Refuting Creationism - Scientists Now have the Genome of a Mammoth from 42,000 Years Before 'Creation Week'.

Model of a Woolly mammoth

By Thomas Quine, via Wikimedia (CC BY 2.0)

52,000-year-old wooly mammoth skin recovered from permafrost and found that it contained fossils of ancient chromosomes.

Love Dalén/Stockholm University

First ever 3D reconstruction of 52,000-year-old woolly mammoth chromosomes thanks to serendipitously freeze-dried skin | ScienceDaily

52,000 years ago, a full 42,000 years before creationism’s putative creator god created a universe comprised of a small flat planet with a dome over it, under which there was nothing that wasn't known to Bronze Age Canaanite hill farmers, a wooly mammoth somehow contrived to die and be quickly preserved in permafrost near what is now Belaya Gora, Sakha Republic, Siberia, where it was recovered in 2018, preserved in such a condition that skin cells could be identified under a microscope.

Mammoths, of course, along with their close relatives, elephants, were unknown to the authors of the tales in the Bible which creationists think are real history and science.

A microscope image of subdermal muscle from the ancient skin shows remnants of mammoth nuclei. The new study revealed that fossils of ancient chromosomes survive in this skin sample.

Elena Kizilova/Institute of Cytology and Genetics SB RAS

Carbon dating has shown the preserved mammoth to be more than 42,000 years old and an analysis of its mitochondrial DNA (mtDNA) gives a date close to 52,000 years old.

The research team co-led by Marcela Sandoval-Velasco and Juan Antonio Rodríguez of the Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark, and Olga Dudchenko and Cynthia Pérez Estrada of The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA, used STAR Methods combined with Hi-C to analyse and reconstruct the genome from the ancient DNA (aDNA) recovered from the mammoth skin.

What are STAR methods in the context of ancient DNA analysis? In the context of ancient DNA analysis, the STAR (Stable Tandem Repeat) method refers to a specific approach for examining and analyzing ancient DNA (aDNA). Ancient DNA analysis is crucial for understanding genetic information from past organisms, which helps in studying evolutionary history, population migrations, and historical interrelationships among species.

Key Aspects of STAR Methods in Ancient DNA Analysis:

1. Stable Tandem Repeats (STRs): STRs are short sequences of DNA that are repeated in tandem. These regions are highly polymorphic, meaning they vary greatly between individuals, making them useful for genetic analysis, including studying genetic diversity and relationships.
2. Extraction of aDNA:
   • Sample Preparation: aDNA is typically extracted from ancient biological samples such as bones, teeth, and preserved tissues.
   • Decontamination: Due to the degraded nature and potential contamination of aDNA, strict decontamination procedures are employed to avoid modern DNA contamination.
3. Amplification and Sequencing:
   • PCR Amplification: The regions containing STRs are amplified using polymerase chain reaction (PCR) techniques, which are optimized for the often fragmented and damaged nature of aDNA.
   • Next-Generation Sequencing (NGS): Modern methods may use NGS to sequence aDNA, providing high-throughput and detailed data on STR variations.
4. Data Analysis:
   • Sequence Alignment: Sequences are aligned against reference genomes to identify and compare STR regions.
   • Genetic Diversity and Population Structure: Analysis of STR data helps infer genetic diversity, population structure, and evolutionary relationships.
   • Phylogenetic Analysis: By comparing STR profiles, researchers can construct phylogenetic trees to understand the evolutionary history of the species being studied.
5. Applications:
   • Evolutionary Biology: Understanding the evolution of species, including extinct ones.
   • Anthropology: Studying ancient human populations, migrations, and interactions.
   • Archaeology: Providing insights into the genetic makeup of ancient civilizations and their domesticated animals.
   • Conservation Biology: Informing conservation strategies for endangered species by understanding their historical genetic diversity.

Advantages of STAR Methods:

• High Polymorphism: STRs' high variability makes them powerful markers for genetic analysis.
• Sensitivity: STR analysis can work with the highly degraded and fragmented nature of aDNA.
• Specificity: STRs can provide detailed genetic information, even from small and ancient samples.

