Geology topics

Edward J. Heist

Publications and source records attributed to Edward J. Heist.

9 recordsLinked to original sources

USGS2026

GT-Seq panel development for species identification and parentage analysis of closely related hybridising Scaphirhynchus sturgeons

Hatchery supplementation is vital for conserving dwindling fish populations. Effective augmentation requires distinguishing hatchery-origin from wild individuals and accurately identifying species, particularly in systems where closely related species coexist. Genetic monitoring is key to quantifying genetic differences, but conventional markers do not distinguish hybrids, especially backcrosses. Misidentifying hybrids in hatchery programs compromises wild gene pools because hatchery broodstock contributes to numerous offspring being released into the wild. Here, we present a workflow for developing and evaluating the Genotyping-in-Thousands by sequencing (GT-seq) single nucleotide polymorphism (SNP) panel for North American river sturgeons ( Scaphirhynchus spp.). This panel is designed to detect complex hybrid classes and to determine parent-offspring relationships. Our species identification panel (S-loci) contains 155 SNPs selected for high genetic differentiation (F ST ) between Pallid Sturgeon ( S. albus ) and Shovelnose Sturgeon ( S. platorynchus ), and the parentage assignment panel (P-loci) includes 112 SNPs with high heterozygosity within Pallid Sturgeon. Simulation analyses demonstrated that our GT-seq S-loci panel reliably classifies pure species, F1, F2 and backcross hybrids, even with up to 70% missing data. The P-loci panel achieves high-confidence parentage assignment with ≥ 80% typed loci, with performance influenced by the proportion of sampled parents. Overall, the novel Scaphirhynchus GT-seq panel developed in this study represents a robust and efficient tool for detecting hybridisation, assigning parentage and providing critical information for management decisions in ongoing Pallid Sturgeon conservation.

lower Mississippi River, Missouri River↗

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

Diet composition and overlap of larval pallid sturgeon and shovelnose sturgeon from the upper Missouri River, USA

Early life stages of pallid sturgeon Scaphirhynchus albus are rarely collected, and thus information on their biology and ecology is extremely limited. We sampled 75 larval pallid sturgeon (25-110 mm) and 148 larval shovelnose sturgeon S. platorynchus (15-95 mm) by trawl from the upper Missouri River (USA) in 2019. Stomach contents were identified to compare food use and diet overlap between the 2 sturgeon species at the order, family, and genus levels of taxonomic prey identification. Analyses were conducted with sites pooled and with sites separated by the confluence of the Yellowstone River (upper and lower). Abundance of dominant prey in the gut (Diptera larvae) increased with fish length for both species, and regression slopes were similar. Diet overlap at pooled sites decreased from 0.94 to 0.49 when prey were identified to order and genus, respectively, and decreases in diet overlap at individual sites were more pronounced. Larval pallid sturgeon consumed a maximum of 11 unique taxa, whereas shovelnose sturgeon consumed 6 taxa that were not consumed by pallid sturgeon. These results indicate that larval diets are similar between species when evaluated at coarse taxonomic scales, but at fine taxonomic scales, notable differences exist. As information about the diets of larval pallid sturgeon captured from a riverine environment are scarce and the use of shovelnose sturgeon as an indicator of available suitable food and habitat and as a dietary surrogate for pallid sturgeon has been under consideration, our results suggest that caution be exercised in modeling efforts or management actions relating to surrogacy.

Montana, North Dakota↗

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

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↗

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↗

USGS2014

Novel single-nucleotide polymorphism markers confirm successful spawning of endangered pallid sturgeon in the upper Missouri River Basin

