This dataset contains sample information about the origin of the Desmognathus wrighti and Plethodon jordani salamanders collected from Great Smoky Mountains National Park and sequenced, and their corresponding SNP genotype data. These data were used to examine patterns of genomic structure of these two salamander species within Great Smoky Mountains National Park. The raw sequence data are archived in the GenBank Bioproject PRJNA1062342 at: https://www.ncbi.nlm.nih.gov/bioproject/

Aquatic and terrestrial invertebrate density and biomass datasets at genus and family taxonomic levels. This dataset is associated with the following publication: Fritz, K., R. Kashuba, G. Pond, J. Christensen, L. Alexander, B.J. Washington, B. Johnson, D. Walters, W. Thoeny, and P. Weaver. Identifying invertebrate indicators for streamflow duration assessments in forested headwater streams. Freshwater Science. The Society for Freshwater Science, Springfield, IL, 42(3): 247-267, (2023).

We provide genetic and distribution data for the Louisiana Pigtoe, Pleurobema riddellii, to guide decisions related to federal protection for the species under the U.S. Endangered Species Act. Our final dataset includes 125 COI sequences generated as part of our study representing P. riddellii from eight North American river basins. This includes the COI sequence we generated from a museum specimen collected from the Trinity River in the late 1900s, which is the first genetic confirmation of P. riddellii in the Trinity River basin. Also included are sequences from specimens initially identified as Fusconaia cerina (n=3) Fusconaia flava (n=1), Fusconaia sp. (n=5), Pleurobema sintoxia (n=10), and Pustulosa pustulosa (n=1) that were genetically confirmed to be P. riddellii. Additionally, we provide distribution data from freshwater mussel surveys, museum records, and field notes representing 467 records of P. riddellii collected from pre-1900 - 2022. The occurrence data includes records from 9 river basins (Amite, Calcasieu, Neches, Ouachita, Pearl, Red, Sabine, San Jacinto, Trinity), 54 HUC-10 watersheds, and 5 states (Arkansas, Louisiana, Mississippi, Oklahoma, Texas).

Field Methods: I will collect individual sample branches (one for each population to make specimens) and few leaves for the other species without hurting the plants. I would only need population samples for Streptopus lanceolatus, Goodyera pubescens and Gaultheria procumbens. The leaves will be dried in silica gel and for DNA extraction. The species include: Prosartes languinosa, Prosartes matculata, Goodyera pubescens, Gaultheria procumbens, Streptopus amplexifolius, Streptopus lanceolatus.

Biological indicator taxa have long been used for integrative assessments of water quality, particularly benthic invertebrate groups such as arthropods. While standardized protocols have been developed to calculate 'biological index' scores based on the abundances of these taxa, such systems are challenging to implement at large scales due to the sampling effort required, taxonomic expertise needed, and the need for repeated sampling to reliably discriminate sites. Many of the same taxa detected by traditional surveys can also be detected by genetic analysis of environmental DNA (eDNA), potentially allowing for an alternative formulation of biological indexes that might be faster and more economical to produce. The current data were produced to evaluate eDNA-derived biological indexes at sites within the Potomac River watershed of the eastern United States, specifically within units of the National Park Service for which previous biological assessment data were available. This data release consists of five files: 1. sample.metadata.txt, which contains sampling metadata and identifiers linking to sample-derived sequence data that has been deposited in the Sequence Read Archive of the National Center for Biotechnology Information (NCBI). This database is authoritative and comprehensive for sharing high-throughput sequence data produced with public funds. All accessions listed in the file can be searched to retrieve sample and sequence information at www.ncbi.nlm.nih.gov. 2. cox1.references.fasta, which contains reference sequences of the cytochrome c oxidase 1gene of arthropods (typically abbreviated cox1 or COI), identified from regional checklists. The file is a text file in FASTA format. 3. mt16S.references.fasta, which contains reference sequences of the mitochondrial 16S ribosomal RNA (mt16S) gene of arthropods identified from regional checklists. The file is a text file in FASTA format. 4. first.stage.counts.txt, which is a tab-delimited table of counts of sequences that are attributed to each taxon from each sample for the first stage of the study. Whether the taxon attribution is from the mt16S or cox1 locus is also indicated. 5. second.stage.counts.txt, which is a tab-delimited table of counts of sequences that are attributed to each taxon from each sample for the second stage of the study. Whether the taxon attribution is from the mt16S or cox1 locus is also indicated.

