Introduction

The Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus, Acipenseridae) is an anadromous fish that currently inhabits the east coast of North America from Labrador, CA to Florida, USA [1, 2, 3, 4, 5]. Atlantic sturgeon (AS) were very abundant during European establishment of North America but were heavily exploited during the late 1800s, particularly for flesh and roe [1, 5, 6, 7, 8, 9, 10]. By the end of the 19^th century most of the “inexhaustible” AS populations were decimated and most fisheries collapsed [1, 5, 6, 10]; however, these populations still experienced commercial fishing pressure until the later part of the 20^th century when a moratorium was imposed by the Atlantic States Marine Fisheries Commission [11]. Unfortunately, as a result of AS’s long generation time in combination with continued habitat impairment such as dams and sedimentation, AS populations have been very slow to recover [4, 12, 13] which resulted in all US distinct population segments being listed as either threatened or endangered by the National Oceanic and Atmospheric Administration in 2012 [14, 15].

Previously, it was commonly accepted that AS only spawned during the spring along with most of the other anadromous fish on the east coast of the US [1, 4]. However, relatively recently researchers have shown via several lines of telemetry evidence that some rivers likely have dual-spawning groups of AS, one group spawning in the spring and another group spawning in the fall [10, 16, 17, 18]. Additionally, river-resident juvenile AS (<530 mm TL) from the Edisto River, SC were assigned to either fall or spring spawning events based on total length at day of year over a 15 year period and subsequently determined to be genetically distinct with little admixture between the spawning groups [19]. Currently dual-spawning in the James River, VA has been documented based on collections of pre- and post-spawn AS accompanied by telemetry data [10, 18]. Due to the lack of juvenile AS captures in the James River, genetics from the two spawning populations cannot be compared in the same river-resident juvenile design similar to the Edisto River study; however, adult samples are available with substantial collection information to attempt to genetically address these putative spawning groups. As such, the main objective of our study was to determine if genetic differences were present between spring and fall run AS by sampling the adult populations during the spawning seasons. Secondary objectives included determining the genetic health of the population(s) and evaluating if the use of appropriate sample selection criteria with adult AS can be used to identify dual-spawning group genetic signatures.

Study area

The James River, river mouth located at N 36.98889, W 76.30365, is the southern-most major tributary of the Chesapeake Bay, is 696 km long and drains 26,164 km². The tidal portion of the river extends up to Richmond, VA located at rkm 155. The river width varies between 0.7 and 7.1km up to rkm 120 and then narrows substantially (0.1–0.4 km). The federal navigation channel maintained by the US Army Corps of Engineers runs from the river mouth at Hampton Roads, VA to rkm 150 and is maintained to a minimum depth of 7.6 m and a minimum width of 91.4 m. AS in the James River were exploited by Europeans since the founding of Jamestown Colony in 1607 [20] and harvest continued in some capacity until 1974 when the Virginia Marine Resources Commission implemented a state-wide ban on all AS harvest [21].

Materials and methods

Results and discussion

Locus LS39 was dropped from all analyses due to substantial problems with its amplification throughout the sample set. In fall-spawning AS dataset, three loci were observed to be out of Hardy-Weinberg equilibrium (HWE): LS-68, AoxD241, and Aox12; in spring-spawning AS dataset, one locus was observed to be out of HWE: AoxD170. Given the lack of consistency in deviations from HWE and the prior use of this marker set in multiple AS studies, these loci were retained. All genotypes were checked for individual recaptures; two were identified and removed from further analysis. Three other samples could not be genotyped successfully and were excluded.

Each COLONY run produced minor variations in relatedness with 21, 22, and 18 full-sibling pairs identified in each of the three runs of the combined dataset. Individual full-sibling pairs were generally consistent between runs with the combined dataset and runs with fall and spring datasets separately. Based on the long run length and high precision (theoretically the most accurate analysis run), 17 full-sibling pairs were found in the fall-spawning dataset and 1 full-sibling pair was found in the spring-spawning dataset. Given the low number of siblings to the total sample size, these fish were not removed prior to the Structure analyses.

The results from Structure and Structure Harvester (ΔK = 31.6) indicated that there were two population clusters in the James River, with distinct signatures assigned to AS from fall and spring spawning events (Fig 1). When fall and spring spawning sturgeon were evaluated independently, both resulted in K = 1, indicating that there was no further population or family structure present. Similar results were obtained with and without location used as a prior.

