Abstract
Identifying units for appropriate management and conservation of rare species is an important and challenging process, and population genetics can inform this decision making. Using Phlox hirsuta, a rare species restricted to serpentine soils in Northern California and with a geographic range of less than 15 km, we examined genetic variation within and among populations, using tunable Genotyping-by-Sequencing (tGBS) to generate single nucleotide polymorphisms (SNPs) as well as 11 microsatellite loci, to identify population structure, patterns of migration and selection, and units for conservation. Multiple methods recognized three geographically structured population clusters. The species has undergone a recent genetic bottleneck, and the increase in population size may be influenced by the changing climate. Patterns of gene flow are greater from south to north than in the opposite direction. Some of the genes under selection are putatively involved in adaptation to edaphic conditions, and genes under selection differ among the populations. Four population units were identified as suitable for conservation purposes based on various partitions of the SNPs.
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Data availability
The VCF, microsatellite, and beagle data files that support the findings of this study are deposited and openly available at Dryad: https://doi.org/10.5061/dryad.gmsbcc2q4. Individual geographic coordinates are excluded because P. hirsuta is a rare species. The fastq files are available at the SRA at NCBI (BioProject PRJNA862075).
Change history
13 February 2023
A Correction to this paper has been published: https://doi.org/10.1007/s10592-022-01482-2
References
Anacker BL (2014) The nature of serpentine endemism. Am J Bot 101:219–224
Anacker BL, Whittall JB, Goldberg EE, Harrison SP (2011) Origins and consequences of serpentine endemism in the California flora. Evolution: Int J Org Evol 65:365–376
Baldwin BG, Goldman DH, Keil DJ, Patterson R, Rosatti TJ, Vorobik LA (2012) The Jepson manual: vascular plants of California. Universityof California Press, Berkeley
Barron JA, Heusser L, Herbert T, Lyle M (2003) High-resolution climatic evolution of coastal northern California during the past 16,000 years. Paleoceanography. https://doi.org/10.1029/2002PA000768
Baskauf CJ, McCauley DE, Eickmeier WG (1994) Genetic analysis of a rare and a widespread species of Echinacea (Asteraceae). Evolution 48:180–188
Beerli P (2009) How to use MIGRATE or why are Markov chain Monte Carlo programs difficult to use. Popul Genet Anim Conserv 17:42–79
Beerli P, Palczewski M (2010) Unified framework to evaluate panmixia and migration direction among multiple sampling locations. Genetics 185:313–326
Bradburd GS, Coop GM, Ralph PL (2018) Inferring continuous and discrete population genetic structure across space. Genetics 210:33–52
Briggs D, Walters SM (2016) Plant variation and evolution. Cambridge University Press, Cambridge
Caye K, Jay F, Michel O, Francois O (2017) Fast inference of individual admixture coefficients using geographic data. bioRxiv. https://doi.org/10.1101/080291
Chan WY, Hoffmann AA, van Oppen MJ (2019) Hybridization as a conservation management tool. Conserv Lett 12:e12652
Chen KY, Marschall EA, Sovic MG, Fries AC, Gibbs HL, Ludsin SA (2018) Assign POP: an r package for population assignment using genetic, non-genetic, or integrated data in a machine‐learning framework. Methods Ecol Evol 9:439–446
Coates BS, Sumerford DV, Miller NJ, Kim KS, Sappington TW, Siegfried BD, Lewis LC (2009) Comparative performance of single nucleotide polymorphism and microsatellite markers for population genetic analysis. J Hered 100:556–564
Cohen JI (2019) The conservation genomics of the endangered distylous gypsophile Oreocarya crassipes (Boraginaceae). Conserv Genet 20:1315–1328
Conesa A, Götz S (2008) Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genom. https://doi.org/10.1155/2008/619832
