Appendix A: Technical Summary

STUDY TITLE: Using Advanced Population Genomics to Better Understand the Relationship 

Between Offshore and Spawning Habitat Use for Atlantic Sturgeon

REPORT TITLE: Using Advanced Population Genomics to Better Understand the Relationship 

Between Offshore and Spawning Habitat Use for Atlantic Sturgeon

OCS STUDY NUMBER: BOEM 2020-062

NUMBER OF PAGES: 70

CONTRACT NUMBERS: M15PG00044

SPONSORING OCS REGION: Headquarters

APPLICABLE PLANNING AREAS: North Atlantic, Mid-Atlantic, South Atlantic

FISCAL YEARS OF PROJECT FUNDING: FY2016–2018

COSTS BY FISCAL YEAR: FY2016: $66,666; FY2017: $66,666; FY2018: $66,667

CUMULATIVE PROJECT COST: $200,000

COMPLETION DATE OF REPORT: January 2020

PROJECT MANAGERS: Tim L. King, David C. Kazyak, and Aaron W. Aunins

AFFILIATION OF PROJECT MANAGERS: USGS Leetown Science Center

ADDRESS: 11649 Leetown Rd., Kearneysville, WV 25430

PRINCIPAL INVESTIGATORS: Tim L. King, David C. Kazyak, and Aaron W. Aunins

KEY WORDS: Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus, population genomics, single 

nucleotide polymorphisms (SNPs), genetic assignment testing

NOTE: References for the information presented below can be found in the text of the full report.

BRIEF ABSTRACT: Federal management of Atlantic sturgeon presents challenges, as sturgeon from 

each of the five Distinct Population Segments (DPSs) mix extensively in coastal and marine habitats,but

take and recovery progress must be evaluated separately for each unit. Genetic assignment testing allows 

individuals to be assigned back to their natal river and DPS. However, this approach is not perfect, and 

some individuals may be incorrectly assigned. Recent advances in genomics offer the potential of a higher 

resolution approach to genetic assignment testing which may reduce uncertainty. We used nextgeneration sequencing to develop a draft genome for Atlantic sturgeon and identify single nucleotide 

polymorphisms (SNPs) that could be used to resolve the origin of Atlantic sturgeon. We identified 1,210 

candidate SNPs within the nuclear genome and 49 SNPs within the mitochondrial genome, from which 

we selected 161 nuclear SNPs and 39 mitochondrial SNPs for further evaluation. We used genotyping-inthousands by sequencing (GT-seq) to simultaneously sequence nuclear and mitochondrial SNP loci. 

Using baseline data from the nine populations, we ran a series of genomic analyses to characterize 

diversity within and among populations, providing a benchmark for this species using the new SNP 

markers. Allelic richness was similar for all populations, although there was a general trend of more 

northern population containing greater levels of allelic richness. Pairwise differentiation among 
populations varied among the populations (FST range: 0.010–0.098) and was significantly correlated (r = 

0.771; P < 0.001) to pairwise FST observed using microsatellite markers). Population clustering and 

ordination techniques using the new genomic data both support an overall population structure that is 

similar to the current DPS management units developed primarily based on using microsatellite genetic 

data. The nuclear SNP markers showed utility for identifying the origin of unknown Atlantic sturgeon 

samples, as 86.5% were assigned to the correct DPS, and 66.3% were assigned to the correct natal river. 

The SNPs were less effective at assigning Atlantic sturgeon than the existing microsatellite markers, 

which correctly assign 95.8% of individuals to DPS and 84.9% of individuals to their natal population 

using 12 microsatellite loci. However, a much larger number of SNP loci (which if identified could be 

sequenced using other available methods) could produce assignment efficiencies that are greater than 

what is currently feasible using microsatellites.

BACKGROUND: Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) are a large, ancient fish native to 

the Atlantic Coast of North America. Due to overexploitation and other anthropogenic impacts, Atlantic 

sturgeon are protected under the Endangered Species Act. The species is listed and managed as five DPSs 

based on distinct genetic and physical characteristics. This presents a significant challenge for Atlantic 

sturgeon, as sub-adult and adult Atlantic sturgeon frequently form mixed-stock aggregations in marine 

and estuarine waters. Consequently, non-breeding sub-adult and adult individuals can only be assigned to 

their DPS using molecular genetic techniques. To date, most molecular work on Atlantic sturgeon has 

employed a modest number of microsatellite markers to assess population structure and run individualbased assignment tests. Although these approaches are reasonably effective, rapid advances in genomics 

offer new opportunities to enhance our understanding of stock structure and improve assignment 

efficiency in support of Federal management activities.

