TY  - GEN
A1  - Mohandesan, Elmira
A1  - Speller, Camilla F.
A1  - Peters, Joris
A1  - Uerpmann, Hans-Peter
A1  - Uerpmann, Margarethe
A1  - De Cupere, Bea
A1  - Hofreiter, Michael
A1  - Burger, Pamela A.
T1  - Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel
T2  - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 789 
KW  - ancient DNA
KW  - Camelus dromedarius
KW  - capture enrichment
KW  - degraded DNA
KW  - mitochondrial genome (mtDNA)
KW  - next-generation sequencing
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439955
SN  - 1866-8372
IS  - 789
SP  - 300
EP  - 313
ER  - 
TY  - JOUR
A1  - Mohandesan, Elmira
A1  - Speller, Camilla F.
A1  - Peters, Joris
A1  - Uerpmann, Hans-Peter
A1  - Uerpmann, Margarethe
A1  - De Cupere, Bea
A1  - Hofreiter, Michael
A1  - Burger, Pamela A.
T1  - Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel
JF  - Molecular ecology resources
N2  - 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.
KW  - ancient DNA
KW  - Camelus dromedarius
KW  - capture enrichment
KW  - degraded DNA
KW  - mitochondrial genome (mtDNA)
KW  - next-generation sequencing
Y1  - 2017
U6  - https://doi.org/10.1111/1755-0998.12551
SN  - 1755-098X
SN  - 1755-0998
VL  - 17
IS  - 2
SP  - 300
EP  - 313
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - GEN
A1  - Hofreiter, Michael
A1  - Paijmans, Johanna L. A.
A1  - Goodchild, Helen
A1  - Speller, Camilla F.
A1  - Barlow, Axel
A1  - Gonzalez-Fortes, Gloria M.
A1  - Thomas, Jessica A.
A1  - Ludwig, Arne
A1  - Collins, Matthew J.
T1  - The future of ancient DNA
BT  - technical advances and conceptual shifts
T2  - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe
N2  - Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 908 
KW  - ancient DNA
KW  - hybridisation capture
KW  - multi-locus data
KW  - next generation sequencing (NGS)
KW  - palaeogenomics
KW  - population genomics
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-438816
SN  - 1866-8372
IS  - 908
SP  - 284
EP  - 295
ER  - 
TY  - JOUR
A1  - Hofreiter, Michael
A1  - Paijmans, Johanna L. A.
A1  - Goodchild, Helen
A1  - Speller, Camilla F.
A1  - Barlow, Axel
A1  - González-Fortes, Gloria M.
A1  - Thomas, Jessica A.
A1  - Ludwig, Arne
A1  - Collins, Matthew J.
T1  - The future of ancient DNA: Technical advances and conceptual shifts
JF  - Bioessays : ideas that push the boundaries
N2  - Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.
KW  - ancient DNA
KW  - hybridisation capture
KW  - multi-locus data
KW  - next generation sequencing (NGS)
KW  - palaeogenomics
KW  - population genomics
Y1  - 2015
U6  - https://doi.org/10.1002/bies.201400160
SN  - 0265-9247
SN  - 1521-1878
VL  - 37
IS  - 3
SP  - 284
EP  - 293
PB  - Wiley-Blackwell
CY  - Hoboken
ER  -