Molecular Ecology (2008) 17, 3147–3159 doi: 10.1111/j.1365-294X.2008.03817.x © 2008 The Authors Journal compilation © 2008 Blackwell Publishing Ltd Blackwell Publishing Ltd The history of Seasonally Dry Tropical Forests in eastern South America: inferences from the genetic structure of the tree Astronium urundeuva (Anacardiaceae) S. CAETANO,* D. PRADO,† R. T. PENNINGTON,‡ S. BECK,§ A. OLIVEIRA-FILHO,¶ R. SPICHIGER* and Y. NACIRI* *Laboratoire de Systématique et de Biodiversité, Unité de Phylogénie et Génétique Moléculaires, Conservatoire et Jardin botaniques, 1 Chemin de l’Impératrice, CP 60, CH-1292 Chambésy, Genève, Switzerland, †Cátedra de Botánica Morfológica y Sistemática, Facultad de Ciencias Agrarias, UNR, Casilla de Correo No. 14, S2125ZAA, Zavalla, Argentina, ‡Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK, §Herbario Nacional de Bolivia, P.O. BOX 10077, Correo Central La Paz, Bolivia, ¶Departamento de Ciências Florestais, Universidade de Lavras, 37200-000, Lavras, MG, Brazil Abstract Today, the Seasonally Dry Tropical Forests (SDTF) of eastern South America occur as large, well-defined nuclei (e.g. Caatinga in the northeast) and as smaller enclaves within other vegetations (e.g. Cerrado and Chaco). In order to infer the way the present SDTF distribution was attained, the genetic structure of Astronium urundeuva, a tree confined to SDTF, was assessed using two chloroplast spacers and nine microsatellite loci. Five haplotypes were identified, whose distribution was spatially structured. The distribution of the two most common and divergent haplotypes suggested former vicariance and progressive divergence due to isolation. More recent range expansions of these two lineages subsequently occurred, leading to a secondary contact at the southern limit of the Caatinga SDTF nucleus. The multilocus-Bayesian approach using microsatellites consistently identified three groups of populations (Northeast, Central and Southwest). Isolation by distance was found in Northeast and Southwest groups whereas admixture was detected in the Central group, located at the transition between Caatinga and Cerrado domains. All together, the results support the existence of range expansions and secondary contact in the Central group. This study provides arguments that favour the existence of a previously more continuous formation of SDTF in eastern South America. Keywords: chloroplast spacers, genetic boundaries, isolation by distance, microsatellites, Pleistocenic Arc, secondary contact, spatial analyses, vicariance events Received 21 October 2007; revision received 24 February 2008; accepted 20 March 2008 Introduction The present-day distribution of a taxon is both the outcome of habitat preferences and colonization history. The way species reacted to past climatic changes, such as those experienced in the Pleistocene, reflects the dynamics of ecosystems in a long-term perspective (Schaal et al. 1998). In this context, exploring the genetic patterns of trees is of great interest, because of the general attributes that make them unique in terms of mode and tempo of evolution (see review in Petit & Hampe 2006). How Pleistocenic climate fluctuations influenced different biomes in South America is still poorly understood. Nearly all available data are based on fossil pollen in the Amazon Basin (e.g. Colinvaux et al. 1996), and the few existing studies of molecular phylogeography of trees have focused mainly on rain-forest species (Caron et al. 2000; Cavers et al. 2003; Dutech et al. 2003), or on species from the seasonally dry savanna formations of the Brazilian Cerrado (Lacerda et al. 2001; Collevatti et al. 2003; Ramos et al. 2007). Here, we will address the question of whether the Seasonally Dry Tropical Forests (SDTF) of eastern South America may have been more widespread during drier glacial climates, Correspondence: Y. Naciri, Fax: +41 22 4185101; E-mail: yamama.naciri@ville-ge.ch