Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel.
The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17-95% length coverage and 1.27-47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1-1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.
Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria.|Institute of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.
Elmira
E
Mohandesan
BioArCh, Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK.
Camilla F
CF
Speller
Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität München (LMU Munich), 80539, Munich, Germany.|Staatliche Naturwissenschaftliche Sammlungen Bayerns, Bavarian State Collection of Anthropology and Palaeoanatomy, 80333, Munich, Germany.
Joris
J
Peters
Abteilung Archäozoologie, Institut für Naturwissenschaftliche Archäologie, Eberhard-Karls-Universität Tübingen, Rümelinstrasse 23, 7207, Tübingen, Germany.
Hans-Peter
HP
Uerpmann
Staatliche Naturwissenschaftliche Sammlungen Bayerns, Bavarian State Collection of Anthropology and Palaeoanatomy, 80333, Munich, Germany.
Margarethe
M
Uerpmann
Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000, Brussels, Belgium.
Bea
B
De Cupere
BioArCh, Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK.|Evolutionary and Adaptive Genomics, Department of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Street 24-25, Potsdam, 14476, Germany.
Michael
M
Hofreiter
Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria.
Pamela A
PA
Burger
D000818:Animals; D000829:Animals, Domestic; D000835:Animals, Wild; D018643:Arab World; D002162:Camelus / Q000145:classification* / Q000235:genetics*; D000072441:DNA, Ancient / Q000737:chemistry* / Q000302:isolation & purification*; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D003889:Desert Climate; D009693:Nucleic Acid Hybridization / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013696:Temperature; D013997:Time Factors; D014421:Turkey
D000072441:DNA, Ancient; D004272:DNA, Mitochondrial

Camelus dromedarius
; ancient DNA; capture enrichment; degraded DNA; mitochondrial genome (mtDNA); next-generation sequencing