OBJECTIVES: The objectives of this study were to (1) develop a set of phylogeographically 

informative SNP markers for Atlantic sturgeon and (2) apply the markers to better understand the 

relationship between spawning habitat and offshore use for Atlantic sturgeon.

METHODS: We used next-generation sequencing to develop a draft genome for Atlantic sturgeon and 

identify SNPs that could be used to resolve the origin of Atlantic sturgeon. We identified candidate SNPs 

within the nuclear genome as well as within the mitochondrial genome. After filtering and review, we 

selected a set of nuclear and mitochondrial SNPs for further testing and evaluation. We used GT-seq to 

simultaneously sequence nuclear and mitochondrial SNP loci. This effort required a pilot sequencing run 

on a single sturgeon sample to test marker amplification and refine primer strengths, followed by a series 

of sequencing runs to generate baseline data for individuals representing nine populations of Atlantic 

sturgeon in four DPSs. Using baseline data from the nine populations, we ran a series of genomic 

analyses to characterize diversity within and among populations, providing a benchmark for this species 

using the new SNP markers. We then tested the utility of our new genomic baseline for resolving the 

population and DPS of Atlantic sturgeon and compared our results with the existing microsatellite 

approach. Based on the comparison, we used microsatellite genotyping and assignment testing to provide 

information on stock composition of Atlantic sturgeon captured in another BOEM-funded project titled 

“Monitoring Endangered Atlantic Sturgeon and Commercial Finfish Habitat Use Offshore New York.”

RESULTS: We identified 1,210 candidate SNPs within the nuclear genome, as well as 49 SNPs within 

the mitochondrial genome, and developed a GT-seq assay to efficiently genotype a subset of those loci 

(161 nuclear SNPs and 39 mitochondrial SNPs). We generated baseline genomic data for nine population 

representing four different DPSs. Allelic richness was similar for all populations, although there was a 

general trend of more northern population containing greater levels of allelic richness. Pairwise 

differentiation among populations varied among the populations (FST range: 0.010–0.098) and was 

significantly correlated (r = 0.771; P < 0.001) to pairwise FST observed using microsatellite markers). 

Population clustering and ordination techniques using the new genomic data both support an overall 

population structure that is similar to the current DPS management units developed primarily based on 
using microsatellite genetic data. The nuclear SNP markers showed utility for identifying the origin of 

unknown Atlantic sturgeon samples, as 86.5% were assigned to the correct DPS, and 66.3% were 

assigned to the correct natal river. The SNPs were less effective at assigning Atlantic sturgeon than the 

existing microsatellite markers, which correctly assign 95.8% of individuals to DPS and 84.9% of 

individuals to their natal population using 12 microsatellite loci.

CONCLUSIONS: GT-seq represents a tractable approach to efficiently and repeatably genotype > 100 

SNP loci in Atlantic sturgeon. Population genomic patterns based on nuclear and mitochondrial SNPs 

were broadly similar to those previously reported based on a panel of 12 microsatellite loci and thus 

support an overall population structure similar to the current DPS management units. The SNP markers 

developed in this study are phylogeographically informative and showed utility for running assignment 

tests to related sturgeon captured offshore to their natal habitats and Federal management units (DPSs). 

However, the panel of SNP markers we evaluated was less effective for genetic assignment testing than 

the existing panel of 12 microsatellite markers. Using the microsatellite markers, we determined that most 

of Atlantic sturgeon captured in a BOEM-funded project off the Rockaway Peninsula in New York were 

part of the New York Bight DPS and primarily were spawned in the Hudson River. However, small 

numbers of Atlantic sturgeon were present from other DPSs and natal rivers ranging from the Ogeechee 

River in Georgia to the St. John River in Canada. Genetic assignment testing is an effective tool for 

connecting Atlantic sturgeon encountered on the continental shelf to their natal rivers and Federal 

management units (DPSs).

STUDY PRODUCTS: 

1. BOEM Study Report: Kazyak DC, Aunins A, Johnson R, Lubinski B, Eackles M, King TL. 

2019. Using Advanced Population Genomics to Better Understand the Relationship Between 

Offshore and Spawning Habitat Use for Atlantic Sturgeon. Sterling (VA): US Department of the 

Interior, Bureau of Ocean Energy Management. OCS Study BOEM 2020-062, 70p.

2. Genomic sequence data for Atlantic sturgeon. Archived at GenBank under accession 

JABEPO000000000.