Fact-checked by Grok 2 weeks ago

Paleogenetics

Paleogenetics is the interdisciplinary field that applies molecular genetics to the study of ancient DNA (aDNA) extracted from archaeological, paleontological, and sedimentary remains, enabling the reconstruction of genetic histories of past human populations, extinct species, and microbial pathogens.^[1] This approach overcomes the inherent challenges of DNA degradation and contamination through advanced techniques like next-generation sequencing (NGS), which has revolutionized the analysis of fragmented genetic material from sources such as bones, teeth, and mummified tissues.^[2] The field emerged in the 1980s with pioneering work on mitochondrial DNA, including the first successful sequencing of aDNA from a quagga specimen in 1984, marking the beginning of efforts to retrieve genetic information from remains thousands of years old.^[2] Methodological advancements, such as polymerase chain reaction (PCR) amplification introduced in 1988 and the adoption of NGS around 2006, shifted paleogenetics from limited fragment analysis to whole-genome sequencing, exemplified by the 2010 publication of the first ancient human genome from a 4,000-year-old Paleo-Inuit individual.^[2] These developments have expanded the temporal scope dramatically, with the oldest verified aDNA recovered from 2-million-year-old Greenland sediments in 2022, providing insights into early mammalian evolution, and more recently, in November 2025, the oldest ancient RNA recovered from up to 50,000-year-old mammoth mummies, extending methods to paleotranscriptomics.^[2]^[3] Key applications of paleogenetics include tracing human migrations and admixture events, such as Neanderthal introgression into modern genomes, which influences traits like immune response and disease susceptibility.^[4] It also elucidates the evolution of complex traits, using polygenic risk scores (PRS) derived from genome-wide association studies (GWAS) to infer historical changes in phenotypes like skin pigmentation and height across prehistoric European populations.^[4] Furthermore, paleogenetics has illuminated pathogen histories, such as the Bronze Age origins of Yersinia pestis through analysis of 3,800-year-old genomes, informing our understanding of ancient epidemics like the Black Death.^[2] Despite ethical concerns over sampling irreplaceable remains,^[5] and risks of misinterpretation due to post-mortem DNA damage,^[1] the field continues to integrate with disciplines like anthropology and epidemiology for broader historical reconstructions.

Introduction

Definition

Paleogenetics is the study of preserved genetic material from ancient organisms to reconstruct past biological events, a concept introduced by Émile Zuckerkandl and Linus Pauling in their seminal work on chemical paleogenetics. This field leverages molecular data to infer historical processes that shaped life, focusing on the retrieval and analysis of ancient DNA (aDNA) to address questions beyond the reach of living populations. At its core, paleogenetics relies on extracting aDNA from diverse sources such as fossils, sediments, and mummified remains to elucidate evolutionary relationships, population dynamics, and adaptive changes over time.^[6] These genetic traces, often fragmented and chemically modified due to postmortem degradation, enable researchers to model ancestral states and trace lineage divergences.^[7] Unlike modern genetics, which analyzes high-quality, abundant DNA from contemporary samples, paleogenetics contends with severely degraded and low-quantity aDNA, where endogenous material typically constitutes less than 1% of the total extract, necessitating specialized authentication and amplification techniques to distinguish authentic ancient sequences from contaminants.^[8] The scope of paleogenetics extends to animals, plants, and microbes, though early applications predominantly targeted vertebrates and humans to explore key evolutionary milestones. It differs from paleogenomics, which emphasizes the reconstruction of complete ancient genomes, by encompassing broader genetic analyses that may not require full genomic sequencing.^[9]

Historical Development

The field of paleogenetics originated in the early 1960s with the conceptual framework proposed by Émile Zuckerkandl and Linus Pauling, who envisioned using molecular data from proteins and genes to reconstruct evolutionary history, terming this approach "chemical paleogenetics" or molecular paleontology.^[10] In their 1963 work, they argued that sequences of informational macromolecules, such as hemoglobin, could serve as "documents of evolutionary history," enabling inferences about paleontological events through comparisons with modern sequences.^[10] This idea laid the groundwork for integrating genetic information with fossil records, shifting evolutionary studies from morphological to molecular evidence.^[11] The first empirical advances came in 1984, when Russell Higuchi and colleagues successfully extracted and sequenced mitochondrial DNA from a 140-year-old quagga (Equus quagga quagga) museum specimen, an extinct zebra subspecies, demonstrating that ancient DNA (aDNA) could be viable for genetic analysis despite degradation.^[12] This breakthrough confirmed the potential of aDNA for phylogenetic studies, as the quagga sequences aligned closely with modern zebras, validating the technique's reliability for extinct taxa.^[12] By the 1990s, the invention of polymerase chain reaction (PCR) amplification revolutionized aDNA research, allowing recovery of short, fragmented sequences from subfossil remains and enabling broader applications to extinct species, such as the New Zealand moas (Dinornithiformes). Studies on moa bones and eggshells, for instance, clarified their evolutionary relationships to kiwis and other ratites, highlighting PCR's role in overcoming low DNA yields. A pivotal shift occurred post-2005 with the development of cloning-free methods, such as direct high-throughput sequencing, which alleviated contamination risks from bacterial cloning and facilitated the transition from mitochondrial to nuclear DNA analysis. This enabled whole-genome sequencing in the 2000s and 2010s, exemplified by the 2010 Neanderthal draft genome project, which recovered approximately 63% of the ~3.2-billion-base-pair nuclear genome from three individuals at 1.3-fold coverage, revealing interbreeding with modern humans. These advancements expanded paleogenetics to population-level inferences and functional genomics. The significance of this work was recognized in 2022 when Svante Pääbo, a key figure in the Neanderthal genome project, was awarded the Nobel Prize in Physiology or Medicine for his discoveries concerning the genomes of extinct hominins and the evolution of modern humans.^[13] In the 2020s, the field reached new depths with the sequencing of the oldest aDNA to date—~2-million-year-old environmental DNA from Greenland permafrost sediments—which unveiled an ancient Arctic ecosystem featuring mastodons, hares, and conifers, including early mammoth lineages and canids.^[14]