Challenges:

• Degradation: aDNA is often highly degraded and contaminated, making analysis challenging.
• Technical Limitations: PCR amplification of aDNA requires highly sensitive and precise techniques to avoid errors and contamination.
• Data Interpretation: Ancient genetic data require careful interpretation within the context of potential damage and contamination issues.

Overall, STAR methods in ancient DNA analysis are a crucial tool for extracting valuable genetic information from ancient biological samples, providing insights into evolutionary history, genetic diversity, and historical population dynamics.

What is Hi-C in the same context?

In the context of ancient DNA analysis, Hi-C is a technique used to study the three-dimensional architecture of genomes by capturing spatial interactions between different regions of the DNA. Hi-C can provide insights into the organization of the genome and how different parts of the genome interact within the cell nucleus.

Key Aspects of Hi-C in Ancient DNA Analysis:

1. Principle of Hi-C:
   • Hi-C involves cross-linking DNA to preserve its three-dimensional structure, then cutting the DNA with restriction enzymes, filling in the ends with biotin-labeled nucleotides, ligating the fragments to create chimeric junctions, and sequencing these junctions to identify spatially proximal DNA segments.
2. Application to Ancient DNA (aDNA):
   • Genome Assembly: Hi-C can help in scaffolding and assembling fragmented ancient genomes by providing information about which DNA fragments are physically close to each other in the nucleus.
   • Chromosome Conformation: It allows researchers to study the higher-order structures of ancient genomes, which can provide insights into how genome organization has evolved over time.
   • Interaction Mapping: Hi-C data can reveal interactions between different genomic regions, helping to understand the regulatory landscapes of ancient organisms.
3. Steps in Hi-C Analysis:
   • Cross-Linking: Cells or tissues containing ancient DNA are treated with formaldehyde to cross-link DNA and preserve its spatial interactions.
   • Fragmentation: The cross-linked DNA is digested with restriction enzymes to create smaller fragments.
   • Ligation: Biotin-labeled nucleotides are incorporated, and the DNA fragments are ligated to form chimeric molecules, where fragments that were spatially close are now covalently linked.
   • Purification and Sequencing: The biotinylated junctions are purified and sequenced using high-throughput sequencing technologies.
   • Data Analysis: Sequencing data are analyzed to identify interacting regions and to reconstruct the three-dimensional genome organization.
4. Advantages of Hi-C in aDNA Studies:
   • Improved Genome Assembly: Helps in assembling ancient genomes from highly fragmented DNA, which is common in ancient samples.
   • Structural Insights: Provides insights into the chromosomal architecture and how it might have changed over evolutionary time.
5. Functional Genomics: Enables the study of regulatory elements and their interactions, shedding light on gene regulation in ancient organisms.
6. Challenges:
   • DNA Degradation: aDNA is often degraded and contaminated, which can complicate Hi-C experiments.
   • Complexity of Analysis: Hi-C data are complex and require sophisticated computational tools for analysis and interpretation.
   • Sample Quality: High-quality ancient samples are rare, and the preservation of three-dimensional structures in ancient samples can be challenging.

Applications:

• Evolutionary Biology: Understanding the evolution of genome architecture and its functional implications.
• Anthropology: Investigating the genomic organization of ancient human populations and their relatives.
• Archaeology: Providing insights into the genetic and regulatory landscapes of ancient organisms and their adaptations.

Overall, Hi-C is a powerful tool in the toolkit of ancient DNA analysis, offering unique insights into the spatial organization and interaction networks within ancient genomes. It complements other genomic techniques by providing a three-dimensional perspective on the genetic information from ancient samples.

The DNA and Chromosome structures recovered are about a million times longer than are typically recovered from ancient samples.

