Evolution Human evolution

Researchers: Jumping genes play extensive role in human evolution

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Abstract: Transposable Elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) extensively shaped the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage. Briefly, we first identified species-specific N-LTRrs and established their distribution in present day human populations. These analyses shortlisted a group of N-LTRr insertions that were found exclusively in Anatomically Modern Humans. Notably, these insertions targeted genes more frequently than randomly expected and are associated with an increase in the number of transcriptional/splicing variants of those genes they inserted in. The analysis of the functionality of genes targeted by human-specific N-LTRr insertions seems to reflect phenotypic changes that occurred during human evolution. Furthermore, the expression of genes containing the most recent N-LTRr insertions is enriched in the brain, especially in undifferentiated neurons, and these genes associate in networks related to neuron maturation and migration. Additionally, we also identified candidate N-LTRr insertions that have likely produced new functional variants exclusive to modern humans, which show traces of positive selection and are now fixed in all present-day human populations. In sum, our results strongly suggest that N-LTRr impacted our differentiation as a species and have been a constant source of genomic variability all throughout the evolution of the human lineage. (public access) – Etienne Guichard, Valentina Peona, Guidantonio Malagoli-Tagliazucchi, Lucia Abitante, Evelyn Jagoda, Margherita Musella, Marco Ricci, Alejandro Rubio-Roldán, Stefania Sarno, Donata Luiselli, Davide Pettener, Cristian Taccioli, Luca Pagani, Jose Luis Garcia-Perez, Alessio Boattini
doi: https://doi.org/10.1101/207241More.

And each and every accidental change was a benefit? Wow. There must be a lot of extinct species out there that we haven’t found yet, for which the change didn’t work.

See also: Jumping’ Genes!: A quarter of cow DNA came from reptiles? If jumping genes can be this prevalent, evolution is about to become way more complex than the storied Tree of Life hammered into kids at school. They could be like migrating populations.

17 Replies to “Researchers: Jumping genes play extensive role in human evolution

  1. 1
    gpuccio says:

    News:

    Very good paper.

    Design by transposons is definitely the answer! Or at least one of them.

  2. 2
    Dionisio says:

    gpuccio,

    You’ve been saying this long ago.

  3. 3
  4. 4
    ET says:

    TE’s play a big role in Perry Marshall’s Evolution 2.0. Dr Spetner also says they are used in evolution by design- Not By Chance!.

    This research appears to support their cases.

  5. 5
    Dionisio says:

    gpuccio,

    In the abstract of the same paper referenced @3 we can read this:

    “…there have been multiple waves of LINE retrotransposition as well as

    the birth of new mobile elements

    such as the SINEs Alu and SVA…”

    As far as you’re aware of, is there any literature explaining how

    the birth of new mobile elements

    may have occurred?

    Thanks.

  6. 6
    Dionisio says:

    @5 text formatting error correction

    gpuccio,

    In the abstract of the same paper* referenced @3 we can read this:

    “…there have been multiple waves of LINE retrotransposition as well as the birth of new mobile elements such as the SINEs Alu and SVA…”

    As far as you’re aware of, is there any literature explaining how the birth of new mobile elements may have occurred?

    It would be interesting to review such a literature and learn more about that important topic.

    Thanks.

    (*) Linker, S.B., Marchetto, M.C., Narvaiza, I. et al. BMC Biol (2017) 15: 68. https://doi.org/10.1186/s12915-017-0409-z

    [emphasis added]

  7. 7
    Dionisio says:

    @3 & @6 follow-up

    “Unique qualities of the human brain such as a relatively large cortical volume, surface area, and altered connectivity are often cited as key structural reasons for this increased complexity with respect to physiology.

    A yet unresolved question is the identification of the genetic modifications that underlie these physiological and cognitive complexities.”

    Linker, S.B., Marchetto, M.C., Narvaiza, I. et al. BMC Biol (2017) 15: 68. https://doi.org/10.1186/s12915-017-0409-z
    https://link.springer.com/content/pdf/10.1186%2Fs12915-017-0409-z.pdf

    Juicy material to dissect, isn’t it?

  8. 8
    Dionisio says:

    @7 follow-up

    […] all forms of mutation work together with selection and drift to produce the ever-dynamic phenotype […]

    Cognitive differences exist between humans and nonhuman primates that allow for the development of sophisticated behaviors such as language, self-awareness, symbolic thought, and cultural learning […]

    […] the functional contribution of RTs to these differences is still largely unknown.

    Linker, S.B., Marchetto, M.C., Narvaiza, I. et al. BMC Biol (2017) 15: 68. https://doi.org/10.1186/s12915-017-0409-z
    https://link.springer.com/content/pdf/10.1186%2Fs12915-017-0409-z.pdf

  9. 9
    Dionisio says:

    @8 follow-up

    While RTs can influence the host independently of mobility, the number of active elements and their genomic locations will be instrumental in understanding their role in human biology, especially in somatic cells.

