Computational challenges in the analysis of ancient DNA

Kay Pruefer; Udo Stenzel; Michael Hofreiter; Svante Paeaebo; Janet Kelso; Richard E. Green

doi:10.1186/gb-2010-11-5-r47

Computational challenges in the analysis of ancient DNA

Kay Pruefer, Udo Stenzel, Michael Hofreiter, Svante Paeaebo, Janet Kelso, Richard E. Green

Biology

Research output: Contribution to journal › Article › peer-review

Abstract

High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.

Original language	English
Article number	R47
Pages (from-to)	-
Number of pages	15
Journal	Genome biology
Volume	11
Issue number	5
DOIs	https://doi.org/10.1186/gb-2010-11-5-r47
Publication status	Published - 6 May 2010

Keywords

MITOCHONDRIAL GENOME
NEANDERTHAL GENOME
SEQUENCE
EVOLUTION
MAMMOTH
MOUSE
BLAST
AMPLIFICATION
ALIGNMENTS
PHYLOGENY

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10.1186/gb-2010-11-5-r47

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AU - Pruefer, Kay

AU - Stenzel, Udo

AU - Hofreiter, Michael

AU - Paeaebo, Svante

AU - Kelso, Janet

AU - Green, Richard E.

PY - 2010/5/6

Y1 - 2010/5/6

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AB - High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.

KW - MITOCHONDRIAL GENOME

KW - NEANDERTHAL GENOME

KW - SEQUENCE

KW - EVOLUTION

KW - MAMMOTH

KW - MOUSE

KW - BLAST

KW - AMPLIFICATION

KW - ALIGNMENTS

KW - PHYLOGENY

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SP - -

JO - Genome biology

JF - Genome biology

SN - 1474-760X

IS - 5

M1 - R47

ER -

Computational challenges in the analysis of ancient DNA

Abstract

Keywords

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