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Piquerobi
06-05-2020, 11:52 PM
The oldest remains whose DNA has been analysed so far:


Article Published: 01 April 2020

The dental proteome of Homo antecessor

The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain) and Homo erectus from Dmanisi (Georgia), two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor—that is, similar to that of modern humans—may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.
https://www.nature.com/articles/s41586-020-2153-8


An important advancement in human evolution studies has been achieved after scientists retrieved the oldest human genetic data set from an 800,000-year-old tooth belonging to the hominin species Homo antecessor.

The findings by scientists from the University of Copenhagen (Denmark), in collaboration with colleagues from the CENIEH (National Research Center on Human Evolution) in Burgos, Spain, and other institutions, are published April 1st in Nature.

"Ancient protein analysis provides evidence for a close relationship between Homo antecessor, us (Homo sapiens), Neanderthals, and Denisovans. Our results support the idea that Homo antecessor was a sister group to the group containing Homo sapiens, Neanderthals, and Denisovans," says Frido Welker, Postdoctoral Research Fellow at the Globe Institute, University of Copenhagen, and first author on the paper.

Reconstructing the human family tree

By using a technique called mass spectrometry, researchers sequenced ancient proteins from dental enamel, and confidently determined the position of Homo antecessor in the human family tree.

The new molecular method, palaeoproteomics, developed by researchers at the Faculty of Health and Medical Sciences, University of Copenhagen, enables scientists to retrieve molecular evidence to accurately reconstruct human evolution from further back in time than ever before.

The human and the chimpanzee lineages split from each other about 9-7 million years ago. Scientists have relentlessly aimed to better understand the evolutionary relations between our species and the others, all now extinct, in the human lineage.

"Much of what we know so far is based either on the results of ancient DNA analysis, or on observations of the shape and the physical structure of fossils. Because of the chemical degradation of DNA over time, the oldest human DNA retrieved so far is dated at no more than approximately 400,000 years," says Enrico Cappellini, Associate Professor at the Globe Institute, University of Copenhagen, and leading author on the paper.

"Now, the analysis of ancient proteins with mass spectrometry, an approach commonly known as palaeoproteomics, allow us to overcome these limits," he adds.

Theories on human evolution

The fossils analyzed by the researchers were found by palaeoanthropologist José María Bermúdez de Castro and his team in 1994 in stratigraphic level TD6 from the Gran Dolina cave site, one of the archaeological and paleontological sites of the Sierra de Atapuerca, Spain.

Initial observations led to conclude that Homo antecessor was the last common ancestor to modern humans and Neanderthals, a conclusion based on the physical shape and appearance of the fossils. In the following years, the exact relation between Homo antecessor and other human groups, like ourselves and Neanderthals, has been discussed intensely among anthropologists.

Although the hypothesis that Homo antecessor could be the common ancestor of Neanderthals and modern humans is very difficult to fit into the evolutionary scenario of the genus Homo, new findings in TD6 and subsequent studies revealed several characters shared among the human species found in Atapuerca and the Neanderthals. In addition, new studies confirmed that the facial features of Homo antecessor are very similar to those of Homo sapiens and very different from those of the Neanderthals and their more recent ancestors.

"I am happy that the protein study provides evidence that the Homo antecessor species may be closely related to the last common ancestor of Homo sapiens, Neanderthals, and Denisovans. The features shared by Homo antecessor with these hominins clearly appeared much earlier than previously thought. Homo antecessor would therefore be a basal species of the emerging humanity formed by Neanderthals, Denisovans, and modern humans," adds José María Bermúdez de Castro, Scientific Co-director of the excavations in Atapuerca and co-corresponding author on the paper.

World class-expertise

Findings like these are made possible through an extensive collaboration between different research fields: from paleoanthropology to biochemistry, proteomics and population genomics.

Retrieval of ancient genetic material from the rarest fossil specimens requires top quality expertise and equipment. This is the reason behind the now ten-years-long strategic collaboration between Enrico Cappellini and Jesper Velgaard Olsen, Professor at the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen and co-author on the paper.

"This study is an exciting milestone in palaeoproteomics. Using state of the art mass spectrometry, we determine the sequence of amino acids within protein remains from Homo antecessor dental enamel. We can then compare the ancient protein sequences we 'read' to those of other hominins, for example Neanderthals and Homo sapiens, to determine how they are genetically related," says Jesper Velgaard Olsen.