    In the future, we will have to move away from simply annotating transposable elements and take their context and activity state into consideration.

    Linker, S.B., Marchetto, M.C., Narvaiza, I. et al. BMC Biol (2017) 15: 68. https://doi.org/10.1186/s12915-017-0409-z
    https://link.springer.com/content/pdf/10.1186%2Fs12915-017-0409-z.pdf

  10. 10
    Dionisio says:

    @9 follow-up

    Only a multi-species, comprehensive analysis and catalog of transposable elements will allow a true understanding of the influence of transposable elements on human brain evolution.

    Linker, S.B., Marchetto, M.C., Narvaiza, I. et al. BMC Biol (2017) 15: 68. https://doi.org/10.1186/s12915-017-0409-z
    https://link.springer.com/content/pdf/10.1186%2Fs12915-017-0409-z.pdf

  11. 11
    Dionisio says:

    @10 follow-up

    […] the direct impact of RTs on the human brain currently remains under debate.

    Therefore, future studies, such as those using these induced pluripotent stem cell models, will help to define the role of RTs in the function of the human neuron.

    Linker, S.B., Marchetto, M.C., Narvaiza, I. et al. BMC Biol (2017) 15: 68. https://doi.org/10.1186/s12915-017-0409-z
    https://link.springer.com/content/pdf/10.1186%2Fs12915-017-0409-z.pdf

    Work in progress… stay tuned.

  12. 12
    Peer says:

    I missed the release of Perry Marschall’s book, but apparently the author drained from the paradigm of rapid speciation:

    https://creation.com/images/pdfs/tj/j23_1/j23_1_99-106.pdf

    https://creation.com/images/pdfs/tj/j23_1/j23_1_107-114.pdf

    We can now also understand the Origin of RNA viruses:

    https://creation.com/images/pdfs/tj/j27_3/j27_3_105-112.pdf

  13. 13
    Dionisio says:

    Wow!!! Exciting news ahead!!!

    The next decade could be the one in which the regulatory code is cracked, opening the door to reading out the functional effects of non-coding changes that distinguish humans from other primates.

    Human evolution: the non-coding revolution
    Lucía F. Franchini, Katherine S. Pollard
    BMC Biol (2017) 15: 89.
    https://doi.org/10.1186/s12915-017-0428-9
    https://link.springer.com/content/pdf/10.1186%2Fs12915-017-0428-9.pdf

    Somebody in this website has been saying over and over that the most fascinating discoveries are still ahead.
    I don’t think we have to wait till the next decade.
    Before the end of this decade we shall read about very fascinating discoveries.
    But obviously, in the next decade the discoveries should be even more fascinating.
    Work in progress… stay tuned.
    We should look forward to reading future research papers shedding more light on the wonderful molecular and cellular choreographies orchestrated within the biological systems.
    The scientific discoveries should excite us. The knowledge gaps should keep us searching for the necessary information to fill them.

  14. 14
    Dionisio says:

    […] there is not a unique underlying evolutionary mechanism that led to the appearance of all HARs.

    The interpretation of functional differences between orthologous sequences in HARs should consider different evolutionary forces.

    Human evolution: the non-coding revolution
    Lucía F. Franchini, Katherine S. Pollard
    BMC Biol (2017) 15: 89.
    https://doi.org/10.1186/s12915-017-0428-9
    https://link.springer.com/content/pdf/10.1186%2Fs12915-017-0428-9.pdf

    There yet?

    🙂

  15. 15
    Dionisio says:

    […] the human brain seems to be unusual in terms of the number of neurons [93, 96], spatial organization [97], neuropil space, amount of dendritic branching, and synaptic spine density […]

    Human evolution: the non-coding revolution
    Lucía F. Franchini, Katherine S. Pollard
    BMC Biol (2017) 15: 89.
    https://doi.org/10.1186/s12915-017-0428-9
    https://link.springer.com/content/pdf/10.1186%2Fs12915-017-0428-9.pdf

    Well, that’s just a minor difference.

    🙂

  16. 16
    Dionisio says:

    The resulting extensive diversity data will permit the inference of constraint at high resolution and will thus shed light on function and molecular mechanisms.

    It will also help to overthrow misguided notions that function requires between-species sequence conservation or that function is widespread outside constrained sequence.

    Biological function in the twilight zone of sequence conservation
    Ponting, C.P. BMC Biol (2017) 15: 71. https://doi.org/10.1186/s12915-017-0411-5
    https://link.springer.com/content/pdf/10.1186%2Fs12915-017-0411-5.pdf

    Work in progress… stay tuned.

  17. 17
    gpuccio says:

    Dionisio:

    Yes, I think it is! 🙂

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