Molecular Palaeontology

Anthropology: An Overview of Molecular Palaeontology

Molecular palaeontology is the study of ancient complex biomolecules associated with deep-time fossils. The field may provide important information for understanding organisms’ evolution and fossilization processes at the molecular level and make preserved biomarkers easier to recognize to identify life on other planets.

Abelson’s (1956) study on the recovery of proteinaceous fossil components represents the beginning of contemporary molecular palaeontology. New analytical procedures began to be applied to fossil material as technology improved precision, sensitivity, and reliability.

DeJong et al. revealed in 1974 that precipitation reactions with antisera retained the antigenic components of proteins maintained within 70 Ma mollusc shells. Immunogenic reactivity in other Cretaceous fossil shells corroborated these findings (Weiner et al. 1976; Westbroek et al. 1979). Armstrong et al. (1983) found amino acids in a range of bone samples, and Gurley et al. (1991) isolated and identified amino acids in the skeletal tissues of the sauropod dinosaur Seisomosaurus.

Molecular palaeontology, or the recovery of DNA from ancient human, animal, and plant remains, is a cutting-edge study field that has gotten scientists’ attention since the 1980s. Unfortunately, the area has been blighted by claims that piqued people’s attention but ultimately turned out to be faking, the most notable of which was a sequence of dinosaur DNA that was later discovered to be of human origin.

Currently, the discipline is marked by considerable certainty and a great deal of uncertainty. We know, for example, that we have a good possibility of recovering legitimate DNA from a mammoth carcass but that our odds are slim to none (or none at all) in the case of an Egyptian dynastic mummy. Moreover, although we are building DNA breakdown models in bone, we cannot forecast if a paleontological or archaeological site would provide DNA-absorbable material.

Overview of Molecular Palaeontology

Examining Dinosaur Bone
Credit: Earth Magazine

The study of evolutionary events, species diasporas, and the identification and characterization of extinct species have all been aided by the science of molecular palaeontology. In recent years, advances in molecular palaeontology have allowed scientists to investigate evolutionary concerns on a genetic level rather than relying solely on phenotypic variation. The relatedness level between any two organisms for whom DNA has been extracted can be quantified using molecular analytical techniques applied to DNA in recent animal remains. [3] Scientists have obtained expanded new insights into the divergence and evolutionary history of innumerable recently extinct animals using diverse biotechnological techniques such as DNA isolation, amplification, and sequencing[4]. In February 2021, scientists announced the first sequencing of DNA from animal remains, this time a mammoth over a million years old, making it the oldest DNA sequenced to date.

Through a cascade of oxidative fossilization events, compositional heterogeneities in carbonaceous remains of various species ranging period from the Neoproterozoic to the recent have been connected to biological markers recorded in current proteins in deep time. Biological signatures that reflect original biomineralization, different tissues, metabolism, and the relationship affinities are preserved in the macromolecular composition of carbonaceous fossils, some of which are Tonian in age.

History of Molecular Palaeontology

The finding of 360 million-year-old amino acids preserved in fossil shells by Abelson is credited with launching the field of molecular palaeontology.

Svante Pääbo, on the other hand, is frequently credited as the creator of the subject of molecular palaeontology. Since the 1950s, the science of molecular palaeontology has made significant advancements and continues to expand. Following is a comprehensive timeline of important contributions:

Timeline of Molecular Palaeontology

Mid-1950s: Abelson discovered intact amino acids in 360 million-year-old fossil shells in the mid-1950s.

1970s: The amino acid analysis is used to investigate fossil peptides in the 1970s. Next, begin using potent peptides and immunological techniques.

Late 1970s: Palaeobotanists (sometimes spelt Paleobotanists) investigated molecules from well-preserved fossil plants in the late 1970s.

1984: The quagga, a zebra-like species, becomes the first extinct species to have its DNA sequenced successfully.

1991: Article published about the effective extraction of proteins from a dinosaur’s fossil bone, specifically the Seismosaurus.

2005: Scientists resuscitated the 1918 influenza virus in 2005.

2006: Nuclear DNA sequence fragments from Neanderthals began to be examined and published in 2006.

Timeline

2007: Molecular palaeontology scientists create an entirely new version of the extinct human endogenous retrovirus (HERV-K).

2010: Denisovans, a new species of early hominids revealed from mitochondrial and nuclear genomes extracted from bone found in a cave in Siberia, were discovered in 2010. The Denisovan species lived around 41,000 years ago and shared a common progenitor with both modern humans and Neanderthals about 1 million years ago in Africa, according to analysis.

2013: The first complete Neanderthal genome was sequenced in 2013. After that, the Neanderthal genome project has a lot more information.

2013: Homo heidelbergensis, a 400,000-year-old specimen with remnant mitochondrial DNA sequenced, is discovered to represent a common ancestor of Neanderthals and Denisovans.

Denisovan
Credit: National Geographic

2015: A 110,000-year-old fossil tooth-bearing Denisovan DNA was discovered in 2015.

