Abstract
Salvia officinalis is a perennial species, native and endemic to the Western Balkans and the Apennine Peninsula. Due to its medicinal and aromatic properties, it is used in pharmaceutical, cosmetic, and food industries. The main objectives of the study were to infer the genetic structure of S. officinalis populations in the northern and central parts of the eastern Adriatic coast, to detect the phylogeographical barriers among the putative microrefugia and to assess the genetic diversity among the resulting ancestral clusters. Twenty-five populations were assessed using amplified fragment length polymorphism markers. High polymorphism and high diversity within populations were typical for this outcrossing long-lived species. The Fitch–Margoliash tree based on Nei’s genetic distance matrix showed that most of the populations tended to group in accordance with the geographical position of their collecting sites. Spatial analysis of the genetic diversity revealed a typical pattern of isolation by distance. Very low overall among-population differentiation and detection of only three private alleles indicate that there has been high gene flow among populations. By using Bayesian Analysis of Population Structure on population level, two distinct ancestral clusters were obtained. It is likely that these two ancestral clusters were separated for a longer period by Pleistocene glaciation, although the subsequent fast recolonization resulted in diminished genetic differences. High rarity of northern and southern populations of the investigated area indicates that S. officinalis presumably survived in both northern and southern microrefugia and expanded from there resulting in secondary contact zones, characterized by lower rarity and equal genetic diversity.
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Bonin A, Bellemain E, Bronken Eidesen P, Pompanon F, Brochmann C, Taberlet P (2004) How to track and assess genotyping errors in population genetics studies. Molec Ecol 13:3261–3273. https://doi.org/10.1111/j.1365-294X.2004.02346.x
Colantoni P, Gallignani P, Lenaz R (1979) Late pleistocene and holocene evolution of the North Adriatic Continental-Shelf (Italy). Mar Geol 33:M41–M50. https://doi.org/10.1016/0025-3227(79)90130-0
Corander J, Marttinen P (2006) Bayesian identification of admixture events using multilocus molecular markers. Molec Ecol 15:2833–2843. https://doi.org/10.1111/j.1365-294X.2006.02994.x
Corander J, Waldmann P, Sillanpaa MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics 163:367–374
Corander J, Waldmann P, Marttinen P, Sillanpaa MJ (2004) BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics 20:2363–2369. https://doi.org/10.1093/bioinformatics/bth250
Corander J, Marttinen P, Siren J, Tang J (2008) Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinform 9:539. https://doi.org/10.1186/1471-2105-9-539
Corsi G, Bottega S (1999) Glandular hairs of Salvia officinalis: new data on morphology, localization and histochemistry in relation to function. Ann Bot (Oxford) 84:657–664. https://doi.org/10.1006/anbo.1999.0961
Earl DA, Vonholdt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genet Resources 4:359–361. https://doi.org/10.1007/s12686-011-9548-7
Echeverrigaray S, Agostini G (2006) Genetic relationships between commercial cultivars and Brazilian accessions of Salvia officinalis L. based on RAPD markers. Revista Brasil Pl Med 8:13–17
Ehrich D (2006) AFLPDAT: a collection of R functions for convenient handling of AFLP data. Molec Ecol Notes 6:603–604. https://doi.org/10.1111/j.1471-8286.2006.01380.x
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molec Ecol 14:2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes—application to human mitochondrial-DNA restriction data. Genetics 131:479–491
Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinf 1:47–50
Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molec Ecol Notes 7:574–578. https://doi.org/10.1111/j.1471-8286.2007.01758.x
Felsenstein J (1993) Phylogeny inference package (PHYLIP). Version 3.5. Department of genetics, University of Washington, Seattle
