cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1594698
title: Supplementary file

description: Abstract Background. The syngnathid fishes produce three kinds of sound named click, growl and purr. These sounds are generated by different mechanisms to give a consistent signal pattern or signature which is believed to play a role in intraspecific and interspecific communication. Commonly or known are sounds that are produced when the fish feeds (click, purr) or is under duress (growl). While there are more acoustic studies on seahorses, pipefishes have not received much attention. Here we document the differences in feeding click signals between three species of pipefishes and relate them to cranial morphology and kinesis, or the sound producing mechanism. Methods. The feeding clicks of two species of freshwater pipefishes, Doryichthys martensii and Doryichthys deokhathoides, and one species of estuarine pipefish, Syngnathoides biaculeatus, were recorded by a hydrophone in acoustic dampened tanks. The acoustic signals were analysed using time-scale distribution (or scalogram) based on wavelet transform. A detailed time-varying analysis of the spectral contents of the localized acoustic signal was obtained by jointly interpreting the oscillogram, scalogram and power spectrum. The heads of both Doryichthys species were prepared for microtomographical scans which were analysed using a 3D imaging software. Additionally, the cranial bones of all three species were examined using a clearing and double-staining method for histological studies. Results. The sound characteristics of the feeding click of the pipefish is species-specific, appearing to be dependent on three bones, the supraoccipital, 1st postcranial plate and 2nd postcranial plate. The sounds are generated when the head of the Dorichthyes pipefishes flexes backward during the feeding strike, as the supraoccipital slides backwards, striking and pushing the 1st postcranial plate against (and striking) the 2nd postcranial plate. In the Syngnathoides pipefish, in the absence of the 1st postcranial plate, the supraoccipital rubs against the 2nd postcranial plate twice as it is pulled backward and released on the return. Cranial morphology and kinesis produce acoustic signals consistent with the bone strikes that produce sharp energy spikes (discrete or merged), or stridulations between bones that produce repeated or multimodal sinusoidal waveforms. Discussion. The variable structure of the sound producing mechanism explains the unique acoustic signatures of the three species of pipefish. The differences in cranial bone morphology, cranial kinesis and acoustic signatures among pipefishes (and seahorses) could be attributed to independent evolution within the Syngnathidae which warrants further investigation.
DOI: 10.6084/m9.figshare.1594697
title: The 391 CELJs in China

description: The 391 CELJs are collected from various sources, and there may be few missing. Hope everyone can help me.
DOI: 10.6084/m9.figshare.1594698.v1
title: Supplementary file

description: Abstract Background. The syngnathid fishes produce three kinds of sound named click, growl and purr. These sounds are generated by different mechanisms to give a consistent signal pattern or signature which is believed to play a role in intraspecific and interspecific communication. Commonly or known are sounds that are produced when the fish feeds (click, purr) or is under duress (growl). While there are more acoustic studies on seahorses, pipefishes have not received much attention. Here we document the differences in feeding click signals between three species of pipefishes and relate them to cranial morphology and kinesis, or the sound producing mechanism. Methods. The feeding clicks of two species of freshwater pipefishes, Doryichthys martensii and Doryichthys deokhathoides, and one species of estuarine pipefish, Syngnathoides biaculeatus, were recorded by a hydrophone in acoustic dampened tanks. The acoustic signals were analysed using time-scale distribution (or scalogram) based on wavelet transform. A detailed time-varying analysis of the spectral contents of the localized acoustic signal was obtained by jointly interpreting the oscillogram, scalogram and power spectrum. The heads of both Doryichthys species were prepared for microtomographical scans which were analysed using a 3D imaging software. Additionally, the cranial bones of all three species were examined using a clearing and double-staining method for histological studies. Results. The sound characteristics of the feeding click of the pipefish is species-specific, appearing to be dependent on three bones, the supraoccipital, 1st postcranial plate and 2nd postcranial plate. The sounds are generated when the head of the Dorichthyes pipefishes flexes backward during the feeding strike, as the supraoccipital slides backwards, striking and pushing the 1st postcranial plate against (and striking) the 2nd postcranial plate. In the Syngnathoides pipefish, in the absence of the 1st postcranial plate, the supraoccipital rubs against the 2nd postcranial plate twice as it is pulled backward and released on the return. Cranial morphology and kinesis produce acoustic signals consistent with the bone strikes that produce sharp energy spikes (discrete or merged), or stridulations between bones that produce repeated or multimodal sinusoidal waveforms. Discussion. The variable structure of the sound producing mechanism explains the unique acoustic signatures of the three species of pipefish. The differences in cranial bone morphology, cranial kinesis and acoustic signatures among pipefishes (and seahorses) could be attributed to independent evolution within the Syngnathidae which warrants further investigation.
DOI: 10.6084/m9.figshare.1594686
title: Week 6/ Week 7- Experimental Design: Abundance of Plants and Edge Effect Observed within the Grassland and Woodlot regions of York University

