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Kimberly Chojnacki

Publications and source records attributed to Kimberly Chojnacki.

11 recordsLinked to original sources
USGS2023

The effects of substrate and sediment burial on survival of developing pallid sturgeon (Scaphirhynchus albus) and shovelnose sturgeon (S. platorynchus) embryos

The shovelnose sturgeon ( Scaphirhynchus platorynchus ) and endangered pallid sturgeon ( S. albus ) deposit demersal and adhesive eggs in swift currents, near or over coarse substrate. Hydrographic surveys have demonstrated the dynamic nature of spawning habitats and that coarse substrates may episodically be buried (partially or completely) by fine sediments. To evaluate embryo survival of both species in various substrate conditions, laboratory trials were conducted with substrates of clean glass, gravel, medium-coarse sand (MCS), and fine sand-silt (FSS). Embryos in MCS and FSS were tested three ways: unburied, partially buried, and fully buried (1–2-mm depth). Embryos were exposed to trial conditions for 10 days from the day of fertilization (5 days beyond expected hatching). For both species, mean hatch of normally developed free embryos was highest in unburied treatments where embryos were incubated on substrates and not covered with sediments and ranged from 81.0 to 87.1% for shovelnose sturgeon and 55.2–80.0% for pallid sturgeon. Mean hatch of normal free embryos was lowest where incubating embryos were fully buried by MCS or FSS and ranged from 2.4 to 11.6% for shovelnose sturgeon and 4.8–15.2% for pallid sturgeon. We observed free embryos with physical abnormalities in all treatments; however, the occurrence was most variable in treatments fully and partially buried by MCS. Hatch of both species was also delayed in treatments where embryos were incubated fully and partially buried by MCS. Our results may be useful to estimate the relative suitability of spawning substrates in relevant river reaches.

Environmental Biology of Fishes↗
USGS2022

Haploid gynogens facilitate disomic marker development in paleotetraploid sturgeons

Acipenseriformes (sturgeons and paddlefishes) are of substantial conservation concern, and development of genomic resources for these species is difficult due to past whole genome duplication. Development of disomic markers for polyploid organisms can be challenging due to difficulty in resolving alleles at a single locus from those among duplicated loci. In this study, we detail the development of disomic markers for the endangered pallid sturgeon ( Scaphirhynchus albus ) found in North America. One of the strategies for pallid sturgeon conservation is to stock U.S. rivers with offspring of pure pallid sturgeon, but introgression with the sympatric shovelnose sturgeon ( S. platorynchus ) threatens pallid sturgeon genetic integrity. Currently, 19 microsatellite loci are used to differentiate between both species and their hybrids, but the markers are insufficient to robustly identify backcrosses. We performed double digest restriction site-associated DNA sequencing (ddRADseq) on shovelnose sturgeon haploid gynogens to produce a reduced-representation genomic reference. Contiguous sequences that were heterozygous within a haploid individual were flagged as potentially encompassing multiple loci. Approximately 60 individuals of each species from two management units were sequenced, and reads were mapped to the haploid reference to identify single nucleotide polymorphisms (SNPs) at individual loci. The final data set contained 11,082 microhaplotyped loci which offer at least an order of magnitude greater resolution for species discrimination than the current panel of 19 microsatellites. These markers will be used to examine a larger sample of Scaphirhynchus individuals throughout their ranges to determine the extent and trajectory of hybridization.

Molecular Ecology Resources↗
USGS2022

Ontogenetic development of pallid sturgeon (Scaphirhynchus albus) and shovelnose sturgeon (Scaphirhynchus platorynchus) from hatch through yolk absorption

Sturgeons have a complex free-embryo period extending from hatch to the initiation of exogenous feeding. Although available for some sturgeon species of the genus Acipenser , descriptions of the developmental stages of free embryos of the genus Scaphirhynchus are lacking. We characterised the ontogenetic development of pallid sturgeon ( Scaphirhynchus albus ) and shovelnose sturgeon ( S . platorynchus ) free embryos from hatch through melanin plug expulsion. The rate of development was similar between Scaphirhynchus species among free embryos from 4 pallid sturgeon and 7 shovelnose sturgeon crosses reared separately in the laboratory at a mean temperature of 17.8°C. Free embryos required a mean of 18.2 days postfertilisation (DPF; 323.5 cumulative thermal units; CTU) to reach melanin plug expulsion for pallid sturgeon and 17.9 DPF (318.3 CTU) for shovelnose sturgeon. Free embryos of both species showed overlap in lengths among developmental stages indicating that length of free embryos alone is insufficient to estimate age. Description of pallid sturgeon and shovelnose sturgeon free-embryo development provides a template to develop more sophisticated models incorporating length and stage to estimate the age of field-collected specimens. Improved estimates of free-embryo developmental stage and age may aid in the identification of timing and location of spawning and better inform flow manipulation and habitat management actions tailored to increase survival of early life-stage pallid sturgeon.