Methods and Techniques

DNA Extraction and Preservation

The preservation of ancient DNA (aDNA) is fundamentally influenced by environmental conditions and postmortem degradation processes, which limit the recovery of genetic material from archaeological and paleontological samples. DNA molecules degrade primarily through hydrolysis, which cleaves the phosphodiester backbone, oxidation that modifies nucleotide bases, and microbial activity that further breaks down organic remains.^[7]^[15] These processes are accelerated in warm, humid, or oxygen-rich environments but are mitigated in cold, dry, or anaerobic settings such as permafrost, caves, or desiccated sediments.^[16]^[17] For instance, under a burial temperature of approximately 13.1°C, the half-life of a 242 base pair mitochondrial DNA fragment has been estimated at 521 years, providing a benchmark for predicting DNA survival over time.^[18] Suitable sample types for aDNA extraction include dense skeletal elements like bones and teeth, as well as non-skeletal materials such as sediments, coprolites, and dental calculus, which can preserve traces of host, dietary, or environmental DNA.^[19]^[20] However, endogenous DNA—derived from the original organism—typically constitutes less than 1% of the total extract due to extensive postmortem damage, including depurination that leads to strand breaks and base loss.^[7]^[21] Resulting aDNA fragments are highly degraded, with average lengths of 50–100 base pairs, necessitating specialized extraction and preparation techniques to maximize recovery.^[22] Silica-based purification methods, such as the Boom protocol developed in 1990, represent a cornerstone for extracting double-stranded DNA from ancient samples by binding nucleic acids to silica particles under chaotropic conditions like guanidinium thiocyanate.^[23] To accommodate the prevalence of single-stranded, fragmented DNA, single-stranded library preparation protocols, introduced by Gansauge and Meyer in 2013, ligate adapters directly to denatured strands, significantly improving yields from low-input samples.^[24] These approaches are often combined with pretreatment steps, such as decalcification with EDTA for mineralized tissues, to release bound DNA while minimizing further degradation.^[25] Contamination from modern sources poses a persistent risk in aDNA workflows, addressed through rigorous controls including dedicated clean rooms with positive pressure and HEPA filtration, UV irradiation of surfaces and reagents to induce thymine dimers in extraneous DNA, and the use of protective clothing and one-way workflows.^[26] Authentication of endogenous aDNA relies on characteristic postmortem signatures, such as elevated C-to-T transitions at fragment 5' ends due to cytosine deamination, which distinguish ancient molecules from modern contaminants.^[27]^[28] Quantifying endogenous DNA yield is essential for assessing extraction efficiency and guiding downstream analyses, typically achieved via quantitative PCR (qPCR) targeting short, species-specific amplicons to measure preservable DNA content relative to inhibitors or microbial overburden.^[29] Alternatively, initial shotgun sequencing surveys provide comprehensive metrics, including the proportion of mapped endogenous reads and average fragment length, to evaluate sample quality before targeted enrichment.^[30] These methods ensure that only viable extracts proceed to sequencing, optimizing resource use in paleogenetic studies.^[31]

Sequencing and Bioinformatics

In paleogenetics, sequencing of ancient DNA (aDNA) primarily relies on next-generation sequencing platforms like Illumina's short-read technologies, which excel at processing highly fragmented DNA molecules typical of archaeological samples due to their high throughput and base-calling accuracy exceeding 99%. Emerging long-read platforms, such as PacBio, are increasingly applied to resolve complex post-mortem damage (PMD) patterns and sequence longer mitochondrial DNA (mtDNA) amplicons, offering improved assembly of repetitive regions despite higher error rates in raw reads that are mitigated through circular consensus sequencing. Similarly, Oxford Nanopore Technologies (ONT) long-read sequencing enables real-time analysis and direct detection of DNA modifications like methylation in aDNA, with applications in studies of ancient environmental samples as of 2025.^[32]^[33] To enhance yield from low-input libraries, target capture techniques hybridize probes to specific loci like mtDNA, enriching endogenous sequences by orders of magnitude while minimizing off-target microbial DNA.^[34] The bioinformatics pipeline for aDNA begins with preprocessing steps, including adapter trimming and quality filtering to remove low-confidence bases, often using tools like Trim Galore or Cutadapt tailored for short inserts averaging 50-100 base pairs.^[35] Authentication of aDNA authenticity follows, employing software such as mapDamage to quantify characteristic PMD signatures, including elevated C-to-T transitions at fragment ends from cytosine deamination, which confirm the ancient origin and help filter modern contaminants.^[36] Reads are then aligned to reference genomes using specialized mappers like BWA-aln or Bowtie2, which accommodate damage-induced mismatches and short lengths through seeded alignment algorithms, achieving mapping rates of 10-50% in typical paleogenetic datasets.^[37] Downstream analysis addresses the pervasive low coverage in aDNA, often below 1× genome-wide, through pseudohaploidization, where a single allele is randomly selected per heterozygous site based on read evidence to generate a diploid-like consensus without inflating heterozygosity artifacts from uneven coverage.^[38] For missing genotypes, imputation methods like GLIMPSE leverage modern reference panels and hidden Markov models to infer variants with imputation accuracy (r²) exceeding 0.8 for common variants (MAF >5%) even at 0.1× coverage, and approaching 0.95 at 0.75× coverage, enabling scalable population-scale inferences.^[39] Population genetic tools, such as ADMIXTOOLS, compute admixture metrics like f-statistics to quantify shared drift and gene flow, providing robust tests for events like Neanderthal introgression without assuming parametric models.^[40] Coverage metrics in paleogenetics emphasize effective depth, which adjusts raw read counts for PMD and duplication rates; for instance, the first Neanderthal genome achieved 1.3× mean depth but only 63% callable bases due to fragmentation and damage, highlighting the need for multiple individuals to reach genome-wide resolution. Error correction has advanced with post-2020 machine learning models that classify reads or predict contamination probabilities using features like mismatch patterns and fragment lengths, achieving >90% specificity in filtering modern human DNA from ancient libraries.^[41]

