University of North Florida Showcase

These data are the sample information for each of the samples collected for metabarcoding of 16S and rbcL to describe Cyanobacterial and diatom diversity, respectively, in three sites in Alpena, Michigan, one site in Monroe, Michigan, and one site in Palm Coast, Florida. Sample data are for sequenced samples and include their associated water parameter information that was collected simultaneously. Each of these sites are high-sulfur, low-oxygen environments formed by underwater sinkholes and springs that create extreme habitats populated by microbial mat communities. Our study investigated previously undescribed diatom diversity in these habitats, and further explored the bacterial communities as well. Our results provide novel information on microbial mat community composition, and present evidence that microbial biogeography influences these unique communities.

Using the code in this file, we will process rbcL metabarcoding data using the Dada2 pipeline. (DATA REDUCTION STAGE). Our goal is to remove primers, and then use the DADA2 algorithm to assess read quality, denoise, and merge our sequences. Finally, we will assign our sequences to ASVs and assign these to taxonomy using DADA2 and a reference database.

Using the code in this file, we will process 16S metabarcoding data using the Dada2 pipeline. (DATA REDUCTION STAGE). Our goal is to use the DADA2 algorithm to assess read quality, denoise, and merge our sequences. Finally, we will assign our sequences to ASVs and assign these to taxonomy using DADA2 and a reference database.

These data are the information for each of the cultures generated from samples collected from three sites in Alpena, Michigan, one site in Monroe, Michigan, and one site in Palm Coast, Florida. Data are for cultures sequenced using Sanger sequencing and include taxonomic identification, location and water parameter information from samples used to develop the cultures, and growth medium. Each of these cultures was developed from high-sulfur, low-oxygen environments formed by underwater sinkholes and springs that create extreme habitats populated by microbial mat communities. Our study investigated previously undescribed diatom diversity in these habitats. Sequences from these cultures contribute to tying molecular data to morphologically identified isolates, providing a bridge between these two data types that can be used to improve metabarcoding analyses.

These data are the information for each of the cultures generated from samples collected from three sites in Alpena, Michigan, one site in Monroe, Michigan, and one site in Palm Coast, Florida. Data are for cultures sequenced using Sanger sequencing and include taxonomic identification, location and sample type for samples used to develop the cultures. Each of these cultures was developed from high-sulfur, low-oxygen environments formed by underwater sinkholes and springs that create extreme habitats populated by microbial mat communities. Our study investigated previously undescribed diatom diversity in these habitats. Sequences from these cultures contribute to tying molecular data to morphologically identified isolates, providing a bridge between these two data types that can be used to improve metabarcoding analyses.

Human-driven land use change can fundamentally alter ecological communities, especially the diversity and abundance of large-bodied predators. Yet despite the important roles large-bodied predators play in structuring communities through feeding, there have been only a few investigations of how the feeding patterns of large-bodied predators change in human-dominated landscapes. One group of large-bodied predators that has been largely overlooked in the context of land use change is the crocodilians. To help fill these gaps we studied the feeding patterns of juvenile American alligators (Alligator mississippiensis) on neighboring barrier islands on the southeast coast of Georgia, USA. Jekyll Island has multiple golf courses and substantial amounts of human activity, while Sapelo Island does not have any golf courses and a much smaller amount of human activity. We found that juvenile alligator populations on both islands ate the same types of prey but in vastly different quantities. Sapelo Island alligators primarily consumed crustaceans while alligators that lived on Jekyll Island's golf courses ate mostly insects/arachnids. Furthermore, the Jekyll Island alligators exhibited a much more generalist feeding pattern (individuals mostly ate the same types of prey in the same quantities) than the more specialized Sapelo Island alligators (diets were more varied across individuals). The most likely explanation for our results is that alligators living on golf courses have different habitat use patterns and have access to different prey communities relative to alligators in more natural habitats. Thus, land use change can strongly alter the feeding patterns of large-bodied predators and, as a result, may affect their body condition, exposure to human-made chemicals, and role within ecological communities.

In some species, the ability to acquire new vocalizations persists into adulthood and may be an important mediator of social interactions. While it is generally assumed that vocal learning persists undiminished throughout the lifespan of these open-ended learners, the stability of this trait remains largely unexplored. We hypothesize that vocal learning exhibits senescence, as is typical of complex cognitive traits, and that this decline may relate to age-dependent changes in sociality. The budgerigar (Melopsittacus undulatus), an open-ended learner which develops new contact call types that are shared with social associates upon joining new flocks, provides a robust assay for measuring the effects of aging on vocal learning ability. We formed captive flocks of 4 previously unfamiliar adult males of the same age class, either "young adults" (6 mo.-1 yr.) or "older adults" (≥ 3 yr.), and concurrently tracked changes in contact call structure and social interactions over time. Older adults exhibited decreased vocal diversity, which may be related to the sparser and weaker affiliative bonds observed in older adults. Older adults, however, displayed equivalent levels of vocal plasticity and vocal convergence compared to young adults, suggesting vocal learning ability is largely maintained into later adulthood in an open-ended learner.

In some species, the ability to acquire new vocalizations persists into adulthood and may be an important mediator of social interactions. While it is generally assumed that vocal learning persists undiminished throughout the lifespan of these open-ended learners, the stability of this trait remains largely unexplored. We hypothesize that vocal learning exhibits senescence, as is typical of complex cognitive traits, and that this decline may relate to age-dependent changes in sociality. The budgerigar (Melopsittacus undulatus), an open-ended learner which develops new contact call types that are shared with social associates upon joining new flocks, provides a robust assay for measuring the effects of aging on vocal learning ability. We formed captive flocks of 4 previously unfamiliar adult males of the same age class, either “young adults” (6 mo.-1 yr.) or “older adults” (≥ 3 yr.), and concurrently tracked changes in contact call structure and social interactions over time. Older adults exhibited decreased vocal diversity, which may be related to the sparser and weaker affiliative bonds observed in older adults. Older adults, however, displayed equivalent levels of vocal plasticity and vocal convergence compared to young adults, suggesting vocal learning ability is largely maintained into later adulthood in an open-ended learner.

Added Docker image creation via a GitHub Action. This is stored on the GitHub Container Registry (ghcr.io) and made available in this repository as a package. Specific changes are: Creation of a Dockerfile that defines the process of building the Docker image (starting from a mysql image on Dockerhub) Creation of a GitHub Workflow that runs the Dockerfile to create the image and then stores in on ghcr Replacement of database files as .zip with .gz versions, which allows the Dockerfile ADD command on line 21 to send the SQL gzip file to the image and decompress it at the same time

Changed gz SQL file for uncompressed SQL file as encountering 'not in gzip format' in Dockerfile (line 28).