The Evolutionary Genomics of Serpentine Adaptation

. 2020 ; 11 () : 574616. [epub] 20201216

Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic-ecollection

Typ dokumentu časopisecké články, přehledy

Perzistentní odkaz   https://www.medvik.cz/link/pmid33391295

Serpentine barrens are among the most challenging settings for plant life. Representing a perfect storm of hazards, serpentines consist of broadly skewed elemental profiles, including abundant toxic metals and low nutrient contents on drought-prone, patchily distributed substrates. Accordingly, plants that can tolerate the challenges of serpentine have fascinated biologists for decades, yielding important insights into adaptation to novel ecologies through physiological change. Here we highlight recent progress from studies which demonstrate the power of serpentine as a model for the genomics of adaptation. Given the moderate - but still tractable - complexity presented by the mix of hazards on serpentine, these venues are well-suited for the experimental inquiry of adaptation both in natural and manipulated conditions. Moreover, the island-like distribution of serpentines across landscapes provides abundant natural replicates, offering power to evolutionary genomic inference. Exciting recent insights into the genomic basis of serpentine adaptation point to a partly shared basis that involves sampling from common allele pools available from retained ancestral polymorphism or via gene flow. However, a lack of integrated studies deconstructing complex adaptations and linking candidate alleles with fitness consequences leaves room for much deeper exploration. Thus, we still seek the crucial direct link between the phenotypic effect of candidate alleles and their measured adaptive value - a prize that is exceedingly rare to achieve in any study of adaptation. We expect that closing this gap is not far off using the promising model systems described here.

Zobrazit více v PubMed

Aeschbacher S., Selby J. P., Willis J. H., Coop G. (2017). Population-genomic inference of the strength and timing of selection against gene flow. Proc. Natl. Acad. Sci. U. S. A. 114, 7061–7066. 10.1073/pnas.1616755114, PMID: PubMed DOI PMC

Agrawal B., Lakshmanan V., Kaushik S., Bais H. P. (2012). Natural variation among PubMed DOI

Anacker B. L. (2014). The nature of serpentine endemism. Am. J. Bot. 101, 219–224. 10.3732/ajb.1300349, PMID: PubMed DOI

Arnold B. J., Lahner B., DaCosta J. M., Weisman C. M., Hollister J. D., Salt D. E., et al. (2016). Borrowed alleles and convergence in serpentine adaptation. Proc. Natl. Acad. Sci. U. S. A. 113, 8320–8325. 10.1073/pnas.1600405113, PMID: PubMed DOI PMC

Assunção A. G. L., Bookum W. M., Nelissen H. J. M., Vooijs R., Schat H., Ernst W. H. O. (2003). Differential metal-specific tolerance and accumulation patterns among PubMed DOI

Berglund A. N., Dahlgren S., Westerbergh A. (2004). Evidence for parallel evolution and site-specific selection of serpentine tolerance in DOI

Boyd R. S., Wall M. A., Santos S. R., Davis M. A. (2009). Variation of morphology and elemental concentrations in the California nickel hyperaccumulator DOI

Bradshaw H. D. (2005). Mutations in CAX1 produce phenotypes characteristic of plants tolerant to serpentine soils. New Phytol. 167, 81–88. 10.1111/j.1469-8137.2005.01408.x, PMID: PubMed DOI

Brady K. U., Kruckeberg A. R., Bradshaw Jr. H. D. (2005). Evolutionary ecology of plant adaptation to serpentine soils. Annu. Rev. Ecol. Evol. Syst. 36, 243–266. 10.1146/annurev.ecolsys.35.021103.105730 DOI

Bratteler M., Baltisberger M., Widmer A. (2006). QTL analysis of intraspecific differences between two PubMed DOI PMC

Burrell M. A., Hawkins A. K., Pepper A. E. (2012). Genetic analyses of nickel tolerance in a north American serpentine endemic plant, PubMed DOI

Busoms S., Paajanen P., Marburger S., Bray S., Huang X. Y., Poschenrieder C., et al. (2018). Fluctuating selection on migrant adaptive sodium transporter alleles in coastal PubMed DOI PMC