description: The objective of this experiment was to measure the abundance of plants in the Grassland and Woodlot regions and observe edge effects in both areas. A Grassland is observed to be an area dominated largely by grasses. A Woodlot is observed to be an ecosystem dominated by trees. The experiment was conducted from the corners (North-West, North-East, South-West and South-East) to the middle of each region. The experiment was performed on two separate days. This experiment yields discrete data. To begin the experiment, a 50 meter long transect was laid stretching from the North-West edge to the middle of the Grassland region. The edge of the area began at an undisturbed location, where there was minimal human interference. Mowed and cut down areas were likely to produce inaccurate results and were avoided as much as possible. A 1m2 quadrant was laid on at the 0m position along the transect. The abundance of living plants were counted in the quadrant. If the number of plants was too large to count, it was estimated by dividing the quadrant into smaller parts and counting the number of plants within one of the divided parts and multiplying that number by the number of parts the quadrant was divided. The quadrant was picked up and moved 5 meters along the transect once the number of plants was counted and recorded. This process was conducted until a total of 10 quadrant samples were observed along the laid transect. Once all necessary data was obtained, the experimenter folded the quadrant, rolled the transect and repeated the above procedure in the North-East, South-West and South-East corners of the Grassland region. A total of 40 samples were recorded in the Grassland region. This process was repeated in the Woodlot area, where another 40 sample were recorded. At the end of the first day of experimentation, a total of 80 samples were obtained. This entire process was repeated for a second trial. In total 160 samples (n=160) were obtained during the 2 days of conducting the experiment. All data, including the site, location, distance along the transect, date, abundance and general observations were recorded in a chart for later examination The experiment was conducted by Hannan Fayyaz, Gopaul Parbatie, Albert Lin and Gajamugan Rajavarothayan on Thursday October 15th- 2015 and Thursday October 22nd- 2015 during the lab hours of 2:30pm-5:30pm on a Grassland and Woodlot region located on Keele Campus of York University. The weather on October 15th-2015 was observed to be 17oC and the weather on October 22nd-2015 was observed to be 16oC. The tools required to conduct the experiment include a transect and a 1m2 quadrant.
DOI: 10.6084/m9.figshare.1594686.v1
title: Week 6/ Week 7- Experimental Design: Abundance of Plants and Edge Effect Observed within the Grassland and Woodlot regions of York University

