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Genetic structure in peripheral Western European populations of the endangered species Cochlearia pyrenaica (Brassicaceae)

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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.

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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).

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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%)

  1. AFLP profiles obtained for our samples of C. pyrenaica with BW 0.5 were vague, and they were not taken into account for later analyses

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.

Fig. 5a–c
figure 5

Example AFLP profiles. Each profile consists of a plot of fluorescence (relative fluorescent units, rfu) versus fragment mobility/size (base pairs, bp) for one fluorescently tagged primer pair combination. a Visualising polymorphic peaks, b detail of the primer combination EcoRI-ACT/MseI-CAC, c detail of the primer combination EcoRI-AGC/MseI-CTA (Peak Scanner™ Software 1.0 was used to open the profiles)

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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

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