Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments

Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.

Nuclear preservation in the cartilage of the Jehol dinosaur Caudipteryx

Previous findings on dinosaur cartilage material from the Late Cretaceous of Montana suggested that cartilage is a vertebrate tissue with unique characteristics that favor nuclear preservation. Here, we analyze additional dinosaur cartilage in Caudipteryx (STM4-3) from the Early Cretaceous Jehol biota of Northeast China. The cartilage fragment is highly diagenetically altered when observed in ground-sections but shows exquisite preservation after demineralization. It reveals transparent, alumino-silicified chondrocytes and brown, ironized chondrocytes. The histochemical stain Hematoxylin and Eosin (that stains the nucleus and cytoplasm in extant cells) was applied to both the demineralized cartilage of Caudipteryx and that of a chicken. The two specimens reacted identically, and one dinosaur chondrocyte revealed a nucleus with fossilized threads of chromatin. This is the second example of fossilized chromatin threads in a vertebrate material. These data show that some of the original nuclear biochemistry is preserved in this dinosaur cartilage material and further support the hypothesis that cartilage is very prone to nuclear fossilization and a perfect candidate to further understand DNA preservation in deep time.

A genomic exploration of the early evolution of extant cats and their sabre-toothed relatives

Background: The evolutionary relationships of Felidae during their Early–Middle Miocene radiation is contentious. Although the early common ancestors have been subsumed under the grade-group Pseudaelurus, this group is thought to be paraphyletic, including the early ancestors of both modern cats and extinct sabretooths. Methods: Here, we sequenced a draft nuclear genome of Smilodon populator, dated to 13,182 ± 90 cal BP, making this the oldest palaeogenome from South America to date, a region known to be problematic for ancient DNA preservation. We analysed this genome, together with genomes from other extinct and extant cats to investigate their phylogenetic relationships. Results: We confirm a deep divergence (~20.65 Ma) within sabre-toothed cats. Through the analysis of both simulated and empirical data, we show a lack of gene flow between Smilodon and contemporary Felidae. Conclusions: Given that some species traditionally assigned to Pseudaelurus originated in the Early Miocene ~20 Ma, this indicates that some species of Pseudaelurus may be younger than the lineages they purportedly gave rise to, further supporting the hypothesis that Pseudaelurus was paraphyletic.

Field blood preservation and DNA extraction from wild mammals: methods and key factors for biodiversity studies

Studies on public health and wild mammal biodiversity include a genetic component. For blood samples, there must be optimal sample collection conditions since these can affect DNA preservation and extraction. This study evaluated the use of liquid and dry DNA preservation methods and commercial and non-commercial DNA extraction methods on field-collected blood samples. For this, 264 total blood samples were collected from wild mammals. A first group of samples was preserved in guanidine hydrochloride (GuHCl) and DNA was extracted using six commercial kits: Bioline, Norgen, Invitrogen, Promega, and Qiagen, in addition to phenol-chloroform isoamyl alcohol (PC) and guanidine thiocyanate (GIT). Another group of samples was preserved in Whatman® FTA® cards and DNA was extracted with PC and GIT. The extractions with GIT and PC showed the highest values (ng/µL) and variation in DNA concentration, while the commercial kit showed low variation. Sample preservation in Whatman® FTA® cards provided low variation and quantity of the extracted DNA compared with the use of GuHCl. Concerning DNA quality, the commercial kits yielded higher purity, while GIT and PC-based protocols provided highly variable results. Furthermore, the use of GIT and PC yielded a higher amount of DNA, yet, of variable quality. Overall, extraction based on commercial kits and Whatman® FTA® preservation allowed obtaining more standardized DNA qualities and quantities.