Late Pleistocene Population Research Articles

Dental microwear analysis of Kudaro cave bears: Insights into dietary evolution from the Middle to Late Pleistocene

The dietary changes of early cave bear populations from the Middle to Late Pleistocene are poorly understood. In this study, we analysed 60 m1 through dental microwear analysis of three diachronic Middle (Ursus praekudarensis and U. praekudarensis/kudarensis) to Late Pleistocene (U. kudarensis) populations inhabiting the Kudaro 1 and Kudaro 3 caves in the Southern Caucasus. The diet of all populations was inferred to be omnivorous, although it changed over time, adapting to the climatic and ecological conditions of the period. Bones from U. praekudarensis/kudarensis populations accumulated throughout the year; thus, microwear suggests an average annual diet dominated by plant resources. The widespread presence of hypercoarse scratches in U. kudarensis and U. praekudarensis populations suggests animal protein intake during the hyperphagia. The presence of omnivorous guild competitors and harsh conditions in a high-altitude environment could have driven the Caucasian cave bears to consume animal protein as a fallback diet during their predormancy period. Furthermore, the cave bears' capacity for dietary flexibility through time highlights the ability of cave bears to withstand climatic changes, while competition with other omnivorous species could have driven their dietary niche during their hyperphagia period towards animal protein consumption throughout the Middle to Late Pleistocene.

A 47,000 year archaeological and palaeoenvironmental record from Juukan 2 rockshelter on the western Hamersley Plateau of the Pilbara region, Western Australia

Archaeological and palaeoenvironmental investigations at Juukan 2 rockshelter have yielded new information on the ancient Aboriginal occupation of the Pilbara uplands in northwest Australia. Using multiple lines of evidence, including lithic, faunal, pollen, ancient DNA, radiocarbon dating, optically stimulated luminescence, and Bayesian chronological modelling, we show that Aboriginal people occupied the western Hamersley Plateau as early as 47,000 years ago (47 ka). Late Pleistocene populations utilised a diverse range of tool technologies, including bone points, grindstones, and flaked stone artefacts. Palaeoclimatic conditions at Juukan 2 rockshelter varied greatly over the past 47 ka, with repeated site visits by people, including during the peak hyper-arid phase of the Last Glacial Maximum (LGM) c. 21 ± 2 ka. Ancient starch analyses of the ground stone artefacts show the processing of Ipomoea (Bush Potato) from around 42 ka to the present day. Pronounced increases in the discard of stone artefacts and bone in the last 3500 years are interpreted to be the result of increased frequency of site use. A braided hair fragment dated to this period has demonstrated genetic links between the earlier rockshelter occupants and contemporary Puutu Kunti Kurrama and Pinikura peoples, who have maintained strong cultural connections to the area.

New age of the Dingcun 54:100 hominin site in northern China

The Dingcun locality 54:100 site was first excavated in 1950 s and has since yielded abundant stone artefacts and the famous ‘Dingcun human’ fossils, including three teeth and a parietal fragment. The Dingcun teeth has been regarded as a potential evidence of early emergence and development of ‘modern’ anatomic characters, making them key to understanding the origin and evolution of our species. However, there has been considerable debate regarding the chronology of the Dingcun site. Here we establish a new chronology for the site, based on optical dating of the fossil-bearing sediments and U-series dating of fauna fossils from the cultural layers. Our study shows that the age of the Dingcun human fossil ranges from 298,000 to 225,000 years ago (at 95.4 % confidence interval). This new dating result suggest that the Dingcun hominins represent a Late Middle Pleistocene population in East Asia who had borne some modern dental traits.

Climate Niche Modeling Reveals the Fate of Pioneering Late Pleistocene Populations in Northern Europe

Climate Niche Modeling Reveals the Fate of Pioneering Late Pleistocene Populations in Northern Europe

Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals.

The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.

