Gabriela Antunez-de-Mayolo 1 Adriana Antunez-de-Mayolo 1 Pamela Antunez-de-Mayolo 1 Surinder S. Papiha 2 Michael Hammer 3 Juan J. Yunis 4 Emilio J. Yunis 5 Chendi Damodaran 6 Marian Martinez de Pancorbo 7 Jose Luis Caeiro 8 Valery P. Puzyrev 9 Rene J. Herrera 1 1 Department of Biological Sciences, Florida International University, University Park Campus, Miami, FL, USA 2 Department of Human Genetics, University of New Castle upon Thames, New Castle upon Thames, UK 3 Department of EEB, Biosciences West, University of Arizona, Tucson, AZ, USA 4 Instituto de Genética, Universidad Nacional de Colombia, Santa Fe de Bogota, Colombia 5 Servicios Médicos Yunis, Turbay y Cia, Santa Fe de Bogota, Colombia 6 Forensic House 30-A, Kamalajar Salid, Mylapore, Madras, India 7 Departamento de Z. y Dinámica Celular, Facultad de Farmacia, Universidad del Pais Vasco, Vitoria-Lasteiz, España 8 Universidad Santiago de Compostela, Santiago de Compostela, España 9 Institute of Medical Genetics, Tomsk Scientific Center of the Russian Academy of Medical Science, Tomsk, Russia Phylogenetics of worldwide human populations as determined by polymorphic Alu insertions Alu elements, the largest family of interspersed repeats, mobilize throughout the ge- nomes of primates by retroposition. Alu are present in humans in an excess of 500 000 copies per haploid genome. Since some of the insertion alleles have not reached fixa- tion, they remain polymorphic and can be used as biallelic DNA marker systems in investigations of human evolution. In this study, six polymorphic Alu insertional (PAI) loci were used as genetic markers. These markers are thought to be selectively neutral. The presence of these six PAIs was determined by a polymerase chain reaction (PCR)- based assay in 1646 individuals from 47 populations from around the world. Examina- tion of the populations by plotting the first and second principal components, shows the expected segregation of populations according to geographical vicinity and estab- lished ethnic affinities. Centroid analysis demonstrated that sub-Sahara populations have experienced higher than average gene flow and/or represent larger populations as compared to groups in other parts of the globe and especially to known inbreed populations. This is consistent with greater heterogeneity and diversity expected of source groups. In addition, maximum likelihood (ML) analyses were performed with these 47 populations and a hypothetical ancestral group lacking the insertion in all six loci. Analysis of our data supports the Out of Africa hypothesis. African populations and admixed groups of African descent formed a single monophyletic group with a basal placement on the tree, which grouped closest to the hypothetical ancestor. Keywords: Alu family of repetitive elements / Recent human evolution / Short interspersed ele- ments EL 5023 Correspondence: Dr. Rene J. Herrera, Department of Biological Sciences, FL International University, University Park Campus, Miami, FL 33199 USA E-mail: herrerar@fiu.edu Fax: +305-348-1259 Abbreviations: ML, maximum likelihood; PAIs, polymorphic Alu insertions 3346 Electrophoresis 2002, 23, 3346–3356 1 Introduction In this study, six PAIs were utilized as genetic markers to ascertain phylogenetic relationships. Alu sequences are ancestrally related from the 7SL RNA gene [1]. It is believed that a mutated 7SL gene, early in primate evolu- tion, became mobile by transposition via a RNA inter- mediate and reverse transcription prior to insertion into novel sites [2–4]. Alu sequences are subdivided into groups of related subfamilies. One of the most recently formed subfamilies is the human-specific (HS), which was derived from the Catarrhini-specific (CS) subfamily [5]. The number of HS insertions is estimated to be 500– 2000 per haploid genome and are primarily restricted to humans [6, 7]. A second subfamily, Sb2, which is an inde- pendent derivative of the CS lineage, has also been recently expanding within the human genome [5]. PAIs are not unique to humans. These insertional markers have been detected in Baboon species [8]. The distribution of some HS and Sb2 elements varies in geographically distinct human populations [9]. The rate of new insertions that reach polymorphic levels is only about 100–200 per million years, thus the probability for independent insertions of two or more elements at exactly the same nucleotide site is almost nil [5]. Also, Alu ele- ments are stable insertions as they are rarely completely deleted, leaving behind residual and detectable Alu  2002 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim 0173-0835/02/1910–3346 $17.501.50/0