cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1558327.v5
title: Utilizing Line Transect Methods for Sampling Common Milkweed Plants in Grassland near the Danby Woodlot at York University

description: The purpose of this observational study was to utilize the line transect method, i.e., a distance method, for sampling purposes, to meausre characteristics of the Common Milkweed plant (Asclepias syriaca), i.e., plant height, number of leaves, number of flowers, and level of crowding, and to use the distance on the transect measures from the plants as a means to estimate the population abundance of this plant species in the Grassland situated near the Danby Woodlot at York University, which is the location where this study was conducted. This study was conducted by group members Gajamugan Rajavarothayan, Gopaul Parbatie, Albert Lin, and Hannan Fayyaz from 3:25 pm to 4:00 pm EDT. A transect tape was randomly placed in a straight line stretching 20 meters in the Grassland situated near the Danby Woodlot at York University, specifically in an area that had the presence of the target plant species, i.e. the Common Milkweed plants. As we walked along the transect line, we recorded the distance on the transect whenever a Common Milkweed plant was visible near the transect tape, i.e. within 2 meters from the transect tape, to estimate the population abundance of this plant species in this Grassland area near Danby Woodlot at York University. We also measured the plant height using a second transect tape from the ground up to the tip of the largest leaf in the Common Milkweed plant, i.e.. the largest leaf in the plant was actually lifted to as high as possible and this height was recorded as the plant height. Gajamugan was the one who read all the measurements from the transect tape to ensure errors are minimized as the measurements for both the distance on the transect and plant height were recorded consistently by the same person. The number of leaves and number of flowers was recorded for each individual plant, and the level of crowding for each individual plant was scored from 0-3, whereby 0 = open, 1 = some plants nearby, 2 = quite a few plants nearby, and 3 = very crowded bunch of plants nearby within 50 cm. In total, our sample size, n, was 20 individual Common Milkweed plants. The conditions at this site at York University had an atmosphere temperature of 23 degrees Celsius, the weather was partly cloud, wind speed was 16 km/h blowing from the East, and the humidity level was 63% and the soils were not dry but rather they contained some moisture. The height of the grassland vegetation in area we used to sample the Common Milkweed plants was below 0.5 m, I.e., below knee level. However, in neighbouring grassland areas from our site that contained other plant species, the height of the grassland vegetation increased and was around 1-1.5 m, i.e., above knee level. Insects like lady bugs, bees, and flies flew around our site as well. Hence, overall these factors provided adequate conditions for viewing the plants and recording measurements from it.
DOI: 10.6084/m9.figshare.1558285
title: The Study of Plant Abundance Using Quadrats in the Stong Pond Grasslands of York University

description: On Monday September 21st 2015, at approximately 3:30pm, on the sunny day with partial clouds at a temperature of 21 degrees Celsius, an experiment including 25 grassland plots of various different vegetation were examined in the grasslands around Stong Pond. A one by one meter quadrat was randomly placed around different areas of the grassland to determine the abundance and distribution of vegetation and grass. To randomize the selection of the grassland plots chosen, a plastic bowl was thrown backwards while facing the sun. The quadrat was then placed around the bowl and the results were noted. This experiment was repeated 25 times. Among the examined plots, there were many varieties of plants including the Common Plantain (Plantago major), Common Thistle (Cirsium vulgare), Canadian Goldenrod (Solidago canadensis), Late Purple Aster (Aster prenathoides), Heather Aster (Aster ericoides), and Wild Carrot (Daucus carota). The total coverage of vegetation and grass was visually estimated with the assistance of lab members Danika Gordon, Karen Lin, and Raman Singh.
DOI: 10.6084/m9.figshare.1558290.v1
title: Ηχητικά αρχεία

description: Συνοδευτικά ηχητικά αρχεία του ηλεκτρονικού συγγράμματος
DOI: 10.6084/m9.figshare.1558272
title: Simulated Drosophila Larval Chemotaxis (Revised)

description: Trajectories of simulated Drosophila larvae performing chemotaxis in a variety of environments
DOI: 10.6084/m9.figshare.1558285.v1
title: The Study of Plant Distribution and Abundance Using Quadrats in the Grasslands of York University's Stong Pond