description: The objective of this experiment was to measure the abundance of plants in the Grassland and Woodlot regions and observe edge effects in both areas. A Grassland is observed to be an area dominated largely by grasses. A Woodlot is observed to be an ecosystem dominated by trees. The experiment was conducted from the corners (North-West, North-East, South-West and South-East) to the middle of each region. The experiment was performed on two separate days. This experiment yields discrete data. To begin the experiment, a 50 meter long transect was laid stretching from the North-West edge to the middle of the Grassland region. The edge of the area began at an undisturbed location, where there was minimal human interference. Mowed and cut down areas were likely to produce inaccurate results and were avoided as much as possible. A 1m2 quadrant was laid on at the 0m position along the transect. The abundance of living plants were counted in the quadrant. If the number of plants was too large to count, it was estimated by dividing the quadrant into smaller parts and counting the number of plants within one of the divided parts and multiplying that number by the number of parts the quadrant was divided. The quadrant was picked up and moved 5 meters along the transect once the number of plants was counted and recorded. This process was conducted until a total of 10 quadrant samples were observed along the laid transect. Once all necessary data was obtained, the experimenter folded the quadrant, rolled the transect and repeated the above procedure in the North-East, South-West and South-East corners of the Grassland region. A total of 40 samples were recorded in the Grassland region. This process was repeated in the Woodlot area, where another 40 sample were recorded. At the end of the first day of experimentation, a total of 80 samples were obtained. This entire process was repeated for a second trial. In total 160 samples (n=160) were obtained during the 2 days of conducting the experiment. All data, including the site, location, distance along the transect, date, abundance and general observations were recorded in a chart for later examination The experiment was conducted by Hannan Fayyaz, Gopaul Parbatie, Albert Lin and Gajamugan Rajavarothayan on Thursday October 15th- 2015 and Thursday October 22nd- 2015 during the lab hours of 2:30pm-5:30pm on a Grassland and Woodlot region located on Keele Campus of York University. The weather on October 15th-2015 was observed to be 17oC and the weather on October 22nd-2015 was observed to be 16oC. The tools required to conduct the experiment include a transect and a 1m2 quadrant.
DOI: 10.6084/m9.figshare.1594077
title: Correlation between the abundance of invasive species European Buckthorn and surrounding species’ richness

description: This study of correlation between the abundance of invasive species European Buckthorn and surrounding species’ richness was conducted in Boyer Woodlot, Saywell Woodlot and Osgoode Woodlot of York University by myself and two other group member: Laura and Kalvin on Oct 1, 8 and 15. The purpose of this study is to investigate whether there is a connection between the invasive European Buckthorn and the richness of other surrouding species. A transect was used to measure a 3 foot x 3 foot sampling area which was placed on random coordinates from a specified corner of the woodlot using a random number generator on Excel. The total number of buckthorn and other species within the sampling area were recorded separately. The soil temperature was measured with a thermometer and the outside temperature was also taken on each day. The approximate sunlight coverage for each quadrat was recorded as percentage, and the number of people encountered was also counted to see if there is any effect of human distubance on buckthorn abundance. A total of 27 replicates were recorded.
DOI: 10.6084/m9.figshare.1594239
title: Polistes dominula genome annotation

description: This data set is part of the <em>Polistes dominula</em> genome project, and details the annotation of protein coding genes and tRNA genes in the <em>P. dominula</em> genome, as described in (Standage <em>et al.</em>, <i>Molecular Ecology</i>, 2016). Included in this data set are the annotations (gene models in GFF3 format), gene model translations (peptide sequences in Fasta format), and documentation providing complete disclosure of the annotation workflow.
DOI: 10.6084/m9.figshare.1593976
title: The Effect of Sunlight and Crowding Level on Moss Coverage.

description: On Wednesday, October 14 and Wednesday, October 21 at York University between 14:30 and 17:30, an experiment was conducted in the woodlot to determine the effect of level of crowding and sunlight on moss coverage (all type of moss species were observed). A group of four students from BIOL 2050 Lab 3 conducted the experiment using 4 quadrats (1m x 1m) and 4 transects (30 meter long). The weather was between 10°C and 15°C with little to no wind in the two days the experiment was done. First, the student laid out the transect randomly from the edge of the forest until the transect reached thirty meters into the woodlot. Then, every five meters a quadrat was placed on the woodlot ground. Second, the student recorded whether or not there was any moss present. If no, the student placed a zero for moss coverage and if yes, the student would place the percentage of moss that was present in the quadrat. Third, for each quadrat the student recorded if the moss is surrounded by other plant species. The level of surrounding by using a scale of 0-3 (0=open, 1=some plants nearby, 2= quite a few plants nearby, 3= very crowded bunch of plants within 50 cm). Fourth, the student used both of their indexes and thumbs to make a square like shape, holding it up above where the quadrat laid, and the percentage of sunlight that was coming into the woodlot was recorded. Each student collected 20 to 30 data each, then all of the data was combined. Group 3 members: Mary H, Shaneil H, Gamsayini K and Prachi M.
DOI: 10.6084/m9.figshare.1593852
title: Field experiment: Does insect abundance differ in mowed vs. un-mowed grassland and does pan colour influence abundance?

