Skip to main content

Advertisement

SpringerLink
Log in

Population genetic diversity and structure of two rare vernal pool grasses in central California

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

Abstract

Vernal pool ecosystems are declining throughout California, with only 10% of historic habitat remaining. This has endangered many specialist endemic plant species, leaving extant populations fragmented, isolated, and threatened or endangered. Recovery plans for the increasing number of endangered vernal pool species require information on their genetic and ecological status to guide conservation and restoration efforts. Federally threatened Neostapfia colusana (Colusa grass) and federally endangered Tuctoria greenei (Greene’s tuctoria) are two endemic vernal pool grasses of high conservation concern in central California. Remaining populations are highly fragmented due to range-wide habitat destruction. Using five polymorphic microsatellite markers for each species, we performed genetic surveys of 240 individuals from eight vernal pools for N. colusana, and 317 individuals from 13 vernal pools for T. greenei. We detected high within-population genetic diversity for both species, with average allelic diversities of 24 alleles/locus (mean Hobs = 0.68, mean Hexp = 0.71) for N. colusana, and 19 alleles/locus (mean Hobs = 0.77, and mean Hexp = 0.79) for T. greenei. Bayesian clustering and AMOVA indicated two genetically distinct population groups for N. colusana (Fst = 0.268, P < 0.0001), and three for T. greenei (Fst = 0.11, P < 0.0001). We found very slight temporal genetic structure at one N. colusana (Fst = 0.013, P < 0.05) and two T. greenei (Fst = 0.015, Fst = 0.018, P < 0.05) pools. These estimates of population genetic diversity and structure are critical measures for both species that will help inform recovery management actions.

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.

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Alexander DG, Schlising RA (1998) Patterns in time and space for rare macroinvertebrates and vascular plants in vernal pool ecosystems at the Vina plains preserve, and implications for pool landscape management. In: Witham CW, Bauder ET, Belk D, Ferren WRJ, Ornduff R (eds) Ecology, conservation, and management of vernal pool ecosystems. Proceedings of the 1996 conference of the California Native Plant Society

  • Baskin Y (1994) California’s ephemeral vernal pools may be a good model for speciation. Bioscience 44:384–388

    Article  Google Scholar 

  • Beardsmore JA (1983) Extinction, survival and genetic variation. In: Schonewald-Cox CM, Chambers SM, MacBryde B, Thomas WL (eds) Genetics and conservation: a reference for managing wild animal and plant populations. Benjamin/Cummings, California, pp 125–151

    Google Scholar 

  • Black C, Zedler PH (1998) An overview of 15 years of vernal pool restoration and construction activities in San Diego County, California. In: Witham CW, Bauder ET, Belk D, Ferren WRJ, Ornduff R (eds) Ecology, conservation, and management of vernal pool ecosystems. Proceedings of the 1996 conference of the California Native Plant Society

  • Boykin LM, Kubatko LS, Lowrey TK (2010) Comparison of methods for rooting phyologenetic trees: a case study using Orcuttieae (Poaceae: Chloridoideae). Mol Phylogenet Evol 54:687–700

    Article  PubMed  Google Scholar 

  • CNDDB (2006) California Natural Diversity Database, California Department of Fish and Game. http://www.dfg.ca.gov/biogeodata/cnddb. Accessed July 2006

  • 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

    PubMed  CAS  Google Scholar 

  • Davis HG, Sloop CM, Cushman JH (2009) Developing tools to promote the recovery of five federally listed vernal pool grasses. Final Report. United States Fish and Wildlife Service, Sacramento

    Google Scholar 

  • Edmands S (2007) Between a rock and a hard place: evaluating the relative risks of inbreeding and outbreeding for conservation and management. Mol Ecol 16:463–475

    Article  PubMed  Google Scholar 

  • Elam D (1998) Population genetics of vernal pool plants: theory data and conservation implications. In: Witham CW, Bauder ET, Belk D, Ferren WRJ, Ornduff R (eds) Ecology, conservation, and management of vernal pool ecosystems. Proceedings of the 1996 conference of the California Native Plant Society

  • Ellstrand NC, Elam DR (1993) Population genetic consequences of small population size: implications for plant conservation. Annu Rev Ecol Syst 24:217–242

    Article  Google Scholar 

  • Estoup A, Garnery L, Solignac M, Cornuet JM (1995) Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models. Genetics 140:679–695

    PubMed  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  PubMed  CAS  Google Scholar 

  • Excoffier L, Laval G, Schneider S (2005) Arlequin ver 3.11: an integrated software package for population genetic data analysis. Evol Bioinform Online 1:47–50

    CAS  Google Scholar 

  • Falush D, Stephans M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587

    PubMed  CAS  Google Scholar 

  • Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7:574–578

    Article  PubMed  CAS  Google Scholar 

  • Fan Q, Chen S, Zhou R, Xiang X, Liao W, Shi S (2011) Genetic variation of wild litchi (Litchi chinensis Sonn. subsp. chinensis) revealed by microsatellites. Conserv Genet 12:753–760

    Article  Google Scholar 

  • Ferguson NJ, Ellstrand NC (1999) Assessment of seed bank buffering of genetic change in Dodeca hemaleptoceras (Slender-horned Spineflower). Final Report to M. Meyer. Department of Fish and Game, Sacramento

    Google Scholar 

  • Ferren WRJ, Hubbard DM, Wiseman S, Parikh AK, Gale N (1998) Review of 10 years of vernal pool restoration and creation in Santa Barbara, California. In: Witham CW, Bauder ET, Belk D, Ferren WRJ, Ornduff R (eds) Ecology, conservation, and management of vernal pool ecosystems. Proceedings of the 1996 conference of the California Native Plant Society

  • Foin T, Reilly S, Pawley A, Ayres D, Carlson T, Hodem P, Switzer P (1998) Improving recovery planning for the conservation of threatened and endangered taxa. Bioscience 48:177–184

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Frankham R (2010) Where are we in conservation genetics and where do we need to go? Conserv Genet 11:661–663

    Article  Google Scholar 

  • Frankham R, Ballou JD, Brosco DA (2002) Introduction to conservation genetics. Cambridge University Press, Cambridge

    Google Scholar 

  • Gilligan DM, Briscoe DA, Frankham R (2005) Comparative losses of quantitative and molecular genetic variation in finite populations of Drosophila melanogaster. Genet Res 85:47–55

    Article  PubMed  CAS  Google Scholar 

  • Gilpin ME, Soulé ME (1986) Minimum viable populations: processes of species extinction. In: Soulé ME (ed) Conservation biology: the science of scarcity and diversity. Sinauer, Sunderland, pp 19–34

    Google Scholar 

  • Gitzendanner MA, Soltis PE (2000) Patterns of genetic variation in rare and widespread plant congeners. Am J Bot 87(6):783–792

    Article  PubMed  CAS  Google Scholar 

  • Griggs FT (1981) Life histories of vernal pool annual grasses. Fremontia 9:14–17

    Google Scholar 

  • Griggs FT, Jain S (1983) Conservation of vernal pool plants in California, II. Population biology of a rare and unique grass genus Orcuttia. Biol Conserv 27:171–193

    Article  Google Scholar 

  • Hobson WA, Dahlgren RA (1998) A quantitative study of pedogenesis in California vernal pool wetlands. Soil Sci Soc Am Spec Publ 54:107–127

    CAS  Google Scholar 

  • Holland R (1978) The geographic and edaphic distribution of vernal pools in the great central valley, California. California Native Plant Society Special Publication No. 4, Sacramento

  • Holm S (1979) A simple sequentially rejective multiple test procedure. Scand J Stat 6:65–70

    Google Scholar 

  • Karron JD (1987) A comparison of levels of genetic polymorphism and self-compatibility in geographically restricted and widespread plant congeners. Evol Ecol 1:47–58

    Article  Google Scholar 

  • Keeler-Wolf T, Elam DR, Lewis K, Flint SA (1998) California vernal pool assessment preliminary report. State of California. Department of Fish and Game, Sacramento

    Google Scholar 

  • Keeley JE (1998) C4 photosynthetic modifications in the evolutionary transition from land to water in aquatic grasses. Oecologia 116:85–97

    Article  Google Scholar 

  • Lewis PO, Zaykin D (2001) Genetic data analysis: computer program for the analysis of allelic data. Version 1.1 (d16c). Free program distributed by the authors over the internet from http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php. Accessed 19 Jan 2011

  • Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  • Martin MA, Mattioni C, Cherubini M, Taurchini D, Villani F (2010) Genetic diversity in European chestnut populations by means of genomic and genic microsatellite markers. Tree Genet Genomes 6:735–744

    Article  Google Scholar 

  • Miller MP (2005) Alleles in space: computer software for the joint analysis of inter individual spatial and genetic information. J Hered 96:722–724

    Article  PubMed  CAS  Google Scholar 

  • Nikiforoff CC (1941) Hardpan and micro-relief in certain soil complexes of California. USDA Technical bulletin No. 745, Washington DC

  • Peakal 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 

  • Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin L, Estoup A (2004) GeneClass2: a software for genetic assignment and first-generation migrant detection. J Hered 95:536–539

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Ramp Neal JM, Ranker TA, Collinge SK (2008) Conservation of rare species with island-like distributions: a case study of Lasthenia conjugens (Asteraceae) using population genetic structure and the distribution of rare markers. Plant Species Biol 23:97–110

    Article  Google Scholar 

  • Ramp JM, Collinge SK, Ranker TA (2006) Restoration genetics of the vernal pool endemic Lasthenia conjugens (Asteraceae). Conserv Genet 7:631–649

