Skip to main content

Advertisement

SpringerLink
Log in

Genetic characterization of Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus, in the Edisto River, South Carolina and identification of genetically discrete fall and spring spawning

  • Research Article
  • Published:
Conservation Genetics Aims and scope Submit manuscript

Abstract

Once widely abundant, most subpopulations of the endangered Atlantic sturgeon are now estimated to be only 1–10% of their historical levels. The Edisto River has been sampled for a long period and extensively for juvenile Atlantic sturgeon from separate spring- and fall-spawned cohorts. Our objectives are to characterize the genetic diversity, stability, adaptive potential, and potential genetic structure of Atlantic sturgeon in the Edisto River and to identify any past bottlenecks experienced by this species, as well as to conduct forward simulation modeling of the population under multiple population trajectories. Our results indicate that fall- and spring-spawned Atlantic sturgeon in the Edisto River are genetically distinct (overall \({{F}_{ST}}\) = 0.092) with little gene flow or admixture between groups, both of which are diverse from a neutral genetic marker standpoint. Genetic diversity of both groups is on the higher end of published population diversity values. A lack of inbreeding and recent bottlenecks also bode well for these two groups of sturgeon, although future projections indicate a loss of allelic richness and genetic diversity even with population stability. Our effective population size estimates are moderate compared to published estimates for other Atlantic sturgeon populations. The most significant finding of our research is the genetic distinctness of the fall- and spring-spawned Atlantic sturgeon in the Edisto River, which may have several important ramifications for management of the species, including re-evaluating the demarcation of distinct population segments.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Anders PJ, Drauch-Schreier A, Rodzen J, Powell MS, Narum S, Crossman JA (2011) A review of genetic evaluation tools for conservation and management of North American sturgeons: roles, benefits, and limitations. J Appl Ichthyol 27:3–11

    Article  Google Scholar 

  • Anderson EC, Dunham KK (2008) The influence of family groups on inferences made with the program Structure. Mol Ecol Resour 8:1219–1229

    Article  CAS  PubMed  Google Scholar 

  • ASSRT (2007) Status review of Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus). Report to National Marine Fisheries Service, Northeast Regional Office Februrary, 23, 174.

  • Bain MB (1997) Atlantic and shortnose sturgeons of the Hudson River: common and divergent life history attributes. Sturgeon biodiversity and conservation. Springer, The Netherlands. pp. 347–358

    Google Scholar 

  • Balazik MT, Musick JA (2015) Dual annual spawning races in Atlantic sturgeon. PloS ONE 10:e0128234. doi:10.0128210.0121371/journal.pone.0128234

    Article  PubMed  PubMed Central  Google Scholar 

  • Balazik MT, Garman GC, Van Eenennaam JP, Mohler J, Woods LC (2012) Empirical evidence of fall spawning by Atlantic sturgeon in the James River, Virginia. Trans Am Fish Soc 141:1465–1471

    Article  Google Scholar 

  • Banks MA, Rashbrook VK, Calavetta MJ, Dean CA, Hedgecock D (2000) Analysis of microsatellite DNA resolves genetic structure and diversity of chinook salmoon (Oncorhynchus tshawytscha) in California’s central valley. Can J Fish Aquat Sci 57:915–927

    CAS  Google Scholar 

  • Beasley BR, Marshall WD, Miglarese AH, Scurry JD, Vanden Houten C (1996) Managing resources for a sustainable future: the Edisto River Basin Project report. South Carolina Department of Natural Resources, Columbia, SC

    Google Scholar 

  • Blake A, Kineke G, Milligan T, Alexander C (2001) Sediment trapping and transport in the ACE Basin, South Carolina. Estuaries 24:721–733

    Article  Google Scholar 

  • Charlesworth B (2009) Effective population size and patterns of molecular evolution and variation. Nat Rev Genet 10:195–205

    Article  CAS  PubMed  Google Scholar 

  • Collins MR, Smith TI, Post WC, Pashuk O (2000) Habitat utilization and biological characteristics of adult Atlantic sturgeon in two South Carolina rivers. Trans Am Fish Soc 129:982–988

    Article  Google Scholar 

  • Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014

    CAS  PubMed  PubMed Central  Google Scholar 

  • Darden T, Tarpey C (2014) Genetic characterization of the Savannah and Pee Dee River populations of robust redhorse (Moxostoma robustum) with conservation implications. Copeia 2014:70–78

    Article  Google Scholar 

  • Dunton KJ, Chapman D, Jordaan A, Feldheim K, O’Leary SJ, McKown KA, Frisk MG (2012) Genetic mixed-stock analysis of Atlantic sturgeon Acipenser oxyrinchus oxyrinchus in a heavily exploited marine habitat indicates the need for routine genetic monitoring. J Fish Biol 80:207–217

    Article  CAS  PubMed  Google Scholar 

  • Earl DA, vonHoldt BM (2012) Structure harvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Res 4:359–361

    Article  Google Scholar 

  • Erickson DL, Kahnle A, Millard MJ, Mora EA, Bryja M, Higgs A, Mohler J, DuFour M, Kenney G, Sweka J, Pikitch EK (2011) Use of pop-up satellite archival tags to identify oceanic-migratory patterns for adult Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus Mitchell, 1815. J Appl Ichthyol 27:356–365