description: The data was collected on Thursday October 15, 2015 at 3:00-4:20 p.m and on October 22 at 3:07-4:27 p.m. The location of the study was at Danby grasslands at York University. The mowed and un-mowed areas of the grassland were tested for abundance of insects using pans of various colors, transects, tweezers, and soapy water. The sample size for mowed and un-mowed grassland was 24 pans. Data was collected by Stephanie, Alexander, Vivian, and Amandeep. A transect was randomly placed in the mowed and un-mowed area of the grassland. Three different coloured pans (yellow, white, blue) were placed along the transect 1 m apart in that order. The total length of the transect tape was 11 m for all four trials. There were two transects used for day 1 and two for day 2, with one at each site. Soapy water was added to each pan to capture insects. After duration of 1 hour and 20 minutes the number of insects in each pan was counted using tweezers by pointing at the insects. The weather on day 1 and 2 was 16 degrees Celsius. It was cloudy with wind speed of 56 km/h on day 1 and was sunny with wind speed of 30 km/h on day 2. It was raining on day 1 when we ended the study because we did not want rain water to flood the pans while losing the insects captured. This study lasted only 1 hour and 20 minutes as a result. The same duration was used for the rest of the trials to maintain consistency. There were a few scattered trees in the un-mowed grassland, and almost none in mowed. There were lots of leaves on the ground. Common plants in the grassland were milkweed, golden rod, purple aster, white aster, common thistle. The mowed and un-mowed had the same plants but differed in height and density. The purpose of collecting this data set was to test whether there is a difference in abundance between mowed and un-mowed grassland, and if a certain coloured pan attracted more insects.
DOI: 10.6084/m9.figshare.1593958
title: Polistes dominula protein alignment

description: This data set is part of the <em>Polistes dominula</em> genome project, and provides details regarding the alignment of reference proteins to the <em>P. dominula</em> genome, as described in (Standage <em>et al.</em>, <i>Molecular Ecology</i>, 2016). Included in this data set are the alignments themselves (in GenomeThreader format), alignment structures suitable for genome annotation workflows (in GFF3 format), and documentation providing complete disclosure of the alignment procedure.
DOI: 10.6084/m9.figshare.1593958.v1
title: Polistes dominula protein alignment

description: This data set is part of the <em>Polistes dominula</em> genome project, and provides details regarding the alignment of reference proteins to the <em>P. dominula</em> genome, as described in (Standage <em>et al.</em>, <i>Molecular Ecology</i>, 2016). Included in this data set are the alignments themselves (in GenomeThreader format), alignment structures suitable for genome annotation workflows (in GFF3 format), and documentation providing complete disclosure of the alignment procedure.
DOI: 10.6084/m9.figshare.1593839
title: Lab 4: The effect of different coloured pan traps placed in a disturbed vs. undisturbed grassland have on the abundance of insects

description: The data was collected over a period of two weeks on two days. Day 1 was Oct.15, 2015 cloudy with showers 16°C wind 50km/h NE and gusts up to 61km/h making the temperature feel like 10°C. Day 2 was Oct. 22, 2015 sunny16°C with wind 30km/h and gusts up to 41km/h W making the temperature on day 2 feel like 13°C. In order keep the experiment consistent both days were conducted at the same time 3:00pm to 4:15 pm and left for a duration of 1 hour and 15 minutes in the two sites disturbed (mowed) and undisturbed (unmowed), in the Danby grassland on York University's Keele campus. The disturbed site was about 1 month old and contained the following plants that were shorter than what was found in the undisturbed site: grass, milkweed, golden rod, purple aster, white aster, and dominated by common thistle, as well as a few scattered trees. The undisturbed site was also found to be much denser. The data was collected by Vivian D, Amandeep B, Alexander K, and Myself (Stephanie A). The experiment was set up by placing a 12m long transect randomly in both sites, disturbed and undisturbed. Laying down the yellow, white, and blue pan traps in a systematic alternating pattern 1m apart from each other for a total of 12 pan traps (4 of each colour) per site. Once the pans were placed they were filled with soapy water and left for the duration stated above of 1 hour and 15 minutes. After said duration the abundance; total number of individual insects found within each pan trap was recorded using the aid of tweezers to visually count the number of insects. The total sample size was n=48. The purpose of this experiment was to see whether or not different colour pan traps (yellow, white and blue) had an affect on the abundance of insects found in two different sites disturbed (mowed) and undisturbed (unmowed).
DOI: 10.6084/m9.figshare.1594077.v1
title: Correlation between invasive species European Buckthorn and surrounding species’ abundance