Middle Pleistocene Xenocyon lycaonoides Kretzoi, 1938 in northeastern China and the evolution of Xenocyon-Lycaon lineage

ABSTRACT Xenocyon lycaonoides is a well-represented large canid known from the middle Early Pleistocene to Middle Pleistocene in Europe, central Asia, and Alaska, yet its fossil record in eastern Asia is extremely poor. Here we report a well-preserved palatal part of the skull of this species from Jinyuan Cave of Luotuo Hill, Puwan, Dalian of Liaoning Province, northeastern China. The new material confirms the presence of this species in eastern Asia during the early Middle Pleistocene, supporting a Holarctic distribution of this lineage during the Mid-Pleistocene climate change. The morphology of the new material suggests that the Middle Pleistocene X. lycaonoides is more derived than the late Early Pleistocene population, and is distinct from the living Lycaon pictus, and imply the different evolutionary direction from Lycaon. Our analyses support a generic distinction of the Xenocyon from Lycaon. X. lycaonoides can not be the direct ancestor of Lycaon, but is a related taxon that lived in Eurasia and North America. The lineage includes Xenocyon, and Lycaon Brookes, 1827, and partially contributes to Cynotherium Studiati, 1857, showing two independent Island specialisation events, making it one of the most successful lineages of canids ever known.

Genetic Diversity and Population Genetic Structure of Korean Black Scraper Thamnaconus modestus in Korea and Japan Based on the mtDNA Marker

Thamnaconus modestus is a commercially important species that is widely distributed in the Northwest Pacific region. To investigate the genetic diversity, demographic history, and population structure, 84 individuals were collected from two locations in Korea (Geomundo and Jumunjin) and one location in Japan (Wakasa Bay). Analysis of the mitochondrial DNA control region sequence of 373 base pairs from the 84 individuals revealed 39 haplotypes with 50 polymorphic sites. The haplotype diversity and nucleotide diversity of different populations ranged from 0.973 (0.018) to 0.981 (0.013) and from 0.020 (0.011) to 0.021 (0.011), respectively. Phylogenetic analysis revealed three distinct clades of which two were large (clade 1 and clade 2) and one was small clade (clade 3). However, there was no significant geographical clustering of the haplotypes according to the sampling locality. Demographic analysis suggested that both clades experienced Late Pleistocene population expansion. The pairwise FST and AMOVA analysis were insignificant among the populations investigated. This indicated high gene flow among the populations of Korea and Japan. The dispersal capacity of the larvae and juveniles by ocean currents and migration of adult individuals could explain the genetic homogeneity. Insufficient time to accumulate genetic variation might be another reason for the lack of genetic structure.

Dietary stability inferred from dental mesowear analysis in large ungulates from Rancho La Brea and opportunistic feeding during the late Pleistocene

The Rancho La Brea locality is world famous for asphaltic deposits that trapped and preserved late Pleistocene megafauna over the last 50,000 years. This wealth of paleontological data allows for detailed investigation into paleoecological changes through the last glacial maximum into the Holocene. Here, we used dental mesowear analyses to infer dietary behavior in Bison antiquus, Equus occidentalis, and Camelops hesternus from five deposits (“pits”) spanning the latest Pleistocene: pits 77, 91, 13, 3, and 61/67. Mesowear was compared among pits for each taxon and discriminant function and posterior probability analyses were conducted using a modern dataset to predict dietary categories at Rancho La Brea. Published mesowear scores from late Pleistocene Bison, Equus and Camelops from other localities were included in the discriminant function and posterior probability analyses to assess dietary variability among regions. Mesowear for each taxon did not differ among pits. Posterior probabilities and discriminant function analyses recovered E. occidentalis as a strict grazer with B. antiquus and C. hesternus recovered as mixed feeders. The stability of mesowear scores through the latest Pleistocene suggests average diets of these herbivores did not significantly change at Rancho La Brea. This is in contrast to documented changes in climate and flora proxies of southern California. However, it is unclear whether these proxies are representative of climate and floral changes at Rancho La Brea. Mesowear scores from late Pleistocene populations of Equus, Bison, and Camelops indicate little variability in diet in Equus, modest variability in Bison, and high variability in Camelops. These analyses suggest large ungulates may have been more opportunistic in their feeding strategies and highlights the need for using multiple proxies to clarify dietary behavior of herbivores

Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia.

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long‐range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.

Perishable Technology and the Successful Peopling of South America

ABSTRACT Recent research demonstrates that perishable industries – specifically including the manufacture of textiles, basketry, cordage, and netting – were a well-established, integral component of the Upper Paleolithic milieu in many parts of the Old World. Moreover, extant data suggest that not only were these synergistic technologies part and parcel of the armamentarium of the first migrants to the New World, but, also, that these technologies played critical, and hitherto, largely unappreciated roles in the ecological success of late Pleistocene populations, notably including the first South Americans. This paper examines the evidence for, and varied roles of, early plant fiber technology in highland and lowland South America and also examines the adaptive qualities, potential impacts on social organization, and alteration of food procurement strategies implicit in this fundamentally crucial series of interrelated industries.