Ecology of Freshwater Fish↗
USGS2021

Production of haploid gynogens to inform genomic resource development in the paleotetraploid pallid sturgeon (Scaphirhynchus albus)

Order Acipenseriformes (sturgeons and paddlefishes) is an ancient lineage of osteichthyan fishes (>200 million years old) with most extant species at conservation risk. A relatively basal species, the pallid sturgeon, Scaphirhynchus albus, is a federally endangered species native to the Mississippi and Missouri River basins. Hybridization with sympatric shovelnose sturgeon, S. platorynchus, is one of several threats to pallid sturgeon. Current molecular markers cannot reliably distinguish among pure species and multigenerational backcrosses. This information is critical for implementation of management strategies to increase populations through natural reproduction and artificial propagation. Genotypes from a large panel of unlinked single-nucleotide polymorphisms (SNPs) may provide greater resolution of the two species; however, paralogous sequence variants (PSVs) within individuals resulting from an ancient whole genome duplication event confound SNP development. The aim of this study was to produce pallid sturgeon gynogens that contain 100% homozygous DNA contributed by only the maternal parent and have enough DNA for future SNP marker development. When homozygous gynogens are sequenced, heterozygosity at a locus within an individual indicates the presence of incorrectly aligned sequences that contain PSVs; accurate identification of these multi-locus contigs can facilitate their exclusion when developing disomic markers. In this study, we attempted to produce two types of pallid sturgeon gynogens: a) haploid gynogens produced from the activation of pallid sturgeon eggs with ultraviolet-irradiated sperm from the distantly related paddlefish (Polyodon spathula), and b) doubled haploids produced from the activation of pallid sturgeon eggs with irradiated paddlefish milt followed by thermal shock to suppress the first mitotic division. Production of doubled haploids, gynogens with 100% homozygous DNA and double the genome content of haploid gynogens, was pursued because it was originally unknown if haploid gyongens would survive long enough to attain enough genetic material for SNP marker development. We performed flow cytometry and microsatellite genotyping on the specimens in order to confirm haploid and doubled haploid status. Our study was unable to successfully yield doubled haploids; however, we successfully produced haploid gynogens that contained enough nuclear DNA for our future SNP marker development study. Interestingly, this study also produced paddlefish × pallid sturgeon hybrids in the control groups in two separate years; this is the first study to report viable offspring between the paddlefish and a Scaphirhynchus sturgeon species and reflects on the malleability of the genomes of the species in this order.

Louisiana, Arkansas, Missouri, Nebraska, North Dak↗
USGS2020

Physical characteristics and simulated transport of pallid sturgeon and shovelnose sturgeon eggs

The imperiled pallid sturgeon (Scaphirhynchus albus) and closely related, but more common, shovelnose sturgeon (S. platorynchus) are believed to broadcast adhesive, demersal eggs in the current and over coarse substrate in turbid rivers of the North American midcontinent. It has been hypothesized that eggs settle immediately following fertilization, but field conditions preclude direct observation. We conducted laboratory studies to characterize the diameter, shape, settling velocity, and specific gravity of pallid sturgeon and shovelnose sturgeon eggs. Based on these laboratory measurements, we then modeled the potential fate of pallid sturgeon eggs by considering these physical properties in the context of two field sites where spawning has occurred. Although eggs of pallid sturgeon and shovelnose sturgeon were of a similar size and shape, shovelnose sturgeon eggs had slightly higher specific gravity and settling velocity. For representative hydraulic conditions at documented spawning sites in the mainstem Missouri and Lower Yellowstone Rivers, eggs of both species will likely be concentrated near the bed although some eggs may be distributed throughout the water column. Simulations of egg transport indicate that eggs may be transported up to several hundred meters downstream from spawning locations in the approximate length of time required for eggs to become adhesive. Estimates of egg transport presented here rely on simplifying assumptions about river hydraulics and limited understanding of how eggs interact with the complex substrates and flow near the bed; results highlight the need for additional studies to evaluate the fate of eggs and fertilized embryos of both species.

