Extraction of Ancient Insect DNA from Copal!

 

This article discusses the ability to extract ancient DNA from insects trapped in copal. It tests the hypothesis of whether or not aDNA (ancient DNA) could possibly be preserved over such an extensive period of time. They were able to extract endogenous DNA molecules from one of the samples they analyzed, and able to make taxonomic identifications regarding the organism, though it was incredibly degraded. They did so via radiocarbon analysis. They discuss struggles regarding human DNA contamination, and how tedious the separation of modern human DNA from the aDNA was. Additionally, they discuss reasons behind why they advise against this type of analysis- it is highly destructive to the samples.

I am highly interested in the extraction, sequencing, and use of ancient DNA in modern studies. Therefore, it is not surprising that I find this article incredibly fascinating. Scientifically, I find this an incredible feat, which is primarily attributed to the fact that DNA degrades so quickly. It is absolutely insane to think that we may be able to extract ancient biomolecules, and harness the ability to not only make assumptions about ancient organisms, but also use the information gathered to make strides in modern genetic research. 

Potential Recovery of Dinosaur DNA!

 This article details an account which claims that $125 million-year-old DNA has been recovered from a dinosaur called Caudipteryx. Scientists claim that the fragments of chromatin and nuclei within the fossil could contain preserved DNA, which could then be extracted and studied. However, mass skepticism surrounds this idea. Currently, the oldest sequenced DNA belongs to a million year old woolly mammoth, and, given how long ago dinosaurs went extinct, the idea of sequencing multi-millions of years old DNA is nearly unheard of… This is due to DNA's fragility. The dinosaur DNA was allegedly extracted from fossilized femur cartilage, found in China. This fossil was exceptionally preserved, as the site it was found at is known for fossilization via fine volcanic ash- prime preservation conditions. However, the main concern surrounding this is the idea that the genetic material being found could actually be from microbes on the fossils, not the dinosaurs themselves. This is a problem that researchers commonly run into, not only with dinosaurs, but other ancient organisms as well.

Personally, I think that the concept of being able to study ancient DNA, and then further learn from it in the present day, is fantastical. However the obvious problems of being unable to differentiate between modern organisms and fossil DNA is a major setback. Additionally, due to DNA's tendency to break down over time, unfortunately, I am also a skeptic in regards to whether or not DNA was actually recovered from this dinosaur. However, if somehow we were able to develop a way to differentiate modern versus ancient DNA, I think it would be amazing to compare ancient DNA to modern DNA, and see just how similar dinosaur DNA is to that of modern organisms. 

Paleogenetics

 Next-generation sequencing (NGS) technology and the updating of DNA isolation protocols have combined to make the sequencing and genome estimation process of a very fragmented ancient DNA (aDNA) possible. This new technology has furthered the field of paleogenetics to be able to perform metagenomic studies, as opposed to analyzing a singular short DNA sequence, like in the past. It is difficult to extract aDNA and process it without severe degradation, if enough of a sample is still present in a fossil, to be collected at all. Amplification through the use of primers, selected for the species closest to the species of interest, or primers for interspecies conserved regions, has also been done to analyze aDNA. The mitochondrial DNA from fossils, as well as fragments of their nuclear genomes, are the main focus of study and captured using a hybridization-based capture method.

I have a particular interest in biological archeology. Advancements in paleogenetics could vastly improve identification of extinct species. Amplifying DNA like this, to allow for genome sequencing, will allow for better estimations of their genetic codes. However, the species with no living members cannot be verified and could possibly be providing contaminated DNA strands. This discrepancy is still difficult to rectify. Perhaps further technological advancements could assist in identifying and removing any contaminants.

Link to article “Methodological Changes in the Field of Paleogenetics”:

 https://doi.org/10.3390/genes14010234

Other associated links:

DNA sequences from the quagga, an extinct member of the horse family | Nature

Ancient DNA | definition of Ancient DNA by Medical dictionary (thefreedictionary.com)

We Evolved from Neanderthals

A study has shown that Developmental cells are the cause for the Domestication and Change in Facial Structure between the once Neanderthals and today's "normal" facial structured Humans, as well as some Humans who have rare genetic disorders from prenatal and postnatal growth. It’s all tied around this one gene that goes by the name of BAZ1B. A scientist has concluded that the lack of this "boss-like" cell to be the main reason for the "Williams-Beuren syndrome". The Neural crest cells show up upon the elemental stage of birth as they migrate into different placements throughout the body.  Rising tissues, altering bone and cartilage placements, pigment cells, and other actions take place when these neural crest cells present there presents.

