Skip to main content
SpringerLink
Log in

Population structure and genetic management of Rio Grande cutthroat trout (Oncorhynchus clarkii virginalis)

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

Abstract

The Rio Grande cutthroat trout, Oncorhynchus clarkii virginalis, has declined precipitously over the past century, and currently exhibits a highly fragmented distribution within the Canadian, Pecos and Rio Grande river systems of the western United States. The relationships between populations in the three river drainages, and between O. c. virginalis and the closely related taxa O. c. pleuriticus and O. c. stomias, are not well understood. In order to guide management decisions for the subspecies, we investigated the distribution of variation at 12 microsatellite loci and two regions of the mitochondrial genome. We observed a high level of genetic differentiation between O. c. virginalis populations occupying different headwater streams (global Fst = 0.41). However, we found evidence for previous gene flow within the Rio Grande drainage, indicating that inter-population differentiation may have been exacerbated by the recent effects of population fragmentation. Despite large-scale anthropogenic movement of individuals from the Rio Grande into the Canadian and Pecos, the genetic signature of long-term evolutionary independence between the three drainages has been retained.

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
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Allendorf FW, Leary RF (1988) Conservation and distribution of genetic variation in a polytypic species, the cutthroat trout. Conserv Biol 2:170–184. doi:10.1111/j.1523-1739.1988.tb00168.x

    Article  Google Scholar 

  • Bachhuber FW (1989) The occurrence and paleolimnologic significance of cutthroat trout (Oncorhynchus clarki) in pluvial lakes of the Estancia Valley, central New Mexico. Geol Soc Am Bull 101:1543–1551. doi:10.1130/0016-7606(1989)101<1543:TOAPSO>2.3.CO;2

    Article  Google Scholar 

  • Behnke RJ (2002) Trout and salmon of North America. Free Press, New York

    Google Scholar 

  • Belkhir K, Borsa P, Chiki L, Raufaste N, Bonhomme F (2001) GENETIX 4.02, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions CNRS UMR 5000, Université de Montpellier II, Montpellier (France)

  • Carlsson J, Nilsson J (2001) Effects of geomorphological structures on genetic differentiation among brown trout populations in a northern boreal river drainage. Trans Am Fish Soc 130:36–45. doi:10.1577/1548-8659(2001)130<0036:EOGSOG>2.0.CO;2

    Article  Google Scholar 

  • Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Evol Int J Org Evol 32:550–570. doi:10.2307/2406616

    Google Scholar 

  • Chapman RW, Sedberry GR, Koenig CC, Eleby BM (1999) Stock identification of gag, Mycteroperca microlepis, along the southeast coast of the United States. Mar Biotechnol 1:137–146. doi:10.1007/PL00011761

    Article  CAS  PubMed  Google Scholar 

  • Ciofi C, Bruford MW (1999) Genetic structure and gene flow among Komodo dragon populations inferred by microsatellite loci analysis. Mol Ecol 8(Suppl 1):S17–S30. doi:10.1046/j.1365-294X.1999.00734.x

    Article  CAS  PubMed  Google Scholar 

  • Conner JV, Suttkus RD (1986) Zoogeography of freshwater fishes of the western Gulf Slope of North America. In: Hocutt CH, Wiley EO (eds) The zoogeography of North American freshwater fishes. John Wiley and Sons, New York, pp 413–456

    Google Scholar 

  • Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M (1999) New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153:1989–2000

    CAS  PubMed  Google Scholar 

  • Crispo E, Bentzen P, Reznick DN, Kinnison MT, Hendry AP (2006) The relative influence of natural selection and geography on gene flow in guppies. Mol Ecol 15:49–62. doi:10.1111/j.1365-294X.2005.02764.x

    Article  CAS  PubMed  Google Scholar 

  • Estoup A, Rousset F, Michalakis Y, Cornuet J-M, Adriamange M, Guyomard R (1998) Comparative analysis of microsatellite and allozyme markers: a case study investigating microgeographic differentiation in brown trout (Salmo trutta). Mol Ecol 7:339–353. doi:10.1046/j.1365-294X.1998.00362.x

    Article  CAS  PubMed  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. doi:10.1111/j.1365-294X.2005.02553.x

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences. University of Washington, Seattle, Washington

    Google Scholar 

  • Fumagalli L, Snoj A, Jesenšek D et al (2002) Extreme genetic differentiation among the remnant populations of marble trout (Salmo marmoratus) in Slovenia. Mol Ecol 11:2711–2716. doi:10.1046/j.1365-294X.2002.01648.x