Cecchi L., Selvi F. (2009). Phylogenetic relationships of the monotypic genera Halacsya and Paramoltkia and the origins of serpentine adaptation in circummediterranean Lithospermeae (Boraginaceae): insights from ITS and matK DNA sequences. Taxon 58, 700–714. 10.1002/tax.583002 DOI

Čertner M., Sudová R., Weiser M., Suda J., Kolář F. (2018). Ploidy-altered phenotype interacts with local environment and may enhance polyploid establishment in PubMed DOI

Courbot M., Willems G., Motte P., Arvidsson S., Roosens N., Saumitou-laprade P., et al. (2007). A major quantitative trait locus for cadmium tolerance in PubMed DOI PMC

Davoodian N., Bosworth J., Rajakaruna N. (2012). Mycorrhizal colonization of DOI

Deniau A. X., Pieper B., Ten Bookum W. M., Lindhout P., Aarts M. G. M., Schat H. (2006). QTL analysis of cadmium and zinc accumulation in the heavy metal hyperaccumulator Thlaspi caerulescens. Theor. Appl. Genet. 113, 907–920. 10.1007/s00122-006-0350-y, PMID: PubMed DOI

Dittmar E. L., Oakley C. G., Conner J. K., Gould B. A., Schemske D. W. (2016). Factors influencing the effect size distribution of adaptive substitutions. Proc. R. Soc. B Biol. Sci. 283:20153065. 10.1098/rspb.2015.3065 PubMed DOI PMC

Doubková P., Suda J., Sudová R. (2012). The symbiosis with arbuscular mycorrhizal fungi contributes to plant tolerance to serpentine edaphic stress. Soil Biol. Biochem. 44, 56–64. 10.1016/j.soilbio.2011.09.011 DOI

Eggler J. (1955). Ein Beitrag zur Serpentinvegetation in der Gulsen bei Kraubath in Obersteiermark. Mitt Naturw Ver Steiermark 85, 27–72.

Gabbrielli R., Pandolfini T. (1984). Effect of Mg2+ and Ca2+ on the response to nickel toxicity in a serpentine endemic and nickel-accumulating species. Physiol. Plant. 62, 540–544. 10.1111/j.1399-3054.1984.tb02796.x DOI

Galardi F., Corrales I., Mengoni A., Pucci S., Barletti L., Barzanti R., et al. (2007). Intra-specific differences in nickel tolerance and accumulation in the Ni-hyperaccumulator DOI

Galey M. L., van der Ent A., Iqbal M. C. M., Rajakaruna N. (2017). Ultramafic geoecology of south and Southeast Asia. Bot. Stud. 5818. 10.1186/s40529-017-0167-9, PMID: PubMed DOI PMC

Gilbert K. J., Whitlock M. C. (2017). The genetics of adaptation to discrete heterogeneous environments: frequent mutation or large-effect alleles can allow range expansion. J. Evol. Biol. 30, 591–602. 10.1111/jeb.13029, PMID: PubMed DOI

Hämälä T., Mattila T. M., Savolainen O. (2018). Local adaptation and ecological differentiation under selection, migration, and drift in PubMed DOI

Hämälä T., Savolainen O. (2019). Genomic patterns of local adaptation under gene flow in PubMed DOI

Harrison S., Rajakaruna N. (2011). Serpentine: The evolution and ecology of a model system. University of California Press.

Holliday J. A., Zhou L., Bawa R., Zhang M., Oubida R. W. (2016). Evidence for extensive parallelism but divergent genomic architecture of adaptation along altitudinal and latitudinal gradients in PubMed DOI

Huang X. Y., Salt D. E. E. (2016). Plant ionomics: from elemental profiling to environmental adaptation. Mol. Plant 9, 787–797. 10.1016/j.molp.2016.05.003, PMID: PubMed DOI

Jain S. K., Bradshaw A. D. (1966). Evolutionary divergence among adjacent plant populations I. the evidence and its theoretical analysis. Heredity 21, 407–441. 10.1038/hdy.1966.42 DOI

Jenny H. (1980). The soil resource. Origin of behaviour. New York: Springer.

