Biology subjects

Finger, A. J.

Publications and source records attributed to Finger, A. J..

8 recordsLinked to original sources

bioRxiv2026

Quantifying the evolutionary potential for Delta Smelt persistence in a warming habitat

Long-term persistence of managed species will depend, in part, on whether the species harbors the physiological or genetic potential to adjust to warming temperatures, and whether relevant genetic variation is modified by management practices. The critically endangered Delta Smelt (Hypomesus transpacificus) is intensively managed, but little is known about the presence of genetic variation for resistance to elevated temperature, which will be important to maintain for their persistence in a rapidly warming future. Using a pedigree and whole genome sequencing data, we characterized the genetic variation and genomic architecture for CTMax (as a metric of upper thermal tolerance) across control and elevated rearing temperatures, alongside covarying traits (body size, degree of hatchery ancestry). Warmer rearing temperatures increased CTMax through acclimation but also resulted in reduced additive genetic variation for the trait, which could constrain adaptation under thermal stress. We found that larger fish had reduced CTMax, although this effect was diminished at elevated temperatures. We observed modest heritability for CTMax at rearing temperatures of 15{degrees}C and 18{degrees}C (0.26 and 0.16, respectively), but only a limited number of loci were identified that had consistent effects on CTMax across rearing temperatures. Instead, the genomic basis of thermal tolerance was highly dependent on rearing temperature (many loci detected with a GxE effect). The influence of domestication selection was indicated by changes in allele frequency, and divergence in upper thermal tolerance and plasticity, between low and high hatchery ancestry groups. Minimal overlap between loci associated with domestication and CTMax suggests that these traits possess separate genetic underpinnings. Knowledge of genetic variation supporting ecologically relevant physiological variation may be useful for refuge management and may inform supplementation in an ever-warming environment.

evolutionary biology↗

bioRxiv2026

Alignment-Free Microhaplotype Genotyping for GT-seq (Genotyping-in-Thousands by Sequencing) Using a Diploid Abundance Model

GT-seq (Genotyping-in-Thousands by Sequencing) is widely used for high-throughput amplicon genotyping, but most analytical pipelines focus on single SNPs or rely on alignment-based variant calling. Here we present an alignment-free approach for microhaplotype genotyping that leverages the high read depth and low error rates typical of paired-end Illumina and Element sequencing. The pipeline first identifies primer-bounded reads and resolves paired-end sequences into complete amplicon sequences. Within each sample and locus, unique sequences are ranked by read abundance and the top one or two sequences are retained as candidate diploid alleles. These alleles are aggregated across samples to construct a catalog of unique haplotypes for each locus. In a second pass, reads are assigned to catalog haplotypes by exact sequence matching to produce diploid genotypes. Finally, catalog haplotype sequences are positionally compared to identify phased SNP and collapsed indel variation, generating compact microhaplotype representations suitable for population genetic analysis. This approach enables robust, alignment-free microhaplotype inference directly from high-depth amplicon sequencing data.

genetics↗

bioRxiv2026

Use of SNPs in a low diversity system for genetic monitoring and identifying a successful translocation event in the Paiute Cutthroat Trout (O. henshawi seleniris)

ObjectiveMaintaining genetic diversity in small, isolated populations is a key goal in conservation genetics. Genetic monitoring can guide management decisions, but comparisons across studies and time points are often complicated by differences in genetic markers and data sets. We aimed to develop a consistent, replicable set of genetic markers to support long-term monitoring of Paiute Cutthroat Trout (Oncorhynchus henshawi seleniris), a federally threatened subspecies persisting in a network of isolated refuge populations in California, USA. MethodsWe used RAD (Restriction site-associated DNA) sequencing to identify single nucleotide polymorphisms (SNPs) from 476 individuals representing eight extant refuge populations. Filtering steps included the removal of paralogous loci and exclusion of FST outliers associated with sequencing batch effects. We selected a panel of 1,114 SNPs that were shared across all populations and validated the panel in silico by comparing population structure and genetic diversity estimates to those derived from the full RAD sequencing dataset. ResultsThe candidate panel SNPs captured key patterns of genetic differentiation and diversity consistent with previous studies and the larger RAD dataset. We present updated baseline genetic metrics for each refuge population, providing a consistent reference point for future monitoring efforts. We also demonstrate the ability of our candidate panel SNPs to detect successful spawning after a translocation event. ConclusionThis study provides a set of SNPs tailored for monitoring genetic diversity and structure in Paiute Cutthroat Trout refuge populations. Future work should include development of a high-throughput genotyping assay to implement these candidate panel SNPs for ongoing management. This would enable consistency over time with genetic studies and be a foundational tool for repeated evaluation of conservation actions such as reintroductions and augmentations. Lay SummaryWe identified genetic markers to help track and protect one of the rarest trout in the United States. This work supports long-term conservation by making it easier to monitor isolated populations and measure the success of efforts to restore the species.

