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83 results for “species counts”
Evaluation of Mask R-CNN Model for Counting Reproductive Structures of Six Plant Species 1895-2018
Phenology––the timing of life-history events––is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current common practice of manually harvesting data from individual specimens greatly restricts our ability to scale data collection to entire collections. Recent investigations have demonstrated that machine-learning models can facilitate data collection from herbarium specimens. However, present attempts have focused largely on simplistic binary coding of reproductive phenology (e.g., flowering or not). Here, we use crowd-sourced phenological data of numbers of buds, flowers, and fruits of more than 3000 specimens of six common wildflower species of the eastern United States (Anemone canadensis, A. hepatica, A. quinquefolia, Trillium erectum, T. grandiflorum, and T. undulatum} to train a model using Mask R-CNN to segment and count phenological features. A single global model was able to automate the binary coding of reproductive stage with greater than 90% accuracy. Segmenting and counting features were also successful, but accuracy varied with phenological stage and taxon. Counting buds was significantly more accurate than flowers or fruits. Moreover, botanical experts provided more reliable data than either crowd-sourcers or our Mask R-CNN model, highlighting the importance of high-quality human training data. Finally, we also demonstrated the transferability of our model to automated phenophase detection and counting of the three Trillium species, which have large and conspicuously-shaped reproductive organs. These results highlight the promise of our two-phase crowd-sourcing and machine-learning pipeline to segment and count reproductive features of herbarium specimens, providing high-quality data with which to study responses of plants to ongoing climatic change.
Species-level estimated abundances and zero counts of nighttime collected female mosquitoes 2014 - 2022 (Derived from NEON Mosquitoes sampled from CO2 traps (DP1.10043.001, RELEASE-2024))
This Level 2 data package contains species level estimated abundances, including zero counts, and estimated mean number of female mosquitoes per trap derived from the NEON Mosquitoes sampled from CO2 traps (DP1.10043.001), RELEASE-2024 Level 0 data (https://doi.org/10.48443/3cyq-6v47). The data set includes mosquito records of traps collecting mosquito samples at night, for up to 24 trap hours, across a total of 20 terrestrial core and 27 terrestrial gradient sites from 2014 to 2022. To ensure high confidence in abundance estimates, records were only included when at least 90% of collected individuals were identified to sex, and 90% of female specimens were identified to species. Information across multiple QC/QA fields within the NEON mosquito data was evaluated to identify and exclude records where confidence in estimated abundances may have been compromised. Species level zero counts were added for all species collected at least once within the sampling year and trap location. Additionally, species level zero counts were included for trap events where only male mosquitoes had been collected or where QC/QA remarks indicated traps were inactive due to cold temperatures. The data set provides an analysis ready time series of estimated abundances across NEON sites and plots. An R Markdown file that contains descriptions of the QC/QA and data filtering steps along with annotated code, as well as data tables used to filter active and inactive trap events based on QC/QA fields, are published with the data package. Any questions about this data package should be directed to Amely Bauer listed under contacts.
Nekton species counts and density from flume net collections along Rowley River tidal creeks associated with long term fertilization experiments, Rowley, MA.
The flume nets were deployed with the purpose of capturing salt marsh nekton. Nekton species were identified to the lowest taxonomic level using species keys. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70μM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2016 and at Clubhead Creek in 2005 and from 2009 till 2016. Years 2017-2020 are enrichment recovery years.
[DEPRECATED] Vegetation Plots of the Bonanza Creek LTER Control Plots: Species Count (1975 - 2004) (Reformatted to ecocomDP Design Pattern)
This ecocomDP data package has been deprecated due to issues in the L0 source dataset that prohibits the creation of an L1 ecocomDP dataset. This data package is formatted according to the "ecocomDP", a data package design pattern for ecological community surveys, and data from studies of composition and biodiversity. For more information on the ecocomDP project see https://github.com/EDIorg/ecocomDP/tree/master, or contact EDI https://environmentaldatainitiative.org. This Level 1 data package was derived from the Level 0 data package found here: https://portal.edirepository.org/nis/mapbrowse?scope=knb-lter-bnz&identifier=175&revision=20 The abstract below was extracted from the Level 0 data package and is included for context: These data are the vegetation datasets for 27 LTER sites in Bonanza Creek Experimental Forest. The 27 sites are divided into three replicates for six primary successional stages on the floodplains (3 replicates X 6 successional stages = 18 sites) and three replicates for three secondary successional stages in the uplands (3 replicates X 3 successional stages = 9 sites). Data include: 1) Visual estimates of percent cover, 2) Stem counts (the number of individuals/species), and 3) Heights (cm) for "tall shrub species" in twenty 4 m2 plots. Shrubs are considered "Tall shrubs" if they are Salix sp., Alnus sp., Rosa acicularis, Viburnum edule, Betula nana, Betula glandulosa, or Rubus idaeus. Initial colonziations plots (FP0s, SL1s, HR1A) were remeasured every year. Early successional plots were remeasured every 2-4 years. Later succesional plots were remeasured approximately every five years. For a detail schedule of plot measurements please see the file: Vegetation Monitoring Schedule.xls Although most sites were established in 1988 some sites have vegetation plots that have been sampled periodically since 1965. In 2006 shrub data collection was changed to a transect method of sampling. These data can be found in the file: <a href="http://www.lte
Invert species counts and density along transects on the high marsh along Rowley River tidal creeks associated with long term fertilization experiments, Rowley, MA.