description: This study of correlation between invasive species European Buckthorn and surrounding species’ abundance was conducted in Boyer Woodlot, Saywell Woodlot and Osgoode Woodlot of York University by myself and two other group member: Laura and Kalvin on Oct 1, 8 and 15. The purpose of this study is to investigate whether there is a connection between the invasive European Buckthorn and the richness of other surrouding species. A transect was used to measure a 3 foot x 3 foot sampling area which was placed on random coordinates from a specified corner of the woodlot using a random number generator on Excel. The total number of buckthorn and other species within the sampling area were recorded separately. The soil temperature was measured with a thermometer and the outside temperature was also taken on each day. The approximate sunlight coverage for each quadrat was recorded as percentage, and the number of people excountered was also counted to see if there is any effect of human distubance on buckthorn abundance. A total of 27 replicates were recorded.
DOI: 10.6084/m9.figshare.1593728
title: WK6 & WK7. Experimental design: field experiment

description: There are two sets of data in this experiment. For the first set of data 72 total pan traps were placed in the grassland area of York University's Keele Campus. Pan traps were approximately halfway filled with soapy water in order to catch the insects that they attracted. This was split over two days. On each day four pan traps of each colour, red, white, and yellow were placed near the edge of the grassland, in the middle of the grassland, and near the pond beside the grassland. All the pan traps were distributed 1m apart from each other in no specific colour order or linear pattern. This was done in 10 degrees C on day 1, and 9 degrees C on day 2. After leaving the pan traps for 1.5 hours, the number of insects in each, as well as the specific types of insects, were recorded for all pan traps.This process was the same for both days. For the second set of data there were a total of 54 pan traps placed around six different woodlots on York University's Keele Campus. The woodlots were WSC (William Small Centre woodlot), SWL (Stong Wood Lot), WL (Wood Lot), D (Denbi Woodlot), V (Vari Woodlot), and L (Lassonde Woodlot). This was split over two days. On each day, 9 pan traps, 3 of each colour, red, white and yellow, were distributed at random at each of the 6 woodlots.After 1.5 hours, the number of insects in each, as well as the specific types of insects, were recorded for all pan traps. This process was the same for both days.
DOI: 10.6084/m9.figshare.1593728.v1
title: WK6 & WK7. Experimental design: field experiment

description: There are two sets of data in this experiment. For the first set of data 72 total pan traps were placed in the grassland area of York University's Keele Campus. Pan traps were approximately halfway filled with soapy water in order to catch the insects that they attracted. This was split over two days. On each day four pan traps of each colour, red, white, and yellow were placed near the edge of the grassland, in the middle of the grassland, and near the pond beside the grassland. All the pan traps were distributed 1m apart from each other in no specific colour order or linear pattern. This was done in 10 degrees C on day 1, and 9 degrees C on day 2. After leaving the pan traps for 1.5 hours, the number of insects in each, as well as the specific types of insects, were recorded for all pan traps.This process was the same for both days. For the second set of data there were a total of 54 pan traps placed around six different woodlots on York University's Keele Campus. The woodlots were WSC (William Small Centre woodlot), SWL (Stong Wood Lot), WL (Wood Lot), D (Denbi Woodlot), V (Vari Woodlot), and L (Lassonde Woodlot). This was split over two days. On each day, 9 pan traps, 3 of each colour, red, white and yellow, were distributed at random at each of the 6 woodlots.After 1.5 hours, the number of insects in each, as well as the specific types of insects, were recorded for all pan traps. This process was the same for both days.