Molecular Ecology (2003) 12, 2201–2214 doi: 10.1046/j.1365-294X.2003.01899.x © 2003 Blackwell Publishing Ltd Blackwell Publishing Ltd. Phylogeography of the rock partridge (Alectoris graeca) E. RANDI,* C. TABARRONI,* S. RIMONDI,* V. LUCCHINI * and A. SFOUGARIS † *Istituto Nazionale per la Fauna Selvatica (INFS), Ozzano Emilia (BO), Italy, †Department of Agriculture, Crop Production and Rural Environment, University of Thessaly, Volos, Greece Abstract We used mitochondrial DNA control-region and microsatellite data to infer the evolutionary history and past demographic changes in 332 rock partridges (Alectoris graeca) sampled from throughout the species’ distribution range, with the exception of the central Balkans region. Maternal and biparental DNA markers indicated concordantly that rock partridge populations are structured geographically (mtDNA φ ST = 0.86, microsatellite F ST = 0.35; R ST = 0.31; P < 0.001). Phylogenetic analyses of 22 mtDNA haplotypes identified two major phylogroups (supported by bootstrap values = 93%), splitting partridges from Sicily vs. all the other sampled populations at an average Tamura–Nei genetic distance of 0.035, which corresponds to 65% of the average distance between closely related species of Alectoris. Coalescent estimates of divergence times suggested that rock partridges in Sicily were isolated for more than 200 000 years. This deep subdivision was confirmed by multivariate, Bayesian clustering and population assignment analyses of microsatellite genotypes, which supported also a subdivision of partridges from the Alps vs. populations in the Apennines, Albania and Greece. Partridges in the Apennines and Albania–Greece were probably connected by gene flow since recently through a late Pleistocene Adriatic landbridge. Deglaciated Alps were probably colonized by distinct and, perhaps, not yet sampled source populations. Bottleneck and mismatch analyses indicate that rock par- tridges have lost variability through past population declines, and did not expand recently. Deglaciated areas could have been recolonized without any strong demographic expansion. Genetic data partially supported subspecies subdivisions, and allowed delimiting distinct conservation units. Rock partridges in Sicily, formally recognized as A. g. whitakeri, met the criteria for a distinct evolutionary significant unit. Keywords: Alectoris graeca, demographic changes, microsatellites, mtDNA control-region, phylo- geography, population structure, rock partridge Received 30 January 2003; revision received 2 May 2003; accepted 2 May 2003 Introduction Pleistocene climate changes have shaped the patterns of geographical distribution, demographic history and genetic diversification in a number of plant and animal species in the Palaearctic (Avise 2000; Hewitt 2000). During cold-dry glacial periods arctic tundra ecosystems covered most of northern and central Europe. For thousand of years the Alps, Pyrenees and parts of the Apennines were glaciated. In these periods populations adapted to temperate climates were forced to retreat to southern refuges. During glacials the Mediterranean Sea level was 100 –120 m lower than present, many islands were interconnected or united to the mainland and a wide landbridge filled the gap between the eastern and western Adriatic coasts (Dawson 1996: 35 – 36), thus providing occa- sions for dispersal of animal populations (Fig. 1). Glaciations predictably shaped the patterns of genetic diversity in Mediterranean species that inhabit mid- latitude temperate zones or formerly glaciated mountains. Among them, the Alectoris partridges (Aves, Galliformes) constitute an interesting case study. The fossil record documents the presence of Alectoris in Europe in the Correspondence: Ettore Randi. Istituto Nazionale per la Fauna Selvatica, Via Cà Fornacetta 9, 40064 Ozzano Emilia (BO), Italy. Fax: + 39 051796 628; E-mail: met0217@iperbole.bo.it