Kazakou E., Dimitrakopoulos P. G., Baker A. J. M., Reeves R. D., Troumbis A. Y. (2008). Hypotheses, mechanisms and trade-offs of tolerance and adaptation to serpentine soils: from species to ecosystem level. Biol. Rev. Camb. Philos. Soc. 83, 495–508. 10.1111/j.1469-185X.2008.00051.x, PMID: PubMed DOI

Kolář F., Dortová M., Lepš J., Pouzar M., Krejčová A. (2014). Serpentine ecotypic differentiation in a polyploid plant complex: shared tolerance to Mg and Ni stress among di‐ and tetraploid serpentine populations of. Plant Soil 374, 435–447. 10.1007/s11104-013-1813-y DOI

Kolář F., Fér T., Štech M., Trávníček P., Dušková E., Schönswetter P., et al. (2012). Bringing together evolution on serpentine and polyploidy: spatiotemporal history of the diploid-tetraploid complex of PubMed DOI PMC

Kruckeberg A. R. (1950). An experimental inquiry into the nature of endemism on serpentine soils. Berkeley: University of California.

Kruckeberg A. R. (1951). Intraspecific variability in the response of certain native plant species to serpentine soil. Am. J. Bot. 38, 408–419. 10.1002/j.1537-2197.1951.tb14842.x DOI

Kruckeberg A. R. (1954). The ecology of serpentine soils: a symposium. III. Plant species in relation to serpentine soils. Ecology 35, 267–274.

Kruckeberg A. R. (1967). Ecotypic response to ultramafic soils by some plant species of northwestern United States. Brittonia 19, 133–151. 10.2307/2805271 DOI

Kruckeberg A. R. (1984). California serpentines: Flora, vegetation, geology, soils and management problems. University of California Press.

Lämmermayr L. (1927). Materialien zur Systematik und Ökologie der Serpentinflora. II. Das Problem der, Serpentinpflanzen “–Eine kritische ökologische Studie, Sitzungsber. Akad. Wiss. Wien, math.-naturw. Kl., Abt., 25–69.

Lee K. M., Coop G. (2019). Population genomics perspectives on convergent adaptation. Philos. Trans. R Soc. Lond. B Biol. Sci. 374, 1–19. 10.1098/rstb.2018.0236, PMID: PubMed DOI PMC

Leigh Broadhurst C., Tappero R. V., Maugel T. K., Erbe E. F., Sparks D. L., Chaney R. L. (2009). Interaction of nickel and manganese in accumulation and localization in leaves of the Ni hyperaccumulators Alyssum murale and DOI

Losos J. B. (2011). Convergence, adaptation, and constraint. Evolution 65, 1827–1840. 10.1111/j.1558-5646.2011.01289.x, PMID: PubMed DOI

Mayer M., Soltis P. S. (1994). The evolution of serpentine endemics : a chloroplast DNA phylogeny of the DOI

Mengoni A., Baker A. J. M., Bazzicalupo M., Reeves R. D., Adigüzel N., Chianni E., et al. (2003). Evolutionary dynamics of nickel hyperaccumulation in alyssum revealed by ITS nrDNA analysis. New Phytol. 159, 691–699. 10.1046/j.1469-8137.2003.00837.x PubMed DOI

Mengoni A., Barzanti R., Gonnelli C., Gabbrielli R., Bazzicalupo M. (2001). Characterization of nickel-resistant bacteria isolated from serpentine soil. Environ. Microbiol. 3, 691–698. 10.1046/j.1462-2920.2001.00243.x, PMID: PubMed DOI

Moyle L. C., Levine M., Stanton M. L., Wright J. W. (2012). Hybrid sterility over tens of meters between ecotypes adapted to serpentine and non-serpentine soils. Evol. Biol. 39, 207–218. 10.1007/s11692-012-9180-9 DOI

Nosil P., Funk D. J., Ortiz-Barrientos D. (2009). Divergent selection and heterogeneous genomic divergence. Mol. Ecol. 18, 375–402. 10.1111/j.1365-294X.2008.03946.x, PMID: PubMed DOI

Novák F. A. (1928). Ekologické úvahy o hadcových rasách a hadcové vegetaci. Věda přírodní 9.

