Abstract
Cochlearia pyrenaica is one of the most endangered plant species in Europe, listed in many European and regional conservation policy documents (e.g. Spain, France, Belgium, Switzerland). To study its genetic structure, define its conservation units and propose a management strategy for this species, amplified fragment length polymorphism markers were used to analyse the genetic diversity within and between five representative populations of the species distribution in Western Europe (Cantabrian Range, North of Spain; Pyrenees, France; Wallonia, Belgium). Low levels of genetic diversity were revealed by the population percentage of polymorphic bands (PPB = 36.56%), average within-population diversity (H S = 0.0990) and genetic diversity within populations (H pop = 0.1541), although high levels were reported at species level (PPB = 81.16%; total genetic diversity for the species, H T = 0.0990; and genetic diversity within whole species, H sp = 0.2515). The coefficient of genetic differentiation among populations (G ST) was 0.3869. The analysis of Shannon diversity index in population and for the total data set partitioned (38.72%) and AMOVA (53%) detected a high level of interpopulation diversity, in broad agreement with the result of genetic differentiation analysis. NeighborNet network and principal coordinate analyses clustered the populations in three major groups congruent with geographical regions. Bayesian clustering also confirmed these three distinct genetic clusters. The level of gene flow (Nm) was estimated as 0.3961 individuals per generation among populations, with the genetic identity (I) and genetic distance (D) among populations ranging from 0.8679 to 0.9651 and from 0.0355 to 0.1417, respectively. Therefore, the low levels of genetic variation and high divergence of regional gene pools indicate that there is a need to protect each disjunct region of Western Europe.
Similar content being viewed by others
References
Abs C (1999) Differences in the life histories of two Cochlearia species. Folia Geobot 34:33–45
Al-Shehbaz IA, Beilstein MA, Kellogg EA (2006) Systematics and phylogeny of the Brassicaceae: an overview. Plant Syst Evol 259:89–120
Bailey CD, Koch MA, Mayer M, Mummenhoff K, O’Kane SL Jr, Warwick SI, Windham MD, Al-Shehbaz IA (2006) Toward a global phylogeny of the Brassicaceae. Molec Biol Evol 23:2142–2160
Bañares Á, Blanca G, Güemes J, Moreno JC, Ortíz S (eds) (2004) Atlas y libro rojo de la flora vascular amenazada de España. Dirección General de Conservación de la Naturaleza, Madrid
Bonin A, Bellemain E, Bronken Eidesen P, Pompanon F, Brochmann C (2004) How to track and assess genotyping errors in population genetics studies. Mol Ecol 13:3261–3273. doi:10.1111/j.1365-294X.2004.02346.x
Chater AO, Heywood VH (1964) Cochlearia L. In: Tutin TG, Heywood VH, Burges NA, Valentine DH, Walters SM, Webb DA (eds) Flora Europaea, vol I. Cambridge University Press, Cambridge, pp 313–314
Chater AO, Heywood VH, Wyse Jackson P, Akeroyd JR (1993) Cochlearia L. In: Tutin TG, Heywood VH, Burges NA, Valentine DH, Moore DM (eds) Flora Europaea, vol I, 2nd edn. Cambridge University Press, Cambridge, pp 378–380
Cieślak E, Korbecka G, Ronikier M (2007a) Genetic structure of the critically endangered endemic Cochlearia polonica (Brassicaceae): efficiency of the last-chance transplantation. Bot J Linn Soc 155:527–532
Cieślak E, Ronikier M, Koch MA (2007b) Western Ukrainian Cochlearia (Brassicaceae)—the identity of an isolated edge population. Taxon 56:112–118
Daneck H, Abraham V, Fér T, Marhold K (2011) Phylogeography of Lonicera nigra in Central Europe inferred from molecular and pollen evidence. Preslia 83:237–257
Dixon C, Schönswetter P, Schneeweiss GM (2007) Traces of ancient range shifts in a mountain plant group (Androsace halleri complex, Primulaceae). Mol Ecol 16:3890–3901
Dixon C, Schönswetter P, Vargas P, Ertl S, Schneeweiss GM (2009) Bayesian hypothesis testing supports long-distance Pleistocene migrations in a European high mountain plant (Androsace vitaliana, Primulaceae). Mol Phylogenet Evol 53:580–591
Eckstein RL, O’Neill RA, Danihelka J, Otte A, Köhler W (2006) Genetic structure among and within peripheral and central populations of three endangered floodplain violets. Mol Ecol 15:2367–2379
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 HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10(3):564–567
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
Grundt HH, Obermayer R, Borgen L (2005) Ploidal levels in the arctic-alpine polyploid Draba lactea (Brassicaceae) and its low-ploid relatives. Bot J Linn Soc 147:333–347