The finding is the subject of an open access paper in Cell and was explained in information made available ahead of publication by Cell Press, and reported in Science Daily:

First ever 3D reconstruction of 52,000-year-old woolly mammoth chromosomes thanks to serendipitously freeze-dried skin

---

An international research team has assembled the genome and 3D chromosomal structures of a 52,000-year-old woolly mammoth -- the first time such a feat has been achieved for any ancient DNA sample. The fossilized chromosomes, which are around a million times longer than most ancient DNA fragments, provide insight into how the mammoth's genome was organized within its living cells and which genes were active within the skin tissue from which the DNA was extracted. This unprecedented level of structural detail was retained because the mammoth underwent freeze-drying shortly after it died, which meant that its DNA was preserved in a glass-like state. The results are presented July 11 in the journal Cell.

---

This is a new type of fossil, and its scale dwarfs that of individual ancient DNA fragments -- a million times more sequence. It is also the first time a karyotype of any sort has been determined for an ancient sample.

Erez Lieberman Aiden, co-corresponding author
Director of the Center for Genome Architecture
Baylor College of Medicine
Baylor, TX, USA.

Knowing the three-dimensional architecture of a genome provides a lot of additional information beyond its sequence, but most ancient DNA specimens consist of very small, scrambled DNA fragments. Building off work mapping the 3D structure of the human genome, Aiden thought that if the right ancient DNA sample could be found -- one with the 3D organization of the fragments still intact -- it would be possible to use the same strategies to assemble ancient genomes.

The researchers tested dozens of samples over the course of five years before landing on an unusually well-preserved woolly mammoth that was excavated in northeastern Siberia in 2018.

We think it spontaneously freeze-dried shortly after its death. The nuclear architecture in a dehydrated sample can survive for an incredibly long period of time.

Olga Dudchenko, co-corresponding author
Center for Genome Architecture
Baylor College of Medicine
Baylor, TX, USA.

To reconstruct the mammoth's genomic architecture, the researchers extracted DNA from a skin sample taken behind the mammoth's ear. They used a method called Hi-C that allows them to detect which sections of DNA are likely to be in close spatial proximity and interact with each other in their natural state in the nucleus.

Imagine you have a puzzle that has three billion pieces, but you don't have the picture of the final puzzle to work from. Hi-C allows you to have an approximation of that picture before you start putting the puzzle pieces together.

Professor Marc A. Marti-Renom, co-corresponding author
Centre Nacional d'Anàlisi Genòmica (CNAG)
and the Centre for Genomic Regulation (CRG)
Barcelona, Spain.

Then, they combined the physical information from the Hi-C analysis with DNA sequencing to identify the interacting DNA sections and create an ordered map of the mammoth's genome, using the genomes of present-day elephants as a template. The analysis revealed that woolly mammoths had 28 chromosomes -- the same number as present-day Asian and African elephants. Remarkably, the fossilized mammoth chromosomes also retained a huge amount of physical integrity and detail, including the nanoscale loops that bring transcription factors in contact with the genes they control.

By examining the compartmentalization of genes within the nucleus, the researchers were able to identify genes that were active and inactive within the mammoth's skin cells -- a proxy for epigenetics or transcriptomics. The mammoth skin cells had distinct gene activation patterns compared to the skin cells of its closest relative, the Asian elephant, including for genes potentially related to its woolly-ness and cold tolerance.

For the first time, we have a woolly mammoth tissue for which we know roughly which genes were switched on and which genes were off. This is an extraordinary new type of data, and it's the first measure of cell-specific gene activity of the genes in any ancient DNA sample.

Professor Marc A. Marti-Renom.

Although the method used in this study hinges on unusually well-preserved fossils, the researchers are optimistic that it could be used to study other ancient DNA specimens -- from mammoths to Egyptian mummies -- as well as more recently preserved museum specimens.

For mammoths, the next steps would include examining the epigenetic patterns of other tissues.

These results have obvious consequences for contemporary efforts aimed at woolly mammoth de-extinction.

M. Thomas P. Gilbert, co-corresponding author
Center for Evolutionary Hologenomics
University of Copenhagen, Copenhagen, Denmark.

Researchers examine the mammoth skin after it was excavated from permafrost.