2018: Molecular Paleobiologists have discovered a mechanical relationship between polymers of N-, O-, and S-heterocycle composition in ancient carbonaceous remnants and structural biomolecules in original tissues. Nucleophilic amino acid residues effectively condense with Reactive Carbonyl Species generated from lipids and sugars through oxidative crosslinking, a process analogous to the Maillard reaction. Advanced Glycosylation and Advanced Lipoxidation are two biomolecule fossilization mechanisms. They are identified by Raman spectroscopy of present and fossil tissues and focus on experimental modelling and statistical data analysis.

Timeline

2019: An independent laboratory of Molecular Paleontologists reveals advanced glycosylation and epoxidation change biomolecules during fossilization. The authors use synchrotron Fourier-Transform Infrared spectroscopy.

2020: Wiemann and colleagues uncover biological fingerprints in preserved compositional heterogeneities of various carbonaceous animal fossils that represent original biomineralization, tissue types, metabolism, and connection affinity (phylogeny). It is the first large-scale study of fossils from the Neoproterozoic to the Recent and the first record of life signals discovered in complex organic matter. The authors base their findings on statistical studies of a massive Raman spectroscopy data collection.

2021: Geochemists discover tissue type indications in the chemistry of Tonian carbonaceous fossils and use these signs to identify epibionts in 2021. The writers use Raman spectroscopy.

2022: Fourier-Transform Infrared spectroscopy and various Raman instruments, filters, and excitation sources were used to duplicate Raman spectroscopy data. They indicated patterns in the fossilization of structural biomolecules.

Important Molecular Palaeontology Research

Quagga
Credit: Wikipedia

The Quagga

In 1984, a 150-year-old museum specimen of the quagga, a zebra-like creature, was used to sequence the first DNA of an extinct species. The Mitochondrial DNA (or mtDNA) was sequenced from dehydrated quagga muscle and found to differ from mountain zebra mitochondrial DNA by 12 nucleotide alterations. It was determined that these two species shared a common ancestor 3-4 million years ago, which agrees with the species’ existing fossil evidence.

Denisovans

DNA sequencing of a 41,000-year-old material unearthed in 2008 led to the discovery of the Denisovans of Eurasia. It was a hominid species related to Neanderthals and humans. A mitochondrial DNA analysis of a salvaged finger bone revealed genetically distinct from both humans and Neanderthals. Later, there was a discovery that two teeth and a toe bone belonged to distinct people from the same group.

According to the evidence, both Neanderthals and Denisovans were already living in Eurasia when modern humans arrived. [20] Scientists discovered a fossil tooth-bearing Denisovan DNA in November 2015 and calculated its age to be 110,000 years old.

Denisovan mtDNA in molecular palaeontology differs from modern human mtDNA by 385 bases (nucleotides) in the mtDNA strand out of roughly 16,500, whereas the difference between modern humans and Neanderthals is around 202 bases. The distance between chimps and modern humans, on the other hand, is around 1,462 mtDNA base pairs. It pointed to a time of divergence of roughly one million years ago.

The mtDNA of a tooth and a finger bone shared a high similarity, indicating that they came from the same population. An mtDNA sequence from a second tooth revealed a surprisingly large number of genetic changes compared to the other tooth and finger, indicating a high degree of mtDNA diversity. These two individuals from the same cave displayed more diversity than Neanderthals from Eurasia and were as diverse as modern-day humans from other continents.

The Nuclear Genome

Nuclear DNA has also been isolated and sequenced from the Denisova finger bone in molecular palaeontology. This material has a very high level of DNA preservation and a low contamination level. As a result, they achieved near-complete genetic sequencing, which allowed them to make extensive comparisons between Neanderthals and modern humans. Despite the apparent diversity of their mitochondrial sequences, they found that the Denisova and Neanderthal populations shared a good common branch from the lineage that led to current African humans.

The time of divergence between Denisovan and Neanderthal sequences was 640,000 years ago. In comparison, the time between these and modern African sequences is estimated to be 804,000 years ago. They believe the Denisova mtDNA divergence is due to the persistence of a lineage that has been purged from other branches of humanity due to genetic drift or introgression from an older hominin lineage.

Homo Heidelbergensis

Homo Heidelbergensis Skull
Credit: Encyclopedia Britannica

Homo heidelbergensis was first discovered at Heidelberg, Germany, in 1907 through molecular palaeontology and has since been found throughout Europe, Africa, and Asia. However, it wasn’t until 2013 that a specimen with retrievable DNA was discovered in the Sima de los Huesos Cave in Spain, in a 400,000-year-old femur. Both mtDNA and nuclear DNA were discovered in the femur. MtDNA was successfully recovered and sequenced thanks to advancements in DNA extraction and library preparation procedures.