    Article  Google Scholar 

  • Estoup A, Angers B (1998) Theoretical and empirical considerations. Adv. Mol Ecol 306:55

    CAS  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47

    CAS  Google Scholar 

  • Frankham R (2005) Genetics and extinction. Biol Conserv 126:131–140

    Article  Google Scholar 

  • Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10:305–318

    Article  CAS  PubMed  Google Scholar 

  • Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86:485–486

    Article  Google Scholar 

  • Grunwald C, Maceda L, Waldman J, Stabile J, Wirgin I (2008) Conservation of Atlantic sturgeon Acipenser oxyrinchus oxyrinchus: delineation of stock structure and distinct population segments. Conserv Genet 9:1111–1124

    Article  Google Scholar 

  • Henderson A, Spidle A, King T (2005) Genetic diversity, kinship analysis, and broodstock management of captive Atlantic sturgeon for population restoration. American Fisheries Society Symposium 2005:621–633

    Google Scholar 

  • Henderson-Arzapalo A, King T (2002) Novel microsatellite markers for Atlantic sturgeon (Acipenser oxyrinchus) population delineation and broodstock management. Mol Ecol Notes 2:437–439

    Article  CAS  Google Scholar 

  • Holm S (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 65–70

  • Jones OR, Wang J (2010) Colony: a program for parentage and sibship inference from multilocus genotype data. Mol Ecol Resour 10:551–555

    Article  PubMed  Google Scholar 

  • Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program cervus accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106

    Article  PubMed  Google Scholar 

  • King T, Lubinski B, Spidle A (2001) Microsatellite DNA variation in Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) and cross-species amplification in the Acipenseridae. Conserv Genet 2:103–119

    Article  CAS  Google Scholar 

  • Kuo CH, Janzen FJ (2003) Bottlesim: a bottleneck simulation program for long-lived species with overlapping generations. Mol Ecol Notes 3:669–673

    Article  CAS  Google Scholar 

  • May B, Krueger CC, Kincaid HL (1997) Genetic variation at microsatellite loci in sturgeon: primer sequence homology in Acipenser and Scaphirhynchus. Can J Fish Aquat Sci 54:1542–1547

    Article  CAS  Google Scholar 

  • McCord JW, Collins MR, Post WC, Smith TI (2007) Attempts to develop an index of abundance for age-1 Atlantic sturgeon in South Carolina, USA. In: American Fisheries Society Symposium, p. 397. American Fisheries Society.

  • Meirmans PG (2006) Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution Int J org Evolution 60:2399–2402

    Article  Google Scholar 

  • Meirmans PG, Hedrick PW (2011) Assessing population structure: \({{F}_{ST}}\) and related measures. Mol Ecol Resour 11:5–18

    Article  PubMed  Google Scholar 

  • Moyer GR, Sweka JA, Peterson DL (2012) Past and present processes influencing genetic diversity and effective population size in a natural population of Atlantic sturgeon. Trans Am Fish Soc 141:56–67

    Article  Google Scholar 

  • Murawski SA, Pacheco AL (1977) Biological and fisheries data on Atlantic sturgeon, Acipenser oxyrhynchus (Mitchill). Sandy Hook Laboratory, Northeast Fisheries Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, US Department of Commerce.

  • Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

  • Newman D, Pilson D (1997) Increased probability of extinction due to decreased genetic effective population size: experimental populations of Clarkia pulchella. Evolution, 354–362

  • Nielsen EE, Hansen MM (2008) Waking the dead: the value of population genetic analyses of historical samples. Fish Fish 9:450–461

    Article  Google Scholar 

  • NMFS (2012a) Endangered and threatened wildlife and plants; threatened and endangered status for distinct population segments of Atlantic sturgeon in the Northheast Region. Fed Reg 77:5880–5912

    Google Scholar 

  • NMFS (2012b) Endangered and threatened wildlife and plants; final listing determinations for two distinct population segments of Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) in the Southeast. Fed Reg 77:5914–5982

    Google Scholar 

  • O’Leary SJ, Dunton KJ, King TL, Frisk MG, Chapman DD (2014) Genetic diversity and effective size of Atlantic sturgeon, Acipenser oxyrhinchus oxyrhinchus river spawning populations estimated from the microsatellite genotypes of marine-captured juveniles. Conserv Genet 15:1173–1181

    Article  Google Scholar 

  • Ohta T, Kimura M (1973) A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet Res 22:201–204

    Article  CAS  PubMed  Google Scholar 

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peterson DL, Bain MB, Haley N (2000) Evidence of declining recruitment of Atlantic sturgeon in the Hudson River. N Am J Fish Manage 20:231–238

    Article  Google Scholar 

  • Piry S, Luikart G, Cornuet J-M (1999) BOTTLENECK: a program for detecting recent effective population size reductions from allele data frequencies. J Hered 90:502–503