genomics↗

bioRxiv2025

Highly and lowly domesticated endangered fish from a conservation hatchery diverge in their thermal physiology, transcriptome, and methylome

Conservation hatcheries aim to produce fish for supplementation of wild populations, but hatchery environments may drive phenotypic divergence from wild fish. These diverged traits may have reduced fitness in the wild, which could compromise wild population sustainability and evolutionary potential, such as in response to climate change. Delta smelt are a critically endangered fish species that are safeguarded against extinction with a hatchery refuge population. We investigated whether elevated rearing temperature through larval development adjusted upper thermal tolerance limits (acclimation) in Delta smelt, whether upper thermal tolerance and plasticity (acclimation ability) differed between fish with old or recent hatchery ancestry (high or low domestication index; DI), and temperature and DI effects on liver transcriptome and methylome patterns. We observed that elevated rearing temperatures induced higher thermal tolerance (acclimation). Individuals with higher DI also had higher upper thermal tolerances, but high DI families had reduced thermal plasticity between rearing temperatures. This is consistent with domestication causing heritable elevation of upper thermal tolerance but at the cost of reduced thermal plasticity. High and low DI fish were differentiated in both genetic variation and methylome variation, suggesting the influence of both during domestication. But methylome differences distinguishing high and low DI fish did not overlap with temperature-induced methylome changes, and do not appear to be stably inherited in the hatchery. We conclude that domestication selection has altered thermal physiology within the refuge hatchery despite careful genetic management, underpinned by shifts in the transcriptome and methylome. These changes could affect Delta smelt fitness upon reintroduction to habitats that continue to warm, and show that physiological traits can diverge even within carefully genetically managed hatchery populations.

evolutionary biology↗

bioRxiv2024

MAXTEMP: A method to maximize precision of the temporal method for estimating Ne in genetic monitoring programs

We introduce a new software program, MAXTEMP, that maximizes precision of the temporal method for estimating effective population size (Ne) in genetic monitoring programs, which are increasingly used to systematically track changes in global biodiversity. Scientists and managers are typically most interested in Ne for individual generations, either to match with single-generation estimates of census size (N) or to evaluate consequences of specific management actions or environmental events. Systematically sampling every generation produces a time series of single-generation estimates of temporal [Formula], which can then be used to estimate Ne; however, these estimates have relatively low precision because each reflects just a single episode of genetic drift. Systematic sampling also produces an array of multigenerational temporal estimates that collectively contain a great deal of information about genetic drift that, however, can be difficult to interpret. Here we show how additional information contained in multigenerational temporal estimates can be leveraged to increase precision of [Formula] for individual generations. Using information from one additional generation before and after a target generation can reduce the standard deviation of [Formula] by up to 50%, which not only tightens confidence intervals around [Formula] but also reduces the incidence of extreme estimates. Practical application of MAXTEMP is illustrated with data for a long-term genetic monitoring program for California delta smelt. A second feature of MAXTEMP, which allows one to estimate Ne in an unsampled generation using a combination of temporal and single-sample estimates of Ne from sampled generations, is also described and evaluated.

genetics↗

bioRxiv2022

Experimental evaluation of environmental DNA methods for detection of a rare fish in turbid water