Evolutionary Applications

Human and Hominin Evolution

Paleogenetics has significantly refined the Out-of-Africa model of human evolution by analyzing ancient DNA (aDNA) from early Homo sapiens remains, placing the origins of anatomically modern humans in Africa between approximately 130,000 and 250,000 years ago. This timeline emerges from genomic comparisons of African and non-African populations, which reveal a deep divergence within African lineages predating major dispersals out of the continent around 60,000–70,000 years ago. Evidence for back-migrations into Africa is supported by the genome of the ~45,000-year-old Ust'-Ishim individual from Siberia, whose DNA shows a basal position relative to present-day Eurasians and indicates gene flow returning to African populations after initial out-of-Africa expansions. Archaic admixture events have been illuminated through paleogenetics, demonstrating interbreeding between Homo sapiens and extinct hominins. Non-African populations carry 1–2% Neanderthal DNA, resulting from admixture events approximately 50,000–60,000 years ago, as quantified by f4-statistics that detect excess allele sharing between Neanderthals and modern Eurasians beyond what would be expected from shared ancestry alone. Similarly, Denisovan contributions are prominent in Oceanic populations, reaching up to 6% in some groups like Papuans and Aboriginal Australians, with gene flow inferred via shared archaic segments and admixture graphs showing multiple pulses of introgression.^[42] These findings highlight how paleogenetics uses statistical tools like f4-ratios to confirm directional gene flow from archaic groups into expanding Homo sapiens lineages. Population turnovers in human history are vividly reconstructed by aDNA, particularly in Europe where Yamnaya steppe pastoralists migrated westward around 5,000 years ago, contributing up to 75% of ancestry to later Bronze Age populations and replacing approximately 90% of pre-existing male lineages through the introduction of Y-chromosome haplogroup R1b. This demographic shift is evidenced by principal component analyses and admixture modeling of over 200 ancient European genomes, revealing a rapid influx that reshaped genetic landscapes. Additionally, ghost populations—unsampled ancient groups inferred from genomic residuals—have been detected using D-statistics, which identify excess shared drift between modern and ancient samples inconsistent with a simple tree-like model, such as an extinct African lineage contributing to West Africans or archaic introgressors in Denisovans. Adaptive traits under selection are traceable via paleogenetics through scans of aDNA for allele frequency changes over time. In Europe, the lactase persistence allele (LCT -13910T) was rare in Neolithic farmers but rose sharply post-Neolithic, driven by strong positive selection linked to dairy pastoralism, as shown by temporal sampling of over 100 ancient individuals where the allele's frequency increased from <5% to >50% within 4,000 years.^[43] Such analyses employ site frequency spectrum methods on aDNA to estimate selection coefficients, confirming the trait's rapid spread in response to dietary shifts. Recent paleogenetic studies from the 2020s, leveraging datasets exceeding 10,000 ancient genomes, have developed multi-ancestry models revealing complex pre-Columbian admixture in the Americas. These models, built on qpAdm and ADMIXTURE frameworks, show that Native American populations derive from at least three streams of Siberian-related ancestry, with evidence of local admixture between northern and southern lineages around 15,000–20,000 years ago, prior to continental diversification. For instance, genomes from the Andes and Amazon indicate ghost admixture from unsampled Paleoamerican groups, contributing 10–20% to modern indigenous profiles and underscoring a more intricate migration history than previously thought.

Cultural and Behavioral Evolution

Paleogenetics provides insights into ancient kinship structures by analyzing sex-biased genetic patterns, such as Y-chromosome bottlenecks and mitochondrial DNA (mtDNA) diversity. In Bronze Age Europe, genomic data from multiple sites reveal sharp reductions in Y-chromosome diversity, indicative of patrilineal social organization where male lineages dominated due to factors like kin-group competition or segmentary systems, rather than widespread violence.^[44] This bottleneck, observed across post-Neolithic populations, suggests patrilocal residence patterns that restricted male dispersal while allowing higher female mobility.^[45] Complementing this, elevated mtDNA diversity in the same archaeological contexts points to female exogamy, where women moved between groups to forge alliances, as evidenced by strontium isotope ratios showing non-local female burials in sites from the third millennium BCE.^[46] Genetic evidence also illuminates cultural adaptations in diet, linking subsistence shifts to selection on specific loci. The spread of lactase persistence, enabling adult milk digestion, coincided with the rise of pastoralism around 7,500 years ago in Europe and Central Asia, driven by mutations in the LCT gene enhancer that rose rapidly under positive selection from dairy consumption.^[47] Similarly, variation in AMY1 gene copy number, which encodes salivary amylase for starch breakdown, increased in frequency in ancient farming populations compared to pre-Neolithic hunter-gatherers, reflecting adaptation to cereal-based diets.^[48] These changes highlight how paleogenetics traces the co-evolution of genes and cultural practices like herding and cultivation. Mobility patterns, integral to trade, conflict, and cultural exchange, are reconstructed by integrating ancient DNA with isotope analyses. In the Bell Beaker culture (ca. 2750-1800 BCE), genome-wide data indicate large-scale male-mediated migrations across western Europe, replacing up to 90% of Britain's Neolithic ancestry, while oxygen and strontium isotopes from tooth enamel confirm long-distance movements of individuals over hundreds of kilometers, suggestive of raids, alliances, or resource networks. Such correlations reveal dynamic social behaviors, including the spread of metallurgical innovations tied to mobile groups rather than purely local diffusion.^[49] Paleogenetics further probes behavioral modernity through variants associated with cognition and social traits. Neanderthals carried the derived FOXP2 allele shared with modern humans, implicated in orofacial motor control and potentially speech, as sequencing of Neanderthal nuclear DNA from multiple fossils confirms the presence of these substitutions predating Homo sapiens divergence.^[50] In human contexts, variants in the serotonin transporter gene (SLC6A4), such as the 5-HTTLPR polymorphism, have been examined in modern studies for potential links to stress reactivity and behavior, though evidence is mixed.^[51] While direct ancient DNA evidence for such variants in specific historical contexts remains limited, these genetic markers highlight the potential of paleogenetics to explore social dynamics and cultural behaviors.