Shallow Genetic Structure of Pholis fangi in Bohai Sea and Yellow Sea Inferred from mtDNA Control Region

Pholis fangi is an ecologically important fish species inhabiting Chinese coastal waters of Yellow Sea and Bohai Sea. To investigate the genetic diversity and population genetic structure of P. fangi, a fragment of 487 bp in the first hypervariable region (HVR-1) of the mitochondrial DNA (mtDNA) control region was sequenced for 181 individuals collected from Bohai Sea and Yellow Sea. A total of 18 polymorphic sites were detected, which defined 25 haplotypes. A moderate level of haplotype diversity (h = 0.7052) and a low level of nucleotide diversity (π = 0.0028) were detected. Both the phylogenetic tree and the haplotype network showed no significant genealogical structure difference among sampling locations. Pairwise FST comparison and hierarchical molecular variance analysis (AMOVA) revealed that no significant genetic structure difference existed throughout the investigated regions, suggesting a high gene exchange among different populations. The results of neutrality test and mismatch distribution analysis indicated that a late Pleistocene population expansion (38000–127000 years ago) happened. Seasonal schooling migration may contribute to the genetically homogeneous population structure of the species.

The population history of northeastern Siberia since the Pleistocene.

Northeastern Siberia has been inhabited by humans for more than 40,000years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.

Comparative observations on the premolar root and pulp canal configurations of Middle Pleistocene Homo in China.

The aim of this study is to explore the root and root canal morphology of Homo fossil occupying China during the Middle Pleistocene period. Human occupation and evolutionary dynamics in East Asia during the Middle Pleistocene period is one of the most intriguing issues in paleoanthropology, with the coexistence of multiple lineages and regional morphs suggesting a complex population interaction scenario. Although premolar root and canal morphology has certain phylogenetic, taxonomic, and functional implications, its morphological diversity, possible evolutionary trend and characteristics regarding Middle Pleistocene hominins inhabiting East Asia are still insufficiently understood; where these populations fits within the Homo lineage (with respect to root and pulp canal structure) needs to be explored. Using microtomography, we directly observed and assessed the nonmetric variability of root and canal forms in maxillary and mandibular premolars of Chinese Middle Pleistocene Homo (N = 19), and compared our observed variations with Eurasian Early Pleistocene specimens from the Asia continent (N = 1) and Java (N = 2), as well as with Neanderthals (N = 28) and recent modern humans (N = 67). A total number of nine types of root-canal forms were recorded. As a whole, the Chinese Middle Pleistocene record shows an evolutionary trend toward a modern human-like condition (a reduction of root/canal number and a simplification of root surface structure). We documented primitive signals like high percentage of Tomes' root in lower premolars. A considerable occurrence of incompletely separated root branches and bifid root and canal apices, representing evolutionary transformation from multi-root to single-root condition was also noticed. The results were compared with previous publications on Early and Middle Pleistocene Homo in East Africa, North Africa, and Eurasia. This work provides new original data, incorporates the latest human fossil discoveries and suggests that analyzing the variation of premolar root structural organization, notably integrating together root/canal form and number, could possibly contribute to taxonomic and phylogenetic assessments. The mid-Middle Pleistocene populations, or "classic" Homo erectus, in our study show closer affinity to Early and Middle Pleistocene hominins in Eurasia, than to East African early Homo, which supports the suggestion that at least some of the Early Pleistocene hominin groups in Eurasia contribute to the later population; on the other hand, it is still difficult to clearly trace the evolutionary fate of those late Middle Pleistocene populations (roughly assigned as archaic Homo sapiens through a craniodental perspective). More comparable materials from the Early to Middle Pleistocene period as well as precise chronological framework is needed to further explore the evolutionary trends of archaic hominins in the Asian continent before the arrival of modern humans.

