Ancient DNA Sequencing Service

Overview

CD Genomics provides internationally leading ancient DNA (aDNA) sequencing solutions, specifically designed to decode the genetic secrets of ancient organisms. By integrating targeted capture techniques with ultra-high-throughput sequencing platforms, we achieve in-depth analysis of highly degraded samples, enabling groundbreaking advancements in research on human evolution, species adaptation, and cultural heritage.

What is aDNA Sequencing Service

Ancient DNA (aDNA) refers to DNA fragments extracted from the remains of ancient organisms, such as fossils, bones, and sediments. aDNA sequencing, a cornerstone methodology in paleogenetics, archaeology, and forensic science, faces significant challenges due to severe degradation and contamination. To overcome these obstacles, researchers employ uracil glycosylase to repair deamination damage and reduce sequencing errors, while utilizing RNA/DNA probes to isolate target aDNA from heavily contaminated samples. Beyond human evolution, aDNA sequencing currently helps with many tasks such as confirming ancient artifacts, agricultural/animal domestication studies and reconstruction of ancient societies.

Schematic of aDNA analysis. (Carpenter, et al., 2013)

Sequencing Platforms

NextSeq 500

Illumina NovaSeq

PacBio Sequel II

Workflow of aDNA Sequencing in Population Genetics

Our aDNA sequencing service workflow includes sample collection, library preparation, high-throughput sequencing, quality control, and detailed variant analysis to uncover genetic variations and population insights. Customers are encouraged to ensure proper sample handling and share specific research goals for tailored analysis. For any questions about sample requirements, sequencing, or data interpretation, our team is always ready to assist.

Bioinformatics Content

Basic Analysis	Advanced Analysis
Raw Data Quality Control: Per-base sequence quality, GC content distribution and adapter contamination ratio. Adapter Trimming: Clean reads (>30bp fragments) after adapter removal. Deamination Check: Terminal C→T mutation rates. Ancient Alignment: Alignment to ancient genomes. Variant Calling: SNP and indel identification.	Contamination Estimate: Exogenous DNA contamination rate. Damage Correction: Corrects aDNA-specific C→T errors. Population Structure Analysis: Ancestry decomposition and admixture modeling. Functional Annotation: Pathogenic mutations and disease risk loci.

Why CD Genomics

Cutting-edge Sequencing Platforms: Compatible with NGS (Illumina) and third-gen (PacBio/Nanopore) platforms.
High-throughput, High-quality Sequencing: Deliver premium-quality sequencing data faster, at lower cost, and with unmatched efficiency.
One-Stop Service: End-to-end analysis from raw data QC, variant calling to population structure analysis, and provide expert data interpretation support.
Integration of Comprehensive Genomics Analysis: Offer various omics technology services, including advanced and customized genomics analysis solutions.
Ethical Compliance Guarantee: Strict adherence to IRB (Institutional Review Board) -approved ethical frameworks for ancient specimen research.

Sample Requirements

Must adhere to institutional safety and ethical guidelines.
All wet lab procedures must be conducted in an aDNA cleanroom to prevent cross-contamination.
Prioritize dense skeletal elements (e.g., teeth or limb bones), avoiding marrow cavity contamination.
Multiple sub-samples may enhance DNA yield from low-quality specimens.
Short-term storage at –20°C or –80°C.

Demo Results

Yield of unique fragments for NA40 (Peruvian bone) precapture (blue) and postcapture (red) libraries.

Venn diagram showing the overlap between the NA40 pre- and postcapture libraries.

Percent GC content of reads for NA40 pre- and postcapture libraries.
(Carpenter et al., AJHG, 2013）

Case Study

Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments.