Missouri River basin↗
USGS2020

Improved genetic identification of acipenseriform embryos with application to the endangered pallid sturgeon Scaphirhynchus albus

We produced pallid sturgeon Scaphirhynchus albus embryos at five pre‐hatch developmental stages and isolated and quantified genomic DNA from four of the stages using four commercial DNA isolation kits. Genomic DNA prepared using the kit that produced the largest yields and concentrations were used for microsatellite DNA analyses of 10–20 embryos at each of the five developmental stages. We attempted to genotype the hatchery‐produced embryos at 19 microsatellite loci and confirmed reliable genotyping by comparing the microsatellite genotypes to those of known parents. Embryos at stages 5 and 8 did not produce reliable genotyping while those at stages 14, 24 and 33 did. We used the same DNA isolation method on 262 wild‐caught acipenseriform embryos collected from the lower Yellowstone River. A total of 200 of the wild embryos were successfully identified to stages 8 to 34 and the rest could not be staged. Using a combination of single nucleotide polymorphism and microsatellite markers, 249 of the wild‐caught embryos were genetically identified as paddlefish Polyodon spathula , five were identified as shovelnose sturgeon Scaphirhynchus platorynchus and eight failed to amplify. None were identified as pallid sturgeon. This study demonstrates that early‐stage wild‐spawned acipenseriform embryos can be genetically identified less than 24 h post‐spawn. This methodology will be useful for recovery efforts for endangered pallid sturgeon and can be applied to other acipenseriform species.

Journal of Fish Biology↗
USGS2020

Characterization of pallid sturgeon (Scaphirhynchus albus) spawning habitat in the Lower Missouri River

Acipenseriformes (sturgeons and paddlefish) globally have declined throughout their range due to river fragmentation, habitat loss, overfishing, and degradation of water quality. In North America, pallid sturgeon (Scaphirhynchus albus) populations have experienced poor to no recruitment, or substantial levels of hybridization with the closely related shovelnose sturgeon (S. platorynchus). The Lower Missouri River is the only portion of the species’ range where successful reproduction and recruitment of genetically pure pallid sturgeon have been documented. This paper documents spawning habitat and behavior on the Lower Missouri River, which comprises over 1,300 km of unfragmented river habitat. The objective of this study was to determine spawning locations and describe habitat characteristics and environmental conditions (depth, water velocity, substrate, discharge, temperature, and turbidity) on the Lower Missouri River. We measured habitat characteristics for spawning events of ten telemetry‐tagged female pallid sturgeon from 2008–2013 that occurred in discrete reaches distributed over hundreds of kilometers. These results show pallid sturgeon select deep and fast areas in or near the navigation channel along outside revetted banks for spawning. These habitats are deeper and faster than nearby river habitats within the surrounding river reach. Spawning patches have a mean depth of 6.6 m and a mean depth‐averaged water‐column velocity of 1.4 m per second. Substrates in spawning patches consist of coarse bank revetment, gravel, sand, and bedrock. Results indicate habitat used by pallid sturgeon for spawning is more common and widespread in the present‐day channelized Lower Missouri River relative to the sparse and disperse coarse substrates available prior to channelization. Understanding the spawning habitats currently utilized on the Lower Missouri River and if they are functioning properly is important for improving habitat remediation measures aimed at increasing reproductive success. Recovery efforts for pallid sturgeon on the Missouri River, if successful, can provide guidance to sturgeon recovery on other river systems; particularly large, regulated, and channelized rivers.

