A combined method for DNA analysis and radiocarbon dating from a single sample

Chronological and genetic analysis of an Upper Palaeolithic female infant burial from Borsuka Cave, Poland

Six infant human teeth and 112 animal tooth pendants from Borsuka Cave were identified as the oldest burial in Poland. However, uncertainties around the dating and the association of the teeth to the pendants have precluded their association with an Upper Palaeolithic archaeological industry. Using <67 mg per tooth, we combined dating and genetic analyses of two human teeth and six herbivore tooth pendants to address these questions. Our interdisciplinary approach yielded informative results despite limited sampling material, and high levels of degradation and contamination. Our results confirm the Palaeolithic origin of the human remains and herbivore pendants, and permit us to identify the infant as female and discuss the association of the assemblage with different Palaeolithic industries. This study exemplifies the progress that has been made toward minimally destructive methods and the benefits of integrating methods to maximize data retrieval from precious but highly degraded and contaminated prehistoric material.

On Roth's "human fossil" from Baradero, Buenos Aires Province, Argentina: morphological and genetic analysis

The "human fossil" from Baradero, Buenos Aires Province, Argentina, is a collection of skeleton parts first recovered by the paleontologist Santiago Roth and further studied by the anthropologist Rudolf Martin. By the end of the nineteenth century and beginning of the twentieth century it was considered one of the oldest human skeletons from South America's southern cone. Here, we present the results of an interdisciplinary approach to study and contextualize the ancient individual remains. We discuss the context of the finding by first compiling the available evidence associated with the historical information and any previous scientific publications on this individual. Then, we conducted an osteobiographical assessment, by which we evaluated the sex, age, and overall preservation of the skeleton based on morphological features. To obtain a 3D virtual reconstruction of the skull, we performed high resolution CT-scans on selected skull fragments and the mandible. This was followed by the extraction of bone tissue and tooth samples for radiocarbon and genetic analyses, which brought only limited results due to poor preservation and possible contamination. We estimate that the individual from Baradero is a middle-aged adult male. We conclude that the revision of foundational collections with current methodological tools brings new insights and clarifies long held assumptions on the significance of samples that were recovered when archaeology was not yet professionalized.

Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.

A 23,000-year-old southern Iberian individual links human groups that lived in Western Europe before and after the Last Glacial Maximum

Human populations underwent range contractions during the Last Glacial Maximum (LGM) which had lasting and dramatic effects on their genetic variation. The genetic ancestry of individuals associated with the post-LGM Magdalenian technocomplex has been interpreted as being derived from groups associated with the pre-LGM Aurignacian. However, both these ancestries differ from that of central European individuals associated with the chronologically intermediate Gravettian. Thus, the genomic transition from pre- to post-LGM remains unclear also in western Europe, where we lack genomic data associated with the intermediate Solutrean, which spans the height of the LGM. Here we present genome-wide data from sites in Andalusia in southern Spain, including from a Solutrean-associated individual from Cueva del Malalmuerzo, directly dated to ~23,000 cal yr BP. The Malalmuerzo individual carried genetic ancestry that directly connects earlier Aurignacian-associated individuals with post-LGM Magdalenian-associated ancestry in western Europe. This scenario differs from Italy, where individuals associated with the transition from pre- and post-LGM carry different genetic ancestries. This suggests different dynamics in the proposed southern refugia of Ice Age Europe and posits Iberia as a potential refugium for western European pre-LGM ancestry. More, individuals from Cueva Ardales, which were thought to be of Palaeolithic origin, date younger than expected and, together with individuals from the Andalusian sites Caserones and Aguilillas, fall within the genetic variation of the Neolithic, Chalcolithic and Bronze Age individuals from southern Iberia.