Archaeological Applications

Ancient Pathogens and Diseases

Paleogenetics has revolutionized the study of ancient infectious diseases by enabling the recovery of pathogen DNA from archaeological remains, particularly through metagenomic shotgun sequencing of skeletal materials. This approach allows for the unbiased detection of microbial genetic material in human samples, revealing the presence and genetic diversity of pathogens that afflicted past populations. For instance, genomes of Yersinia pestis, the causative agent of plague, have been reconstructed from Black Death victims dated to 1347–1351 CE, demonstrating that the pandemic resulted from multiple independent introductions of the bacterium into Europe from diverse Asian sources.30208-6) Phylogenetic analyses of ancient pathogen genomes have illuminated the evolutionary histories of major diseases. Hepatitis B virus (HBV) strains, including extinct genotypes, have been identified in human skeletons dating back approximately 4,500 years from sites across Eurasia, indicating that the virus circulated widely during the Bronze Age and diversified alongside human migrations. Similarly, ancient DNA evidence supports the diversification of Mycobacterium tuberculosis lineages around 6,000 years ago, coinciding with the Neolithic expansion of agriculture and denser human settlements in Eurasia, which likely facilitated the pathogen's spread.^[52] A prominent example of pathogen detection in preserved human remains is the case of Ötzi the Iceman, a ~5,300-year-old mummy discovered in the European Alps. Whole-genome sequencing conducted in 2012 identified DNA from Borrelia burgdorferi, the spirochete responsible for Lyme disease, marking the earliest known human infection with this pathogen around 3,300 BCE; the analysis also detected sequences from intestinal parasites such as Helicobacter pylori. Techniques for DNA extraction from such mummified tissues, involving careful decontamination and targeted enrichment, have been essential for these recoveries.^[53] Distinctions between endemic and epidemic disease dynamics have emerged from paleogenetic studies of plague and other infections. Y. pestis was present in Europe as an endemic pathogen at least 5,000 years ago, with early divergent strains identified in Neolithic and Bronze Age teeth from Germany and Russia, predating the Black Death by millennia and suggesting sporadic outbreaks rather than the later pandemic scale. Likewise, the variola virus, cause of smallpox, has been detected in Viking-era remains (~600–1050 CE) from northern Europe, including diverse strains in mass graves, indicating widespread circulation during this period and challenging prior assumptions about the virus's antiquity.01163-3)^[54] Host-pathogen co-evolution is evident in the genetic adaptations of human immune systems to ancient infections, particularly through selection on human leukocyte antigen (HLA) alleles that enhance pathogen recognition and clearance. Ancient DNA from medieval European populations reveals rapid changes in HLA allele frequencies following the Black Death, with variants conferring resistance to Y. pestis rising in frequency due to selective pressure from the plague. Such dynamics extend to other pathogens, including ancient influenza strains, where HLA class I and II alleles have been implicated in modulating immune responses and viral evasion over millennia.^[55]

Domestication and Subsistence

Paleogenetics has provided critical evidence for the timing and genetic signatures of animal domestication, revealing bottlenecks and founder effects that shaped early human-animal relationships. For instance, ancient DNA analyses indicate that dogs diverged from wolf ancestors between 20,000 and 40,000 years ago, with a genetic bottleneck around 27,000 years ago marking the onset of domestication from an extinct Pleistocene wolf lineage.^[56] This single domestication event in Eurasia facilitated the dual dispersal of dogs alongside human migrations into the Americas.^[57] Similarly, taurine cattle (Bos taurus) were domesticated from wild aurochs in the Near East approximately 10,500 years ago, descending from a small founder population of fewer than 80 individuals, which imposed a severe genetic bottleneck.^[58]^[59] The divergence between taurine and indicine (Bos indicus) cattle lineages occurred later, around 7,000 years ago in the Indus Valley, reflecting independent domestication events tied to regional pastoralism.^[60] These genetic insights underscore how domestication reduced diversity in livestock, influencing modern breeds and human subsistence economies. In plant domestication, ancient DNA from archaeological seeds has illuminated selective pressures for traits enhancing harvestability and yield. Einkorn wheat (Triticum monococcum), one of the earliest domesticated crops in the Fertile Crescent around 10,000 years ago, shows genomic evidence of selection for a non-brittle rachis, which prevents natural seed shattering and allows easier collection.^[61]^[62] This mutation, identified through comparisons of ancient and modern genomes, arose rapidly post-domestication, transforming wild progenitors into viable agricultural staples.^[63] In Mesoamerica, ancient DNA from amaranth (Amaranthus spp.) seeds demonstrates genetic continuity between wild and domesticated forms, indicating local domestication and sustained cultivation without complete loss of ancestral diversity, as seen in South American grain amaranth varieties.^[64]^[65] Such findings highlight parallel evolutionary paths in independent domestication centers, where human selection favored nutritional and adaptive traits over millennia. Domestication also facilitated zoonotic pathogen transmission, with paleogenetic evidence linking animal husbandry to human disease emergence. The measles virus (MeV) likely diverged from the rinderpest virus (RPV) of cattle around 2,500 years ago, but the broader zoonotic framework traces to cattle domestication approximately 10,000 years ago, enabling spillover in dense agro-pastoral communities.^[66]^[67] This event exemplifies how intensified animal-human contact post-domestication amplified infectious disease reservoirs. Subsistence shifts driven by these practices are evident in human genetic adaptations; for example, variants in the FADS gene cluster, involved in polyunsaturated fatty acid metabolism, underwent positive selection in ancient European coastal populations reliant on marine diets, enhancing efficiency in processing fish-derived omega-3s before and after the Neolithic transition.^[68] Likewise, the lactase persistence (LP) allele (e.g., -13910*T) spread rapidly across Eurasia between 4,000 and 3,000 years ago, correlating with the expansion of dairy farming and enabling adult milk consumption in pastoralist societies.^[69]^[70] Hybridization events further illustrate the dynamic genetic interplay in domesticated species. Ancient DNA from ~4,500-year-old equid remains in the Near East reveals the "kunga"—an elite hybrid pack animal—as a cross between domesticated donkeys and Syrian wild asses, combining traits for strength and endurance in early urban economies.^[71] In ancient Egyptian contexts, genomic analyses confirm admixture between domestic donkeys and African wild asses, contributing to breed diversity and supporting long-distance trade networks.^[72] These findings demonstrate how intentional or opportunistic hybridization bolstered the utility of domesticated animals in subsistence systems.