Journal: Science

Published: 2021

https://doi.org/10.1126/science.abf1667

While bones and teeth are critical sources of Pleistocene hominin DNA, they are infrequently preserved at archaeological sites. Although mitochondrial DNA (mtDNA) has been successfully retrieved from cave sediments, its utility for elucidating population relationships is constrained by its uniparental inheritance. To address this limitation, this study developed novel methods for enriching and analyzing nuclear DNA from sedimentary archives and applied them to Late Pleistocene cave deposits (approximately 200,000–50,000 years old) in Western Europe and Southern Siberia. Their analysis revealed a population replacement in northern Spain occurring ~100,000 years ago, concurrent with a complete turnover of mtDNA lineages. Furthermore, they identified two distinct radiation events during the early Late Pleistocene that reshaped Neanderthal evolutionary history. This work establishes a foundational approach for reconstructing ancient hominin population dynamics using trace nuclear DNA preserved in environmental samples.

aDNA sequencing
Bioinfomatics

Mitochondrial DNA (mtDNA) analysis in Pleistocene hominins has been constrained by maternal inheritance patterns and the fragmented fossil record, limiting insights into population dynamics. To reconstruct Neanderthal maternal lineages and temporal population shifts independently of skeletal remains, researchers analyzed sediment-derived mtDNA from Estatuas Cave (Spain) and Chagyrskaya Cave (Siberia). Hominin mtDNA was enriched from sediment extracts using hybridization capture. It enables assembly of near-complete mtDNA genomes (>17-fold coverage). These genomes were utilized for phylogeny reconstruction with BEAST2. A novel probabilistic placement method assigned fragmentary data to known haplotypes based on diagnostic positions distinguishing Neanderthal subgroups. Their mtDNA phylogeny identified five distinct Neanderthal haplogroups. Furthermore, they observed stratigraphic mtDNA turnover at Estatuas Cave. Crucially, sediment mtDNA resolved a previously undetectable Neanderthal population turnover in Iberia, characterized by the loss of basal genetic diversity. In contrast, Siberian populations exhibited continuity. This demonstrates the power of sedimentary ancient DNA to reveal fine-scale demographic histories beyond the scope of fossil evidence.

mtDNA from sediments.

They studied Neanderthal population relationships using nuclear DNA from cave sediments. They developed maximum likelihood models to estimate Neanderthal population split times from these sediment samples. Diagnostic SNPs and metagenomic filtering were used to reduce contamination. Their methods were validated using down-sampled skeletal genomes. Sediment layers in Estatuas Cave showed distinct divergence times. Two Late Pleistocene radiation events reshaped Neanderthal populations: an older expansion around 135 thousand years ago (ka) and a younger one around 105 ka. This history was confirmed using nuclear DNA from sediments, without needing skeletal remains.

Sediment samples placed on Neanderthal phylogeny.
(Vernot, et al. 2021)

FAQs

What types of samples are suitable for ancient DNA sequencing?

Suitable samples for ancient DNA (aDNA) analysis including archaeological remains like bones and teeth, as well as ancient sediments. Within osseous materials, denser internal regions (e.g., cortical bone) are ideal for DNA extraction due to their enhanced molecular integrity. Notably, teeth and the petrous portion of the temporal bone are particularly good sources of endogenous aDNA.

What kind of data and results can you expect?

You will receive information about the sample' s DNA content, including the amount of DNA that maps to a reference genome.
The analysis indicates if the DNA is ancient based on damage patterns.
Contamination levels are assessed.
If enough data is generated, species, sex, maternal ancestry (mitochondrial haplotype), and paternal ancestry (Y-chromosome haplotype) can be determined.
Close kinship between sampled individuals can be investigated.
Further analysis of ancestry and traits may be available upon request.

Are there any limitations or potential issues with ancient DNA sequencing?

aDNA is usually badly damaged and broken into very small pieces. This makes it hard to prepare for sequencing and to match the pieces together correctly. Contamination with exogenous DNA is a major problem, necessitating rigorous authentication protocols such as deamination pattern analysis and mitochondrial haplogroup verification. In poor conditions like acidic soil or hot climates, less than 1% of the DNA recovered may actually belong to the ancient person or animal. However, dense bones (like the petrous bone near the ear) or the cementum at the root of a tooth often protect DNA much better.

References

Carpenter, M. L., Buenrostro, J. D., et al. (2013). Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries. AJHG, 93(5), 852-864. http://dx.doi.org/10.1016/j.ajhg.2013.10.002
Vernot, B., Zavala, E. I., et al. (2021). Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments. Science, 372(6542). https://doi.org/10.1126/science.abf1667

* Designed for biological research and industrial applications, not intended for individual clinical or medical purposes.