Damschen EI, Harrison S, Ackerly DD, Fernandez-Going BM, Anacker BL (2012) Endemic plant communities on special soils: early victims or hardy survivors of climate change? J Ecol 100:1122–1130
De Meeûs T, Goudet J (2007) A step-by-step tutorial to use HierFstat to analyse populations hierarchically structured at multiple levels. Infect Genet Evol 7:731–735
Díaz-Arce N, Rodríguez-Ezpeleta N (2019) Selecting RAD-Seq data analysis parameters for population genetics: the more the better? Front Genet 10:533
Dobzhansky T (1948) Genetics of natural populations. XVIII. Experiments on chromosomes of Drosophila pseudoobscura from different geographic regions. Genetics 33:588
Earl DA (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361
Edwards AL, Wyatt R (1994) Population genetics of the rare Asclepias texana and its widespread sister species, A. perennis. Syst Bot 19:291–307
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
Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587
Fehlberg SD (2013) Personal communication
Fehlberg SD, Ford KA, Ungerer MC, Ferguson CJ (2008) Development, characterization and transferability of microsatellite markers for the plant genus Phlox (Polemoniaceae). Mol Ecol Resour 8:116–118
Ferguson CS, Filipski J, Donham K (2006) The mating system of the Yreka Phlox (Phlox hirsuta E.E. Nelson). Southern Oregon University, Ashland, p 80
Fischer MC, Rellstab C, Leuzinger M, Roumet M, Gugerli F, Shimizu KK, Holderegger R, Widmer A (2017) Estimating genomic diversity and population differentiation–an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri. BMC Genom 18:69
Foll M (2012) Bayescan v2. 1 user manual. Ecology 20:1450–1462
Foll M, Gaggiotti O (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180:977–993
Frichot E, François O (2015) LEA: an R package for landscape and ecological association studies. Methods Ecol Evol 6:925–929
Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28:3150–3152
Funk WC, McKay JK, Hohenlohe PA, Allendorf FW (2012) Harnessing genomics for delineating conservation units. Trends Ecol Evol 27:489–496
Garcia-Erill G, Albrechtsen A (2020) Evaluation of model fit of inferred admixture proportions. Mol Ecol Resour 20:936–949
Gibson JP, Rice SA, Stucke CM (2008) Comparison of population genetic diversity between a rare, narrowly distributed species and a common, widespread species of Alnus (Betulaceae). Am J Bot 95:588–596
Gitzendanner MA, Soltis PS (2000) Patterns of genetic variation in rare and widespread plant congeners. Am J Bot 87:783–792
Gitzendanner M, Soltis P (2001) Genetic variation in rare and widespread Lomatium species (Apiaceae): a comparison of AFLP and SSCP data. Edinb J Bot 58:347–356
Goudet J (2005) Hierfstat, a package for R to compute and test hierarchical F-statistics. Mol Ecol Resour 5:184–186
Gruenthal KM, Larson WA (2021) Efficient genotyping with backwards compatibility: converting a legacy microsatellite panel for muskellunge (Esox masquinongy) to genotyping-by-sequencing chemistry. Conserv Genet Resour 13:151–159
Hey J, Chung Y, Sethuraman A, Lachance J, Tishkoff S, Sousa VC, Wang Y (2018) Phylogeny estimation by integration over isolation with migration models. Mol Biol Evol 35:2805–2818
Hodel RG, Chen S, Payton AC, McDaniel SF, Soltis P, Soltis DE (2017) Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering. Sci Rep 7:1–14
Honnay O, Jacquemyn H (2007) Susceptibility of common and rare plant species to the genetic consequences of habitat fragmentation. Conserv Biol 21:823–831
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806
Janes JK, Miller JM, Dupuis JR, Malenfant RM, Gorrell JC, Cullingham CI, Andrew RL (2017) The K = 2 conundrum. Mol Ecol 26:3594–3602
Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genet 6:13
Jombart T, Ahmed I (2011) adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27:3070–3071
Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11:94
