface roughness) and an outcome of interest (mobile dunes). It is hoped that the results of this work will help guide decision-making with regards the location, scale and morphology of future interventions in order to maximise their sustainability, minimising the need for maintenance and further intervention.</p><p>References</p><p>Arens, S.M., Slings, Q.L., Geelen, L.H. and Van der Hagen, H.G., 2013. Restoration of dune mobility in the Netherlands. In Restoration of coastal dunes (pp. 107-124). Springer, Berlin, Heidelberg.</p><p>Delgado-Fernandez, I., O'Keeffe, N., & Davidson-Arnott, R. G. (2019). Natural and human controls on dune vegetation cover and disturbance. Science of The Total Environment, 672, 643-656.</p><p>Howe, M. A., Knight, G. T., & Clee, C. (2010). The importance of coastal sand dunes for terrestrial invertebrates in Wales and the UK, with particular reference to aculeate Hymenoptera (bees, wasps & ants). Journal of Coastal Conservation, 14(2), 91-102.</p><p>Jackson, D. W., Costas, S., González-Villanueva, R., & Cooper, A. (2019). A global ‘greening’of coastal dunes: An integrated consequence of climate change?. Global and Planetary Change, 182, 103026.</p><p>Pye, K., Blott, S. J., & Howe, M. A. (2014). Coastal dune stabilization in Wales and requirements for rejuvenation. Journal of coastal conservation, 18(1), 27-54.</p>

scholarly journals Evaluation of Genotypic and Phenotypic Methods to Detect Carbapenemase Production in Gram-Negative Bacilli

2017 ◽  
Vol 63 (3) ◽  
pp. 723-730 ◽  
Author(s):  
Allison R McMullen ◽  
Melanie L Yarbrough ◽  
Meghan A Wallace ◽  
Angela Shupe ◽  
Carey-Ann D Burnham
Keyword(s):  
Carbapenem Resistance ◽  
Accurate Method ◽  
Genetic Determinants ◽  
Accurate Identification ◽  
Gram Negative ◽  
Healthcare Facilities ◽  
Carbapenem Resistant ◽  
Phenotypic Screen ◽  
Acinetobacter Baumannii Complex ◽  
Phenotypic Methods

Abstract BACKGROUND Carbapenemase-producing gram-negative bacteria (CP-GNB) are an urgent and expanding public health threat. Rapid and accurate identification of these organisms facilitates infection prevention efforts in healthcare facilities. The objective of our study was to evaluate methods to detect and identify CP-GNB. METHODS We examined 189 carbapenem-resistant GNB(CR-GNB), including Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii complex, using 3 different methods: 2 methods to screen isolates of GNB for carbapenemase production [the carbapenem inactivation method (CIM) and 2 chromogenic agars] and a molecular method (Cepheid GeneXpert Carba-R) to identify the mechanism of carbapenem resistance and the associated resistance genes (blaKPC, blaNDM, blaIMP, blaOXA-48-like, and blaVIM). RESULTS The CIM was a simple and inexpensive phenotypic screen to differentiate between CR-GNB and CP-GNB, with improved analytical performance characteristics and inter-reader correlation compared to the modified Hodge test. Both chromogenic agars evaluated (HardyCHROM CRE and chromID CARBA) were able to support growth of most of the organisms tested, including isolates possessing the blaOXA-48-like gene. However, these media had a low analytical specificity for carbapenemase production, with breakthrough of CR-GNB that did not produce a carbapenemase. The Xpert Carba-R assay was rapid and easy to perform, and demonstrated 100% positive and negative agreement for characterization of genetic determinants of carbapenem resistance. CONCLUSIONS Screening by CIM followed by the Xpert Carba-R PCR is an accurate method for detecting and characterizing CP-GNB, including Enterobacteriaceae, P. aeruginosa, and A. baumannii complex.

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