On the traces of lost identities: chronological, anthropological and taphonomic analyses of the Late Neolithic/Early Eneolithic fragmented and commingled human remains from the Farneto rock shelter (Bologna, northern Italy)

The present study examines the prehistoric human skeletal remains retrieved starting from the 1920s in the deposit of the Farneto rock shelter, situated in the area of the 'Parco dei Gessi Bolognesi e Calanchi dell'Abbadessa' (San Lazzaro di Savena, Bologna, northern Italy). An exact dating and a reliable interpretation of the assemblage had not been reached so far because of the lack of contextual data useful for dating purposes, the inaccurate recovery procedures of the remains and their state of preservation. In fact, the skeletal remains from the Farneto rock shelter are highly fragmented and commingled, whereas reliable information about their original position and their recovery procedures are not available. Despite these difficulties, radiocarbon analyses allowed the precise dating of the remains to a final phase of the Neolithic and an early phase of the Eneolithic period in Emilia Romagna (northern Italy). The study of the assemblage enabled to clarify the use of the context for funerary purposes. Moreover, the anthropological and taphonomic analyses of the skeletal remains shed light on the biological profile of the individuals and on some events that occurred after their death. In particular, the analysis of perimortem lesions highlighted the existence of intentional interventions related to corpse treatment, referable to dismembering/disarticulation and scarnification, i.e. cleaning of bones from soft tissues. Finally, the comparison with other Italian and European Neo/Eneolithic funerary contexts enabled a better understanding of these complex ritual practices.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12520-023-01727-2.

The Quaternary lions of Ukraine and a trend of decreasing size in Panthera spelaea

The fossil record of the cave lion, Panthera spelaea, suggests a gradual decrease in body size, the process peaking just before the extinction of the species at the end of the Late Pleistocene. Such an evolutionary trend appears rather unusual for a large felid species and requires further investigation. This study reviews the cave lions of Ukraine, whose fossils are known from 46 localities dated from 800 kyr to 18–17 kyr ago, with a special emphasis on size changes through time. We describe several important finds including those of Panthera spelaea fossilis from Sambir, Panthera spelaea ssp. from Bilykh Stin Cave and Panthera spelaea spelaea from Kryshtaleva Cave. We make subspecific identifications of specimens from the region and focus on their size characteristics. Our analysis of Ukrainian cave lions agrees with the temporal trend of decreasing size, particularly accelerating during MIS 2, as exemplified by the extremely small female skull from Kryshtaleva Cave. We provide a direct AMS date for this specimen (22.0–21.5 cal kyr BP), which suggests that the Kryshtaleva lioness must have belonged to a Panthera spelaea spelaea population forced south by the spreading ice sheet. We discuss some palaeoecological aspects of the evolutionary history and eventual extinction of the cave lion. Finally, we review the subfossil records of the extant lion Panthera leo known from several Ukrainian sites archaeologically dated to 6.4–2.0 kyr BP. These finds most probably represent the Persian lion Panthera leo persica.

Temporal population structure, a genetic dating method for ancient Eurasian genomes from the past 10,000 years

Radiocarbon dating is the gold standard in archeology to estimate the age of skeletons, a key to studying their origins. Many published ancient genomes lack reliable and direct dates, which results in obscure and contradictory reports. We developed the temporal population structure (TPS), a DNA-based dating method for genomes ranging from the Late Mesolithic to today, and applied it to 3,591 ancient and 1,307 modern Eurasians. TPS predictions aligned with the known dates and correctly accounted for kin relationships. TPS dating of poorly dated Eurasian samples resolved conflicting reports in the literature, as illustrated by one test case. We also demonstrated how TPS improved the ability to study phenotypic traits over time. TPS can be used when radiocarbon dating is unfeasible or uncertain or to develop alternative hypotheses for samples younger than 10,000 years ago, a limitation that may be resolved over time as ancient data accumulate.