description: On Monday September 21st 2015, at approximately 3:30pm, on the sunny day with partial clouds at a temperature of 21 degrees Celsius, an experiment including 25 grassland plots of various different vegetation were examined in the grasslands around Stong Pond. A one by one meter quadrat was randomly placed around different areas of the grassland to determine the abundance and distribution of vegetation and grass. To randomize the selection of the grassland plots chosen, a plastic bowl was thrown backwards while facing the sun. The quadrat was then placed around the bowl and the results were noted. This experiment was repeated 25 times. Among the examined plots, there were many varieties of plants including the Common Plantain (<em>Plantago major</em>), Common Thistle (<em>Cirsium vulgare</em>), Canadian Goldenrod (<em>Solidago canadensis</em>), Late Purple Aster (<em>Aster prenathoides</em>), Heather Aster (<em>Aster ericoides</em>), and Wild Carrot (<em>Daucus carota</em>). The total coverage of vegetation and grass was visually estimated with the assistance of lab members Danika Gordon, Karen Lin, and Raman Singh.
DOI: 10.6084/m9.figshare.1558290.v2
title: Ηχητικά αρχεία

description: Συνοδευτικά ηχητικά αρχεία του ηλεκτρονικού συγγράμματος
DOI: 10.6084/m9.figshare.1558285.v2
title: The Study of Plant Distribution and Abundance Using Quadrats in the Grasslands of York University

description: On Monday September 21st 2015, at approximately 3:30pm, on the sunny day with partial clouds at a temperature of 21 degrees Celsius, an experiment including 25 grassland plots of various different vegetation were examined in the grasslands around Stong Pond. A one by one meter quadrat was randomly placed around different areas of the grassland to determine the abundance and distribution of vegetation and grass. To randomize the selection of the grassland plots chosen, a plastic bowl was thrown backwards while facing the sun. The quadrat was then placed around the bowl and the results were noted. This experiment was repeated 25 times. Among the examined plots, there were many varieties of plants including the Common Plantain (<em>Plantago major</em>), Common Thistle (<em>Cirsium vulgare</em>), Canadian Goldenrod (<em>Solidago canadensis</em>), Late Purple Aster (<em>Aster prenathoides</em>), Heather Aster (<em>Aster ericoides</em>), and Wild Carrot (<em>Daucus carota</em>). The total coverage of vegetation and grass was visually estimated with the assistance of lab members Danika Gordon, Karen Lin, and Raman Singh.
DOI: 10.6084/m9.figshare.1558263
title: In-Place Query Driven Big Data Platform: Applications to Post Processing of Environmental Monitoring

description: This is a paper accepted by PRAGMA-ICDS-15
DOI: 10.6084/m9.figshare.1558272.v1
title: Simulated Drosophila Larval Chemotaxis (Revised)

description: Trajectories of simulated Drosophila larvae performing chemotaxis in a variety of environments
DOI: 10.6084/m9.figshare.1558290.v3
title: Ηχητικά αρχεία

description: Συνοδευτικά ηχητικά αρχεία του ηλεκτρονικού συγγράμματος
DOI: 10.6084/m9.figshare.1558272.v3
title: Simulated Drosophila Larval Chemotaxis (Revised)

description: Trajectories of simulated Drosophila larvae performing chemotaxis in a variety of environments
DOI: 10.6084/m9.figshare.1558285.v3
title: The Study of Insect Abundance Using Quadrats in the Stong Pond Grasslands and Saywell Woodlots of York University

