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Thread: More analysis of older DNA and discoveries shed light on human relatives

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    tWebber shunyadragon's Avatar
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    More analysis of older DNA and discoveries shed light on human relatives

    Source: https://www.sciencemag.org/news/2020/04/mysterious-human-ancestor-finds-its-place-our-family-tree



    Mysterious human ancestor finds its place in our family tree
    By Michael PriceApr. 1, 2020 , 11:00 AM

    When it comes to deciphering our ancient family tree, DNA from fossils is the new gold standard. But after about half a million years, even the best-preserved DNA degrades into illegibility, leaving the story of our early evolution shrouded in mystery. A new study of proteins taken from the tooth of an enigmatic human ancestor reveals their rough place in the family tree—and shows how ancient proteins can push beyond the limits of DNA.

    The new study is “a landmark paper,” says Mark Collard, an archaeologist at Simon Fraser University who wasn’t involved with the work. “Ancient protein analysis promises to be as exciting as ancient DNA analysis for shedding light on human evolution.”

    DNA, made of chains of nucleic acids, can remain embedded inside fossilized bones (and prehistoric “chewing gum”) for up to about 500,000 years, explains Enrico Cappellini, a geneticist at the University of Copenhagen’s Natural History Museum of Denmark. That time frame covers the rise of our species, Homo sapiens, in Africa sometime about 300,000 years ago. But before then, many other kinds of humans roamed Earth, including our close cousins the Neanderthals, and their Siberian kin, the Denisovans. Another early relative is H. antecessor, known chiefly from northern Spain’s Gran Dolina cave.

    The physical features of H. antecessor have left anthropologists puzzling over its relationships with other early humans. It has big teeth, as do more primitive members of our genus such as H. erectus, but its face shape is remarkably similar to that of modern humans. Some have argued it could be the last common ancestor of Neanderthals, Denisovans, and H. sapiens. Others argue it is actually a member of H. erectus.

    In the new study, Cappellini’s team used mass spectrometry—a technique that can sort out a sample’s chemical composition, including the peptides that make up proteins—to analyze proteins in a sliver of enamel from an 800,000-year-old H. antecessor molar from Gran Dolina. Proteins are much hardier and longer lived than DNA: In just the past 6 months, Cappellini and colleagues have published ancient proteins found in a 1.77-million-year-old rhinoceros and a 1.9-million-year-old primate, Gigantopithecus blacki. But they also contain less genetic information than DNA, and they vary less between species.

    Cappellini’s team identified peptide sequences from seven proteins in the ancient tooth enamel—essentially all the proteins found there—including a peptide specific to the Y-chromosome that marks the individual as a male. Next, researchers compared these protein sequences with their equivalents in modern humans, other living apes, Neanderthals, and Denisovans.

    The proteins suggest H. antecessor was a close relative of the last common ancestor to humans, Neanderthals, and Denisovans, the researchers report today in Nature. “We see that antecessor falls as a sister group—close, very close—to the branch that leads to us,” Cappellini says.

    That solidifies what many suspected, but it’s far from conclusive, says Tim Weaver, an anthropologist at the University of California, Davis, who wasn’t involved in the study. Either way, it offers fantastic proof of the power of proteomics to reveal ancient events in human evolution. “It’s really exciting that we’re starting to get proteins from some of these older fossils,” he says.

    Posted in: ArchaeologyEvolution
    doi:10.1126/science.abc0184

    © Copyright Original Source

    Last edited by shunyadragon; 04-01-2020 at 05:23 PM.
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  2. #2
    Evolution is God's ID rogue06's Avatar
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    Quote Originally Posted by shunyadragon View Post
    Source: https://www.sciencemag.org/news/2020/04/mysterious-human-ancestor-finds-its-place-our-family-tree



    Mysterious human ancestor finds its place in our family tree
    By Michael PriceApr. 1, 2020 , 11:00 AM

    When it comes to deciphering our ancient family tree, DNA from fossils is the new gold standard. But after about half a million years, even the best-preserved DNA degrades into illegibility, leaving the story of our early evolution shrouded in mystery. A new study of proteins taken from the tooth of an enigmatic human ancestor reveals their rough place in the family tree—and shows how ancient proteins can push beyond the limits of DNA.