People who have Williams-Beuren syndrome are known to be more talkative, outgoing and not aggressive in any manner. But on the flip side, there is a disorder that includes that extra BAZ1B crest cell that results in the person having difficulty speaking and tend to come off more aggressive than the norm. They also have a different facial structure, more narrow opposed to the Williams-Beuren syndrome. This disorder is formally known as 7q11.23 Duplication syndrome.  All in all, evolution has allowed us to change in appearance, giving rise to less harsh facial features. Imagine how different human beings would look in the next hundred years compared to how we appear today!

Original link: Gene Tied to Facial Development

Extinct Ancestor to Orangutan Opens up Doors for Further Human Evolution Research

Ancient protein sequencing has been used to determine the genetic position of the Gigantopithecus blacki. It revealed that the orangutan is its closest living relative. This is the first time that genetic information this old has been able to be used from such a warm, damp environment. This is important because primates are closely related to humans, meaning it may be possible to retrieve similar information on the evolutionary line leading to humans. We used to only be able to go back about 400,000 years, but now it may be possible to trace human evolution as far back as two million years. The sequencing of proteins from dental enamel also proved to be useful when studying lineage of species, when there is no surviving DNA. Only a few jaws, but a lot of teeth were found from this species. This protein sequencing of the enamal showed that the orangutan and Gigantopithecus blacki split up about 12 million years ago. Mass spectrometry was used to analyze these protein sequences. Because there are not a lot of fossils found from Gigantopithecus blacki, a lot of speculation surrounds what its physical characteristics may have been.

A lot is already known about the evolution of a lot of animals and of humans, but there is still so much missing. When new fossils are found and they are sequenced to find out which species they are closest related to, a whole new door is opened. From there other lineages can be mapped out and we can get a clearer understanding of how evolution occurred. What's even more interesting about this case, is that the way these fossils were sequenced opened up new possibilities for the sequencing of future fossils from extinct human species. Now more questions about the evolution of humans can be answered.

Link:
https://www.sciencedaily.com/releases/2019/11/191113153053.htm

Related Article:
https://healthsciences.ku.dk/newsfaculty-news/2019/11/extinct-giant-ape-directly-linked-to-the-living-orangutan/

The First Denisovan Fossil From Outside Siberia Has Been Found in China

In 2016, Jean-Jacques Hublin, paleoanthropologist and director of the Department of Human Evolution at the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany, was emailed by archaeologist Dongju Zhang about a highly unusual hominin mandible found in a cave on the Tibetan Plateau in Xiahe, China. The photos she attached stunned Hublin. This fossil was quite complete and clearly nonmodern. It wasn’t long after that they met in Leipzig and began planning their collaboration and recruiting a team of specialists for a study on this strange fossil.

On May 1st of this year, Hublin, Zhang, and their team published the results of their study in the journal Nature. Their analysis confirmed that it belonged to the mysterious branch of hominins known as Denisovans, which were first identified in 2010. Never before had a bone fragment from a Denisovan been found outside a single cave in the Altai Mountains of Siberia.

Moreover, this is the most complete fossil of one ever discovered, as all the previous ones, including the recently uncovered skull piece I reported on in an earlier article, have been small and fragmented. The Xiahe jaw will help scientists tremendously, as now they will have a reference specimen to compare currently unidentified fossils to. Until this point, the anatomy of Homo denisova has been almost entirely unknown and speculative. This finding will thankfully add another eye-opening piece to the puzzle.

Hublin and his team were able to identify the fossil as Denisovan thanks to the work of his PhD student, Frido Welker, who had figured out that ancient proteins can be preserved much longer than ancient DNA, and therefore they could be used to map hominin groups in the absence of the latter material. Genome sequencing of Denisovans and their famous “sister” hominin, Neandertals, allowed the researchers to suppose the structure of these proteins and subsequently flesh out the separate branches. In the case of the Xiahe jaw, there was no ancient DNA, but the teeth yielded some proteins. These were then analyzed and matched using the aforementioned technique. The results were clear, this Tibetan fossil was a Denisovan.

