TY  - JOUR
A1  - Barlow, Axel
A1  - Cahill, James A.
A1  - Hartmann, Stefanie
A1  - Theunert, Christoph
A1  - Xenikoudakis, Georgios
A1  - Gonzalez-Fortes, Gloria M.
A1  - Paijmans, Johanna L. A.
A1  - Rabeder, Gernot
A1  - Frischauf, Christine
A1  - Garcia-Vazquez, Ana
A1  - Murtskhvaladze, Marine
A1  - Saarma, Urmas
A1  - Anijalg, Peeter
A1  - Skrbinsek, Tomaz
A1  - Bertorelle, Giorgio
A1  - Gasparian, Boris
A1  - Bar-Oz, Guy
A1  - Pinhasi, Ron
A1  - Slatkin, Montgomery
A1  - Dalen, Love
A1  - Shapiro, Beth
A1  - Hofreiter, Michael
T1  - Partial genomic survival of cave bears in living brown bears
JF  - Nature Ecology & Evolution
N2  - Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.
Y1  - 2018
U6  - https://doi.org/10.1038/s41559-018-0654-8
SN  - 2397-334X
VL  - 2
IS  - 10
SP  - 1563
EP  - 1570
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Pinhasi, Ron
A1  - Fernandes, Daniel
A1  - Sirak, Kendra
A1  - Novak, Mario
A1  - Connell, Sarah
A1  - Alpaslan-Roodenberg, Songul
A1  - Gerritsen, Fokke
A1  - Moiseyev, Vyacheslav
A1  - Gromov, Andrey
A1  - Raczky, Pal
A1  - Anders, Alexandra
A1  - Pietrusewsky, Michael
A1  - Rollefson, Gary
A1  - Jovanovic, Marija
A1  - Trinhhoang, Hiep
A1  - Bar-Oz, Guy
A1  - Oxenham, Marc
A1  - Matsumura, Hirofumi
A1  - Hofreiter, Michael
T1  - Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone
JF  - PLoS one
N2  - The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (similar to 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,0001,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.
Y1  - 2015
U6  - https://doi.org/10.1371/journal.pone.0129102
SN  - 1932-6203
VL  - 10
IS  - 6
PB  - PLoS
CY  - San Fransisco
ER  -