Hammer Ø, Harper DAT, Ryan PD (2001) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4(1):1–9
Heuertz M, Fineschi S, Anzidei M, Pastorelli R, Salvini D, Paule L, Frascaria-Lacoste N, Hardy OJ, Vekemans X, Vendramin GG (2004) Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe. Mol Ecol 13:3437–3452
Holt RD (2003) On the evolutionary ecology of species’ ranges. Evol Ecol Res 5:159–178
Huck S, Büdel B, Kadereit JW, Printzen C (2009) Range-wide phylogeography of the European temperate-montane herbaceous plant Meum athamanticum Jacq.: evidence for periglacial persistence. J Biogeogr 36:1588–1599
Hurka H, Neuffer B (1997) Evolutionary processes in the genus Capsella (Brassicaceae). Plant Syst Evol 206:295–316
Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Molec Biol Evol 23:254–267
Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A (1997) Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breed 3:381–390
Jork KB, Kadereit JW (1995) Molecular phylogeny of the Old World representatives of Papaveraceae subfamily Papaveroideae with special emphasis on the genus Meconopsis. Plant Syst Evol Suppl 9:171–180
Kadereit JW, Schwarzbach AE, Jork KB (1997) The phylogeny of Papaver s.l. (Papaveraceae): polyphyly or monophyly? Plant Syst Evol 204:75–98
King RA, Ferris C (1998) Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn. Mol Ecol 7:1151–1161
Koch M (2002) Genetic differentiation and speciation in prealpine Cochlearia (Brassicaceae): allohexaploid Cochlearia bavarica (Brassicaceae) compared to its diploid ancestor Cochlearia pyrenaica in Germany and Austria. Plant Syst Evol 232:35–49
Koch M, Al-Shehbaz IA (2000) Molecular systematics of the Chinese Yinshania (Brassicaceae): evidence from plastid and nuclear its DNA sequence data. Ann Missouri Bot Gard 87:246–272
Koch M, Bernhardt K-G (2004) Cochlearia macrorrhiza, a highly endangered lowland species from eastern Austria. Conservation genetics, ex situ and in situ conservation efforts. Scripta Bot Belg 29:157–164
Koch M, Hurka H, Mummenhoff K (1996) Chloroplast DNA restriction site variation and RAPD-analyses in Cochlearia (Brassicaceae): biosystematics and speciation. Nord J Bot 16:585–604
Koch M, Huthmann M, Hurka H (1998) Isozymes, speciation and evolution in the polyploid complex Cochlearia L. (Brassicaceae). Bot Acta 111:451–466
Koch M, Mummenhoff K, Hurka H (1999) Molecular phylogenetics of Cochlearia (Brassicaceae) and allied genera based on nuclear ribosomal ITS DNA sequence analysis contradict traditional concepts of their evolutionary relationship. Plant Syst Evol 216:207–230
Koch M, Dobeš C, Bernhardt KG, Kochjarová J (2003) Cochlearia macrorrhiza (Brassicaceae): a bridging species between Cochlearia taxa from the eastern Alps and the Carpathians? Plant Syst Evol 242:137–147
Kochjarová J, Valachovič M, Bureš P, Mráz P (2006) The genus Cochlearia L. (Brassicaceae) in the eastern Carpathians and adjacent area. Bot J Linn Soc 151:355–364
Kramp K, Huck S, Niketić M, Tomović G, Schmitt T (2009) Multiple glacial refugia and complex postglacial range shifts of the obligatory woodland plant Polygonatum verticillatum (Convallariaceae). Plant Biol 11:392–404
Kropf M, Kadereit JW, Comes HP (2003) Differential cycles of range contraction and expansion in European high mountain plants during the Late Quaternary: insights from Pritzelago alpina (L.) O. Kuntze (Brassicaceae). Mol Ecol 12:931–949
Kučera J, Valko I, Marhold K (2005) On-line database of the chromosome numbers of the genus Cardamine (Brassicaceae). Biologia (Bratislava) 60:473–476
Légifrance (2004a) Arrêté du 30 mars 1990 relatif à la liste des espèces végétales protégées en région Auvergne complétant la liste nationale. http://www.legifrance.gouv.fr/affichTexte.do?cidTexte=JORFTEXT000000349624&dateTexte
Légifrance (2004b) Arrêté du 30 décembre 2004 relatif à la liste des espèces végétales protégées en région Midi-Pyrénées complétant la liste nationale. http://www.legifrance.gouv.fr/affichTexte.do?cidTexte=JORFTEXT000000628251&dateTexte
Lesica P, Allendorf FW (1995) When are peripheral populations valuable for conservation? Conserv Biol 9(4):753–760
Lewontin RC (1972) The apportionment of human diversity. In: Dobzhansky T, Hecht MK, Steere WC (eds) Evolutionary biology, vol 6. Appleton-Century-Crofts, New York, pp 381–398
Lin J-J, Kuo J, Ma J, Saunders JA, Beard HS, Macdonald MH, Kenworthy W, Ude GN, Matthews BF (1996) Identification of molecular markers in soybean comparing RFLP, RAPD and AFLP DNA mapping techniques. Plant Mol Biol Rep 14:156–159