Man's Genome from 45,000 Years Ago is Reconstructed

The genome of a man who lived 45,0000 years ago has now be reconstructed, from a fossil thighbone found in Siberia. Not only do the results give insight into the expansion of modern humans from Africa into Eurasia, but it is strong supportive evidence for the hypothesis that at one point, modern humans interbred with Neanderthals. This was accomplished by a team of scientists, led by geneticist Svante Pablo in Leipzig, Germany.

The team was able to do this by retrieving small parts of genes, reading the sequences and joining the fragments together to make larger pieces of the genome. They found that this man (who they deemed Ust’-Ishim man) was part of a lineage that eventually gave rise to all non-African humans, living after homo sapiens migrated from Africa, but before the species split between Europe and Asia.

The team was also able to reconstruct a Neanderthal’s genome from a single toe bone. Comparing a Neanderthal’s genome to that of Ust’-Ishim man, it was found that he had pieces of Neanderthal DNA in his genome, but with the significant difference that he had much longer pieces of Neanderthal DNA, compared to the much shorter fragments you would find in humans today. Thus showing that he was part of a lineage more closely related to Neanderthals.

From the findings, the scientists hypothesize that humans and Neanderthals interbred between 50,000 and 60,000 years ago, and that non-Africans descended from a group of people this man belonged to, who moved out of Africa, also around 60,000 years ago.

It’s very interesting to see the gaps in the history of our species slowly be reconstructed. Although we may never know everything, this is a great discovery. The hypothesis that we only just moved out of Africa, and were interbreeding with another species, just 60,000 years ago is astonishing; since that is not a long time ago in the great scheme of things, and much less than the hypothesis 100,000 years ago. I hope that more discoveries like this will not only reveal the past, but reveal how we slowly evolved into modern humans.

Link to article: http://www.nytimes.com/2014/10/23/science/research-humans-interbred-with-neanderthals.html

The Lost Identity of Man's Best Friend

We believe that the origin of Earth was caused by the Big Bang 13.7 billion years ago, but what can we say about the origin of dogs?

Comparing the two, the origin of dogs may seem minuscule and unimportant but just how much do we know about our best friend? Some people agreed on the fact dogs came from wolves, aside that we only know dogs appeared around 15,000 to 100,000 years ago somewhere in Asia or Africa.

According to Dr. Greger Larson at University of Durham, England, it is currently improbable to trace when and where dogs originated from the DNA of modern dogs. Larson and twenty other authors have been working on a paper about the origins of dog domestication. Currently the team has analyzed 49,024 locations on dog DNA; working with 1,375 DNA samples from 121 breed, and 19 wolves.So far they have only been successful tracing back to about a hundred years.

Larson and his colleagues concluded on how modern dog breeding is making it more difficult to locate when or where dogs were first domesticated. In fact, dog breeding had been so mixed, that the genetic history for dogs became very obscured; with the exception of basenji, shar-pei, Saluki, Akita, Finnish spitz, and Eurasier bring slightly less mixed.

What Larson and his team found out was that, dogs that are most genetically distinct were not from the places where the oldest dog fossil was found. Larson expected if these breeds were closer genetically to the first domesticated dogs, they would be geographically closer to sites of early dog fossils or ancient dog breeds. However, their studies shows the more genetically distinct dogs had been geographically isolated quite recent in the history of domestication. For instance, dingoes, basenjis, and New Guinea singing dogs came from southeast Asia and southern Africa about 3,500 and 1,400 years ago.

Larson concluded that there is still hope to learn about the origin of dogs. People have burying their dogs for a long amount of history, thus somewhere, there really is a fossil of an ancient dog--we just have to find it.

I think dog breeding is one of the things we, as humans take for granted. We decide on the breed that we want for our own purposes, not knowing the consequences of our selfishness. In order to create a companion to cuddle and be dog show material--we have made our best friend lost his identity. Everyone kept saying how much they love their dogs, but just how much do we know about their history?

Original article: http://www.nytimes.com/2012/05/22/science/dogs-genetic-roots-remain-obscure.html?_r=0

Related article: http://www.npr.org/2013/07/10/200498354/barking-up-the-family-tree-american-dogs-have-surprising-genetic-roots