An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data.

Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA.

Geochemical Behaviors of Rare Earth Elements (REEs) in Karst Soils under Different Land-Use Types: A Case in Yinjiang Karst Catchment, Southwest China.

The geochemical characteristics of rare earth elements (REEs) can be employed to identify the anthropogenic and natural influence on the distributions of REEs in soils. A total of 47 soil samples from the three soil profiles of the secondary forest land, abandoned cropland, and shrubland in the Yinjiang county of Guizhou province, southwest China, were collected to determine the contents and distribution of REEs in the soil environment. The total REEs (ΣREE) contents in different soil profiles are in the following sequence: secondary forest land (mean: 204.

Climatic and anthropogenic driving forces of the nitrogen cycling in a subtropical river basin.

To date, basin-scale understanding of nitrogen (N) cycling is lacking, which undermines riverine N pollution control efforts. Applying a multiple-isotopic approach, this study provided insights into the impacts of climate and anthropogenic activities on the N cycling at a basin scale. The isotopic compositions of the river water were regulated by a simple mixing process in winter, while unconservative processes (nitrification and denitrification) occurred in warm seasons.

Early Pleistocene hominin teeth from Meipu, southern China.

The rarity and poor preservation of hominin fossils from the East Asian Early Pleistocene hamper our understanding of their taxonomy and possible phylogenetic relationship with other members of the genus Homo. In the 1970s, four isolated hominin teeth were recovered from the Meipu site, southern China, which biostratigraphic analysis placed in the late Early Pleistocene. Early reports assigned the teeth to late Homo erectus.

Hypercarnivorous teeth and healed injuries to from Early Pleistocene Nihewan beds, China, support social hunting for ancestral wolves.

Collaborative hunting by complex social groups is a hallmark of large dogs (Mammalia: Carnivora: Canidae), whose teeth also tend to be hypercarnivorous, specialized toward increased cutting edges for meat consumption and robust p4-m1 complex for cracking bone. The deep history of canid pack hunting is, however, obscure because behavioral evidence is rarely preserved in fossils. Dated to the Early Pleistocene (>1.

gen. et sp. nov. (Colobodontidae, Neopterygii), a large durophagous predator from the Middle Triassic (Anisian) Luoping Biota, eastern Yunnan, China.

Neopterygii is a large group of ray-finned fishes which underwent a rapid radiation in the Middle Triassic. Until recently, 11 stem neopterygians have been recovered from the early Middle Triassic Luoping Biota in eastern Yunnan, China, and they are small to medium-sized fishes. Here, I report the discovery of a new stem neopterygian, y gen.

Earliest fossils of giant-sized bony-toothed birds (Aves: Pelagornithidae) from the Eocene of Seymour Island, Antarctica.

While pelagornithid or 'bony-toothed' bird fossils representing multiple species are known from Antarctica, a new dentary fragment of a pelagornithid bird from the middle Eocene Submeseta Formation on Seymour Island, Antarctica represents a species with a body size on par with the largest known species in the clade. Measurements from the partial 'toothed' dentary point to a giant body size for the species, although the spacing among the pseudoteeth differs from that published for other pelagornithids. The discrepancy might suggest that previous techniques are not adequate for examination of incomplete material or that another factor such as phylogeny might impact size estimates and comparisons.

Palaeoproteomic analysis of Pleistocene cave hyenas from east Asia.

The spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. However, its origin and evolutionary history is somewhat contentious due to discordances between morphological, nuclear, and mitochondrial data. Due to the limited molecular data from east Asian Crocuta, also known as cave hyena, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China.

The evolutionary history of Neanderthal and Denisovan Y chromosomes.

Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago.

The upper limb skeleton and behavioral lateralization of modern humans from Zhaoguo Cave, southwestern China.

Objectives: Aims of the study are to initially describe and comparatively evaluate the morphology of the new Zhaoguo M1 upper limb remains, and contextualize upper limb functional adaptations among those of other worldwide Upper Paleolithic (UP) humans to make inferences about subsistence-related activity patterns in southwestern China at the Pleistocene-Holocene boundary.

Materials And Methods: The preserved Zhaoguo M1 skeletal remains include paired humeri, ulnae, and radii, among others. These specimens were scanned using micro-computed tomography to evaluate internal structural properties, while external osteometric dimensions of the Zhaoguo M1 upper limb elements also were acquired.

The origin of Rhinocerotoidea and phylogeny of Ceratomorpha (Mammalia, Perissodactyla).

Rhinoceroses have been considered to have originated from tapiroids in the middle Eocene; however, the transition remains controversial, and the first unequivocal rhinocerotoids appeared about 4 Ma later than the earliest tapiroids of the Early Eocene. Here we describe 5 genera and 6 new species of rhinoceroses recently discovered from the early Eocene to the early middle Eocene deposits of the Erlian Basin of Inner Mongolia, China. These new materials represent the earliest members of rhinocerotoids, forstercooperiids, and/or hyrachyids, and bridge the evolutionary gap between the early Eocene ceratomorphs and middle Eocene rhinocerotoids.

Prehistoric agriculture and social structure in the southwestern Tarim Basin: multiproxy analyses at Wupaer.

The oasis villages of the Tarim Basin served as hubs along the ancient Silk Road, and they played an important role in facilitating communication between the imperial centers of Asia. These villages were supported by an irrigated form of cereal farming that was specifically adapted to these early oasis settlements. In this manuscript, we present the results from new archaeobotanical analyses, radiocarbon dating, and organic carbon isotopic studies directly from carbonized seeds at the Wupaer site (1500-400 BC) in the Kashgar Oasis of the western Tarim Basin.

Perissodactyl diversities and responses to climate changes as reflected by dental homogeneity during the Cenozoic in Asia.