Moreno JC (ed) (2008) Lista Roja 2008 de la Flora Vascular Española. Dirección General de Medio Natural y Política Forestal (Ministerio de Medio Ambiente, y Medio Rural y Marino, y Sociedad Española de Biología de la Conservación de Plantas), Madrid
Moritz CS (1994) Defining ‘evolutionarily significant units’ for conservation. Trends Ecol Evol 9:373–375
Moser D, Gygax A, Bäumler B, Wyler N, Palese R (2002) Liste Rouge des fougères et plantes à fleurs menacées de Suisse. Office fédéral de l’environnement, des forêts et du paysage, Berne
Nei M (1972) Genetic distance between populations. Am Nat 106:283–392
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323
Nei M (1977) F-statistics and analysis of gene diversity in subdivided populations. Ann Hum Genet 41:225–233
Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295
Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: causes, consequences and solutions. Nat Rev Genet 6:847–859. doi:10.1038/nrg1707
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Saintenoy-Simon J (2006) Première liste des espèces rares, menacées et protégées de la Région Wallonne (Ptéridophytes et Spermatophytes). Version 1 (avec la collaboration de Barbier Y, Delescaille L-M, Dufrêne M, Gathoye J-L, Verté P). http://biodiversite.wallonie.be/fr/plantes-protegees-et-menacees.html?IDC=3076
Slatkin M, Barton NH (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution 43:1349–1368
Sosa PA, González-Pérez MA, Moreno C, Clarke JB (2010) Conservation genetics of the endangered endemic Sambucus palmensis Link (Sambucaceae) from the Canary Islands. Conserv Genet 11(6):2357–2368
Vargas P (2000) A phylogenetic study of Saxifraga sect. Saxifraga (Saxifragaceae) based on nrDNA ITS sequences. Plant Syst Evol 223:59–70
Vogt R (1985) Die Cochlearia pyrenaica-Gruppe in Zentraleuropa. Ber Bayer Bot Ges 56:5–52
Vogt R (1987) Die Gattung Cochlearia L. (Cruciferae) auf der Iberischen Halbinsel. Mitt Bot Staatssamml München 23:393–421
Vos P, Hogers R, Bleeker M, Reijand M, van de Lee T, Hornes M, Frijers A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414
Yeh FC, Boyle TJB (1997) Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belg J Bot 129:157
Zhang L-B, Comes HP, Kadereit JW (2001) Phylogeny and Quaternary history of the European montane/alpine endemic Soldanella (Primulaceae) based on ITS and AFLP variation. Am J Bot 88:2331–2345
Acknowledgments
The authors wish to thank Laurence Desmet, Veerle Buysens and Jan De Riek for outstanding technical assistance (ILVO-Plant, Melle, Belgium). We are grateful to Juan Homet (Oviedo University) for helping with the sampling, Pieter Asselman (Ghent University) for laboratory expertise, and finally Candela Cuesta (Plant System Biology Department, Gent) and Marcus A. Koch (Heidelberg Institute of Plant Sciences, Heidelberg) for critical comments on the manuscript. This research was conducted during a short stay of E. Cires in the Research Group Spermatophytes (Ghent University).
Author information
Authors and Affiliations
Corresponding author
Appendix: replicate error rates for representative data sets
Appendix: replicate error rates for representative data sets
As a measure of accuracy, for each character matrix, we calculated the number of replicate pairs that were correctly assigned. Representative data were used from two different bin width (BW) and four peak height threshold (PHT) settings in GeneMapper for C. pyrenaica data sets. For each character matrix, we calculated the relative error for every 100 alleles analysed as well as the replicate error rate expressed in percentages (value in brackets) (Bonin et al. 2004; Pompanon et al. 2005). The values we suggest as the most appropriate (i.e. the overall optimal parameter settings) are indicated with an asterisk.
PHT 50 | PHT 100 | PHT 150 | PHT 200 | |
---|---|---|---|---|
BW 1.0 | 0.857 (5.60%)* | 1.156 (5.04%) | 0.985 (3.29%) | 2.038 (5.34%) |
BW 1.5 | 1.360 (6.72%) | 1.46 (4.98%) | 0.920 (2.54%) | 2.42 (5.16%) |
Therefore, the optimal parameter settings in GeneMapper for C. pyrenaica data sets were PHT 50 and BW 0.5. The profiles from two replicates samples from a single individual are shown in Fig. 5a–c.
Rights and permissions
About this article
Cite this article
Cires, E., Samain, MS., Goetghebeur, P. et al. Genetic structure in peripheral Western European populations of the endangered species Cochlearia pyrenaica (Brassicaceae). Plant Syst Evol 297, 75 (2011). https://doi.org/10.1007/s00606-011-0500-9
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00606-011-0500-9