HAPLOFIND: A New Method for High-Throughput mtDNA Haplogroup Assignment

Vianello, Dario; Sevini, Federica; Castellani, Gastone; Lomartire, Laura; Capri, Miriam; Franceschi, Claudio

doi:10.1002/humu.22356

Cited by 132 publications

(103 citation statements)

References 33 publications

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“…The mt‐haplogroup was assigned to T2b (Vianello et al, 2013). The total of 11312749 reads mapped to the human genome.…”

Section: Resultsmentioning

confidence: 99%

“…Levels of contamination were estimated based on the analyses of contradictory positions in mitochondrial sequences (Green et al, 2008). The consensus mitochondrial DNA (mtDNA) sequences were called using samtools package (Li et al 2009) while the initial haplogroup assignment was in HAPLOFIND tool (Vianello et al, 2013). The assignments were inspected manually by checking against PhyloTree–mtDNA tree build 17 (18 February 2016) (van Oven & Kayser, 2009).…”

Section: Methodsmentioning

confidence: 99%

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A female Viking warrior confirmed by genomics

Hedenstierna-Jonson

Kjellström

Zachrisson

et al. 2017

American J Phys Anthropol

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ObjectivesThe objective of this study has been to confirm the sex and the affinity of an individual buried in a well‐furnished warrior grave (Bj 581) in the Viking Age town of Birka, Sweden. Previously, based on the material and historical records, the male sex has been associated with the gender of the warrior and such was the case with Bj 581. An earlier osteological classification of the individual as female was considered controversial in a historical and archaeological context. A genomic confirmation of the biological sex of the individual was considered necessary to solve the issue.Materials and methodsGenome‐wide sequence data was generated in order to confirm the biological sex, to support skeletal integrity, and to investigate the genetic relationship of the individual to ancient individuals as well as modern‐day groups. Additionally, a strontium isotope analysis was conducted to highlight the mobility of the individual.ResultsThe genomic results revealed the lack of a Y‐chromosome and thus a female biological sex, and the mtDNA analyses support a single‐individual origin of sampled elements. The genetic affinity is close to present‐day North Europeans, and within Sweden to the southern and south‐central region. Nevertheless, the Sr values are not conclusive as to whether she was of local or nonlocal origin.DiscussionThe identification of a female Viking warrior provides a unique insight into the Viking society, social constructions, and exceptions to the norm in the Viking time‐period. The results call for caution against generalizations regarding social orders in past societies.

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“…The mt‐haplogroup was assigned to T2b (Vianello et al, 2013). The total of 11312749 reads mapped to the human genome.…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

A female Viking warrior confirmed by genomics

Hedenstierna-Jonson

Kjellström

Zachrisson

et al. 2017

American J Phys Anthropol

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“…All nine complete mitochondrial genomes that fulfilled the criteria of authenticity were assigned to haplogroups using Haplofind 48 . A Maximum Parsimony tree including present day humans and previously published ancient mtDNA sequences was generated with MEGA 49 .…”

Section: Methodsmentioning

confidence: 99%

Ancient human genomes suggest three ancestral populations for present-day Europeans

Lazaridis

Patterson

Mittnik

et al. 2014

Nature

1,227

1,031

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We sequenced the genomes of a ~7,000 year old farmer from Germany and eight ~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other ancient genomes1–4 with 2,345 contemporary humans to show that most present Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations’ deep relationships and show that EEF had ~44% ancestry from a “Basal Eurasian” population that split prior to the diversification of other non-African lineages.

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“…Mitochondrial haplogroups were determined using HaploFind (40). Consensus sequences in FASTA format were created from alignments with SAMtools (41) (SI Appendix, SI4.…”

Section: Methodsmentioning

confidence: 99%

Early farmers from across Europe directly descended from Neolithic Aegeans

Hofmanová

Kreutzer

Hellenthal

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

410

271

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Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.

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HAPLOFIND: A New Method for High-Throughput mtDNA Haplogroup Assignment

Cited by 132 publications

References 33 publications

A female Viking warrior confirmed by genomics

A female Viking warrior confirmed by genomics

Ancient human genomes suggest three ancestral populations for present-day Europeans

Early farmers from across Europe directly descended from Neolithic Aegeans

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