Love Dalén/Stockholm University

Highlights

• 3D genome architecture is preserved in a 52,000-year-old woolly mammoth sample.
• PaleoHi-C makes it possible to assemble the woolly mammoth’s genome.
• Chromatin compartments also persist, enabling study of mammoth gene expression.
• We propose that dehydration led to a glass transition arresting molecular movement.

Summary
Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth’s death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.

Graphical abstract

Introduction
Study of ancient DNA (aDNA) began with the sequencing of mitochondrial fragments from historic samples^1,2 and has subsequently undergone a remarkable expansion. Current paleogenomic analyses involve DNA sequencing of whole genomes (aDNA-Seq) from a plethora of extinct and archaic humans (e.g., Green et al., Rasmussen et al.^3,4), animals (e.g., Miller et al., Orlando et al.^5,6), plants (e.g., Martin et al., Ramos-Madrigal et al.^7,8), and pathogens (e.g., Bos et al., Smith et al.^9,10) spanning over one million years.¹¹

Yet given the fragmentary nature of typical aDNA molecules,^12,13 such analyses invariably rely on mapping short reads to a modern reference genome. This enables the identification of single-nucleotide polymorphisms (SNPs) and small indels for phylogenomic and population analyses, and identification of variants with functional consequences.^3,4,5 But such methods overlook larger-scale differences, such as chromosomal rearrangements. In fact, the only large-scale differences that can be identified are cases where a modern sequence is absent in the ancient genome.⁷
aDNA studies have also explored epigenetic differences by recovering methylated cytosines from ancient templates^14,15,16 or through DNA decay patterns, which can indicate nucleosome positioning.¹⁵ Yet there is no genome-wide epigenetic data for many ancient species of interest, such as the woolly mammoth (†Mammuthus primigenius). Here, too, the short length of aDNA makes it difficult to place epigenetic features in their genomic context.

One useful class of techniques for generating larger-scale insights into genomes is based on Hi-C,¹⁷ which interrogates the shape of whole chromosomes. Hi-C exploits DNA-DNA proximity ligation^18,19 to ligate DNA sequences that are nearby in 3D within the cell nucleus, even if the sequences are distant along the 1D contour of the chromosome. Contact data can also determine the relative positioning of sequences along chromosomes, since sequences that tend to be in contact are more likely to be nearby in 1D. Consequently, Hi-C facilitates genome assembly, finds errors in draft contigs (contiguous sequences) that turn out to be incorrectly assembled, and reliably orders and orients contigs into chromosome-length scaffolds.^20,21,22 In addition, contact patterns reflect the epigenetic state and activity level of loci genome-wide.^17,23 Thus, generating Hi-C data for ancient samples would be valuable.

However, Hi-C might be impossible in ancient samples, because the surviving aDNA fragments are so short that they may diffuse through space, gradually erasing the ancient chromosomal morphology (Figure 1A).

Figure 1 PaleoHi-C reveals that the morphology of chromosomes is preserved in a 52,000-year-old sample of woolly mammoth skin

1. Ancient DNA is fragmented. The fragments may be free to diffuse through space, erasing the 3D morphology of ancient chromosomes (left), including chromosome territories (top), chromatin compartments (middle), and point-to-point loops (bottom). If so, assays like Hi-C will fail. If diffusion is limited, these features may survive (right) and potentially be examined using Hi-C.
2. Primary mammoth sample used in this study.
3. Histology of skin (left), hair follicles (center), and subdermal muscle (right).
4. PaleoHi-C overview. Samples are collected into ethanol in the field. In the laboratory, samples are crosslinked with formaldehyde. Tissue is disrupted and ground. Instead of isolating nuclei, as in in situ Hi-C, chromatin bodies are bound to beads and cut with a restriction enzyme. Ends are repaired and blunted, introducing biotin. After DNA-DNA proximity ligation, junctions are captured onto streptavidin beads, built into libraries using a paleo-compatible workflow, and sequenced.
5. PaleoHi-C data (yellow) and aDNA-Seq data (purple) for the same sample were aligned to African elephant. The log-log histogram shows relative contact probability vs. 1D genomic distance between read ends. A fraction of PaleoHi-C reads reflects contacts between loci that lie far away in 1D. Not so for aDNA-Seq. For the (E) inset, similar plot comparing PaleoHi-C on woolly mammoth skin vs. in situ Hi-C on Asian elephant skin. Power laws are seen in the 1–10 Mb distance range (solid lines), with nearly identical scalings (mammoth: −0.96; elephant: −0.98).
6. PaleoHi-C summary statistics.

