ORIGINAL ARTICLE Phylogeography and population genetics of black alder (Alnus glutinosa (L.) Gaertn.) in Ireland: putting it in a European context Philippe Cubry 1,2 & Evelyn Gallagher 1 & Ellen O’Connor 3,4 & Colin T. Kelleher 1 Received: 9 December 2014 /Revised: 18 July 2015 /Accepted: 28 August 2015 # Springer-Verlag Berlin Heidelberg 2015 Abstract 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 ob- tained from chloroplast DNA (cpDNA) polymorphisms and from nuclear microsatellites. In silico PCR-RFLP was used to locate cpDNA sequence polymorphisms in order to de- velop 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 dif- ferentiation 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 addi- tional 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. Keywords Alnus glutinosa . Breeding population . cpDNA . High-resolution melting analysis . HRM Introduction Alnus glutinosa (L.) Gaertn (black or common European al- der) is a widespread broadleaf species common in many Eu- ropean forests. It ranges across Eurasia from Russia in the east to Ireland in the west and from southern Europe to southern Scandinavia (Euforgen 2009). It is also present in isolated populations further south, such as in the north of Morocco and Algeria. Alder grows best on deep moist soils or riparian habitats where it contributes to soil stabilisation and water filtration and provides habitat for fauna and flora (McVean Communicated by S. C. González-Martínez This article is part of the Topical Collection on Population Structure Electronic supplementary material The online version of this article (doi:10.1007/s11295-015-0924-4) contains supplementary material, which is available to authorized users. * Colin T. Kelleher colin.kelleher@opw.ie Philippe Cubry philippe.cubry@hotmail.fr Ellen O’Connor elaine.oconnor@teagasc.ie 1 DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Glasnevin, Dublin 9, Ireland 2 INRA, UR 629 Ecologie des Forêts Méditerranéennes, URFM, Domaine Saint Paul, Site Agroparc, 84914 Avignon Cedex 9, France 3 School of Biological, Earth and Environmental Sciences, University College Cork, Butler Building, Distillery Field, North Mall, Cork, Ireland 4 Teagasc Ashtown Food Research Centre, Dunsinea, Castleknock, Dublin 15, Ireland Tree Genetics & Genomes (2015) 11:99 DOI 10.1007/s11295-015-0924-4