Environmental DNA (eDNA) approaches enable sensitive detection of rare aquatic species. However, water conditions like turbidity can limit sensitivity, resulting in false negative detections. The dynamics of eDNA detection in turbid conditions are poorly understood, but can be better characterized through experimental work. In this study, 1-L field-collected water samples were spiked with tank-sourced eDNA from a rare, endangered estuarine fish at concentrations similar to eDNA samples collected from the natural environment. Samples using non-turbid water (5 NTU), turbid water (50 NTU), and prefiltered turbid water were filtered using four filter types (pore size range 0.45 m-10 m). Detection success using a species-specific Taqman qPCR assay was assessed as both eDNA copy number and detection/non-detection. Glass fiber filters (nominal pore size 1.6 m) yielded the highest number of eDNA copies and detections in non-turbid water and the highest detection rate in turbid water when used without a prefilter. Detection was a more robust metric for evaluating species presence across turbidity conditions compared with eDNA copy number. Prefiltration improved detection rates for the other filters tested (polycarbonate and cartridge filters). Filter material and design appear to interact differently with the prefiltration step, and may be more important considerations than pore size for eDNA capture in turbid water. Interactions between eDNA particles, suspended particulate matter, and filters are important to consider for eDNA methods optimization and interpretation of rare species detections in turbid water.

molecular biology↗

bioRxiv2021

Population genomic analysis of the speckled dace species complex (Rhinichthys osculus) identifies three species-level lineages in California

The speckled dace (Rhinichthys osculus) is small cyprinid fish that is widespread in the Western USA. Currently treated as a single species, speckled dace consists of multiple evolutionary lineages that can be recognized as species and subspecies throughout its range. Recognition of taxonomic distinctiveness of speckled dace populations is important for developing conservation strategies. In this study, we collected samples of speckled dace from 38 locations in the American West, with a focus on California. We used RAD sequencing to extract thousands of SNPs across the genome from samples to identify genetic differences among seven California populations informally recognized as speckled dace subspecies: Amargosa, Owens, Long Valley, Lahontan, Klamath, Sacramento, and Santa Ana speckled dace. We performed principal component analysis, admixture analysis, estimated pairwise Fst, and constructed a phylogeny to explore taxonomic relationships among these groups and test if these subspecies warrant formal recognition. Our analyses show that the seven subspecies fit into three major lineages equivalent to species: western (Sacramento-Klamath), Santa Ana, and Lahontan speckled dace. Death Valley speckled dace were determined to be two lineages (Amargosa and Long Valley) within Lahontan speckled dace. Western and Lahontan speckled dace lineages had branches that can be designated as subspecies. These designations fit well with the geologic history of the region which has promoted long isolation of populations. This study highlights the importance of genetic analysis for conservation and management of freshwater fishes.

genomics↗

bioRxiv2020

Environmental DNA sampling provides new management strategies for vernal pool branchiopods in California

Californias vernal pools are declining ecosystems that support valuable native plant and animal diversity. Vernal pool branchiopods are particularly at risk from vernal pool habitat loss and conservation efforts have targeted their long-term protection through the establishment of preserves and conservation banks. These conservation strategies require repeated, perpetual monitoring of preserved habitat, which is currently carried out through dip-net surveys and visual identification of specimens. Dip-netting may be destructive and frequently requires some sacrifice of protected species. Environmental DNA offers a new, modern method to monitor many protected freshwater organisms. We designed qPCR-based species-specific assays for four of Californias vernal pool branchiopods: The Vernal Pool Fairy Shrimp Branchinecta lynchi (BRLY), the Midvalley Fairy Shrimp Branchinecta mesovallensis (BRME), and the Conservancy Fairy Shrimp Branchinecta conservatio (BRCO), and the Vernal Pool Tadpole Shrimp Lepidurus packardi (LEPA). We tested these assays using eDNA sampling protocols alongside traditional dip-net surveys to assess their viability as an alternative method to monitor vernal pool branchiopods. Based on occupancy modeling, each of our assays achieved a 95% or higher detection rate when using optimized sampling protocols.

genetics↗