Recurrent Quaternary magma generation at Baekdusan (Changbaishan) volcano: New zircon U-Th ages and Hf isotopic constraints from the Millennium Eruption

It is well known that Baekdusan (Changbaishan), an active 2744-m-high stratovolcano located on the border between North Korea and China, initiated trachytic/commenditic eruption in the Pleistocene but the petrogenetic and temporal evolutions of this alkaline magma system remain insufficiently constrained. The so-called “Millennium Eruption” (ME) in the mid-10th century, which resulted in the formation of the world's highest caldera lake (Cheonji, or Tianchi) atop the mountain, was one of the largest and most violently explosive volcanic eruptions to have occurred on Earth in the past 2000 years. Here, we present U–Th disequilibrium ages and Hf isotopic compositions of zircons from trachydacitic pumices ejected during the ME. Taken together with the previous U–Th isotope data, our laser ablation-multicollector ICPMS analyses of the zircons yielded multiple age components consisting of an earliest Holocene cluster (11.3 ± 1.3 ka) and Middle–Late Pleistocene populations (ca. 230 and 110 ka), which indicates that Baekdusan magma has been generated episodically at intervals of ca. 120–100 ky. If the eruption ages assigned for the samples analyzed in the previous isotopic studies are correct, the consistent age pattern of zircon may suggest the persistent existence of the same magmatic plumbing system beneath Baekdusan since the ME. The wide range of zircon εHf values (+5.8 to −3.5) reflects an interaction between the EM1-type primitive magma and pre-existing crustal materials, evidenced by the presence of a xenocrystic zircon core showing a significantly negative εHf value (=−21). A broad negative correlation observed between zircon εHf and the published δ18O values can be ascribed to the progressive assimilation of weathered supracrustal rocks, likely in the course of magma chamber expansion.

Genetic diversity analysis of the oriental river prawn (Macrobrachium nipponense) in Huaihe River

The oriental river prawn (Macrobrachium nipponense) is an economically and nutritionally important species of decapod crustaceans in China. Genetic structure and demographic history of Macrobrachium nipponense were examined using sequence data from portions of the mitochondrial DNA cytochrome oxidase subunit I (COI) gene. Samples of 191 individuals were collected from 10 localities in the upper to middle reaches of the Huaihe River. Variability was detected at a total of 42 nucleotide sites along 684 bp length of homologous sequence (6.14%), and base substitutions occurred mostly at the second codon position. Haplotype diversity (h) and nucleotide diversity (π) of all populations were 0.9136 ± 0.0116 and 0.0078 ± 0.0042, respectively. Phylogenetic tree constructed using the maximum-likelihood (ML) method showed that the 44 haplotypes were assigned to two obvious clades associated with geographic regions. Moreover, the median-joining network was similar to the topology of the phylogenetic tree with 44 haplotypes. The pairwise FST values between the populations varied from −0.0298 to 0.2994. Generally, moderate genetic differentiation (FST = 0.1598, p = .0000) among different geographic populations was detected, with the significant differentiation between the Huaibin (HB) and other Macrobrachium nipponense populations. Both mismatch distribution analyses and neutrality tests suggested the early stage of Late Pleistocene population expansion 85,500 years before present for the species, which was consistent with the palaeoclimatic condition of the Huaihe River Basin.

Population Genetic Structure of Rock Bream (Oplegnathus fasciatus Temminck & Schlegel, 1884) Revealed by mtDNA COI Sequence in Korea and China

The rock bream, Oplegnathus fasciatus, is a common rocky reef game fish in East Asia and recently has become an aquaculture species. Despite its commercial importance, the population genetic structure of this fish species remains poorly understood. In this study, 163 specimens were collected from 6 localities along the coastal waters of Korea and China and their genetic variation was analyzed with mtDNA COI sequences. A total of 34 polymorphic sites were detected which determined 30 haplotypes. The genetic pattern reveals a low level of nucleotide diversity (0.04 ± 0.003) but a high level of haplotype diversity (0.83 ± 0.02). The 30 haplotypes are divided into two major genealogical clades: one that consists of only Zhoushan (ZS, East China Sea) specific haplotypes from the southern East China Sea and the other that consists of the remaining haplotypes from the northern East China Sea, Yellow Sea, Korea Strait, and East Sea/Sea of Japan. The two clades are separated by approximately 330~435 kyBP. Analyses of AMOVA and Fst show a significant population differentiation between the ZS sample and the other ones, corroborating separation of the two genealogical clades. Larval dispersal and the fresh Yangtze River plume are invoked as the main determining factors for this population genetic structure of O. fasciatus. Neutrality tests and mismatch distribution analyses indicate late Pleistocene population expansion along the coastal waters of Korea and China approximately 133–183 kyBP during which there were periodic cycles of glaciations and deglaciations. Such population information needs to be taken into account when stock enhancement and conservation measures are implemented for this fisheries species.