Challenges and Limitations

Technical and Preservation Issues

Ancient DNA (aDNA) is highly susceptible to postmortem damage (PMD), which includes hydrolytic processes leading to single- and double-strand breaks, as well as chemical modifications such as depurination and cytosine deamination that result in characteristic C-to-T transitions at fragment ends.^[7] These degradation mechanisms fragment DNA into short molecules, typically under 100 base pairs in length, and introduce errors that complicate downstream analyses.^[73] Environmental factors, particularly elevated temperatures and humidity, accelerate this decay qualitatively following an exponential rate, with half-lives estimated around 500 years under temperate conditions but dropping sharply in warmer settings.^[73] Contamination poses a major technical challenge in aDNA studies, often originating from modern human handlers, laboratory reagents, or environmental microbes, where present-day human DNA can constitute up to 99% of sequences in poorly controlled extracts.^[74] Authentication relies on verifying PMD signatures, such as elevated C-to-T and G-to-A substitution rates, alongside independent replication of results across labs to distinguish ancient from contaminant molecules.^[75] Low sequencing coverage, typically ranging from 0.1x to 5x for many ancient genomes, results in incomplete data recovery and ascertainment bias, where variants in low-coverage regions are underrepresented or miscalled, limiting reliable inferences like heterozygosity estimates.^[39] For instance, the 2010 Neanderthal genome assembly from Vindija achieved only about 4% endogenous DNA recovery, constraining variant calling and population genetic analyses.^[76] Preservation of aDNA varies dramatically by environment, with permafrost sites yielding viable sequences from samples over 10,000 years old, such as woolly mammoth remains, due to consistently low temperatures that inhibit microbial activity and hydrolysis.^[77] In contrast, tropical regions experience rapid degradation from heat and moisture, often restricting recoverable aDNA to less than 1,000 years, as seen in limited successes from rodent bones in Southeast Asian forests.^[78] To ensure reproducibility, 2025 guidelines emphasize mandatory archiving of raw sequencing data in public repositories, validation of bioinformatics pipelines against standardized datasets, and documentation of batch effects to mitigate variability in processing ancient samples. These standards promote transparent workflows, enabling independent verification and reducing false positives in paleogenetic interpretations.^[79]

Ethical and Interpretive Challenges

Paleogenetics faces significant interpretive biases due to the over-reliance on ancient DNA samples from European contexts, which constitute the vast majority of published datasets. This Eurocentric focus limits the understanding of global human history, as regions like Africa and Asia remain underrepresented, leading to skewed narratives that prioritize continental-scale migrations in Europe over local dynamics elsewhere. For instance, early ancient DNA research emphasized broad demographic questions in Europe, often neglecting finer-scale regional histories in the Global South.^[80] Colonial legacies further exacerbate these biases in studies of Indigenous ancestry, where extractive research practices have historically marginalized descendant communities without meaningful involvement. Such approaches perpetuate harm by misrepresenting Indigenous histories, as seen in cases where ancient DNA results have been used to label groups like the Taíno as "extinct," ignoring living descendants' perspectives. Ethical issues surrounding consent for analyzing ancestral remains are central, with scholars advocating for informed proxy consent through relational autonomy, where living representatives or communities provide permission on behalf of the deceased to protect intergenerational impacts. Repatriation demands have intensified in the 2020s, particularly among Native American tribes under the Native American Graves Protection and Repatriation Act (NAGPRA), where debates center on the destructive nature of DNA sampling and the right to reclaim ancestors for reburial rather than continued scientific use. Dual-use risks also arise, as ancient DNA data could be misused for population profiling or to reinforce discriminatory narratives, underscoring the need for safeguards against non-scientific applications.^[81]^[82]^[83] Data access and equity present ongoing tensions between open-access mandates for scientific progress and community veto rights to prevent exploitation. International frameworks, such as the United Nations Declaration on the Rights of Indigenous Peoples (UNDRIP) and UNESCO's bioethics declarations, emphasize Indigenous data sovereignty, requiring consultation and control over genetic information from ancestral remains. Overinterpretation risks compound these challenges, particularly in admixture models where correlation is mistaken for causation; for example, STRUCTURE and ADMIXTURE bar plots may suggest distinct ancestral sources when alternative explanations like genetic bottlenecks better fit the data, leading to flawed historical inferences. Cultural sensitivity in reporting kinship findings is essential to avoid inflammatory narratives, such as framing migrations as "invasions," which can perpetuate stereotypes; instead, results should be contextualized with community input to respect diverse cultural interpretations of ancestry and relatedness.^[84]^[85] To address these gaps, there are increasing calls for diverse global collaborations that prioritize equitable partnerships with African and Asian researchers and communities. Such efforts aim to expand ancient DNA datasets beyond Europe, fostering local laboratories to investigate region-specific histories while ensuring ethical standards like community engagement from project inception. These initiatives, aligned with guidelines from bodies like the World Archaeological Congress, promote sustainable research that benefits all stakeholders and mitigates interpretive biases through inclusive perspectives.^[80]^[81]