Glasnović P, Temunović M, Lakušić D, Rakić T, Brečko Grubar V, Surina B (2018) Understanding biogeographical patterns in the western Balkan Peninsula using environmental niche modelling and geostatistics in polymorphic Edraianthus tenuifolius. AoB PLANTS 10:ply064. https://doi.org/10.1093/aobpla/ply064
Gomez A, Lunt DH (2007) Refugia within refugia: patterns of phylogeographic concordance in the Iberian Peninsula. In: Weiss S, Ferrand N (eds) Phylogeography of Southern European Refugia. Springer, Dordrech, pp 155–188
Grdiša M, Liber Z, Radosavljević I, Carović-Stanko K, Kolak I, Šatović Z (2014) Genetic diversity and structure of Dalmatian Pyrethrum (Tanacetum cinerariifolium Trevir./Sch./Bip., Asteraceae) within the Balkan Refugium. PLoS ONE 9:e105265. https://doi.org/10.1371/journal.pone.0105265
Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electronica 4:9
Hamrick JL, Godt MJ (1990) Allozyme diversity in plant species. In: Brown AHD, Clegg MT, Kahler AL, Weir BS (eds) Plant population genetics, breeding, and genetic resources. Sinauer, Sunderland, pp 43–63
Hamrick JL, Godt MJW (1996) Conservation genetics of endemic plant species. In: Avise JC, Hamrick JL (eds) Conservation genetics: case histories from nature. Chapman and Hall, New York, pp 281–304
Hamrick L, Godt MJW, Murawski DA, Loveless MD (1991) Correlations between species traits and allozyme diversity: implications for conservation biology and conservation of rare plants. In: Falk DA, Holsinger KE (eds) Genetics. Oxford University Press, New York, pp 75–86
Hardy OJ (2003) Estimation of pairwise relatedness between individuals and characterization of isolation-by-distance processes using dominant genetic markers. Molec Ecol 12:1577–1588. https://doi.org/10.1046/j.1365-294X.2003.01835.x
Hardy OJ, Vekemans X (2002) SPAGEDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molec Ecol Notes 2:618–620. https://doi.org/10.1046/j.1471-8286.2002.00305.x
Hardy OJ, Vekemans X (2007) SPAGeDi 1.2: a program for spatial pattern analysis of genetic diversity—user’s manual. Laboratoire Eco-éthologie Evolutive, Université Libre de Bruxelles
Herrmann D, Poncet N, Manel S, Rioux D, Gielly L et al (2010) Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates. Genome 310:302–310. https://doi.org/10.1139/G10-006
Holsinger KE, Lewis PO (2003) Hickory: a package for analysis of population genetic data v1.1. Distributed by the authors, Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs. Available at: http://www.academia.edu/1839794/. Accessed 29 Dec 2017
Holsinger KE, Wallace LE (2004) Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (Orchidaceae). Molec Ecol 13:887–894. https://doi.org/10.1111/j.1365-294X.2004.02052.x
Holsinger KE, Lewis PO, Dey DK (2002) A Bayesian approach to inferring population structure from dominant markers. Molec Ecol 11:1157–1164. https://doi.org/10.1046/j.1365-294X.2002.01512.x
Hughes PD, Woodward JC, van Calsteren PC, Thomas LE (2011) The glacial history of the Dinaric Alps, Montenegro. Quatern Sci Rev 30:3393–3412. https://doi.org/10.1016/j.quascirev.2011.08.016
Kintzios SE (2000) Sage: the genus Salvia. Harwood Academic Publishers, Amsterdam
Kryštufek B, Buzan EV, Hutchinson WF, Hanfling B (2007) Phylogeography of the rare Balkan endemic Martino’s vole, Dinaromys bogdanovi, reveals strong differentiation within the western Balkan Peninsula. Molec Ecol 16:1221–1232. https://doi.org/10.1111/j.1365-294X.2007.03235.x
Kučera J, Tremetsberger K, Vojta J, Marhold K (2008) Molecular study of the Cardamine maritima group (Brassicaceae) from the Balkan and Apennine Peninsula based on amplified fragment length polymorphism. Pl Syst Evol 275:193–207. https://doi.org/10.1007/s00606-008-0061-8
Kučera J, Marhold K, Lihova J (2010) Cardamine maritima group (Brassicaceae) in the amphi-Adriatic area: a hotspot of species diversity revealed by DNA sequences and morphological variation. Taxon 59:148–164. https://doi.org/10.1002/Tax.591015
Kullback S, Leibler RA (1951) On information and sufficiency. Ann Math Stat 22:79–86