    Article  CAS  PubMed  Google Scholar 

  • Goudet J (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from: http://www.unil.ch/izea/softwares/fstat.html

  • Gum B, Gross R, Rottmann O, Schröder W, Kühn R (2003) Microsatellite variation in Bavarian populations of European grayling (Thymallus thymallus): Implications for conservation. Conserv Genet 4:659–672. doi:10.1023/B:COGE.0000006106.64243.e6

    Article  CAS  Google Scholar 

  • Hedrick PW (1999) Highly variable loci and their interpretation in evolution and conservation. Evol Int J Org Evol 53:313–318. doi:10.2307/2640768

    Google Scholar 

  • Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231. doi:10.1007/BF01245622

    Article  Google Scholar 

  • Huelsenbeck JP, Ronquist F (2001) MRBAYES: BAYESIAN inference of phylogenetic trees. Bioinformatics 17:754–755. doi:10.1093/bioinformatics/17.8.754

    Article  CAS  PubMed  Google Scholar 

  • Keeler-Foster CL (2003) Rio Grande cutthroat trout (Oncorhynchus clarki virginalis): Population genetics and hybridization with introduced rainbow trout (Oncorhynchus mykiss). Ph.D. thesis, New Mexico State University

  • Kinnison MT, Bentzen P, Unwin MJ, Quinn TP (2002) Reconstructing recent divergence: evaluating nonequilibrium population structure in New Zealand chinook salmon. Mol Ecol 11:739–754. doi:10.1046/j.1365-294X.2002.01477.x

    Article  CAS  PubMed  Google Scholar 

  • Leary RF, Allendorf FW, Phelps SR, Knudsen KL (1987) Genetic divergence among seven subspecies of cutthroat trout and rainbow trout. Trans Am Fish Soc 116:580–587. doi:10.1577/1548-8659(1987)116<580:GDAIOS>2.0.CO;2

    Article  Google Scholar 

  • Loudenslager EJ, Gall GAE (1980) Geographic patterns of protein variation and subspeciation in the cutthroat trout. Syst Zool 29:27–42. doi:10.2307/2412624

    Article  CAS  Google Scholar 

  • Mäkinen HS, Cano JM, Merilä J (2006) Genetic relationships among marine and freshwater populations of the European three-spined stickleback (Gasterosteus aculeatus) revealed by microsatellites. Mol Ecol 15:1519–1534. doi:10.1111/j.1365-294X.2006.02871.x

    Article  PubMed  Google Scholar 

  • Metcalf JL, Pritchard VL, Silvestri SM et al (2007) Across the great divide: genetic forensics reveals misidentification of endangered cutthroat trout populations. Mol Ecol 16:4445–4454. doi:10.1111/j.1365-294X.2007.03472.x

    Article  CAS  PubMed  Google Scholar 

  • Moritz C (1994) Applications of mitochondrial DNA analysis in conservation: a critical review. Mol Ecol 3:401–411. doi:10.1111/j.1365-294X.1994.tb00080.x

    Article  CAS  Google Scholar 

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

    Google Scholar 

  • Nielsen JL, Sage GK (2002) Population genetic structure in Lahontan cutthroat trout. Trans Am Fish Soc 131:376–388. doi :10.1577/1548-8659(2002)131<0376:PGSILC>2.0.CO;2

    Article  Google Scholar 

  • Novinger DC, Rahel FJ (2003) Isolation management with artificial barriers as a conservation strategy for cutthroat tout in headwater streams. Conserv Biol 17:772–781. doi:10.1046/j.1523-1739.2003.00472.x

    Article  Google Scholar 

  • Nylander JAA (2004) MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Uppsala

    Google Scholar 

  • Peacock MM, Kirchoff VS (2004) Assessing the conservation value of hybridized cutthroat trout populations. Trans Am Fish Soc 133:309–325. doi:10.1577/03-017

    Article  Google Scholar 

  • Peterson DP, Fausch KD, White DC (2004) Population ecology of an invasion, Effects of brook trout on native cutthroat trout. Ecol Appl 14:754–772. doi:10.1890/02-5395

    Article  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Pritchard VL, Jones K, Cowley DE (2007a) Estimation of introgression in cutthroat trout populations using microsatellites. Conserv Genet 8:1311–1329. doi:10.1007/s10592-006-9280-0