Cenozoic mammal evolution and faunal turnover are considered to have been influenced and triggered by global climate change. Teeth of large terrestrial ungulates are reliable proxies to trace long-term climatic changes due to their morphological and physicochemical properties; however, the role of premolar molarization in ungulate evolution and related climatic change has rarely been investigated. Recently, three patterns of premolar molarization among perissodactyls have been recognized: endoprotocrista-derived hypocone (type I); paraconule-protocone separation (type II); and metaconule-derived pseudohypocone (type III).

Confirmation of ovarian follicles in an enantiornithine (Aves) from the Jehol biota using soft tissue analyses.

The remains of ovarian follicles reported in nine specimens of basal birds represents one of the most remarkable examples of soft-tissue preservation in the Early Cretaceous Jehol Biota. This discovery was immediately contested and the structures alternatively interpreted as ingested seeds. Fragments of the purported follicles preserved in an enantiornithine (STM10-12) were extracted and subjected to multiple high-resolution analyses.

Sequential Molt in a Feathered Dinosaur and Implications for Early Paravian Ecology and Locomotion.

Feather molt is an important life-history process in birds, but little is known about its evolutionary history. Here, we report on the first fossilized evidence of sequential wing feather molt, a common strategy among extant birds, identified in the Early Cretaceous four-winged dromaeosaurid Microraptor. Analysis of wing feather molt patterns and ecological properties in extant birds imply that Microraptor maintained its flight ability throughout the entire annual cycle, including the molt period.

A new genus of pliopithecoid from the late Early Miocene of China and its implications for understanding the paleozoogeography of the Pliopithecoidea.

A diversity of pliopithecoids is known from Miocene localities in Europe, but until recently, this group was relatively poorly represented in China. However, new discoveries have shown that Chinese pliopithecoids were taxonomically diverse and geographically widespread. The earliest pliopithecoids in China (and Eurasia) are Dionysopithecus and Platodontopithecus from the Early Miocene of Sihong, Jiangsu (∼19-18 Ma).

Developmental biology of reveals holozoan affinity, cryptic diversity, and adaptation to heterogeneous environments in the early Ediacaran Weng'an biota (Doushantuo Formation, South China).

The exceptional fossil preservation of the early Ediacaran Weng'an biota provides a unique window on the interval of Earth history in which animal lineages emerged. It preserves a diversity of similarly ornamented encysted developmental stages previously interpreted as different developmental stages of one taxon. Although is distinguished from other forms by a helical groove or canal, it has been interpreted as a developmental stage of cooccurring metazoan, nonmetazoan holozoan, or green algal taxa.

Cranial endocast of the stem lagomorph and brain structure of basal Euarchontoglires.

Early lagomorphs are central to our understanding of how the brain evolved in Glires (rodents, lagomorphs and their kin) from basal members of Euarchontoglires (Glires + Euarchonta, the latter grouping primates, treeshrews, and colugos). Here, we report the first virtual endocast of the fossil lagomorph , from the Orella Member of the Brule Formation, early Oligocene, Nebraska, USA. The specimen represents one of the oldest nearly complete lagomorph skulls known.

The Earliest Ursine Bear Demonstrates the Origin of Plant-Dominated Omnivory in Carnivora.

In Carnivora, increases in body size often lead to dietary specialization toward hypercarnivory. Ursine bears (Tremarctos and Ursus), however, are the only omnivorous Carnivora that evolved large body sizes (i.e.

Intra-assemblage variation in the macro-blade assemblage from the 1963 excavation at Shuidonggou locality 1, northern China, in the context of regional variation.

The emergence of the Upper Paleolithic and regional variability in early Upper Paleolithic industries are prominent topics in Paleolithic archaeology, with special relevance to the dispersal and differentiation of early modern human cultures across Eurasia. The so-called Initial Upper Paleolithic (IUP) has been considered a key element in the emergence of the Upper Paleolithic in northern Asia. Here, we examine the intra-assemblage variation in the collection from the 1963 excavation at Shuidonggou locality 1, a major IUP site in northern China.

Imputation for sequencing variants preselected to a customized low-density chip.

The sequencing variants preselected from association analyses and bioinformatics analyses could improve genomic prediction. In this study, the imputation of sequencing SNPs preselected from major dairy breeds in Denmark-Finland-Sweden (DFS) and France (FRA) was investigated for both contemporary animals and old bulls in Danish Jersey. For contemporary animals, a two-step imputation which first imputed to 54 K and then to 54 K + DFS + FRA SNPs achieved highest accuracy.

The tetrapod fauna of the upper Permian Naobaogou Formation of China: 5. gen. et sp. nov., a new peculiar therocephalian.

The upper Permian Naobaogou Formation has been the goal of recent contributions that notably increased the knowledge of its terrestrial vertebrate fauna and unravelled a hidden late Permian therocephalian diversity in China. Two very different species of therocephalians have been documented in the Naobaogou Formation and they were recovered as basal akidnognathids in cladistic analyses. In this contribution we describe gen.

The 3D Reconstruction of Pocillopora Colony Sheds Light on the Growth Pattern of This Reef-Building Coral.

Coral reefs are formed by living polyps, and understanding the dynamic processes behind the reefs is crucial for marine ecosystem restoration. However, these processes are still unclear because the growth and budding patterns of living polyps are poorly known. Here, we investigate the growth pattern of a widely distributed reef-building coral Pocillopora damicornis from Xisha Islands using high-resolution computed tomography.

Evolution of vegetation and climate variability on the Tibetan Plateau over the past 1.74 million years.

The Tibetan Plateau exerts a major influence on Asian climate, but its long-term environmental history remains largely unknown. We present a detailed record of vegetation and climate changes over the past 1.74 million years in a lake sediment core from the Zoige Basin, eastern Tibetan Plateau.