Karron JD, Falk D, Holsinger K (1991) Breeding systems in rare plant species. In: Genetics and conservation of rare plants. Oxford University Press on Demand, Oxford, pp 87–98
Konečná V, Yant L, Kolář F (2020) The evolutionary genomics of serpentine adaptation. Front Plant Sci 11:2004
Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I (2015) Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Eesour 15:1179–1191
Kruckeberg AR (1951) Intraspecific variability in the response of certain native plant species to serpentine soil. Am J Bot 38:408–419
Levin DA, Francisco-Ortega J, Jansen RK (1996) Hybridization and the extinction of rare plant species. Conserv Biol 10:10–16
Lewis DH, Jarvis DE, Maughan PJ (2020) SSRgenotyper: a simple sequence repeat genotyping application for whole-genome resequencing and reduced representational sequencing projects. Appl Plant Sci 8:e11402
Li YL, Liu JX (2018) StructureSelector: a web-based software to select and visualize the optimal number of clusters using multiple methods. Mol Ecol Resour 18:176–177
López-Cortegano E, Pérez‐Figueroa A, Caballero A (2019) metapop2: Re‐implementation of software for the analysis and management of subdivided populations using gene and allelic diversity. Mol Ecol Resour 19:1095–1100
Lowe WH, Allendorf FW (2010) What can genetics tell us about population connectivity? Mol Ecol 19:3038–3051
Lynch M (1991) The genetic interpretation of inbreeding depression and outbreeding depression. Evolution 45:622–629
Mansour M (2000) Nitrogen containing compounds and adaptation of plants to salinity stress. Biol Plant 43:491–500
Meirmans PG, Van Tienderen PH (2004) GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Resour 4:792–794
Minnaar C, Anderson B (2019) Using quantum dots as pollen labels to track the fates of individual pollen grains. Methods Ecol Evol 10:604–614
Moore MJ, Mota JF, Douglas NA, Olvera HF, Ochoterena H (2014) The ecology, assembly and evolution of gypsophile floras. In: Rajakaruna N, Boyd RS, Harris T (eds) Plant ecology and evolution in harsh environments. Nova Science Publishers, New York, pp 97–128
Ott A, Liu S, Schnable JC, Yeh C-TE, Wang K-S, Schnable PS (2017) tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci. Nucleic Acids Res 45:e178–e178
Palm ER, Van Volkenburgh E (2014) Physiological adaptations of plants to serpentine soils. Plant ecology and evolution in harsh environments. Nova Science Publishers, Hauppauge, pp 129–148
Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Resour 6:288–295
Pina-Martins F, Silva DN, Fino J, Paulo OS (2017) Structure_threader: an improved method for automation and parallelization of programs structure, fastStructure and MavericK on multicore CPU systems. Mol Ecol Resour 17:e268–e274
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Puechmaille SJ (2016) The program structure does not reliably recover the correct population structure when sampling is uneven: subsampling and new estimators alleviate the problem. Mol Ecol Resour 16:608–627
R Core Team (2013) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http://www.R-project.org/
Raj A, Stephens M, Pritchard JK (2014) fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197:573–589
Reeves RD, Macfarlane RM, Brooks RR (1983) Accumulation of nickel and zinc by western North American genera containing serpentine-tolerant species. Am J Bot 70:1297–1303
Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Resour 4:137–138
Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348
Ruane LG, Rotzin AT, Congleton PH (2014) Floral display size, conspecific density and florivory affect fruit set in natural populations of Phlox hirsuta, an endangered species. Ann Bot 113:887–893
Ruane LG, Dickens ME, Wall ME (2015) Fitness consequences of short-and long‐distance pollinations in Phlox hirsuta, an endangered species. Am J Bot 102:1659–1665
Schulz MH, Weese D, Holtgrewe M, Dimitrova V, Niu S, Reinert K, Richard H (2014) Fiona: a parallel and automatic strategy for read error correction. Bioinformatics 30:i356–i363