Still, nuclear DNA was discovered to be too degraded in the observed specimen, which was also contaminated with DNA from an old cave bear located in the cave. The mtDNA research revealed an unexpected link between the specimen and the Denisovans, which prompted a lot of issues. In a January 2014 publication titled “A mitochondrial genome sequence of a hominin from Sima de los Huesos,” several possibilities were offered, clarifying the scientific community’s lack of consensus on how Homo heidelbergensis is related to other known hominin groupings.

The scientists argued that H. heidelbergensis was a common ancestor of both Denisovans and Neanderthals. Completely sequenced nuclear genomes from Denisovans and Neanderthals point to a 700,000-year-old common ancestor. One of the field’s leading researchers, Svante Paabo, argues that this new hominin group could be that ancestor.

The Accuracy of Molecular Paleontology Results

Experts agree that no completely convincing authentication can be accomplished only based on a nucleotide sequence extracted from old material through molecular palaeontology. Rather, sequence analysis should come at the end of several tests. First, there should be an examination of the specimen for cell and tissue preservation before being subjected to geochemical testing.

It would help determine whether the material’s diagenetic state is consistent with DNA survival. Then, after at least some of these assays have been completed, the remaining DNA can be amplified using PCR. The amplification product should then be cloned, sequenced, and the sequences compared to the specimen for phylogenetic consistency.

The degree of racemization of some amino acids is a well-known diagenetic test. This assay works on a simple basis, and geochemists and palaeontologists have been using it for a long time. However, recent research has demonstrated that it may also be a highly useful tool in studying ancient DNA.

Applications of Molecular Paleontology

De-extinction
Credit: Science News

De-extinction

Extinct species can now be resurrected utilizing molecular palaeontology techniques. For example, the Pyrenean ibex, a type of wild goat that became extinct in 2000, was the first to be cloned in 2003. Nuclei from Pyrenean ibex cells were transplanted into surrogate goat moms after being injected into goat eggs emptied of their DNA.

Unfortunately, the offspring only lived for seven minutes after birth due to lung problems. Similar lung abnormalities have been observed in other cloned animals.

As a direct result of human activities, many species have become extinct. One can bring an extinct species back to life by using allelic substitution from a closely related extant species. It may be possible to bring back multiple species, including Neanderthals, by replacing a few genes within an organism rather than having to rebuild the extinct species’ genome from the start.

The ethics of reintroducing extinct creatures into the wild are hotly debated. Extinctionists argue that bringing extinct animals back to life through molecular palaeontology will divert scarce funds and resources from addressing the world’s present biodiversity challenges. Furthermore, with current extinction rates estimated to be 100 to 1,000 times higher than the background extinction rate.

There is a fear that a de-extinction programme could reduce public concern about the current mass extinction crisis. So it is if it is believed that these species are resurrectable. However, the loss of habitat is the primary cause of extinction for most species in this era (post 10,000 BC). Therefore, momentarily resurrecting an extinct species would not rebuild their previously inhabited environment.

Many potential benefits are mentioned by proponents of de-extinction, such as George Church. Extinct essential keystone species, like the woolly mammoth, could be reintroduced to assist in rebalancing ecosystems that formerly depended on them. If extinct animals were to be reintroduced, they might have a significant positive impact on the formerly inhabited areas.

Woolly mammoths, for example, may be able to prevent the melting of the Russian and Frigid tundra by eating dead grass, allowing new grass to grow and take root, and periodically breaking up the snow, exposing the ground below to arctic air. In addition, researchers can use these procedures of molecular palaeontology to reintroduce genetic variety in a threatened species and introduce new genes and traits to help animals compete more effectively in a changing environment.

Discovery and Characterization of New Species through Molecular Palaeontology

The discovery of several new species, including the Denisovans as well as the Homo heidelbergensis, have been aided by molecular palaeontology techniques applied to fossils. As a result, we’ve gained a greater understanding of the path humans followed as they spread over the globe and the species that were present at the time.

Conclusion

The recovery and analysis of truly ancient molecules, i.e. those older than tens of thousands of years, is a source of great debate in molecular palaeontology. It is partly due to practical ideas about the ultimate durability and survivability of molecules in the fossil record and to difficulties distinguishing between endogenous and foreign contamination. In addition, molecular and chemical analytical methods are costly and destructive to rare fossils.

The fossils that are most amenable to molecular analyses and most likely to yield positive results are usually those that have been preserved exceptionally, making them too valuable for destructive analyses. As a result, the value of molecular palaeontology and the methodologies and procedures it employs are frequently questioned.

Molecular palaeontology is the recovery, analysis, and characterization of DNA, much like molecular biology. However, the molecular record of an organism is preserved in molecules other than DNA. Also, the information in these other life molecules varies in terms of phylogenies, evolutionary history, and other properties.

Therefore, protein, carbohydrate, and lipid analyses and their breakdown products and products of interactions with geochemical are usable in molecular palaeontology. Furthermore, the study of all macromolecules or their breakdown products can be traced back to their source. Therefore, it can offer insight into an organism’s molecular diagenetic history called molecular palaeontology.

Leave a Reply