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249

    Article  Google Scholar 

  • Rice WR (1989) Analyzing tables of statistical tests. Evolution, 223–225

  • Rodríguez-Ramilo ST, Wang J (2012) The effect of close relatives on unsupervised Bayesian clustering algorithms in population genetic structure analysis. Mol Ecol Resour 12:873–884

    Article  PubMed  Google Scholar 

  • Saccheri I, Kuussaari M, Kankare M, Vikman P, Fortelius W, Hanski I (1998) Inbreeding and extinction in a butterfly metapopulation. Nature 392:491–494

    Article  CAS  Google Scholar 

  • Schueller P, Peterson DL (2010) Abundance and recruitment of juvenile Atlantic sturgeon in the Altamaha River, Georgia. Trans Am Fish Soc 139:1526–1535

    Article  Google Scholar 

  • Smith TI (1985) The fishery, biology, and management of Atlantic sturgeon, Acipenser oxyrhynchus, in North America. Environ Biol Fish 14:61–72

    Article  CAS  Google Scholar 

  • Smith TI, DE Marchette, GF Ulrich (1984) The Atlantic sturgeon fishery in South Carolina. N Am J Fish Manage 4:164–176

    Article  Google Scholar 

  • Smith JA, Flowers HJ, Hightower JE (2015) Fall spawning of Atlantic sturgeon in the Roanoke River, North Carolina. Trans Am Fish Soc 144:48–54

    Article  Google Scholar 

  • Tranah G, Campton DE, May B (2004) Genetic evidence for hybridization of pallid and shovelnose sturgeon. J Hered 95:474–480

    Article  CAS  PubMed  Google Scholar 

  • Van Oosterhout C, Hutchinson WF, Wills DP, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538

    Article  Google Scholar 

  • Waldman JR, Hart JT, Wirgin II (1996) Stock composition of the New York Bight Atlantic sturgeon fishery based on analysis of mitochondrial DNA. Trans Am Fish Soc 125:364–371

    Article  CAS  Google Scholar 

  • Waldman J, Grunwald C, Stabile J, Wirgin I (2002) Impacts of life history and biogeography on the genetic stock structure of Atlantic sturgeon Acipenser oxyrinchus oxyrinchus, Gulf sturgeon A. oxyrinchus desotoi, and shortnose sturgeon A. brevirostrum. J Appl Ichthyol 18:509–518

    Article  Google Scholar 

  • Waples RS (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conserv Genet 7:167–184

    Article  Google Scholar 

  • Waples RS, Antao T, Luikart G (2014) Effects of overlapping generations on linkage disequilibrium estimates of effective population size. Genetics 197:769–780

    Article  PubMed  PubMed Central  Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 1358–1370

  • Wirgin I, Waldman JR, Rosko J, Gross R, Collins MR, Rogers SG, Stabile J (2000) Genetic structure of Atlantic sturgeon populations based on mitochondrial DNA control region sequences. Trans Am Fish Soc 129:476–486

    Article  CAS  Google Scholar 

  • Wirgin I, Waldman J, Stabile J, Lubinski B, King T (2002) Comparison of mitochondrial DNA control region sequence and microsatellite DNA analyses in estimating population structure and gene flow rates in Atlantic sturgeon Acipenser oxyrinchus. J Appl Ichthyol 18:313–319

    Article  CAS  Google Scholar 

  • Wirgin I, Maceda L, Waldman JR, Wehrell S, Dadswell M, King T (2012) Stock origin of migratory Atlantic sturgeon in Minas Basin, Inner Bay of Fundy, Canada, determined by microsatellite and mitochondrial DNA analyses. Trans Am Fish Soc 141:1389–1398

    Article  Google Scholar 

Download references

Acknowledgements

We would like to thank the assistance of J. Carter and National Oceanic and Atmospheric Administration (NOAA) Northwest Fisheries Science Center (NWFSC) Forensics Laboratory (formerly in Charleston, SC) for the archiving and access to Atlantic sturgeon genetic samples. We would also like to thank the Diadromous Fishes Research team at SCDNR for the collection of the samples, the Hollings Marine Laboratory for laboratory space, and the Fish Population Genetics research group at SCDNR for lab assistance, especially T. O’Donnell for laboratory optimization. This project was funded by a Sect. 6 Species Recovery Grants to States from the National Marine Fisheries Service (Grant No. NA13NMF4720044). This manuscript represents publication number 755 from the SCDNR Marine Resources Research Institute.

Author information

Authors and Affiliations

  1. Hollings Marine Laboratory, South Carolina Department of Natural Resources, Marine Resources Research Institute, 331 Fort Johnson Road, Charleston, SC, 29412, USA

    Daniel J. Farrae, William C. Post & Tanya L. Darden

Authors
  1. Daniel J. Farrae
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. William C. Post
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tanya L. Darden
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Daniel J. Farrae.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 18 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Farrae, D.J., Post, W.C. & Darden, T.L. Genetic characterization of Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus, in the Edisto River, South Carolina and identification of genetically discrete fall and spring spawning. Conserv Genet 18, 813–823 (2017). https://doi.org/10.1007/s10592-017-0929-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10592-017-0929-7

Keywords

Search

Navigation