description: On Monday September 28st 2015, at approximately 3:30pm to 5:00 pm an experiment including 10 grassland plots around Stong Pond and 10 woodlot plots at Saywell Lot at York University were examined to collect data on insect abundance and diversity. The goal was to identify the abundance and richness of incest’s found in each location. The weather that day was slightly breezy, approximately a 2 on the beaufort scale, cloudy, with previous rainfall of 0.5 mm on the ground, and at a temperature of 21 degrees Celsius. A one by one-meter quadrat was randomly placed around different areas of the grassland and woodlot to determine the abundance and diversity of incest’s present. To randomize the selection of the grassland and woodlot plots chosen, a plastic bottle was thrown backwards while facing the sun. The quadrat was then placed around the bottle and the results were noted over a period of 4 minutes. The results were then classified into abundance and recognizable taxonomic units (RTUs). The only tool used during the experiment was the quadrat, a plastic bottle and a timer, the incest’s were visually classified by the experimenters. Among the examined plots, there were many varieties of incest’s including the Grasshopper, Moth, Beetle, Wasp, Butterfly, Spider, Ant, Ladybug, Mosquito, Snail, Cricket and Dragonfly. This experiment was done with the assistance of lab members Danika Gordon, Karen Lin, Israt Hossain and Raman Singh.
DOI: 10.6084/m9.figshare.1558272.v2
title: Simulated Drosophila Larval Chemotaxis (Revised)

description: Trajectories of simulated Drosophila larvae performing chemotaxis in a variety of environments
DOI: 10.6084/m9.figshare.1558290.v4
title: Ηχητικά αρχεία

description: Συνοδευτικά ηχητικά αρχεία του ηλεκτρονικού συγγράμματος
DOI: 10.6084/m9.figshare.1558261
title: Liquid sand burrowing and mucus utilisation as novel adaptations to a structurally-simple environment in Octopus kaurna

description: Cephalopods are often celebrated as masters of camouflage, but their exploitation of the soft-sediment habitats that dominate the ocean floor has demanded other anti-predator strategies. Previous research has identified a small number of cephalopods capable of burying into sand and mud, but the need to directly access the water column for respiration has restricted them to superficial burying. Here, we report on the first known sub-surface burrowing in the cephalopods, by <em>Octopus kaurna</em>, a small benthic species that uses advanced sand-fluidisation and adhesive mucus for sediment manipulation. This burrowing strategy appears linked to easily fluidised sediments as shown in experimental trials in three size-grades of sediment. While the selective pressures that drove evolution of this behaviour are unknown, its identification enriches our understanding of the possible life-history traits and functional role of mucus in other benthic octopus species living in soft-sediment environments.
DOI: 10.6084/m9.figshare.1558290.v6
title: Ηχητικά αρχεία

description: Συνοδευτικά ηχητικά αρχεία του ηλεκτρονικού συγγράμματος
DOI: 10.6084/m9.figshare.1558257
title: A benchmark of gene expression tissue-specificity metrics

description: Supplementary figures to the paper "A benchmark of gene expression tissue-specificity metrics".
DOI: 10.6084/m9.figshare.1558261.v1
title: Liquid sand burrowing and mucus utilisation as novel adaptations to a structurally-simple environment in Octopus kaurna

description: Cephalopods are often celebrated as masters of camouflage, but their exploitation of the soft-sediment habitats that dominate the ocean floor has demanded other anti-predator strategies. Previous research has identified a small number of cephalopods capable of burying into sand and mud, but the need to directly access the water column for respiration has restricted them to superficial burying. Here, we report on the first known sub-surface burrowing in the cephalopods, by <em>Octopus kaurna</em>, a small benthic species that uses advanced sand-fluidisation and adhesive mucus for sediment manipulation. This burrowing strategy appears linked to easily fluidised sediments as shown in experimental trials in three size-grades of sediment. While the selective pressures that drove evolution of this behaviour are unknown, its identification enriches our understanding of the possible life-history traits and functional role of mucus in other benthic octopus species living in soft-sediment environments.
DOI: 10.6084/m9.figshare.1558290.v5
title: Ηχητικά αρχεία

description: Συνοδευτικά ηχητικά αρχεία του ηλεκτρονικού συγγράμματος
DOI: 10.6084/m9.figshare.1558254
title: Evolution and role of the follicular epidermal gland system in non-ophidian squamates

