Large-scale, volunteer-collected datasets of community-identified natural world imagery like iNaturalist have enabled marked performance gains for fine-grained visual classification of species using machine learning methods. However, such data---sometimes referred to as citizen science data---are opportunistic and lack a structured sampling strategy. This volunteer-collected biodiversity data contains geographic, temporal, taxonomic, observers, and sociopolitical biases that can have significant effects on biodiversity model performance, but whose impacts are unclear for fine-grained species recognition performance. Here we introduce Diversity Shift (DivShift), a framework for quantifying the effects of domain-specific distribution shifts on machine learning model performance. To diagnose the performance effects of biases specific to volunteer-collected biodiversity data, we also introduce DivShift - North American West Coast (DivShift-NAWC), a curated dataset of almost 7.5 million iNaturalist images across the western coast of North America partitioned across five types of expert-verified bias. We compare species recognition performance across these bias partitions using a diverse variety of species- and ecosystem-focused accuracy metrics. We observe that these biases confound model performance less than expected from the underlying label distribution shift, and that more data leads to better model performance but the magnitude of these improvements are bias-specific. These findings imply that while the structure within natural world images provides generalization improvements for biodiversity monitoring tasks, the biases present in volunteer-collected biodiversity data can also affect model performance; thus these models should be used with caution in downstream biodiversity monitoring tasks.

SUMMARY: Pool sequencing is an efficient method for capturing genome-wide allele frequencies from multiple individuals, with broad applications such as studying adaptation in Evolve-and-Resequence experiments, monitoring of genetic diversity in wild populations, and genotype-to-phenotype mapping. Here, we present grenedalf, a command line tool written in C++ that implements common population genetic statistics such as θ, Tajima's D, and FST for Pool sequencing. It is orders of magnitude faster than current tools, and is focused on providing usability and scalability, while also offering a plethora of input file formats and convenience options. AVAILABILITY AND IMPLEMENTATION: grenedalf is published under the GPL-3, and freely available at github.com/lczech/grenedalf.

SUMMARY: We developed grenepipe, an all-in-one Snakemake workflow to streamline the data processing from raw high-throughput sequencing data of individuals or populations to genotype variant calls. Our pipeline offers a range of popular software tools within a single configuration file, automatically installs software dependencies, is highly optimized for scalability in cluster environments and runs with a single command. AVAILABILITY AND IMPLEMENTATION: grenepipe is published under the GPLv3 and freely available at github.com/moiexpositoalonsolab/grenepipe.