Spawning of the federally endangered Pallid Sturgeon Scaphirhynchus albus is known to occur in the upper Missouri River basin, but progeny from natural reproductive events have not been observed and recruitment to juvenile or adult life stages has not been documented in recent decades. Identification of Pallid Sturgeon progeny is confounded by the fact that Shovelnose Sturgeon S. platorynchus occurs throughout the entire range of Pallid Sturgeon and the two species are essentially indistinguishable (morphometrically and meristically) during early life stages. Moreover, free embryos of sympatric Paddlefish Polyodon spathula are very similar to the two sturgeon species. In this study, three single-nucleotide polymorphism (SNP) assays were employed to screen acipenseriform free embryos and larvae collected from the upper Missouri River basin in 2011, 2012, and 2013. A mitochondrial DNA SNP discriminates Paddlefish from sturgeon, and specific multilocus genotypes at two nuclear DNA SNPs occurred in 98.9% of wild adult Pallid Sturgeon but only in 3% of Shovelnose Sturgeon sampled in the upper Missouri River. Individuals identified as potential Pallid Sturgeon based on SNP genotypes were further analyzed at 19 microsatellite loci for species discrimination. Out of 1,423 free embryos collected over 3 years of sampling, 971 Paddlefish, 446 Shovelnose Sturgeon, and 6 Pallid Sturgeon were identified. Additionally, 249 Scaphirhynchus spp. benthic larvae were screened, but no Pallid Sturgeon were detected. These SNP markers provide an efficient method of screening acipenseriform early life stages for the presence of Pallid Sturgeon in the Missouri River basin. Detection of wild Pallid Sturgeon free embryos in the upper Missouri and Yellowstone rivers supports the hypothesis that the failure of wild Pallid Sturgeon to recruit to the juvenile life stage in the upper Missouri River basin is caused by early life stage mortality rather than by lack of successful spawning.

Transactions of the American Fisheries Society↗

USGS2009

Bycatch of the endangered pallid sturgeon (Scaphirhynchus albus) in a commercial fishery for shovelnose sturgeon (Scaphirhynchus platorynchus)

We quantified the bycatch of pallid sturgeon Scaphirhynchus albus in Tennessee's shovelnose sturgeon ( Scaphirhynchus platorynchus ) fishery by accompanying commercial fishers and monitoring their catch on five dates in spring 2007. Fishers were free to keep or discard any sturgeon they collected in their gillnets and trotlines and we were afforded the opportunity to collect meristic and morphometric data and tissue samples from discarded and harvested specimens. Fishers removed 327 live sturgeon from their gear in our presence, of which 93 were harvested; we also obtained the carcasses of 20 sturgeon that a fisher harvested out of our sight while we were on the water with another fisher. Two of the 113 harvested sturgeon were confirmed pallid sturgeon based on microsatellite DNA analyses. Additionally, fishers gave us five, live pallid sturgeon that they had removed from their gear. If the incidental harvest rate of pallid sturgeon (1.8% of all sturgeon harvested) was similar in the previous two commercial seasons, at least 169 adult pallid sturgeon were harvested by commercial fishers in the Tennessee waters of the Mississippi River in 2005-2007. If fishers altered their behavior because of our presence (i.e. if they were more conservative in what they harvested), the pallid sturgeon take was probably higher when they fished unaccompanied by observers. While retrieving a gill net set the previous day, a fisher we were accompanying retrieved a gillnet lost 2 days earlier; this ghost net caught 53 sturgeon whereby one fish was harvested but most fish were dead, including one confirmed pallid sturgeon.

Journal of Applied Ichthyology↗

USGS2009

Genetic conservation and paddlefish propagation

The conservation of genetic diversity of our natural resources is overwhelmingly one of the central foci of 21st century management practices. Three recommendations related to the conservation of paddlefish Polyodon spathula genetic diversity are to (1) identify genetic diversity at both nuclear and mitochondrial DNA loci using a suggested list of 20 sampling locations, (2) use genetic diversity estimates to develop genetic management units, and (3) identify broodstock sources to minimize effects of supplemental stocking on the genetic integrity of native paddlefish populations. We review previous genetic work on paddlefish and described key principles and concepts associated with maintaining genetic diversity within and among paddlefish populations and also present a genetic case study of current paddlefish propagation at the U.S. Fish and Wildlife Service Gavins Point National Fish Hatchery. This study confirmed that three potential sources of broodfish were genetically indistinguishable at the loci examined, allowing the management agencies cooperating on this program flexibility in sampling gametes. This study also showed significant bias in the hatchery occurred in terms of male reproductive contribution, which resulted in a shift in the genetic diversity of progeny compared to the broodfish. This shift was shown to result from differential male contributions, partially attributed to the mode of egg fertilization. Genetic insights enable implementation of a paddlefish propagation program within an adaptive management strategy that conserves inherent genetic diversity while achieving demographic goals.

American Fisheries Society Symposium↗