    Article  CAS  Google Scholar 

  • Reed DH, Frankham R (2003) Correlation between fitness and genetic diversity. Conserv Biol 17:230–237

    Article  Google Scholar 

  • Reeder JR (1982) Systematics of the tribe Orcuttieae (Gramineae) and the description of a new segregate genus Tuctoria. Am J Bot 69:1082–1095

    Article  Google Scholar 

  • Riley L, McGlaughlin ME, Helenurm K (2010) Genetic diversity following demographic recovery in the insular endemic plant Galium catalinense subspecies acrispum. Conserv Genet 11:2015–2025

    Article  Google Scholar 

  • Segelbacher G, Cushman SA, Epperson BK, Fortin MJ, Francois O, Hardy OJ, Holderegger R, Taberlet P, Waits LP, Manel S (2010) Applications of landscape genetics in conservation biology: concepts and challenges. Conserv Genet 11:375–385

    Article  Google Scholar 

  • Sloop, CM (in press) The population and genetic status of the endangered vernal pool annual Limnanthes floccosa Howell ssp. californica Arroyo: implications for species recovery. In: Schlising RA, DG Alexander (eds) Vernal pool conservation: research, progress and problems: is recovery possible? Studies from the Herbarium, California State University, Chico

  • Sloop, CM, Ayres DR (in press) Conservation genetics of two endangered vernal pool plants of the Santa Rosa Plain, Sonoma County. Proceedings of the CNPS conservation conference, 17–19 Jan 2009

  • Sloop CM, Eberl R, Ayres DR (In review) Genetic diversity and structure in the annual vernal pool endemic Limnanthes vinculans Ornduff (Limnanthaceae): implications of breeding system and restoration practices. Conserv Genet

  • Sloop CM, Pickens C, Gordon SP (2011) Conservation genetics of Butte County meadowfoam (Limnanthes floccosa ssp. californica Arroyo), an endangered vernal pool endemic. Conserv Genet 12:211–323

    Article  Google Scholar 

  • Solomeshch AI, Barbour MG, Holland RF (2007) Vernal pools. In: Barbour MG, Keeler-Wolf T, Schoenherr AA (eds) Terrestrial vegetation of California, 3rd edn. University of California Press, California, pp 394–424

    Google Scholar 

  • Stone RD (1990) California’s endemic vernal pool plants: some factors influencing their rarity and endangerment. In: Ikeda DH, Schlising RA (eds) Vernal pools plants: their habitat and biology. Studies from the Herbarium, California State University, Chico

  • Sun G, Salomon B (2003) Microsatellite variability and heterozygote deficiency in the arctic-alpine Alaskan wheatgrass (Elymus alaskanus) complex. Genome 46:729–737

    Article  PubMed  CAS  Google Scholar 

  • Tallmon DA, Luikart G, Waples RS (2004) The alluring simplicity and complex reality of genetic rescue. Trends Ecol Evol 19:489–496

    Article  PubMed  Google Scholar 

  • US Fish and Wildlife Service (2005) Recovery plan for vernal pool ecosystems of California and Southern Oregon. http://www.fws.gov/sacramento/es/recovery_plans/vp_recovery_plan_links.htm. Accessed 11 Oct 2010

  • Weitkamp WA, Graham RC, Anderson MA, Amrhein C (1996) Pedogenesis of a vernal pool Entisol-Alfisol-Vertison catena in southern California. Soil Sci Soc Am 60:316–323

    Article  CAS  Google Scholar 

  • Young AG, Clarke GM (2000) Genetics, demography and viability of fragmented populations. Cambridge University Press, Cambridge

    Book  Google Scholar 

Download references

Acknowledgments

We thank the U.S. Fish & Wildlife Service (Agreement No.: 802706G122) for funding support. We thank Dr. Derek Girman for use of the Sonoma State Core DNA Facility and Dr. Richard Whitkus for providing laboratory and office space. We further acknowledge the many local experts, land managers, and landowners who helped locate and obtain access to a majority of the extant sites, including Joe Silveira (USFWS), Carol Witham (CNPS), John Vollmer and Rich Reiner (The Nature Conservancy).

Author information

Authors and Affiliations

  1. Department of Biology, Sonoma State University, Rohnert Park, CA, 94928, USA

    Sarah P. Gordon, Christina M. Sloop, Heather G. Davis & J. Hall Cushman

  2. San Francisco Bay Joint Venture, 735 B Center Blvd, Fairfax, CA, 94930, USA

    Christina M. Sloop

Authors
  1. Sarah P. Gordon
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Christina M. Sloop
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Heather G. Davis
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. J. Hall Cushman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sarah P. Gordon.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gordon, S.P., Sloop, C.M., Davis, H.G. et al. Population genetic diversity and structure of two rare vernal pool grasses in central California. Conserv Genet 13, 117–130 (2012). https://doi.org/10.1007/s10592-011-0269-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10592-011-0269-y

Keywords

Search

Navigation