Missouri, Nebraska, Wyoming, Montana, North Dakota↗
USGS2019

Evidence of limited recruitment of Pallid Sturgeon in the Lower Missouri River

Pallid Sturgeon Scaphirhynchus albus are endemic to the Missouri and Mississippi river basins and are rare throughout their range. The species was listed as federally endangered with little to no evidence of natural recruitment. Since population augmentation was initiated as a recovery objective in the early 1990s, thousands of hatchery-origin Pallid Sturgeon have been stocked in the lower Missouri River (Gavins Point Dam [river kilometer 1,305.1] to the confluence of the Mississippi River [river kilometer 0.0]). Efforts to discriminate natural reproduction and recruitment of wild-origin Pallid Sturgeon from hatchery-origin fish has been hampered by tag loss in hatchery-origin sturgeon, inconsistent documentation of hatchery parental crosses, and the failure to collect tissue samples for genotyping all broodstock. However, the recent reconstruction of missing parental genotypes from known hatchery-origin progeny and from cryopreserved milt made it possible to examine Pallid Sturgeon recruitment. Therefore, our objectives were to 1) determine the likelihood that unmarked Pallid Sturgeon captured from the lower Missouri River were the result of natural recruitment and 2) examine the length distribution of wild- and hatchery-origin fish to determine if a difference exists by origin and examine the life-stage distribution. Genetic analysis showed that from 2003 to 2015, 358 “presumptive wild-origin” Pallid Sturgeon were captured in the lower Missouri River and the comparison between the length distributions of wild- and hatchery-origin fish did not provide any additional clarification into potential wild-origin fish. Low recruitment may be due to a small breeding population, high mortality of early life stages, hybridization with Shovelnose Sturgeon Scaphirhynchus platorynchus , or transport of drifting free embryos or larvae into inhospitable habitats. Determining what factors are limiting recruitment is the important next step for the recovery of Pallid Sturgeon in the lower Missouri River.

Iowa, Kansas, Missouri, Nebraska, South Dakota↗
USGS2018

Diet and condition of age‐0 Scaphirhynchus Sturgeon: Implications for shallow‐water habitat restoration

Insufficient food during early life could limit the population growth of endangered Pallid Sturgeon Scaphirhynchus albus in the lower Missouri River. Shallow‐water habitat restoration is intended to provide nursery benefits, including food, for young sturgeon, but the effect of shallow‐water habitat on their diet is unknown. Age‐0 Pallid Sturgeon are rare, providing little opportunity for direct evaluation; however, studying the closely related and abundant Shovelnose Sturgeon S. platorynchus may provide valuable information to guide habitat restoration efforts. We compared diet, body condition (lipid content), and change in body weight (24‐h bioenergetics simulation) for postdrift, age‐0 sturgeon among five reaches ranging widely in shallow‐water habitat availability. Lipid content of satiated and emaciated laboratory‐reared individuals were compared with that of wild‐caught fish. In general, shallow‐water habitat availability appeared to have little effect on the variables examined. Regardless of reach, wild‐caught fish primarily consumed chironomids, and empty stomachs were rare. Additionally, differences in prey weight, lipid content, or the modeled change in body weight did not usually correspond to differences in shallow‐water habitat availability. Instead, we found annual differences, as prey weight consumed and the percentage of fish with modeled weight gain was often higher in 2015 than 2014, while the opposite was true for the percentage of fish with lipid content values that were comparable with the emaciated laboratory standard. Overall, our findings complement recent suggestions that shallow‐water habitat restoration efforts, as previously implemented, may not benefit sturgeon populations. Our results coupled with previous research suggest that the lower Missouri River prey base can support a stable Shovelnose Sturgeon population; however, additional research is needed to determine whether this applies to Pallid Sturgeon.

Missouri↗
USGS2011

A geospatial approach to identify water quality issues for National Wildlife Refuges in Oregon and Washington

Many National Wildlife Refuges (Refuges) have impaired water quality resulting from historic and current land uses, upstream sources, and aerial pollutant deposition. Competing duties limit the time available for Refuge staff to identify and evaluate potential water quality issues. As a result, water quality–related issues may not be resolved until a problem has already arisen. This study developed a geospatial approach for identifying and prioritizing water quality issues affecting natural resources (including migratory birds and federally listed species) within Refuge boundaries. We assessed the location and status of streams pursuant to the Clean Water Act in relation to individual Refuges in Oregon and Washington, United States. Although twelve Refuges in Oregon (60%) and eight Refuges in Washington (40%) were assessed under the Clean Water Act, only 12% and 3% of total Refuge stream lengths were assessed, respectively. Very few assessed Refuge streams were not designated as impaired (0% in Oregon, 1% in Washington). Despite the low proportions of stream lengths assessed, most Refuges in Oregon (70%) and Washington (65%) are located in watersheds with approved total maximum daily loads. We developed summaries of current water quality issues for individual Refuges and identified large gaps for Refuge-specific water quality data and habitat utilization by sensitive species. We conclude that monitoring is warranted on many Refuges to better characterize water quality under the Clean Water Act.

Oregon, Washington↗