description: Many lizard and amphisbaenian lineages possess follicular glands in the dermis of the inner thighs and/or the area anterior to the cloaca. These tubular glands produce a holocrine secretion that finds its way to the external world through pore-bearing scales (femoral and/or preanal pores). Secretions are composed of proteins and many lipophilic compounds that may function as chemosignals in lizard and amphisbaenian communication. In recent years, we have begun to develop an understanding of the adaptive significance of these secretions, and they are currently thought to play an important role in a variety of processes in these animals. While it appears that epidermal gland secretions function in intra- and interspecific recognition and territoriality, research has focused largely on their role in mate assessment. Despite these recent studies, our knowledge on the true role of the chemicals found in epidermal secretions remains poorly studied, and there are many possible avenues for future research on this topic. Here, we review the literature on the follicular epidermal glands of non-ophidian squamates and provide a first taxon-wide overview of their distribution.
DOI: 10.6084/m9.figshare.1558256
title: Beam Brook revisited: a molecular study of a historically introduced non-native amphibian (Triturus carnifex) and its limited introgression into native UK Triturus cristatus populations

description: Human mediated introductions of non-native species can pose a major threat to global biodiversity on several accounts i.e. through competition, the introduction of novel pathogens, and genetic pollution. Where hybridization occurs between two closely related species the F1 offspring are usually phenotypically discernible whereas F2 hybrid, backcrossed or admixed individuals become more difficult to separate. At this point the utilization of molecular methods is required in conservation efforts to differentiate and manage populations. This study demonstrated how a possible threat of hybridization from an introduced non-native (<em>T. carnifex</em>) with a protected native newt species (<em>T. cristatus</em>) could be investigated with molecular tools, and examined the current extent of its genetic introgression over an 80 years period. The results confirmed that hybridization had taken place at the site of introduction (and continues to do so), and that historically limited local dispersal of both non-natives and/or hybrids had occurred sometime in the past. However, the data suggests that although dispersal of hybrids into a local satellite site may still be occuring, hybridization with native species appears limited.
DOI: 10.6084/m9.figshare.1558246
title: Genetic structure and differentiation of the fire salamander Salamandra salamandra at the northern margin of its range in the Carpathians

description: Amphibian populations occurring at the margin of the species range exhibit lower genetic variation due to strong genetic drift and long-term isolation. Limited mobility and site fidelity together with habitat changes may accelerate genetic processes leading to local extinction. Here, we analyze genetic variation of the fire salamander subspecies <em>Salamandra s. salamandra </em>inhabiting the Outer Carpathian region in Poland, at the northern border of its distribution. Nuclear DNA polymorphism based on 10 microsatellite loci of 380 individuals sampled in 11 populations were analysed to measure gene flow between subpopulations and possible long-term isolation. Mitochondrial DNA control region analysis among 17 individuals representing 13 localities was used to detect the origin of populations which colonized Northern Europe after the last glaciation. Overall, pairwise F ST’s and AMOVA test of ‘among group’ variation showed little differences in the allele frequencies and relatively high local gene flow. However, Bayesian clustering results revealed subtle structuring between eastern and western part of the studied region. Two extreme marginal populations from the Carpathian Piedmont revealed reduced genetic variation which may be attributed to strong influence of genetic drift. Only one mitochondrial DNA haplotype (type IIb) was found in all individuals and suggest that after the Last Glacial Maximum <em>Salamandra salamandra </em>migrated to the North-Western Europe from the single glacial refugium placed in the Balkan Peninsula.
DOI: 10.6084/m9.figshare.1558256.v1
title: Beam Brook revisited: a molecular study of a historically introduced non-native amphibian (Triturus carnifex) and its limited introgression into native UK Triturus cristatus populations

description: Human mediated introductions of non-native species can pose a major threat to global biodiversity on several accounts i.e. through competition, the introduction of novel pathogens, and genetic pollution. Where hybridization occurs between two closely related species the F1 offspring are usually phenotypically discernible whereas F2 hybrid, backcrossed or admixed individuals become more difficult to separate. At this point the utilization of molecular methods is required in conservation efforts to differentiate and manage populations. This study demonstrated how a possible threat of hybridization from an introduced non-native (<em>T. carnifex</em>) with a protected native newt species (<em>T. cristatus</em>) could be investigated with molecular tools, and examined the current extent of its genetic introgression over an 80 years period. The results confirmed that hybridization had taken place at the site of introduction (and continues to do so), and that historically limited local dispersal of both non-natives and/or hybrids had occurred sometime in the past. However, the data suggests that although dispersal of hybrids into a local satellite site may still be occuring, hybridization with native species appears limited.
DOI: 10.6084/m9.figshare.1558246.v1
title: Genetic structure and differentiation of the fire salamander Salamandra salamandra at the northern margin of its range in the Carpathians

