Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone

Objective: A key challenge in ancient DNA research is massive microbial DNA contamination from the deposition site which accumulates post mortem in the study organism’s remains. Two simple and cost-effective methods to enrich the relative endogenous fraction of DNA in ancient samples involve treatment of sample powder with either bleach or Proteinase K pre-digestion prior to DNA extraction. Both approaches have yielded promising but varying results in other studies. Here, we contribute data on the performance of these methods using a comprehensive and systematic series of experiments applied to a single ancient bone fragment from a giant panda (Ailuropoda melanoleuca). Results: Bleach and pre-digestion treatments increased the endogenous DNA content up to ninefold. However, the absolute amount of DNA retrieved was dramatically reduced by all treatments. We also observed reduced DNA damage patterns in pre-treated libraries compared to untreated ones, resulting in longer mean fragment lengths and reduced thymine over-representation at fragment ends. Guanine–cytosine (GC) contents of both mapped and total reads are consistent between treatments and conform to general expectations, indicating no obvious biasing effect of the applied methods. Our results therefore confirm the value of bleach and pre-digestion as tools in palaeogenomic studies, providing sufficient material is available

Uncertainty assessment in aboveground biomass estimation at the regional scale using a new method considering both sampling error and model error

Uncertainty associated with multiple sources of error exists in biomass estimation over large areas. This uncertainty affects the accuracy of the resultant biomass estimates. A new method that introduces Taylor series principles into a Monte Carlo simulation procedure was proposed and developed for estimating regional-scale aboveground biomass, along with quantifying the corresponding uncertainty arising from both sampling and model predictions. Additionally, the effect of sample size on estimates during model fitting was studied based on the new method in order to determine whether the effect of the size of the calibration data set can be neglected when the number of simulations is sufficiently large. The results revealed that the proposed method not only produces more reliable estimates of both biomass and uncertainty but also effectively and separately quantifies the uncertainties associated with different sources of error. The new method also reduced the effect of model uncertainty on final estimates. The uncertainty that was associated with model error increased significantly with decreasing sample sizes during model fitting, and the error was not reduced by increasing the number of Monte Carlo simulations.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Ancient DNA of northern China Hystricidae sub-fossils reveals the evolutionary history of old world porcupines in the Late Pleistocene

Abstract Background Old World porcupines (Family: Hystricidae) are the third-largest rodents and inhabit southern Europe, Asia, and most regions of Africa. They are a typical indicator of warm climate and their distribution is restricted to tropical and subtropical zones. In China, porcupines are widely distributed in southern areas of the Yangtze River. However, fossil remains have been identified in a few sites in northern China, among which Tianyuan Cave—near Zhoukoudian site—represents the latest known porcupine fossil record. So far, studies have focused mainly on porcupines’ husbandry and domestication but little is known about their intrafamilial phylogenetic relationships and evolutionary history. Results In this study, we sequence partial mitochondrial 12S rRNA and cyt b genes for seven Late Pleistocene porcupine individuals from Northern, Southern and Central China. Phylogenetic analyses show that the Tianyuan Cave porcupines, which had been morphologically identified as Hystrix subcristata, have a closer relationship to Hystrix brachyura. Conclusion Together with morphological adaptation characteristics, associated fauna, and climate change evidence, the molecular results reveal that a Late Quaternary extirpation has occurred during the evolutionary history of porcupines

Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genus Crocuta

Cave hyenas (genus Crocuta) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta. Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta. Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62–2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas

Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China

Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct