Tree Genetics & Genomes

, 11:99 | Cite as

Phylogeography and population genetics of black alder (Alnus glutinosa (L.) Gaertn.) in Ireland: putting it in a European context

  • Philippe Cubry
  • Evelyn Gallagher
  • Ellen O’Connor
  • Colin T. Kelleher
Original Article
Part of the following topical collections:
  1. Population structure


Black alder (Alnus glutinosa (L.) Gaertn.) is a widespread tree of European forests with a high potential for wood and biomass production. This study investigated the genetic origin and diversity in remnants of putative native alder forest stands in Ireland and compared it with other European populations to determine phylogeographic patterns. The efficiency of capture of the genetic diversity in a breeding population was also assessed. Data were obtained from chloroplast DNA (cpDNA) polymorphisms and from nuclear microsatellites. In silico PCR-RFLP was used to locate cpDNA sequence polymorphisms in order to develop flanking primers for high-resolution melting (HRM) analysis. The cpDNA polymorphism analysis detected two main haplotypes in Ireland. The same two are also found in Wales and England while only one is found in Scotland. The results suggest that Irish populations of alder have originated from at least two European glacial refugia. Black alder in Ireland exhibited no or very weak population differentiation using nuclear microsatellite markers, which is consistent for a wind-dispersed, outcrossing species. Based on the nuclear microsatellite data, a decline in population sizes is estimated to have occurred around a timeframe that coincides with a period of large-scale deforestation. The breeding population contained two haplotypes and showed a high level of genetic capture (86 % of microsatellite alleles) when compared with all samples combined. This study fills a gap in previous knowledge, provides an additional marker and an additional method for future studies. The characterisation of a breeding population provides valuable baseline data for a national alder tree improvement programme.


Alnus glutinosa Breeding population cpDNA High-resolution melting analysis HRM 



The authors thank Oliver Sheridan (Teagasc) for assistance with obtaining samples. We also thank Olivier Lepais for samples provided from Scotland. The authors would also like to thank the editor and the anonymous reviewers for helpful comments and suggestions.


Funding for this research was received from the Department of Agriculture, Food and the Marine, Ireland under the Conservation of Genetic Resources Grant Aid Scheme (project 11/GR/12) and the COFORD Science Technology and Innovation Platform (Project ForGen—Forest Genetic Resources Research Programme).

Data Archiving Statement

Microsatellite raw data is presented as supplemental material.

DNA sequence GenBank accessions for the different haplotypes sequenced are H1-KR014254, H2-KR014252, H4-KR014253, and H5-KR014251.

Supplementary material

11295_2015_924_MOESM1_ESM.pdf (1 mb)
Table S1 A list of samples and sample locations used in this study with raw data for nuclear and cpDNA markers. (PDF 1062 kb)
11295_2015_924_MOESM2_ESM.pdf (36 kb)
Table S2 Haplotype counts for the populations and groups. (PDF 35 kb)
11295_2015_924_MOESM3_ESM.pdf (41 kb)
Table S3 AMOVA based on cpDNA polymorphisms. (PDF 41 kb)
11295_2015_924_MOESM4_ESM.pdf (43 kb)
Table S4 Descriptive statistics and HW tests at the country level per marker. (PDF 42 kb)
11295_2015_924_MOESM5_ESM.pdf (41 kb)
Table S5 Descriptive statistics and HW tests at the sets level within Irish samples per marker. (PDF 41 kb)
11295_2015_924_MOESM6_ESM.pdf (32 kb)
Table S6 R st matrices for different groups and sets of samples. (PDF 32 kb)
11295_2015_924_MOESM7_ESM.pdf (33 kb)
Table S7 AMOVA based on nuclear microsatellites within the whole sample (groups = Irish, Scottish, French). (PDF 32 kb)
11295_2015_924_MOESM8_ESM.pdf (3.2 mb)
Fig. S1 Map of the sampled populations. In red squares and green circles the initial populations sampled as part of the national breeding population and the wild set, respectively. (PDF 3298 kb)
11295_2015_924_MOESM9_ESM.png (1.1 mb)
Fig. S2 A map of the distribution of the five detected haplotypes obtained by combining cpDNA indel and microsatellites. Light green haplotype H1, dark green haplotype H2, light blue haplotype H3, dark blue haplotype H4, and red haplotype H5. (PNG 1092 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Philippe Cubry
    • 1
    • 2
  • Evelyn Gallagher
    • 1
  • Ellen O’Connor
    • 3
    • 4
  • Colin T. Kelleher
    • 1
  1. 1.DBN Plant Molecular LaboratoryNational Botanic Gardens of IrelandDublin 9Ireland
  2. 2.INRA, UR 629 Ecologie des Forêts MéditerranéennesURFMAvignon Cedex 9France
  3. 3.School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
  4. 4.Teagasc Ashtown Food Research CentreDublin 15Ireland

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