Biological indicator taxa have long been used for integrative assessments of water quality, particularly benthic invertebrate groups such as arthropods. While standardized protocols have been developed to calculate 'biological index' scores based on the abundances of these taxa, such systems are challenging to implement at large scales due to the sampling effort required, taxonomic expertise needed, and the need for repeated sampling to reliably discriminate sites. Many of the same taxa detected by traditional surveys can also be detected by genetic analysis of environmental DNA (eDNA), potentially allowing for an alternative formulation of biological indexes that might be faster and more economical to produce. The current data were produced to evaluate eDNA-derived biological indexes at sites within the Potomac River watershed of the eastern United States, specifically within units of the National Park Service for which previous biological assessment data were available. This data release consists of five files: 1. sample.metadata.txt, which contains sampling metadata and identifiers linking to sample-derived sequence data that has been deposited in the Sequence Read Archive of the National Center for Biotechnology Information (NCBI). This database is authoritative and comprehensive for sharing high-throughput sequence data produced with public funds. All accessions listed in the file can be searched to retrieve sample and sequence information at www.ncbi.nlm.nih.gov. 2. cox1.references.fasta, which contains reference sequences of the cytochrome c oxidase 1gene of arthropods (typically abbreviated cox1 or COI), identified from regional checklists. The file is a text file in FASTA format. 3. mt16S.references.fasta, which contains reference sequences of the mitochondrial 16S ribosomal RNA (mt16S) gene of arthropods identified from regional checklists. The file is a text file in FASTA format. 4. first.stage.counts.txt, which is a tab-delimited table of counts of sequences that are attributed to each taxon from each sample for the first stage of the study. Whether the taxon attribution is from the mt16S or cox1 locus is also indicated. 5. second.stage.counts.txt, which is a tab-delimited table of counts of sequences that are attributed to each taxon from each sample for the second stage of the study. Whether the taxon attribution is from the mt16S or cox1 locus is also indicated.

The North American freshwater mussel tribe Quadrulini has a suite of life history adaptations, however, the evolution of life histories in this group has yet to be explored using comparative phylogenetic methods. Here we provide the AHE DNA sequence alignment representing 27 species from the subfamily Ambleminae that was used to estimate a phylogenomic reconstruction of Quadrulini. Additionally, we provide a compilation of host use information and larval length and height measurements utilized to trace the evolution of life history characteristics, such as larval morphology and host attraction strategy. Phylogenetic trees are presented representing phylogenetic inference performed under Maximum Likelihood, Maximum Parsimony, Bayesian Inference, and coalescent-based approaches. Findings from these datasets and analyses suggest the diversification of Quadrulini has been influenced by the codiversification of their larval hosts.

The North American freshwater mussel tribe Quadrulini has a suite of life history adaptations, however, the evolution of life histories in this group has yet to be explored using comparative phylogenetic methods. Here we provide the AHE DNA sequence alignment representing 27 species from the subfamily Ambleminae that was used to estimate a phylogenomic reconstruction of Quadrulini. Additionally, we provide a compilation of host use information and larval length and height measurements utilized to trace the evolution of life history characteristics, such as larval morphology and host attraction strategy. Phylogenetic trees are presented representing phylogenetic inference performed under Maximum Likelihood, Maximum Parsimony, Bayesian Inference, and coalescent-based approaches. Findings from these datasets and analyses suggest the diversification of Quadrulini has been influenced by the codiversification of their larval hosts.