References

[1]
https://doi.org/10.32074/1591-951X-146
[2]
https://doi.org/10.3390/genes14010234
[3]
https://www.science.org/content/article/forty-thousand-year-old-mammoth-mummies-yield-oldest-rna-yet-found
[4]
Methodological Changes in the Field of Paleogenetics - PMC
Jan 16, 2023 · Ancient DNA (aDNA) refers to genetic material recovered from ancient, partially preserved material, including parts of dead organisms, sediments ...Missing: aspects | Show results with:aspects
[5]
Ancient DNA Damage - PMC - NIH
DNA fragments from ancient specimens are short (40–500 bp) and contain lesions that block DNA polymerases and cause replication errors.
[6]
Fragmentation of Contaminant and Endogenous DNA in Ancient ...
The efficiency of retrieval of endogenous sequences is below 1% in all cases. We have used the non-human samples to identify human sequences (0.35 and 1.4%, ...Missing: quantity | Show results with:quantity
[7]
Nobel shines light on paleogenetics, study of ancient DNA - Phys.org
Oct 3, 2022 · New Nobel laureate Svante Paabo is considered the father of both paleogenetics and paleogenomics, which aims to reconstruct the genetic information of long ...
[8]
[PDF] Molecular Restoration Studies of Extinct Forms of Life
17 (1963) Suppl. 1. Page 2. S 10. PAULING AND ZUCKERKANDL. Time. A. Present. Time ... Fossil remains no doubt express the activity of only a fraction of the genes.
[9]
Emile Zuckerkandl, Linus Pauling & Molecular Clock
In 1965, in an often-cited paper, Emile Zuckerkandi and Linus Pauling coined a term to describe a hypothesis that they had been promoting for the previous.
[10]
DNA sequences from the quagga, an extinct member of the horse ...
Nov 15, 1984 · We report that DNA was extracted from this tissue in amounts approaching 1% of that expected from fresh muscle, and that the DNA was of relatively low ...
[11]
A 2-million-year-old ecosystem in Greenland uncovered by ... - Nature
Dec 7, 2022 · Here we report an ancient environmental DNA 6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland.
[12]
Differential preservation of endogenous human and microbial DNA ...
Jun 29, 2018 · These degradative processes include oxidative and hydrolytic damage to individual bases, hydrolytic lesions on the sugar-phosphate backbone, DNA ...
[13]
Effects of different environmental factors on preservation of DNA in ...
Temperature, humidity, the presence of microorganisms, and the chemical properties of the soil have the most significant influence on DNA preservation [8].
[14]
Environment and excavation: Pre-lab impacts on ancient DNA ...
Water is a main degradative factor; it dissolves the bone apatite, allows growth of microorganisms and leads to hydrolytic and oxidative damages of the DNA.2. Data Basis · 3.1. Environment And Dna... · 4. Conclusions And...
[15]
The half-life of DNA in bone: measuring decay kinetics in 158 dated ...
Dec 7, 2012 · The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence.
[16]
Ancient DNA extraction from bones and teeth - PubMed
The protocol presented here allows DNA extraction from ancient bone and teeth with a minimum of working steps and equipment and yields DNA extracts within 2 ...
[17]
The Technological Advance and Application of Coprolite Analysis
Ancient DNA (aDNA), the genetic material isolated from ancient organisms, has various sources in coprolites, including producers, faunal organisms that ...
[18]
Assessing the impact of post-mortem damage and contamination on ...
Mar 14, 2024 · Microbial and environmental contamination are responsible for the underrepresentation of endogenous DNA. The competitive amplification of this ...
[19]
Ancient DNA: the past for the future - PMC - NIH
Jun 8, 2023 · However, aDNA, like any chemical substance, interacts with the environment, degrades into short DNA fragments (approximately 50–100 base pairs ( ...
[20]
Rapid and simple method for purification of nucleic acids - PubMed
The method uses guanidinium thiocyanate and silica particles to purify DNA and RNA from serum and urine in under 1 hour.
[21]
Single-stranded DNA library preparation for the sequencing of ...
Single-stranded library preparation is performed by ligating a biotinylated adapter oligonucleotide to the 3' ends of heat-denatured DNA. The resulting strands ...Missing: 2012 | Show results with:2012
[22]
[PDF] Extraction of highly degraded DNA from ancient bones, teeth and ...
DNA preserved in ancient bones, teeth and sediments is typically highly fragmented and present only in minute amounts. Here, we provide a highly versatile ...<|control11|><|separator|>
[23]
From the field to the laboratory: Controlling DNA contamination in ...
Abstract. High-Throughput DNA Sequencing (HTS) technologies have changed the way in which we detect and assess DNA contamination in ancient DNA studies.Contaminating Dna · Contaminating Human Dna · What To Sample?
[24]
Patterns of damage in genomic DNA sequences from a Neandertal
Sep 11, 2007 · In summary, the patterns of C to T and G to A substitutions along ancient DNA molecules strongly suggest that the overwhelming majority of ...Missing: authentication | Show results with:authentication
[25]
AuthentiCT: a model of ancient DNA damage to estimate the ...
Sep 15, 2020 · We present AuthentiCT, a command-line tool to estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded ...
[26]
Full article: Quantitative PCR as a Predictor of Aligned Ancient DNA ...
Here, we evaluate whether quantitative PCR (qPCR) measurements of aDNA samples correlate with on-target read counts before and after EHC. Our data indicate that ...
[27]
Next Generation Sequencing of Ancient DNA - NIH
A further quality measure that can be determined from shotgun sequencing of aDNA is the average fragment length of the endogenous DNA. Fragment length hardly ...
[28]
Improving access to endogenous DNA in ancient bone and teeth