Nunvářová Kabátová K., Kolář F., Jarolímová V., Krak K., Chrtek J. (2019). Does geography, evolutionary history or ecology drive ploidy and genome size variation in the DOI

O’Dell R. E., Claassen V. P. (2006). Serpentine and nonserpentine DOI

O’Dell R. E., Rajakaruna N. (2011). “Intraspecific variation, adaptation, and evolution” in Serpentine: Evolution and ecology in a model system. eds. Harrison S., Rajakaruna N. (University of California Press; ), 97–137.

Oline D. K. (2006). Phylogenetic comparisons of bacterial communities from serpentine and nonserpentine soils. Appl. Environ. Microbiol. 72, 6965–6971. 10.1128/AEM.00690-06, PMID: PubMed DOI PMC

Ostevik K. L., Moyers B. T., Owens G. L., Rieseberg L. H. (2012). Parallel ecological speciation in plants? Int. J. Ecol. 2012, 1–17. 10.1155/2012/939862 DOI

Pal A., Paul A. K. (2004). Aerobic chromate reduction by chromium-resistant bacteria isolated from serpentine soil. Microbiol. Res. 159, 347–354. 10.1016/j.micres.2004.08.001, PMID: PubMed DOI

Palm E., Brady K., Van Volkenburgh E. (2012). Serpentine tolerance in PubMed DOI

Palm E. R., Van Volkenburgh E. (2014). “Physiological adaptation of plants to serpentine soil” in Plant ecology and evolution in harsh environments. eds. Rajakaruna N., Boyd R. S., Harris T. B. (New York: Nova Science Publishers; ), 129–148.

Pančić J. (1859). Die Flora der Serpentinberge in Mittel-Serbien. Verhandl. Zool.-Bot. Gesell. Wien 9, 139–150.

Peer W. A., Mahmoudian M., Freeman J. L., Lahner B., Richards E. L., Reeves R. D., et al. (2006). Assessment of plants from the Brassicaceae family as genetic models for the study of nickel and zinc hyperaccumulation. New Phytol. 172, 248–260. 10.1111/j.1469-8137.2006.01820.x, PMID: PubMed DOI

Preite V., Sailer C., Syllwasschy L., Bray S., Kraemer U., Yant L. (2019). Convergent evolution in PubMed DOI PMC

Proctor J. (1971). The plant ecology of serpentine: II. J. Ecol. 59, 397–410. 10.2307/2258320 DOI

Proctor J., Woodell S. R. (1975). The ecology of serpentine soils. Adv. Ecol. Res. 9, 255–366.

Rajakaruna N. (2018). Lessons on evolution from the study of edaphic specialization. Bot. Rev. 84, 39–78. 10.1007/s12229-017-9193-2 DOI

Rajakaruna N., Baldwin B. G., Chan R., Desrochers A. M., Bohm B. A., Whitton J. (2003a). Edaphic races and phylogenetic taxa in the PubMed DOI

Rajakaruna N., Bradfield G. E., Bohm B. A., Whitton J. (2003b). Adaptive differentiation in response to water stress by edaphic races of DOI

Rajakaruna N., Siddiqi M. Y., Whitton J., Bohm B. A., Glass A. D. M. (2003c). Differential responses to Na+/K+ and Ca2+/Mg2+ in two edaphic races of the PubMed DOI

Rajakaruna N., Whitton J. (2004). “Trends in the evolution of edaphic specialists with an example of parallel evolution in the

Reeves R. D., Baker A. J. M. (1984). Studies on metal uptake by plants from serpentine and non-serpentine populations of Thlaspi goesingense Hálácsy (Crycuferae). New Phytol. 98, 191–204. 10.1111/j.1469-8137.1984.tb06108.x, PMID: PubMed DOI

Rellstab C., Gugerli F., Eckert A. J., Hancock A. M., Holderegger R. (2015). A practical guide to environmental association analysis in landscape genomics. Mol. Ecol. 24, 4348–4370. 10.1111/mec.13322, PMID: PubMed DOI

Roberts B. A., Proctor J. (1992). The ecology of areas with Serpentinized rocks. A World View. Dordrecht: Kluwer Academic Press.