At PIE, mummichog (Fundulus heteroclitus) use the spring-cycle high tides to access the flooded high marsh platform and consume invertebrate prey. Invertebrate surveys were conducted before and after spring tides that flooded the high marsh area to determine the effect of mummichog predation that occurs on the high marsh during the flood events and to assess the impact of low marsh geomorphology on top-down control by mummichog. These data were included in part of the study "Cross-habitat access modifies the ‘trophic relay’ in New England saltmarsh ecosystems” (Lesser et al. 2021) as well as a part of a NEU Three Seas Master's thesis.
Vegetation Plots of the Bonanza Creek LTER Control Plots: Species Count (1975 - 2004)
These data are the vegetation datasets for 27 LTER sites in Bonanza Creek Experimental Forest. The 27 sites are divided into three replicates for six primary successional stages on the floodplains (3 replicates X 6 successional stages = 18 sites) and three replicates for three secondary successional stages in the uplands (3 replicates X 3 successional stages = 9 sites). Data include: 1) Visual estimates of percent cover, 2) Stem counts (the number of individuals/species), and 3) Heights (cm) for "tall shrub species" in twenty 4 m2 plots. Shrubs are considered "Tall shrubs" if they are Salix sp., Alnus sp., Rosa acicularis, Viburnum edule, Betula nana, Betula glandulosa, or Rubus idaeus. Initial colonziations plots (FP0s, SL1s, HR1A) were remeasured every year. Early successional plots were remeasured every 2-4 years. Later succesional plots were remeasured approximately every five years. For a detail schedule of plot measurements please see the file: Vegetation Monitoring Schedule.xls Although most sites were established in 1988 some sites have vegetation plots that have been sampled periodically since 1965. In 2006 shrub data collection was changed to a transect method of sampling. These data can be found in the file: <a href="http://www.lter.uaf.edu/data_detail.cfm?datafile_pkey=530"> Shrub, Seedling and Sapling Density at Bonanza Creek LTER Research Sites (2006-Present) </a>.
Tree regeneration after fire: Delta 1994 burn surveys, pre-fire stem counts and basal areas, for species other than black spruce
Data for this study were collected in 2001 and 2002 by Jill Johnstone (University of Alaska Fairbanks) and Eric Kasischke (University of Maryland). Sites were located within the perimeter of the 1994 burn southeast of Delta Junction Alaska, USA, bordering the Alaska Highway to the North and the Gerstle River to the West. Sites were selected from satellite classifications prepared by Eric Kasischke to represent different levels of burn severity and post-fire vegetation canopy greenness (NDVI). Site selection was constrained by road access, and only areas where all trees had been killed by the fire were selected. At each site, a central point was located in an area of visually homogeneous vegetation. Five parallel transects, each 50 m long, were laid out as follows: 1) the first transect started at the central point and followed a randomly-selected compass direction, 2) two additional transects were established parallel to the first, but at a random distance from the central transect up to 25 m distant. Vegetation was sampled in a 2-m wide belt centered on each transect, and soil samples were made at intervals along the transect line. Vegetation measurements included: a) basal diameters of all pre-fire trees greater than 1.3 m in height, b) counts of all post-fire tree seedlings, and c) basal diameters of tree seedlings and willows, measured in a randomly chosen 5x2 m portion of each transect. General notes were made on visual percent cover of different vegetation growth forms at the site. Destructive measurements of tree seedlings and willows made in 2001 were used to develop allometric equations to predict dry biomass from basal diameter. Measurements of soil organic layer depth were made at 5 m intervals with the use of a spade to excavate small chunks of sod. At one randomly-selected sample point per transect, a 10x10 cm sample of the organic layer was collected for bulk density measurements. Bulk density samples were dried in a 60degC oven for 48 hours and then w
Marsh plant species stem counts for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA.
Marsh plant species stem counts for Rowley River tidal creeks associated with long term fertilization experiments, Rowley and Ipswich, MA. The TIDE project aims to simulate eutrophication on a large scale by the addition of NO3- aiming to reach 70µM concentrations from May to September every year during the growing season. This fertilization of the marsh has been going on at Sweeney Creek since the 2004 growing season through 2012 and at Clubhead Creek in 2005 and from 2009 till 2012. The reference creeks, West and Nelson, have been sampled in pair with the nutrient enriched creeks.
