Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia

PLoS One. 2015 Dec 7;10(12):e0144391. doi: 10.1371/journal.pone.0144391. eCollection 2015.

Abstract

Genetic signatures from the Paleolithic inhabitants of Eurasia can be traced from the early divergent mitochondrial DNA lineages still present in contemporary human populations. Previous studies already suggested a pre-Neolithic diffusion of mitochondrial haplogroup HV*(xH,V) lineages, a relatively rare class of mtDNA types that includes parallel branches mainly distributed across Europe and West Asia with a certain degree of structure. Up till now, variation within haplogroup HV was addressed mainly by analyzing sequence data from the mtDNA control region, except for specific sub-branches, such as HV4 or the widely distributed haplogroups H and V. In this study, we present a revised HV topology based on full mtDNA genome data, and we include a comprehensive dataset consisting of 316 complete mtDNA sequences including 60 new samples from the Italian peninsula, a previously underrepresented geographic area. We highlight points of instability in the particular topology of this haplogroup, reconstructed with BEAST-generated trees and networks. We also confirm a major lineage expansion that probably followed the Late Glacial Maximum and preceded Neolithic population movements. We finally observe that Italy harbors a reservoir of mtDNA diversity, with deep-rooting HV lineages often related to sequences present in the Caucasus and the Middle East. The resulting hypothesis of a glacial refugium in Southern Italy has implications for the understanding of late Paleolithic population movements and is discussed within the archaeological cultural shifts occurred over the entire continent.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Lineage / genetics
  • DNA, Mitochondrial / genetics*
  • Ethnicity / genetics*
  • Europe
  • Genetic Variation / genetics
  • Genetics, Population*
  • Geography
  • Haplotypes
  • Humans
  • Mitochondria / genetics*
  • Molecular Sequence Data
  • Phylogeography
  • White People / genetics*

Substances

  • DNA, Mitochondrial

Associated data

  • GENBANK/KP340126
  • GENBANK/KP340127
  • GENBANK/KP340128
  • GENBANK/KP340129
  • GENBANK/KP340130
  • GENBANK/KP340131
  • GENBANK/KP340132
  • GENBANK/KP340133
  • GENBANK/KP340134
  • GENBANK/KP340135
  • GENBANK/KP340136
  • GENBANK/KP340137
  • GENBANK/KP340138
  • GENBANK/KP340139
  • GENBANK/KP340140
  • GENBANK/KP340141
  • GENBANK/KP340142
  • GENBANK/KP340143
  • GENBANK/KP340144
  • GENBANK/KP340145
  • GENBANK/KP340146
  • GENBANK/KP340147
  • GENBANK/KP340148
  • GENBANK/KP340149
  • GENBANK/KP340150
  • GENBANK/KP340151
  • GENBANK/KP340152
  • GENBANK/KP340153
  • GENBANK/KP340154
  • GENBANK/KP340155
  • GENBANK/KP340156
  • GENBANK/KP340157
  • GENBANK/KP340158
  • GENBANK/KP340159
  • GENBANK/KP340160
  • GENBANK/KP340161
  • GENBANK/KP340162
  • GENBANK/KP340163
  • GENBANK/KP340164
  • GENBANK/KP340165
  • GENBANK/KP340166
  • GENBANK/KP340167
  • GENBANK/KP340168
  • GENBANK/KP340169
  • GENBANK/KP340170
  • GENBANK/KP340171
  • GENBANK/KP340172
  • GENBANK/KP340173
  • GENBANK/KP340174
  • GENBANK/KP340175
  • GENBANK/KP340176
  • GENBANK/KP340177
  • GENBANK/KP340178
  • GENBANK/KP340179
  • GENBANK/KP340180

Grants and funding

This work was supported by the PRIN Progetti di Ricerca di Interesse Nazionale 2010EL8TXP_006 grant to DL, http://prin.miur.it/; the European Research Council ERC-2011-AdG 295733 (Langelin) to DP and CB, http://erc.europa.eu/; the Institutional Research Funding from the Estonian Research Council [IUT24-1], http://www.etag.ee/en/estonian-research-council/; and by the European Regional Development Fund (European Union), http://ec.europa.eu/regional_policy/index.cfm/en/funding/erdf/, through the Centre of Excellence in Genomics to Estonian Biocentre and University of Tartu, http://genomics.ebc.ee/. MvO was supported in part by an Estonian Biocentre EBC ECOGENE student fellowship, https://edukad.etag.ee/project/3010. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.