Rockman M. V. (2012). The QTN program and the alleles that matter for evolution: all that’s gold does not glitter. Evolution 66, 1–17. 10.1111/j.1558-5646.2011.01486.x, PMID: PubMed DOI PMC

Rundle H. D., Nosil P. (2005). Ecological speciation. Ecol. Lett. 8, 336–352. 10.1111/j.1461-0248.2004.00715.x DOI

Rune O. (1953). Plant life on serpentines and related rocks in the north of Sweden. Sv. växtgeografiska sällsk.

Sakaguchi S., Horie K., Ishikawa N., Nagano A. J., Yasugi M., Kudoh H., et al. (2017). Simultaneous evaluation of the effects of geographic, environmental and temporal isolation in ecotypic populations of PubMed DOI

Sakaguchi S., Horie K., Ishikawa N., Nishio S., Worth J. R. P., Fukushima K., et al. (2019). Maintenance of soil ecotypes of DOI

Sakaguchi S., Horie K., Kimura T., Nagano A. J., Isagi Y., Ito M. (2018). Phylogeographic testing of alternative histories of single-origin versus parallel evolution of early flowering serpentine populations of DOI

Salehi Eskandari B., Ghaderian S. M., Schat H. (2017). The role of nickel (Ni) and drought in serpentine adaptation: contrasting effects of Ni on osmoprotectants and oxidative stress markers in the serpentine endemic, DOI

Salehi-Eskandari B., Ghaderian S. M., Schat H. (2018). Differential interactive effects of the Ca/Mg quotient and PEG-simulated drought in Alyssum inflatum and Fortuynia garcinii. Plant Soil 428, 213–222. 10.1007/s11104-018-3649-y DOI

Salt D. E., Baxter I., Lahner B. (2008). Ionomics and the study of the plant Ionome. Annu. Rev. Plant Biol. 59, 709–733. 10.1146/annurev.arplant.59.032607.092942, PMID: PubMed DOI

Sambatti J. B. M., Rice K. J. (2006). Local adaptation, patterns of selection, and gene flow in the Californian serpentine sunflower ( PubMed DOI

Savolainen O., Lascoux M., Merilä J. (2013). Ecological genomics: genes in ecology and ecology in genes. Nat. Rev. Genet. 14, 807–820. 10.1038/nrg3522, PMID: PubMed DOI

Schechter S., Branco S. (2014). “The ecology and evolution of mycorrhizal fungi in extreme soils” in Plant ecology and evolution in harsh environments. eds. Rajakaruna N., Boyd R. S., Harris T. B. (New York: Nova Science Publishers; ), 33–52.

Schechter S. P., Bruns T. D. (2008). Serpentine and non-serpentine ecotypes of PubMed DOI

Selby J. P. (2014). The genetic basis of local adaptation to serpentine soils in

Selby J. P., Jeong A. L., Toll K., Wright K. M., Lowry D. B. (2014). “Methods and discoveries in the pursuit of understanding the genetic basis of adaptation to harsh environments in Mimulus” in Plant ecology and evolution in harsh environments. eds. Rajakaruna N., Boyd R. S., Harris T. B. (New York: Nova Science Publishers; ), 243–266.