    Article  CAS  Google Scholar 

  • Pritchard VL, Jones K, Cowley DE (2007b) Genetic diversity within fragmented cutthroat trout populations. Trans Am Fish Soc 136:606–623. doi:10.1577/T06-038.1

    Article  Google Scholar 

  • Pritchard VL, Jones K, Metcalf JL , Martin AP, Wilkinson P, Cowley DE (2007c) Characterization of tetranucleotide microsatellites for Rio Grande cutthroat trout and rainbow trout, and their cross-amplification in other cutthroat trout subspecies. Mol Ecol Notes 7:594–596. doi:10.1111/j.1471-8286.2007.01695.x

    Article  CAS  Google Scholar 

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

    Google Scholar 

  • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574. doi:10.1093/bioinformatics/btg180

    Article  CAS  PubMed  Google Scholar 

  • Schmetterling DA, Adams SB (2004) Summer movements within the fish community of a small montane stream. N Am J Fish Manage 24:1163–1172. doi:10.1577/M03-025.1

    Article  Google Scholar 

  • Schneider S, Roessli D, Excoffier L (2000) Arlequin ver 2.000: a software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland

    Google Scholar 

  • Shemai B, Sallenave R, Cowley DE (2007) Competition between hatchery-raised Rio Grande cutthroat trout and wild brown trout. N Am J Fish Manage 27:315–325. doi:10.1577/M06-046.1

    Article  Google Scholar 

  • Swofford DL (2000) PAUP* phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts

    Google Scholar 

  • Taylor EB, Stamford MD, Baxter JS (2003) Population subdivision in westslope cutthroat trout (Oncorhynchus clarki lewisi) at the northern periphery of its range: evolutionary inferences and conservation implications. Mol Ecol 12:2609–2622. doi:10.1046/j.1365-294X.2003.01937.x

    Article  CAS  PubMed  Google Scholar 

  • Tessier N, Bernatchez L (1999) Stability of population structure and genetic diversity across generations assessed by microsatellites among sympatric populations of landlocked Atlantic salmon (Salmo salar L.). Mol Ecol 8:169–179. doi:10.1046/j.1365-294X.1999.00547.x

    Article  Google Scholar 

  • Thomas RG (1972) The geomorphic evolution of the Pecos River system. Bull Bayl Geol Stud 22:1–40

    Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F statistics for the analysis of population structure. Evol Int J Org Evol 38:1358–1370. doi:10.2307/2408641

    Google Scholar 

  • Young MK (1996) Summer movements and habitat use by Colorado River cutthroat trout in small, montane streams. Can J Fish Aquat Sci 53:1403–1408. doi:10.1139/cjfas-53-6-1403

    Article  Google Scholar 

  • Young SF, McLellan JG, Shaklee JB (2004) Genetic integrity and microgeographic population structure of westslope cutthroat trout, Oncorhynchus clarki lewisi, in the Pend Oreille Basin in Washington. Environ Biol Fishes 69:127–142. doi:10.1023/B:EBFI.0000022886.47243.bf

    Article  Google Scholar 

Download references

Acknowledgements

This research was funded by NMDGF through the Federal Aid in Sport Fish Restoration Act, the New Mexico Agricultural Experiment Station, Colorado Division of Wildlife (CDOW), Rocky Mountain National Park and USFWS. Tissue samples were provided by CDOW, NMDGF, USDA Forest Service, Chris Kennedy (USFWS), Jim Melby (CDOW), Dennis Shiozawa and Paul Evans (Monte L. Bean Life Science Museum, Brigham Young University). We thank staff at GIS for technical support.

Author information

Authors and Affiliations

  1. Department of Fishery & Wildlife Sciences, New Mexico State University, Las Cruces, NM, 88003, USA

    V. L. Pritchard & D. E. Cowley

  2. Genetic Identification Services, Chatsworth, CA, 91311, USA

    K. Jones

  3. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA

    J. L. Metcalf & A. P. Martin

  4. University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA

    V. L. Pritchard

Authors
  1. V. L. Pritchard
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J. L. Metcalf
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. K. Jones
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. A. P. Martin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. D. E. Cowley
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to V. L. Pritchard.

Electronic supplementary material

Below is the link to the electronic supplementary material.

(PDF 77 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Pritchard, V.L., Metcalf, J.L., Jones, K. et al. Population structure and genetic management of Rio Grande cutthroat trout (Oncorhynchus clarkii virginalis). Conserv Genet 10, 1209 (2009). https://doi.org/10.1007/s10592-008-9652-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10592-008-9652-8

Keywords

Search

Navigation