A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples

High Throughput DNA Sequencing (HTS) revolutionized the field of paleomicrobiology, leading to an explosive growth of microbial ancient DNA (aDNA) studies, especially from environmental samples. However, aDNA studies that examine environmental microbes routinely fail to authenticate aDNA, examine laboratory and environmental contamination, and control for biases introduced during sample processing. Here, we surveyed the available literature for environmental aDNA projects—from sample collection to data analysis—and assessed previous methodologies and approaches used in the published microbial aDNA studies. We then integrated these concepts into a case study, using shotgun metagenomics to examine methodological, technical, and analytical biases during an environmental aDNA study of soil microbes. Specifically, we compared the impact of five DNA extraction methods and eight bioinformatic pipelines on the recovery of microbial aDNA information in soil cores from extreme environments. Our results show that silica-based methods optimized for aDNA research recovered significantly more damaged and shorter reads (<100 bp) than a commercial kit or a phenol−chloroform method. Additionally, we described a stringent pipeline for data preprocessing, efficiently decreasing the representation of low-complexity and duplicated reads in our datasets and downstream analyses, reducing analytical biases in taxonomic classification.

Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily

Sicily is a key region for understanding the agricultural transition in the Mediterranean because of its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700–4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, whereas Late Mesolithic HGs carry ∼20% ancestry related to northern and (south) eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% of ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match the changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP; however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell’Uzzo, resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition.

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Genetic transition between Early Mesolithic and Late Mesolithic hunter-gatherers

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A near-complete genetic turnover during the Mesolithic-Neolithic transition

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Exchange of subsistence practices between hunter-gatherers and early farmers

An infant burial from Arma Veirana in northwestern Italy provides insights into funerary practices and female personhood in early Mesolithic Europe

The evolution and development of human mortuary behaviors is of enormous cultural significance. Here we report a richly-decorated young infant burial (AVH-1) from Arma Veirana (Liguria, northwestern Italy) that is directly dated to 10,211-9910 cal BP (95.4% probability), placing it within the early Holocene and therefore attributable to the early Mesolithic, a cultural period from which well-documented burials are exceedingly rare. Virtual dental histology, proteomics, and aDNA indicate that the infant was a 40-50 days old female. Associated artifacts indicate significant material and emotional investment in the child's interment. The detailed biological profile of AVH-1 establishes the child as the earliest European near-neonate documented to be female. The Arma Veirana burial thus provides insight into sex/gender-based social status, funerary treatment, and the attribution of personhood to the youngest individuals among prehistoric hunter-gatherer groups and adds substantially to the scant data on mortuary practices from an important period in prehistory shortly following the end of the last Ice Age.

"Here we go again": the inspection of collagen extraction protocols for 14C dating and palaeodietary analysis

Archaeological bone collagen is highly useful for radiocarbon (¹⁴C) dating and palaeodietary reconstruction. However, collagen preservation and carbon contamination are essential considerations when extracting collagen, becoming especially crucial close to the limit of the method (50,000 years before present = BP). Strong progress has been achieved in the past two decades by ¹⁴C and stable isotopic laboratories in removing contamination from archaeological bones, but different pretreatment protocols have been proven to produce varying results. Here we compare three collagen extraction protocols used for palaeodietary studies and ¹⁴C dating, considering collagen yield, elemental and stable isotopic data, FTIR analysis, and ¹⁴C dates. We focus on the impact of ultrafiltration on the yield and quality of the extracted material. The results again underline the importance of rigorous decontamination methods to gain accurate ¹⁴C dates and demonstrate that different protocols have significant effects on the quality and yield of extracted collagen.

Early Alpine occupation backdates westward human migration in Late Glacial Europe

Before the end of the Last Glacial Maximum (LGM, ∼16.5 ka ago)¹ set in motion major shifts in human culture and population structure,² a consistent change in lithic technology, material culture, settlement pattern, and adaptive strategies is recorded in Southern Europe at ∼18-17 ka ago. In this time frame, the landscape of Northeastern Italy changed considerably, and the retreat of glaciers allowed hunter-gatherers to gradually recolonize the Alps.^3-6 Change within this renewed cultural frame (i.e., during the Late Epigravettian phase) is currently associated with migrations favored by warmer climate linked to the Bølling-Allerød onset (14.7 ka ago),^7-11 which replaced earlier genetic lineages with ancestry found in an individual who lived ∼14 ka ago at Riparo Villabruna, Italy, and shared among different contexts (Villabruna Cluster).⁹ Nevertheless, these dynamics and their chronology are still far from being disentangled due to fragmentary evidence for long-distance interactions across Europe.¹² Here, we generate new genomic data from a human mandible uncovered at Riparo Tagliente (Veneto, Italy), which we directly dated to 16,980-16,510 cal BP (2σ). This individual, affected by focal osseous dysplasia, is genetically affine to the Villabruna Cluster. Our results therefore backdate by at least 3 ka the diffusion in Southern Europe of a genetic component linked to Balkan/Anatolian refugia, previously believed to have spread during the later Bølling/Allerød event. In light of the new genetic evidence, this population replacement chronologically coincides with the very emergence of major cultural transitions in Southern and Western Europe.

Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula

Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.

A minimally destructive protocol for DNA extraction from ancient teeth

Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.

Near-infrared hyperspectral imaging (NIR-HSI) and normalized difference image (NDI) data processing: An advanced method to map collagen in archaeological bones

In the present study, an innovative and highly efficient near-infrared hyperspectral imaging (NIR-HSI) method is proposed to provide spectral maps able to reveal collagen distribution in large-size bones, also offering semi-quantitative estimations. A recently introduced method for the construction of chemical maps, based on Normalized Difference Images (NDI), is declined in an innovative approach, through the exploitation of the NDI values computed for each pixel of the hyperspectral image to localize collagen and to extract information on its content by a direct comparison with known reference samples. The developed approach addresses an urgent issue of the analytical chemistry applied to bioarcheology researches, which rely on well-preserved collagen in bones to obtain key information on chronology, paleoecology and taxonomy. Indeed, the high demand for large-sample datasets and the consequent application of a wide variety of destructive analytical methods led to the considerable destruction of precious bone samples. NIR-HSI pre-screening allows researchers to properly select the sampling points for subsequent specific analyses, to minimize costs and time and to preserve integrity of archaeological bones (which are available in a very limited amount), providing further opportunities to understand our past.

Bone need not remain an elephant in the room for radiocarbon dating

Radiocarbon (¹⁴C) analysis of skeletal remains by accelerator mass spectrometry is an essential tool in multiple branches of science. However, bone ¹⁴C dating results can be inconsistent and not comparable due to disparate laboratory pretreatment protocols that remove contamination. And, pretreatments are rarely discussed or reported by end-users, making it an 'elephant in the room' for Quaternary scientists. Through a questionnaire survey, I quantified consensus on the reliability of collagen pretreatments for ¹⁴C dating across 132 experts (25 countries). I discovered that while more than 95% of the audience was wary of contamination and would avoid gelatinization alone (minimum pretreatment used by most ¹⁴C facilities), 52% asked laboratories to choose the pretreatment method for them, and 58% could not rank the reliability of at least one pretreatment. Ultrafiltration was highly popular, and purification by XAD resins seemed restricted to American researchers. Isolating and dating the amino acid hydroxyproline was perceived as the most reliable pretreatment, but is expensive, time-consuming and not widely available. Solid evidence supports that only molecular-level dating accommodates all known bone contaminants and guarantees complete removal of humic and fulvic acids and conservation substances, with three key areas of progress: (i) innovation and more funded research is required to develop affordable analytical chemistry that can handle low-mass samples of collagen amino acids, (ii) a certification agency overseeing dating-quality control is needed to enhance methodological reproducibility and dating accuracy among laboratories, and (iii) more cross-disciplinary work with better ¹⁴C reporting etiquette will promote the integration of ¹⁴C dating across disciplines. Those developments could conclude long-standing debates based on low-accuracy data used to build chronologies for animal domestications, human/megafauna extirpations and migrations, archaeology, palaeoecology, palaeontology and palaeoclimate models.

The early Aurignacian dispersal of modern humans into westernmost Eurasia

We report the remarkable discovery of an early Aurignacian occupation, ∼5,000 years older than any Upper Paleolithic site in westernmost Eurasia. The archaeological and radiocarbon data provide definitive evidence that modern humans were in western Iberia at a time when, if present at all, Neanderthal populations would have been extremely sparse. This discovery has important ramifications for our understanding of the process of modern human dispersal and replacement of Neanderthal populations. The results support a very rapid, unimpeded dispersal of modern humans across western Eurasia and support the notion that climate and environmental change played a significant role in this process.

