Molecular Ecology (2000) 9, 691–698 © 2000 Blackwell Science Ltd Blackwell Science, Ltd Mitochondrial haplotype diversity among Portuguese brown trout Salmo trutta L. populations: relevance to the post-Pleistocene recolonization of northern Europe S. WEISS,*† A. ANTUNES,‡§ C. SCHLÖTTERER† and P. ALEXANDRINO‡§ *Abteilung für Hydrobiologie, Universität für Bodenkultur, Max Emanuel Straße 17, 1180 Vienna, †Institut für Tierzucht und Genetik, Veterinärmedizinische Universität, Veterinärplatz 1, 1210 Vienna, ‡Departmento de Zoologia-Antropologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4050 Porto, Portugal, §Centro de Estudos de Ciência Animal (CECA), ICETA-U.P., Campus Agrário de Vairão, 4480 Vila do Conde, Portugal Abstract Mitochondrial haplotype diversity in seven Portuguese populations of brown trout, Salmo trutta L., was investigated by sequencing the 5′ end of the mitochondrial DNA (mtDNA) control region. Five new haplotypes were described for this species, each two to three mutational steps distant from the common north Atlantic haplotype. Significant population subdivision of mtDNA haplotypes was also apparent. Based on these results, as well as on published data describing the distribution of both mtDNA haplotypes and allozyme alleles throughout Europe, the postglacial recolonization of northern Europe was re-evaluated. It is argued that the available data do not support the contribution of two major glacial refugia (southwest Atlantic and Ponto-Caspian Basin) to this postglacial recolonization, as proposed in a recently published model. The unique genetic architecture of Portuguese brown trout within the Atlantic-basin clade of this species represents a highly valuable genetic resource that should be protected from introgression with nonendemic strains of hatchery fish. Keywords: allozymes, glacial refugia, mtDNA, Pleistocene, Portugal, S. trutta Received 11 July 1999; revision received 18 October 1999; accepted 9 December 1999 Introduction Investigations of mitochondrial DNA (mtDNA) sequence diversity in brown trout, Salmo trutta L. have been used to construct an inferred phylogenetic tree depicting four lineages corresponding to the major drainage basins (Atlantic, Mediterranean, Adriatic and Danube) and a fifth equally divergent lineage corresponding to the morpho- logically distinct marbled trout, S. trutta marmoratus, found in drainages of northern Italy (Bernatchez et al. 1992; Giuffra et al. 1994). Based on 310 bp of the 5′ end of the control region, haplotype diversity within major drainage basins was found to vary considerably. For example, a single haplotype (At1) dominated samples from Atlantic basin sites, and 10 haplotypes were detected in sites within the Caspian–Black–Aral basins (Bernatchez et al. 1992; Bernatchez & Osinov 1995). Allele frequencies at several diagnostic protein loci generally support a subdivision by major drainage basins and have been used to draw inferences on several regionally specific, or more broad-scale, post- Pleistocene recolonization events (Hamilton et al. 1989; Presa et al. 1994; Bernatchez & Osinov 1995; Riffle et al. 1995; Apostolidis et al. 1996; García-Marín & Pla 1996). García-Marín et al. (1999) proposed a postglacial recol- onization model of the north Atlantic, involving three of the four major drainage basins, based primarily on allelic distributions at two enzymatic loci (LDH-C* and CK-A1*). According to this model, following the last glacial maximum (≈ 18 000 years before present [bp]; Frenzel et al. 1992) the north Atlantic was first colonized by northwestwardly migrating populations from undefined passages between the North Sea and the Ponto-Caspian basin, and sub- sequently influenced by gene flow from unglaciated regions of both northern continental Europe as well as Atlantic drainages of the Iberian Peninsula. Correspondence: Steven Weiss. Present address: Centro de Estudos de Ciência Animal (CECA), ICETA-U.P., Campus Agrário de Vairao, 4480 Vila do Conde, Portugal. Fax: +351 252 6611780; E-mail: sjweiss@mail.icav.up.ot