Kutnjak D, Kuttner M, Niketic M, Dullinger S, Schönswetter P, Frajman B (2014) Escaping to the summits: phylogeography and predicted range dynamics of Cerastium dinaricum, an endangered high mountain plant endemic to the western Balkan Peninsula. Molec Phylogen Evol 78:365–374. https://doi.org/10.1016/j.ympev.2014.05.015
Lakušić D, Liber Z, Nikolic T, Surina B, Kovacic S, Bogdanovic S, Stefanovic S (2013) Molecular phylogeny of the Campanula pyramidalis species complex (Campanulaceae) inferred from chloroplast and nuclear non-coding sequences and its taxonomic implications. Taxon 62:505–524. https://doi.org/10.12705/623.1
Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:381–398
Liber Z, Židovec V, Bogdanović S, Radosavljević I, Pruša M, Filipović M, Han Dovedan I, Jug-Dujaković M, Šatović Z (2014) Genetic diversity of dalmatian sage (Salvia officinalis L.) as assessed by RAPD markers. Agric Conspect Sci 79:77–84
Lynch M, Milligan BG (1994) Analysis of population genetic-structure with RAPD markers. Molec Ecol 3:91–99. https://doi.org/10.1111/j.1365-294X.1994.tb00109.x
Marjanac LJ (2012) Pleistocene glacial and periglacial sediments of Kvarner, Northern Dalmatia and Southern Velebit Mt.—evidence of Dinaric glaciation. PhD Thesis, Department of Geology, Faculty of Science, University of Zagreb, Zagreb
Marjanac L, Marjanac T (2004) Glacial history of the Croatian Adriatic and coastal Dinarides. In: Ehlers J, Gibbard PL (eds) Quartenary glaciations—extent and chronology, part I: Europe: developments in quaternary science. Elsevier, Amsterdam, pp 19–26
Marjanac L, Marjanac T (2013) Sedimentological evidence of extensive Dinaric glaciation. In: Marjanac LJ, Mauch Lenardić J (eds) Book of abstracts 3rd scientific INQUA meeting Quaternary geology in Croatia with international participation, 21st–23rd March 2011, Zagreb. Hrvatska akademija znanosti i umjetnosti, Gelogiški zavod Slovenije, Zagreb, pp 37–38
Marjanac T, Marjanac L (2016) The extent of middle Pleistocene ice cap in the coastal Dinaric Mountains of Croatia. Quatern Res 85:445–455. https://doi.org/10.1016/j.yqres.2016.03.006
Marjanac LJ, Hughes P, Marjanac T (2017) A chronostratigraphic framework for Dinaric glaciation: new results and proposal for further investigation and modelling. 5th Regional scientific meeting on quaternary geology dedicated to geohazards and Final conference of the LoLADRIA project “Submerged Pleistocene landscapes of the Adriatic Sea”, 9–10 November 2017, Starigrad-Paklenica, Croatia. Croatian Academy of Sciences and Arts, Zagreb, pp 33–37
Médail F, Diadema K (2009) Glacial refugia influence plant diversity patterns in the Mediterranean Basin. J Biogeogr 36:1333–1345. https://doi.org/10.1111/j.1365-2699.2008.02051.x
Médail F, Quezel P (1999) Biodiversity hotspots in the Mediterranean basin: setting global conservation priorities. Conservation Biol 13:1510–1513. https://doi.org/10.1046/j.1523-1739.1999.98467.x
Meirmans PG (2012) AMOVA-based clustering of population genetic data. J Heredity 103:744–750. https://doi.org/10.1093/jhered/ess047
Nei M (1972) Genetic distance between populations. Amer Naturalist 106:283–292. https://doi.org/10.1086/282771
Nybom H, Bartish IV (2000) Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants. Perspect Pl Ecol Evol Syst 3:93–114. https://doi.org/10.1078/1433-8319-00006
Podnar M, Mayer W, Tvrtkovic N (2004) Mitochondrial phylogeography of the Dalmatian wall lizard, Podarcis melisellensis (Lacertidae). Organisms Diversity Evol 4:307–317. https://doi.org/10.1016/j.ode.2004.04.004
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Randall R (2007) Global compendium of weeds (GCW). Available at: http://www.hear.org/gcw/species/salvia_officinalis. Accessed 24 Jun 2019
Rešetnik I, Baričević D, Batîr Rusu D, Carović-Stanko K, Chatzopoulou P, Dajić-Stevanović Z, Gonceariuc M, Grdiša M, Greguraš D, Ibraliu A, Jug-Dujaković M, Krasniqi E, Liber Z, Murtić S, Pećanac D, Radosavljević I, Gj Stefkov, Stešević D, Šoštarić I, Šatović Z (2016) Genetic diversity and demographic history of wild and cultivated/naturalised plant populations: evidence from Dalmatian sage (Salvia officinalis L., Lamiaceae). PLoS ONE 11:e0159545. https://doi.org/10.1371/journal.pone.0159545