Effects of Pleistocene glaciation on the phylogeographic and demographic histories of chub mackerel Scomber japonicus in the north-western Pacific

Pleistocene glacial cycles associated with geological and climatic changes have been suggested to affect the distribution and abundance of marine organisms in the north-western Pacific. In addition to historical processes, several contemporary forces are associated with spatial distributions and genetic structuring of marine species. Herein, we gathered partial mitochondrial control region sequences of chub mackerel Scomber japonicus from 14 localities over most of its geographical range in the north-western Pacific to infer the effect of Pleistocene climatic fluctuations on its historical demography, and to assess the role of historical process and contemporary factors in shaping present-day patterns of genetic differentiation within this species. Phylogeographic patterns revealed two distinct lineages that originated in vicariance during the Middle Pleistocene. However, there was no evidence of phylogeographic partitioning of haplotypes over the sampled range. Population structure analyses indicated a high degree of genetic homogeneity among chub mackerel populations. Demographic analyses indicated both lineages experienced Late Pleistocene population expansion. The observed genetic pattern of chub mackerel is consistent with a scenario of the survival of this species in at least two allopatric glacial refugia during the glacial maxima of the Pleistocene followed by massive dispersals throughout the north-western Pacific and species-specific ecological processes facilitating contemporary gene flow.

Patterns of variation in Microtus arvalis and Microtus agrestis populations from Middle to Late Pleistocene in southwestern Europe

Fifteen paired fossil populations of Microtus arvalis and Microtus agrestis from southwestern Europe have been analysed from a morphological and morphometric point of view. The sites under consideration are located in the northern Iberian Peninsula and southern France, from the Middle Pleistocene to the end of the Late Pleistocene. The aim of this study is to stress once again the importance of keeping these two species separated in the fossil record in order to recognize specific trends of evolution and divergence and to obtain more precise information on palaeoclimatic and palaeoenvironmental conditions. It was possible to observe remarkable intraspecific differences between Middle and Late Pleistocene populations of both species. Furthermore, in synchronic co-specific populations from the Late Pleistocene, climatic and geographic conditions seem to exert a major influence in shaping intraspecific changes in dental pattern.

Origin and spread of human mitochondrial DNA haplogroup U7

Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16–19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that – analysed alongside 100 published ones – enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the Neolithic (~8 thousand years ago). These findings imply that the carriers of haplogroup U7 spread to South Asia and Europe before the suggested Bronze Age expansion of Indo-European languages from the Pontic-Caspian Steppe region.

Genetic structure and historical demography of the blue swimming crab (Portunus pelagicus) from southeastern sea of China based on mitochondrial COI gene

In this study, the population genetic structure and historical demography of the blue swimming crab, Portunus pelagicus, from southeastern sea of China were investigated using cytochrome c oxidase subunit I (COI) gene of mitochondrion. A total of 889 bp segment of COI gene was sequenced, which showed a high haplotype diversity (0.6833–0.8142) and low nucleotide diversity (0.0021–0.0034). Among 30 haplotypes defined in this study, one (H1) was the most dominant (47.7%) and shared by each locality, while the majority (23) were rare and only existed in one individual. The AMOVA analysis revealed a limited population genetic structure, which suggested a high level of gene flow along the distribution areas of China. This conclusion was supported by the pairwise FST comparison values. The topology of the neighbour-joining tree constructed using 30 haplotypes from four localities presented two distinct clades (clade A and clade B). Meanwhile, three sequences of P. pelagicus downloaded from NCBI database showed a high-level divergence with the individuals collected in our study, which might form a new cryptical species. The individuals of clade B were cryptically embedded in the whole population, with a low frequency (7.7–24.2%), while clade A accounted for 75.8–92.3%. Neutrality tests and mismatch analyses suggested a late Pleistocene population expansion for both clade A (47,000–66,000 years ago) and clade B (74,000–100,000 years ago). This study should provide insight into phylogeny, population genetic structure, conservation genetics, and sustainable management of P. pelagicus.