description: Amphibian populations occurring at the margin of the species range exhibit lower genetic variation due to strong genetic drift and long-term isolation. Limited mobility and site fidelity together with habitat changes may accelerate genetic processes leading to local extinction. Here, we analyze genetic variation of the fire salamander subspecies <em>Salamandra s. salamandra </em>inhabiting the Outer Carpathian region in Poland, at the northern border of its distribution. Nuclear DNA polymorphism based on 10 microsatellite loci of 380 individuals sampled in 11 populations were analysed to measure gene flow between subpopulations and possible long-term isolation. Mitochondrial DNA control region analysis among 17 individuals representing 13 localities was used to detect the origin of populations which colonized Northern Europe after the last glaciation. Overall, pairwise F ST’s and AMOVA test of ‘among group’ variation showed little differences in the allele frequencies and relatively high local gene flow. However, Bayesian clustering results revealed subtle structuring between eastern and western part of the studied region. Two extreme marginal populations from the Carpathian Piedmont revealed reduced genetic variation which may be attributed to strong influence of genetic drift. Only one mitochondrial DNA haplotype (type IIb) was found in all individuals and suggest that after the Last Glacial Maximum <em>Salamandra salamandra </em>migrated to the North-Western Europe from the single glacial refugium placed in the Balkan Peninsula.
DOI: 10.6084/m9.figshare.1558245
title: Lizards along an agricultural land abandonment gradient in Pindos Mountains, Greece

description: Agricultural land abandonment is recognized as one of the main environmental drivers in Southern Europe, affecting ecological communities. Lizards, as ectothermic species with low dispersal capacity, are particularly prone to the threats associated with land use changes. We investigated the effect of land abandonment on lizards in a remote mountainous area in Greece, using line transect sampling, in 20 randomly selected sites [1 km × 1 km], along a four grade abandonment gradient in terms of forest encroachment. We recorded four species: <em>Algyroides nigropunctatus</em>, <em>Lacerta viridis/ trilineata</em>, <em>Podarcis tauricus </em>and <em>Podarcis muralis</em>, the latter being the most abundant. Our results did not provide evidence for a significant effect of forest encroachment or grazing on lizard diversity, given the dominance of <em>P. muralis</em>, the availability of all microhabitat types along the gradient and the low grazing intensity in the study area. Environmental parameters at the macrohabitat scale did not prove determinant for habitat variance, but microhabitat analysis showed a clear preference of <em>P. muralis </em>to bare ground. Despite the non-significant effects of land abandonment on lizard diversity, the dominance of <em>P. muralis </em>tends to indicate a lizard community shift towards species inhabiting forested habitats. The preservation of open microhabitats, such as bare land, is considered of great importance for promoting high levels of lizard diversity, as their loss would affect even species currently widespread in forested ecosystems. Low intensity grazing, as well as the enhancement of wild ungulate populations in abandoned areas, can contribute to halting forest encroachment and maintaining the required habitat heterogeneity.
DOI: 10.6084/m9.figshare.1558244
title: Distance from adult tree to the closest sapling along a transect

description: On Monday September 21st 2015 at approximately 4:00pm in the Saywell Wood lot south east of Stong pond at York University took place an experiment comparing adult trees (all of the same species) along the line of a transect to their nearest sapling. Our team placed the transect starting at the edge of the path and going towards the inside of the wooded area. One tree species was picked that was abundant along the transect tape and chose it as the species for the experiment (it was a pine tree). The experiment was to walk along the transect tape and when we neared our designated adult tree type we measured its DBH, the canopy percentage of the adult tree, the distance to the nearest sapling and the saplings DBH. Collecting this data permits the analysis of how well trees are able to grow and how the distance of its corresponding sapling affects its growth along the transect line that goes from the edge of the woodlot to the dense middle of the woodlot.