Documenting the first appearance of modern humans in a given region is key to understanding the dispersal process and the replacement or assimilation of indigenous human populations such as the Neanderthals. The Iberian Peninsula was the last refuge of Neanderthal populations as modern humans advanced across Eurasia. Here we present evidence of an early Aurignacian occupation at Lapa do Picareiro in central Portugal. Diagnostic artifacts were found in a sealed stratigraphic layer dated 41.1 to 38.1 ka cal BP, documenting a modern human presence on the western margin of Iberia ∼5,000 years earlier than previously known. The data indicate a rapid modern human dispersal across southern Europe, reaching the westernmost edge where Neanderthals were thought to persist. The results support the notion of a mosaic process of modern human dispersal and replacement of indigenous Neanderthal populations.

Not a limitless resource: ethics and guidelines for destructive sampling of archaeofaunal remains

With the advent of ancient DNA, as well as other methods such as isotope analysis, destructive sampling of archaeofaunal remains has increased much faster than the effort to collect and curate them. While there has been considerable discussion regarding the ethics of destructive sampling and analysis of human remains, this dialogue has not extended to archaeofaunal material. Here we address this gap and discuss the ethical challenges surrounding destructive sampling of materials from archaeofaunal collections. We suggest ways of mitigating the negative aspects of destructive sampling and present step-by-step guidelines aimed at relevant stakeholders, including scientists, holding institutions and scientific journals. Our suggestions are in most cases easily implemented without significant increases in project costs, but with clear long-term benefits in the preservation and use of zooarchaeological material.

Microwear and isotopic analyses on cave bear remains from Toll Cave reveal both short-term and long-term dietary habits

Dietary habits of the extinct Ursus spelaeus have always been a controversial topic in paleontological studies. In this work, we investigate carbon and nitrogen values in the bone collagen and dental microwear of U. spelaeus specimens recovered in Level 4 from Toll Cave (Moià, Catalonia, NE Iberian Peninsula). These remains have been dated to > 49,000 ¹⁴C BP. The ability of both proxies to provide data on the diet of U. spelaeus at different times in the life-history (isotopes: average diet of life; microwear: last days/weeks before death), allows us to generate high-resolution and complementary data. Our results show lower values (δ¹³C & δ¹⁵N) in cave bears than in strict herbivores (i.e. Cervus elaphus) recovered from the same level of Toll Cave. On the other hand, 12 lower molars (m1) were analysed through low-magnification microwear technique. The cave bears from Toll Cave show a microwear pattern like that of extant bears with omnivorous and carnivorous diets. These data are discussed in the framework of all available data in Europe and add new information about the plasticity of the dietary habits of this species at the southern latitudes of Europe during Late Pleistocene periods.

Pretreatment and gaseous radiocarbon dating of 40-100 mg archaeological bone

Radiocarbon dating archaeological bone typically requires 300–1000 mg material using standard protocols. We report the results of reducing sample size at both the pretreatment and ¹⁴C measurement stages for eight archaeological bones spanning the radiocarbon timescale at different levels of preservation. We adapted our standard collagen extraction protocol specifically for <100 mg bone material. Collagen was extracted at least twice (from 37–100 mg material) from each bone. Collagen aliquots containing <100 μg carbon were measured in replicate using the gas ion source of the AixMICADAS. The effect of sample size reduction in the EA-GIS-AMS system was explored by measuring ¹⁴C of collagen containing either ca. 30 μg carbon or ca. 90 μg carbon. The gas dates were compared to standard-sized graphite dates extracted from large amounts (500–700 mg) of bone material pretreated with our standard protocol. The results reported here demonstrate that we are able to reproduce accurate radiocarbon dates from <100 mg archaeological bone material back to 40,000 BP.

Reconstructing the Deep Population History of Central and South America

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.