Feb 6, 2015 · We used Next Generation shotgun sequencing to monitor the changes in endogenous DNA content and sequence complexity in DNA extracts from the ...Dna Extraction · Library Preparation And... · Results<|control11|><|separator|>
[29]
Highly-multiplexed and efficient long-amplicon PacBio and ...
May 2, 2023 · We report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing.
[30]
Multiplexed DNA Sequence Capture of Mitochondrial Genomes ...
We describe a novel and economical method in which custom made long-range PCR products are used to capture complete human mitochondrial genomes from complex ...
[31]
Paleogenomics: reconstruction of plant evolutionary trajectories from ...
Feb 11, 2019 · This research field relies on two main complementary approaches that aim to track the evolutionary genomic changes at both the macro-evolutionary and micro- ...
[32]
mapDamage: testing for damage patterns in ancient DNA sequences
mapDamage is a Perl script that computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a ...Abstract · INTRODUCTION · RESULTS · DISCUSSION
[33]
Additional evaluations show that specific BWA‐aln settings still ...
Dec 17, 2021 · Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment ... Fast gapped‐read alignment ...
[34]
Consensify: A Method for Generating Pseudohaploid Genome ...
We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while ...
[35]
Imputation of ancient human genomes | Nature Communications
Jun 20, 2023 · Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling.
[36]
Admixture, Population Structure, and F-Statistics - PubMed Central
A useful methodological framework for this purpose is F-statistics that measure shared genetic drift between sets of two, three, and four populations.
[37]
A Machine Learning Method for Authentication of Human Ancient ...
We present a machine learning approach for human ancient mitochondrial DNA authentication using only FASTA sequences, bypassing the need for read-level data ...
[38]
Denisovan Ancestry in East Eurasian and Native American ...
Jun 23, 2015 · These results suggest that Denisovan ancestry in Oceanians is likely to derive from recent admixture with New Guineans, rather than admixture ...
[39]
Patrilineal segmentary systems provide a peaceful explanation for ...
Apr 24, 2024 · The first socio-cultural model proposed to explain the Y chromosome bottleneck involved violent competition between patrilineal kin groups and ...
[40]
Cultural hitchhiking and competition between patrilineal kin groups ...
May 25, 2018 · Another study of Y-chromosomes of modern humans across Europe confirmed the population bottleneck. Poznik et al. constructed a phylogenetic tree ...Missing: Bronze | Show results with:Bronze
[41]
Female exogamy and gene pool diversification at the transition from ...
Sep 5, 2017 · The striking patterns of patrilocality and female exogamy prevailed over at least 800 y between about 2500 and 1700 BC.
[42]
Evolution of lactase persistence: an example of human niche ...
A study of the development of lactose tolerance, as an example of nutritional genetic adaptation to domesticated animal products in the Old World ...
[43]
Paleolithic Gene Duplications Primed Adaptive Evolution of Human ...
Nov 28, 2023 · Previous studies suggested that the salivary amylase (AMY1) gene copy number increased in response to agricultural diets.Missing: paleogenetics | Show results with:paleogenetics
[44]
Strontium and oxygen isotopes to trace mobility routes during the ...
Oct 1, 2021 · Strontium and oxygen isotopes of individuals from El Hundido and Valdescusa (north of Spain) sites, corresponding to the Bell Beaker culture, were analysed
[45]
The Derived FOXP2 Variant of Modern Humans Was Shared with ...
Nov 6, 2007 · We find that our closest extinct relatives, the Neandertals, share with modern humans two evolutionary changes in FOXP2, a gene that has been implicated in the ...
[46]
Systematic meta-analyses and field synopsis of genetic association ...
Apr 2, 2013 · A large number of candidate gene studies for aggression and violence have been conducted. Successful identification of associations between ...
[47]
Ancient hepatitis B viruses from the Bronze Age to the Medieval period
May 9, 2018 · Nature volume 557, pages 418–423 (2018) ... Ancient hepatitis B viruses from the Bronze Age to the Medieval period. Nature 557, 418–423 (2018).
[48]
New insights into the Tyrolean Iceman's origin and phenotype as ...
Feb 28, 2012 · Sequences corresponding to ∼60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen ...
[49]
Diverse variola virus (smallpox) strains were widespread in northern ...
Jul 24, 2020 · The Viking Age sequences reported here push the definitive date of the earliest VARV infection in humans back by ~1000 years and reveal the ...
[50]
Evolution of immune genes is associated with the Black Death - Nature
Oct 20, 2022 · We characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during ...
[51]
Fossil dogs and wolves from Palaeolithic sites in Belgium, the ...
According to Lindblad-Toh et al. (2005), an ancient genetic bottleneck accompanying the domestication of dogs occurred around 27,000 years ago.
[52]
Dog domestication and the dual dispersal of people and dogs into ...
One possible explanation is that dogs were domesticated from a wolf population somewhere in Siberia or western Beringia during the late Pleistocene, and before ...Missing: 15000-40000 | Show results with:15000-40000
[53]
Modern taurine cattle descended from small number of near-eastern ...
Archaeozoological and genetic data indicate that taurine cattle were first domesticated from local wild ox (aurochs) in the Near East some 10,500 years ago.
[54]
DNA traces cattle back to a small herd domesticated ... - ScienceDaily
Mar 27, 2012 · All cattle are descended from as few as 80 animals that were domesticated from wild ox in the Near East some 10,500 years ago, according to a ...
[55]
Ancient Mitogenomes Reveal the Domestication and Distribution of ...