Selby J. P., Willis J. H. (2018). Major QTL controls adaptation to serpentine soils in PubMed DOI

Sobczyk M. K., Smith J. A. C., Pollard A. J., Filatov D. A. (2017). Evolution of nickel hyperaccumulation and serpentine adaptation in the PubMed DOI PMC

Sork V. L., Aitken S. N., Dyer R. J., Eckert A. J., Legendre P., Neale D. B. (2013). Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate. Tree Genet. Genomes 9, 901–911. 10.1007/s11295-013-0596-x DOI

Southworth D., Tackaberry L. E., Massicotte H. B. (2014). Mycorrhizal ecology on serpentine soils. Plant Ecol. Diversity 7, 445–455. 10.1080/17550874.2013.848950 DOI

Stein R. J., Höreth S., de Melo J. R. F., Syllwasschy L., Lee G., Garbin M. L., et al. (2017). Relationships between soil and leaf mineral composition are element-specific, environment-dependent and geographically structured in the emerging model PubMed DOI PMC

Stern D. L. (2013). The genetic causes of convergent evolution. Nat. Rev. Genet. 14, 751–764. 10.1038/nrg3483, PMID: PubMed DOI

Taylor S. I., Levy F. (2002). Responses to soils and a test for preadaptation to serpentine in PubMed DOI

Teptina A., Paukov A., Rajakaruna N. (2018). Ultramafic vegetation and soils in the circumboreal region of the northern hemisphere. Ecol. Res. 33, 609–628. 10.1007/s11284-018-1577-1 DOI

Turner T. L., Bourne E. C., Von Wettberg E. J., Hu T. T., Nuzhdin S. V. (2010). Population resequencing reveals local adaptation of PubMed DOI

Turner T. L., von Wettberg E. J., Nuzhdin S. V. (2008). Genomic analysis of differentiation between soil types reveals candidate genes for local adaptation in PubMed DOI PMC

Veatch-Blohm M. E., Roche B. M., Campbell M. J. (2013). Evidence for cross-tolerance to nutrient deficiency in three disjunct populations of PubMed DOI PMC

Veatch-Blohm M. E., Roche B. M., Dahl E. E. (2017). Serpentine populations of DOI

Vlamis J. (1949). Growth of lettuce and barley as influenced by degree of calcium-saturation of soil. Soil Sci. 67:453–466. 10.1097/00010694-194906000-00005 DOI

Vlamis J., Jenny H. (1948). Calcium deficiency in serpentine soils as revealed by adsorbent technique. Science 107:549. 10.1126/science.107.2786.549, PMID: PubMed DOI

von Wettberg E. J. B., Ray-Mukherjee J., D’Adesky N., Nesbeth D., Sistla S. (2014). “The Evoltionary ecology and genetics of stress resistance syndrome (SRS) traits: revisiting chapin, autumn and pugnaire (1993)” in Plant ecology and evolution in harsh environments. eds. Rajakaruna N., Boyd R. S., Harris T. B. (New York: Nova Science Publishers; ), 201–226.

Walker R. B., Walker H. M., Ashworth P. (1955). Calcium-magnesium nutrition with special reference to serpentine soils. Plant Physiol. 30, 214–221. 10.1104/pp.30.3.214, PMID: PubMed DOI PMC

Westerbergh A. (1994). Serpentine and non-serpentine DOI

Whittaker R. H. (1954). The ecology of serpentine soils. Ecology 35, 258–288. 10.2307/1931126 DOI

Willems G., Dräger D. B., Courbot M., Godé C. (2007). The genetic basis of zinc tolerance in the metallophyte PubMed DOI PMC

Wright K. M., Lloyd D., Lowry D. B., Macnair M. R., Willis J. H. (2013). Indirect evolution of hybrid lethality due to linkage with selected locus in PubMed DOI PMC

Wright J. W., Stanton M. L., Scherson R. (2006). Local adaptations to serpentine and non-serpentine soils in

Wright J. W., Von Wettberg E. (2009). ‘Serpentinomics’ ‐ an emerging new field of study. Northeast. Nat. 16, 285–296. 10.1656/045.016.0521 DOI

Yeaman S., Whitlock M. C. (2011). The genetic architecture of adaptation under migration-selection balance. Evolution 65, 1897–1911. 10.1111/j.1558-5646.2011.01269.x, PMID: PubMed DOI

Najít záznam

Citační ukazatele

Pouze přihlášení uživatelé

Možnosti archivace

Nahrávání dat ...