See also Figure S1.

The purpose of this paper is, therefore, to answer three questions.

First, to what extent can the 3D morphology of chromosomes be preserved in ancient samples? To answer this question, we developed PaleoHi-C, a variant of the in situ Hi-C protocol23 adapted for ancient samples (Figure 1). We applied PaleoHi-C to a permafrost-preserved woolly mammoth skin sample that is 52,000 years old. We demonstrate that this sample exhibits all the architectural features that are typically visible in modern Hi-C maps—chromosome territories, Barr bodies, active and inactive chromatin compartments, domains, and loops. We confirm the presence of several of these properties in a second sample that is 39,000 years old. Our results demonstrate that the morphological features of chromosomes can remain intact on scales as short as 50 nanometers (nm), forming non-mineralized fossils, or subfossils, that can persist for many millennia.

Second, can the 3D morphology of ancient chromosomes illuminate the biology of ancient species? To answer this question, we use PaleoHi-C data to generate a genome assembly for the woolly mammoth, including the reconstruction of its karyotype. We then compare contact patterns in woolly mammoth skin to those in elephant skin and other mammals. We show that it is possible to identify genes whose transcriptional state is altered in woolly mammoth as compared to elephant. We also show that the woolly mammoth’s Xi exhibits a tetradic architecture that is distinct from the bipartite Xi architecture in human and mouse and confirm that this architecture is also present in modern elephants.

Third, how is it possible that the morphology of chromosomes is not erased by the action of diffusion over such long periods of time? We show that the behavior of the ancient chromatin is consistent with a glass transition, a physical process whereby factors like cooling and dehydration can effectively arrest the diffusion of the molecules in a material. We hypothesize that this glass transition was induced by spontaneous freeze-drying of the woolly mammoth tissue, shortly after death, in the cold Siberian climate. We provide some experimental evidence that supports this hypothesis.

Taken together, our findings highlight new approaches to the study of genome architecture, epigenetics, and gene expression in ancient samples and open the door to generating de novo genome assemblies for ancient and extinct species. They also demonstrate that the morphology of ancient biosamples can be well preserved at scales as fine as 50 nm.

The prospect of palaeontologists being able to assemble the genomes of extinct species will call for some creative misrepresentation by creationists, because it will open up the prospect of science being able to trace the genetic changes that map onto the phenotypic changes as a species evolves over time. This will mean the constant clamour by creationists for evidence of 'macro-evolution', while dismissing the many examples of it in the fossil record as 'not evidence of transitional evolution' can be met with genetic evidence.

---

Advertisement

What Makes You So Special? From The Big Bang To You

How did you come to be here, now? This books takes you from the Big Bang to the evolution of modern humans and the history of human cultures, showing that science is an adventure of discovery and a source of limitless wonder, giving us richer and more rewarding appreciation of the phenomenal privilege of merely being alive and able to begin to understand it all.

Available in Hardcover, Paperback or ebook for Kindle

Advertisement

Ten Reasons To Lose Faith: And Why You Are Better Off Without It

This book explains why faith is a fallacy and serves no useful purpose other than providing an excuse for pretending to know things that are unknown. It also explains how losing faith liberates former sufferers from fear, delusion and the control of others, freeing them to see the world in a different light, to recognise the injustices that religions cause and to accept people for who they are, not which group they happened to be born in. A society based on atheist, Humanist principles would be a less divided, more inclusive, more peaceful society and one more appreciative of the one opportunity that life gives us to enjoy and wonder at the world we live in.

Available in Hardcover, Paperback or ebook for Kindle

Advertisement

Thank you for sharing!

Tweet Link