Both archeological and genetic evidence have demonstrated that taurine cattle and zebu cattle were independently domesticated from aurochs in the Near East ...
[56]
Einkorn genomics sheds light on history of the oldest domesticated ...
Aug 2, 2023 · Einkorn (T. monococcum) was the first wheat species that humans domesticated around 10,000 years ago in the Fertile Crescent, a region in the ...Missing: shattering | Show results with:shattering
[57]
On the Origin of the Non-brittle Rachis Trait of Domesticated Einkorn ...
Jan 3, 2018 · Einkorn and emmer wheat together with barley were among the first cereals to be domesticated by humans more than 10000 years ago, ...
[58]
Review Evolutionary Insights into the Nature of Plant Domestication
Jul 22, 2019 · Together, there appears to be a change in the strength of selection for non-shattering after ∼10,000 years ago in Near Eastern cereals, and ...
[59]
New Evidence for Ancestral Puebloan Use of Domesticated Amaranth
Nov 3, 2021 · The seeds dated to the eleventh to twelfth centuries, and DNA evidence indicated that they were domesticated seeds. The co-occurrence of ...
[60]
Genomic and phenotypic evidence for an incomplete domestication ...
We compared the genomic variation and phenotypic differentiation of the two putative domestication traits seed size and seed colour of the grain amaranth ...Missing: DNA Mesoamerica continuity
[61]
Measles virus and rinderpest virus divergence dated to the ... - Science
Jun 19, 2020 · It is generally accepted that measles emergence resulted from a spillover from cattle to humans, although the directionality of this cross- ...
[62]
Measles virus and rinderpest virus divergence dated to the rise of ...
It is generally accepted that measles emergence resulted from a spill-over from cattle to humans, although the directionality of this cross-species transmission ...
[63]
Dietary adaptation of FADS genes in Europe varied across time and ...
Here, using ancient and modern DNA, we demonstrate that positive selection acted on the same FADS variants both before and after the advent of farming in Europe ...
[64]
Why and when was lactase persistence selected for? Insights from ...
Jun 8, 2020 · This Unsolved Mystery article explores where and when lactase persistence emerged. The mutation rapidly spread throughout Eurasia between 4000 and 3000 BP.
[65]
Absence of the lactase-persistence-associated allele in early ...
Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in ...Sign Up For Pnas Alerts · Discussion · Archaeological Human Nuclear...
[66]
The genetic identity of the earliest human-made hybrid animals, the ...
Jan 14, 2022 · We sequenced the genomes of one of these ~4500-year-old equids, together with an ~11,000-year-old Syrian wild ass (hemippe) from Göbekli Tepe ...
[67]
The genomic history and global expansion of domestic donkeys
Sep 8, 2022 · Pie charts show the ADMIXTURE proportion of domestic ancestry (gray), African wild ass ancestry (white), and kiang ancestry (black) averaged ...
[68]
new model for ancient DNA decay based on paleogenomic meta ...
We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows.
[69]
Present‐Day DNA Contamination in Ancient DNA Datasets
Jul 10, 2020 · Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, ...
[70]
Authentication and Assessment of Contamination in Ancient DNA
Here we present a suite of tools to assist in the assessment of contamination in ancient DNA data sets. These tools perform standard tests of authenticity of ...Missing: machine learning 2021
[71]
Impacts of low coverage depths and post-mortem DNA damage on ...
Jan 23, 2015 · Variant identification from short-read alignment could be hindered, however, by low DNA concentrations common to historic samples, which ...Missing: problems | Show results with:problems
[72]
Deep-time paleogenomics and the limits of DNA survival - Science
Oct 5, 2023 · Deep-time genomics is today mostly conducted on substrates with optimal DNA preservation such as those derived from permafrost or caves. However ...
[73]
Ancient DNA and the tropics: a rodent's tale - PMC - NIH
Ancient DNA work from tropical regions has been precluded owing to factors that limit DNA preservation (e.g. temperature, hydrolytic damage). We analysed ...Missing: variability | Show results with:variability
[74]
Recommendations for reproducible paleogenomic data analyses
Nov 5, 2025 · Developing detailed documentation and clear reporting of analytical workflows will ensure that transparent, robust, and reproducible conclusions ...
[75]
Going local with ancient DNA: A review of human histories ... - Science
Oct 5, 2023 · Upper Paleolithic human genomes, primarily from East Asia and Siberia, have augmented our understanding of the early diversification of modern ...
[76]
Community partnerships are fundamental to ethical ancient DNA ...
Jan 11, 2023 · Indigenous communities need to be equal partners with scientists in ancient DNA (aDNA) research. A recent statement of “five globally applicable ...
[77]
Informed proxy consent for ancient DNA research - Nature
Jul 4, 2024 · We argue for implementation of informed proxy or relational autonomy consent in human aDNA research, where the deceased may be represented by living people.Missing: ancestral | Show results with:ancestral
[78]
[PDF] Repatriation After the 2023 NAGPRA Rule
Nov 2, 2025 · The Native American Graves Protection and Repatriation Act of 1990. (NAGPRA) recognized the rights of Indian Tribes and Native Hawaiian.
[79]
Ethical Guidance in Human Paleogenomics: New and Ongoing ...
Here, we highlight and contextualize the primary sources of professional ethical guidance aimed at paleogenomic researchers. We describe the tension among ...
[80]
A tutorial on how not to over-interpret STRUCTURE and ... - Nature
Aug 14, 2018 · The “admixture model” of STRUCTURE assumes that each individual has ancestry from one or more of K genetically distinct sources. In the case of ...Missing: causation | Show results with:causation