    The new study is “a landmark paper,” says Mark Collard, an archaeologist at Simon Fraser University who wasn’t involved with the work. “Ancient protein analysis promises to be as exciting as ancient DNA analysis for shedding light on human evolution.”

    DNA, made of chains of nucleic acids, can remain embedded inside fossilized bones (and prehistoric “chewing gum”) for up to about 500,000 years, explains Enrico Cappellini, a geneticist at the University of Copenhagen’s Natural History Museum of Denmark. That time frame covers the rise of our species, Homo sapiens, in Africa sometime about 300,000 years ago. But before then, many other kinds of humans roamed Earth, including our close cousins the Neanderthals, and their Siberian kin, the Denisovans. Another early relative is H. antecessor, known chiefly from northern Spain’s Gran Dolina cave.

    The physical features of H. antecessor have left anthropologists puzzling over its relationships with other early humans. It has big teeth, as do more primitive members of our genus such as H. erectus, but its face shape is remarkably similar to that of modern humans. Some have argued it could be the last common ancestor of Neanderthals, Denisovans, and H. sapiens. Others argue it is actually a member of H. erectus.

    In the new study, Cappellini’s team used mass spectrometry—a technique that can sort out a sample’s chemical composition, including the peptides that make up proteins—to analyze proteins in a sliver of enamel from an 800,000-year-old H. antecessor molar from Gran Dolina. Proteins are much hardier and longer lived than DNA: In just the past 6 months, Cappellini and colleagues have published ancient proteins found in a 1.77-million-year-old rhinoceros and a 1.9-million-year-old primate, Gigantopithecus blacki. But they also contain less genetic information than DNA, and they vary less between species.

    Cappellini’s team identified peptide sequences from seven proteins in the ancient tooth enamel—essentially all the proteins found there—including a peptide specific to the Y-chromosome that marks the individual as a male. Next, researchers compared these protein sequences with their equivalents in modern humans, other living apes, Neanderthals, and Denisovans.

    The proteins suggest H. antecessor was a close relative of the last common ancestor to humans, Neanderthals, and Denisovans, the researchers report today in Nature. “We see that antecessor falls as a sister group—close, very close—to the branch that leads to us,” Cappellini says.

    That solidifies what many suspected, but it’s far from conclusive, says Tim Weaver, an anthropologist at the University of California, Davis, who wasn’t involved in the study. Either way, it offers fantastic proof of the power of proteomics to reveal ancient events in human evolution. “It’s really exciting that we’re starting to get proteins from some of these older fossils,” he says.

    Posted in: ArchaeologyEvolution
    doi:10.1126/science.abc0184

    © Copyright Original Source

    Read about this earlier this afternoon.

    Source: The dental proteome of Homo antecessor


    Abstract

    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.



    Source

    © Copyright Original Source




    [*Footnote numbers removed by rogue06*]


    Here's the article about it in phys.org:

    Source: Oldest-ever human genetic evidence clarifies dispute over our ancestors


    Genetic information from an 800,000-year-old human fossil has been retrieved for the first time. The results from the University of Copenhagen shed light on one of the branching points in the human family tree, reaching much further back in time than previously possible.

    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.

    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.

    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 researchers 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 characteristics 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.

    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 10-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 determined the sequence of amino acids within protein remains from Homo antecessor dental enamel. We could then compare the ancient protein sequences 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.


    Source

    © Copyright Original Source


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  3. #3
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by rogue06 View Post
    Read about this earlier this afternoon.

    Source: The dental proteome of Homo antecessor


    Abstract

    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.



    Source

    © Copyright Original Source




    [*Footnote numbers removed by rogue06*]


    Here's the article about it in phys.org:

    Source: Oldest-ever human genetic evidence clarifies dispute over our ancestors


    Genetic information from an 800,000-year-old human fossil has been retrieved for the first time. The results from the University of Copenhagen shed light on one of the branching points in the human family tree, reaching much further back in time than previously possible.

    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.

    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.

    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 researchers 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 characteristics 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.

    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 10-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 determined the sequence of amino acids within protein remains from Homo antecessor dental enamel. We could then compare the ancient protein sequences 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.


    Source

    © Copyright Original Source

    Thank you as usual for y0ur diligence. These are learning threads for me and others, even though it is ignored by many.
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

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