Rohlf FJ (2000) NTSYS-pc. Numerical taxonomy and multivariate analysis system, version 2.1. Exeter Publications, New York
Rousset F (1997) Genetic differentiation and estimation of gene flow form F-statistics under isolation by distance. Genetics 145:1219–1228
SAS Institute (2004) SAS/STAT® 9.1 User’s Guide. SAS Institute Inc, Cary
Schönswetter P, Tribsch A (2005) Vicariance and dispersal in the alpine perennial Bupleurum stellatum L. (Apiaceae). Taxon 54:725–732. https://doi.org/10.2307/25065429
Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, Urbana
Stepišnik U, Žebre M, Tičar J, Lipar M, Ferk M, Kodelja B, Klemenčič I (2010) Obseg pleistocenske poledenitve na Lovčenu v Črni gori. Geogr Vestn 82:9–22
Stojanović D, Aleksić JM, Jančić I, Jančić R (2015) A Mediterranean medicinal plant in the continental Balkans: a plastid DNA-based phylogeographic survey of Salvia officinalis (Lamiaceae) and its conservation implications. Willdenowia 45:103–118. https://doi.org/10.3372/wi.45.45112
Surina B, Schönswetter P, Schneeweiss GM (2011) Quaternary range dynamics of ecologically divergent species (Edraianthus serpyllifolius and E. tenuifolius, Campanulaceae) within the Balkan refugium. J Biogeogr 38:1381–1393. https://doi.org/10.1111/j.1365-2699.2011.02493.x
Ursenbacher S, Schweiger S, Tomovic L, Crnobrnja-Isailovic J, Fumagalli L, Mayer W (2008) Molecular phylogeography of the nose-horned viper (Vipera ammodytes, Linnaeus (1758)): evidence for high genetic diversity and multiple refugia in the Balkan peninsula. Molec Phylogen Evol 46:1116–1128. https://doi.org/10.1016/j.ympev.2007.11.002
Vekemans X, Beauwens T, Lemaire M, Roldan-Ruiz I (2002) Data from amplified fragment length polymorphism (AFLP) markers show indication of size homoplasy and of a relationship between degree of homoplasy and fragment size. Molec Ecol 11:139–151. https://doi.org/10.1046/j.0962-1083.2001.01415.x
Velić J, Velić I, Kljajo D, Protrka K, Škrabić H, Špoljar Z (2017) A geological overview of glacial accumulation and erosional occurrences on the Velebit and the Biokovo Mts., Croatia. Mining-Geol-Petrol Engin Bull 32:77–96. https://doi.org/10.17794/rgn.2017.4.8
Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP—a new technique for DNA-Fingerprinting. Nucl Acids Res 23:4407–4414. https://doi.org/10.1093/nar/23.21.4407
Wright S (1978) Evolution and the genetics of population, variability within and among natural populations. The University of Chicago Press, Chicago
Zhivotovsky LA (1999) Estimating population structure in diploids with multilocus dominant DNA markers. Molec Ecol 8:907–913. https://doi.org/10.1046/j.1365-294x.1999.00620.x
Zutic I, Dudai N (2008) Factors affecting germination of Dalmatian sage (Salvia officinalis) seed. ISHS Acta Hortic 782:121–126. https://doi.org/10.17660/ActaHortic.2008.782.12
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This research has been funded by the Project KK.01.1.1.01.0005 Biodiversity and Molecular Plant Breeding, Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Zagreb, Croatia.
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Conceived and designed the experiments: Zlatko Šatović, Zlatko Liber, and Marija Jug-Dujaković. Performed the experiments: Marija Jug-Dujaković and Zlatko Liber. Analyzed the data: Zlatko Šatović. Contributed reagents/materials/analysis tools: Zlatko Šatović, Marija Jug-Dujaković, and Zlatko Liber. Contributed to the writing of the manuscript: Marija Jug-Dujaković, Tonka Ninčević, Zlatko Šatović, Zlatko Liber, and Martina Grdiša. All the authors have read and approved the final version of the manuscript.
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Jug-Dujaković, M., Ninčević, T., Liber, Z. et al. Salvia officinalis survived in situ Pleistocene glaciation in ‘refugia within refugia’ as inferred from AFLP markers. Plant Syst Evol 306, 38 (2020). https://doi.org/10.1007/s00606-020-01665-9
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DOI: https://doi.org/10.1007/s00606-020-01665-9