Skotte L, Korneliussen TS, Albrechtsen A (2013) Estimating individual admixture proportions from next generation sequencing data. Genetics 195:693–702
Starratt SW, Barron JA, Kneeshaw T, Phillips RL, Bischoff JL, Lowenstern JB, Wanket JA(2003) A Holocene record from Medicine Lake, Siskiyou County, California: preliminary diatom, pollen, geochemical, and sedimentological data. In: Proceedings of the nineteenth annual pacific climate workshop, technical report, pp. 131–148
Templeton AR (1986) Coadaptation and outbreeding depression. In: Soulé M (ed) Conservation biology: the science of scarcity and diversity. Oxford University Press, Minnesota, pp 105–116
U.S. Fish and Wildlife Service (2006) Recovery plan for Phlox hirsuta (Yreka Phlox). Sacramento, CA, pp x + 95
Verity R, Nichols RA (2016) Estimating the number of subpopulations (K) in structured populations. Genetics. https://doi.org/10.1534/genetics.115.180992
Vithanage M, Kumarathilaka P, Oze C, Karunatilake S, Seneviratne M, Hseu Z-Y, Gunarathne V, Dassanayake M, Ok YS, Rinklebe J (2019) Occurrence and cycling of trace elements in ultramafic soils and their impacts on human health: a critical review. Environ Int 131:104974
Whitlock MC, McCauley DE (1999) Indirect measures of gene flow and migration: FST ≠ 1/(4Nm + 1). Heredity 82:117–125
Wu TD, Nacu S (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26:873–881
Wu TD, Reeder J, Lawrence M, Becker G, Brauer MJ (2016) GMAP and GSNAP for genomic sequence alignment: enhancements to speed, accuracy, and functionality. In: Mathé, E, Davis S (eds) Statistical genomics. Humana Press, New York, pp 283–334
Yang W-Y, Novembre J, Eskin E, Halperin E (2012) A model-based approach for analysis of spatial structure in genetic data. Nat Genet 44:725–731
Yuan N, Sun Y, Comes HP, Fu CX, Qiu YX (2014) Understanding population structure and historical demography in a conservation context: population genetics of the endangered Kirengeshoma palmata (Hydrangeaceae). Am J Bot 101:521–529
Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS (2012) A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28:3326–3328
Acknowledgements
The authors would like to thank Nadine Kanim (USFWS), Sheri Hagwood (USFWS), and Merissa Hanisko (California Department of Fish and Wildlife). Dana Shaw prepared the GIS map. Andrew Rotzin and Philip Congleton helped collect leaves and GPS coordinates in the field. The editor and four reviewers provided helpful comments on the manuscript. Funding for the project was made possible by a Traditional Section 6 Grant (#F16AP00010) from USFWS. tGBS sequencing was conducted by data2bio, and Eurofins amplified and sequenced the microsatellite loci. Lisa Coffey and Asgar Shir were quite helpful with these efforts. The KUHPC was from a National Science Foundation Major Research Instrumentation Program award (Award No. 1725938).
Funding
Funding for the project was made possible by a Traditional Section 6 Grant (#F16AP00010) from USFWS. The KUHPC was from a National Science Foundation Major Research Instrumentation Program award (Award No. 1725938).
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JIC and LRG conceptualized the project, investigated the research question, and wrote the manuscript. JIC conducted the formal analyses on the data and undertook data curation. LGR obtained the resources for the project.
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The original online version of this article was revised due to the second author's given and family names were incorrectly structured. The author name has been corrected.
The author Lauren R. Griffen (formally Lauren G. Ruane).
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Cohen, J.I., Griffen, L.R. Conservation genetics of Phlox hirsuta, a serpentine endemic. Conserv Genet 24, 137–152 (2023). https://doi.org/10.1007/s10592-022-01478-y
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DOI: https://doi.org/10.1007/s10592-022-01478-y