"I really look forward to seeing what palaeoproteomics will reveal in the future," concludes Enrico Cappellini.

The study of human evolution by palaeoproteomics will continue in the next years through the recently established EU-funded "Palaeoproteomics to Unleash Studies on Human History (PUSHH)" Marie S. Curie European Training Network (ETN), led by Enrico Cappellini, and involving many of the co-authors on the paper.

The research is mainly funded by VILLUM FONDEN, the Novo Nordisk Foundation, and the Marie Sklowowska-Curie Actions Individual Fellowship and International Training Network programmes.
https://www.sciencedaily.com/releases/2020/04/200401111657.htm

Milkyway
06-08-2020, 03:57 PM
They belonged to a closely related, yet different lineage to that of Neanderthals/AMH/Denisovans.

This means that the ancestors of Neanderthals and Denisovans either lived somewhere in Eurasia and some of them migrated to Africa, or they migrated from Africa to Eurasia in the following 200,000 years (considering they diverged from AMH 600,000 years ago and the H. antecessor tooth is 800,000 years old).


This placement implies that the modern-like face of H. antecessor—that is, similar to that of modern humans—may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form.

What is a "modern-like face"? No brow ridges? A chin?

RP48
06-08-2020, 06:24 PM
It’s confusing to me when H antecessor is declared to be a sister lineage to modern humans (not ancestral) and at the same time postulate that their skull and facial features, similar to anatomically modern humans, suggests that facial/skull morphology of modern humans may have been present for a very long time. Yet in between their MRCA and emergence of anatomically modern humans, are some with less modern features.

Milkyway
06-08-2020, 10:49 PM
It’s confusing to me when H antecessor is declared to be a sister lineage to modern humans (not ancestral) and at the same time postulate that their skull and facial features, similar to anatomically modern humans, suggests that facial/skull morphology of modern humans may have been present for a very long time. Yet in between their MRCA and emergence of anatomically modern humans, are some with less modern features.

Yes, it's a bit confusing... perhaps what they mean is that archaic/gracile facial morphologies can occur in the same (sub)species. We have several examples of this in modern populations: Australian Aboriginals are rather robust, while the San/Bushmen, which have the oldest mtDNA clades, are more gracile.

Anyway, here's a facial reconstruction (https://www.researchgate.net/profile/Israel_Sanchez3/publication/313053422/figure/fig6/AS:[email protected]/The-first-reconstruction-of-Homo-antecessor-Left-column-side-view-Right-column.png) of H. antecessor (they had a receding chin and an elongated skull like that of Neanderthals/Denisovans).

Piquerobi
06-09-2020, 11:42 AM
The analysis is not based on DNA but on proteome. A different way of inferring phylogenetic relationships. An indirect way of checking possible DNA relationships so to say.


The term has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organism's complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome. The term "proteome" has also been used to refer to the collection of proteins in certain sub-cellular biological systems. For example, all of the proteins in a virus can be called a viral proteome. All of the proteins in a mitochondrion make up the mitochondrial proteome which has generated its own field of study mitoproteomics.
https://en.wikipedia.org/wiki/Proteome
https://en.wikipedia.org/wiki/Proteomics

37944

Piquerobi
06-09-2020, 11:44 AM
Proteomics is a rapidly growing field of molecular biology that is concerned with the systematic, high-throughput approach to protein expression analysis of a cell or an organism. Typical results of proteomics studies are inventories of the protein content of differentially expressed proteins across multiple conditions.

In many ways, proteomics runs parallel to genomics. The starting point for genomics is a gene in order to make inferences about its products (i.e. proteins), whereas proteomics begins with the functionally modified protein and works back to the gene responsible for its production.
https://www.azolifesciences.com/article/What-is-Proteomics.aspx

Saetro
06-09-2020, 09:18 PM
Proteomics is something we did back in the 1970s when DNA analysis was in its dragging stage (pre-crawling). (And before.)
Good that people have remembered the value and applied modern equipment and techniques to the task.

Just remember that any comparisons regarding DNA are from inferred DNA.
I would hope that all such comparisons began with protein differences (fact) and then went on to discuss possible DNA ones (inference).

Piquerobi
06-10-2020, 02:11 AM
^ Hopefully they will use it to advance the studies of early hominids. Ancient DNA degradation has hindered it so far.