Annals of Human Genetics

Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade

H.-J.  BANDELT  a1 c1, J.  ALVES-SILVA  a2, P. E. M.  GUIMARÃES  a2, M. S.  SANTOS  a2, A.  BREHM  a3, L.  PEREIRA  a4 a5, A.  COPPA  a6, J. M.  LARRUGA  a7, C.  RENGO  a8 a9, R.  SCOZZARI  a8, A.  TORRONI  a8 a10, M. J.  PRATA  a4 a5, A.  AMORIM  a4 a5, V. F.  PRADO  a2 and S. D. J.  PENA  a2
a1 Fachbereich Mathematik, Universität Hamburg, 20146 Hamburg, Germany
a2 Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte-MG, Brazil 30161-970
a3 Centro de Ciências Biológicas e Geológicas, Universidade da Madeira, 9000 Funchal, Portugal
a4 IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), 4200 Porto, Portugal
a5 Faculdade de Ciências da Universidade do Porto, 4099-002 Porto, Portugal
a6 Dipartimento di Biologia Animale e dell'Uomo, Università ‘La Sapienza’, 00185 Roma, Italy
a7 Departamento de Genética, Universidad de La Laguna, 38271 La Laguna, Tenerife, Spain
a8 Dipartimento di Genetica e Biologia Molecolare, Università ‘La Sapienza’, 00185 Roma, Italy
a9 Istituto di Medicina Legale, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
a10 Dipartimento di Genetica e Microbiologia, Università di Pavia, 27100 Pavia, Italy


The mtDNA haplogroup L3e, which is identified by the restriction site +2349 MboI within the Afro-Eurasian superhaplogroup L3 (−3592 HpaI), is omnipresent in Africa but virtually absent in Eurasia (except for neighbouring areas with limited genetic exchange). L3e was hitherto poorly characterised in terms of HVS-I motifs, as the ancestral HVS-I type of L3e cannot be distinguished from the putative HVS-I ancestor of the entire L3 (differing from the CRS by a transition at np 16223). An MboI screening at np 2349 of a large number of Brazilian and Caribbean mtDNAs (encompassing numerous mtDNAs of African ancestry), now reveals that L3e is subdivided into four principal clades, each characterised by a single mutation in HVS-I, with additional support coming from HVS-II and partial RFLP analysis. The apparently oldest of these clades (transition at np 16327) occurs mainly in central Africa and was probably carried to southern Africa with the Bantu expansion(s). The most frequent clade (transition at np 16320) testifies to a pronounced expansion event in the mid-Holocene and seems to be prominent in many Bantu groups from all of Africa. In contrast, one clade (transition at np 16264) is essentially restricted to Atlantic western Africa (including Cabo Verde). We propose a tentative L3e phylogeny that is based on 197 HVS-I sequences. We conclude that haplogroup L3e originated in central or eastern Africa about 46,000 (±14,000) years ago, and was a hitchhiker of much later dispersal and local expansion events, with the rise of food production and iron smelting. Enforced migration of African slaves to the Americas translocated L3e mitochondria, the descendants of which in Brazil and the Caribbean still reflect their different regional African ancestries.

(Received May 11 2001)
(Accepted August 31 2001)

c1 Correspondence: Prof. Dr. Hans-Jürgen Bandelt, Fachbereich Mathematik der Universität, Bundesstr.55, 20146 Hamburg, Germany. Fax: +49-40-42838-5190. E-mail:,