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Fig 1. Results from Structure displaying the ancestry of fall spawning and spring spawning Atlantic sturgeon in the James River to K = 2 genetic clusters.

Each individual bar represents the ancestry of a single fish, with the colors corresponding to the proportion of population ancestry.

https://doi.org/10.1371/journal.pone.0179661.g001

Pairwise F_ST between fall-spawning and spring-spawning AS was 0.048 (significant); pairwise F’_ST = 0.181. Heterozygosity was moderate overall for both fall (H_O = 0.749, H_E = 0.740) and spring (H_O = 0.708, H_E = 0.717) spawning groups, and no inbreeding was detected during either period (F_IS = -0.008 fall; F_IS = 0.026 spring). Effective population size was similar for both spawning AS groups in the James River (Fall: N_e = 46 (95% CI: 32–71), Spring: N_e = 44 (95% CI: 26–79)).

In the plot of results from Structure (Fig 1), there is a single individual in the fall cluster that appears to have a strong signature associated with the spring cluster. There are several potential explanations for this fish: it may have been mislabeled at initial collection, grouped incorrectly during genetic processing, it may represent an actual stray from the spring cluster, or it may be a stray from elsewhere that more closely resembles the spring cluster than the fall cluster. The fish was originally captured in August 2012 in close proximity to spawning habitat and expelled sperm during capture. The fish returned to the mouth of the James River in 2013 and 2014 during the summer but did not move upstream to the spawning grounds. To our knowledge, the fish has not been detected in another river. The F_ST and F’_ST results indicate that there is some gene flow between the fall and spring clusters, so it is possible that fish from one genetic cluster contribute to the opposite spawning season at times. This gene flow may also be responsible for the higher amount of admixture visible in fish in the spring cluster compared to the fall cluster, though this may also be attributed to a smaller sample size of the spring cluster.

Conclusions

Overall, the results from Structure and the pairwise F_ST and F’_ST values all indicate that the fall and spring spawning adult male groups in the James River are genetically distinct. The degree of genetic differences is not as pronounced as that documented in the Edisto River [19], potentially the result of lower sample sizes from the James River or restrictions within the sample set (i.e., only adult males over a shorter collection period). The genetic diversity within both James River spawning groups are comparable to those measured in the Edisto River [19] and on the high end of genetic diversity measured in other AS populations [34, 35], with no inbreeding detected. The N_e estimates for both James River AS spawning populations were comparable to the estimate for the spring Edisto River population, but were an order of magnitude less than the fall Edisto River population estimate [19].

The genetics results from this study corroborate the telemetry results showing two separate spawning groups utilizing the James River [10]. Managers [2] currently recommend only river-resident AS <50 cm fork length be used for reference genetics samples to characterize populations. However, our study suggests that when eggs, larvae, or juveniles are not available for genetic analysis, spawning adults may be used as a surrogate using appropriate selection criteria, such as adult AS that expel milt or eggs during capture or fish with accompanying telemetry data that show routine returns to a certain river spawning group. Considering genetic differentiation has now been documented between spring and fall spawning AS groups in two river systems along the US Atlantic coast, careful interpretation is clearly warranted if population assignments are made assuming a single spawning population in a river, as other nearby rivers may also have dual spawning groups that either are not accounted for or are potentially pooled in reference databases. As having a biologically correct understanding of stock structure is critical to effective management and conservation, our results suggest the current reference population database should be updated to incorporate both new samples and our increased understanding of Atlantic sturgeon life history.

Supporting information

Acknowledgments

We thank Albert Spells (U.S. Fish and Wildlife Service), William Post (S.C. Department of Natural Resources), Bob Greenlee and Aaron Bunch (Virginia Department of Game and Inland Fisheries), Jason Kahn (National Oceanic and Atmospheric Administration), Carter Watterson (Department of the Navy), Martin Balazik, Chuck Frederickson, and Thiwaporn Balazik (field assistants) for their assistance with this project. We would also like to thank the Hollings Marine Laboratory for laboratory space and the Fish Population Genetics research group at SCDNR for lab assistance. This manuscript represents Rice Rivers Center Publication number 79 and publication number 764 from the SCDNR Marine Resources Research Institute. The authors declare that they have no conflict of interest.