Fig. 4 in The Amount And Distribution Of The Red Data Book Bird Wetland Species In The Azov-Black Sea Region Of Ukraine According To The Results Of August Counts 2004-2015
Fig. 4. Distribution of wetlands number depending on number of species in them (axis X — number of species, axis Y — number of wetlands).
Fig. 5 in The Amount And Distribution Of The Red Data Book Bird Wetland Species In The Azov-Black Sea Region Of Ukraine According To The Results Of August Counts 2004-2015
Fig. 5. Distribution of wetlands depending on species number (axis X) and average amount of birds in them (axis Y).
Figure 2. – Monthly average species richness observed during diurnal counts from June 2013 in Assessing structure and seasonal variations of a temperate shallow water fish assemblage through Snorkel Visual Census
Figure 2. – Monthly average species richness observed during diurnal counts from June 2013 to August 2014. Error bars represent ±SD. Number of counts per month are, indicated at column bases.
Fig. 2. The most numerous RDB wetland birds species, recorded during August Counts 2018 and 2021 in The Red Data Book Waterbirds In The Coastal Wetlands Of The Azov-Black Sea Region Of Ukraine - The Results Of The August Counts 2018 And 2021
Fig. 2. The most numerous RDB wetland birds species, recorded during August Counts 2018 and 2021 (bar chart — amount of birds, line chart — number of sites were species was recorded).
Fig. 31 in Still counting: new records, nomenclatural notes, and three new species of Phaeogenini (Hymenoptera, Ichneumonidae, Ichneumoninae) from the Afrotropical region
Fig. 31. Distribution of Lusius tenuissimus (Heinrich, 1938). A–B. Previous (blue) and new (yellow) records. A. Country records for mainland Africa. B. Regional records for Madagascar.
Fig. 27 in Still counting: new records, nomenclatural notes, and three new species of Phaeogenini (Hymenoptera, Ichneumonidae, Ichneumoninae) from the Afrotropical region
Fig. 27. Kibalus nonnaritae Dal Pos & Di Giovanni sp. nov., holotype, ♂ (TUZ). A. Head, frontal view. B. Metasoma, dorsal view.
Fig. 26 in Still counting: new records, nomenclatural notes, and three new species of Phaeogenini (Hymenoptera, Ichneumonidae, Ichneumoninae) from the Afrotropical region
Fig. 26. Kibalus nonnaritae Dal Pos & Di Giovanni sp. nov., holotype, ♂ (TUZ). A. Habitus, lateral view. B. Head and mesosoma, dorsal view. C. Mesosoma, lateral view.
Fig. 16 in Still counting: new records, nomenclatural notes, and three new species of Phaeogenini (Hymenoptera, Ichneumonidae, Ichneumoninae) from the Afrotropical region
Fig. 16. Distribution of Chauvinia nitida (Heinrich, 1938). A. Previous (blue dots) and new occurrence records (yellow star). B. Previous (blue) and new (yellow) regional records.
Fig. 30 in Still counting: new records, nomenclatural notes, and three new species of Phaeogenini (Hymenoptera, Ichneumonidae, Ichneumoninae) from the Afrotropical region
Fig. 30. Distribution of Lusius tenuissimus (Heinrich, 1938). A–B. Previous (blue dots) and new records (yellow star). A. Mainland Africa. B. Madagascar.
Fig. 20 in Still counting: new records, nomenclatural notes, and three new species of Phaeogenini (Hymenoptera, Ichneumonidae, Ichneumoninae) from the Afrotropical region
Fig. 20. Heterischnus mfongosi Rousse & van Noort, 2013, ♀ (NHMUK). A. Head and mesosoma, lateral view. B. Propodeum, dorso-lateral view.
Fig. 12. Head, frontal view. A–B in Still counting: new records, nomenclatural notes, and three new species of Phaeogenini (Hymenoptera, Ichneumonidae, Ichneumoninae) from the Afrotropical region
Fig. 12. Head, frontal view. A–B. Chauvinia ganota Claridge sp. nov. A. ♀, holotype (EMUS). B. ♂, paratype (EMUS). – C–D. Chauvinia nyanga Rousse & van Noort, 2013. C. ♀ (EMUS). D. ♂ (EMUS).
Fig. 23 in Still counting: new records, nomenclatural notes, and three new species of Phaeogenini (Hymenoptera, Ichneumonidae, Ichneumoninae) from the Afrotropical region
Fig. 23. Distribution of Heterischnus olsoufieffi (Heinrich, 1938). A. Previous (blue dots) and new records (yellow stars). B. Previous (blue) and new (yellow) regional records.
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