Horizontal gene transfer in eukaryotes

[sfs]

A major paper appeared in Nature three days ago, reassessing evidence for horizontal gene transfer from bacteria to eukaryotes and between eukaryotes; the paper is here (behind paywall). The authors' conclusion is that eukaryotes have acquired bacterial genes predominantly through genes transferred from endosymbionts (mitochondria and chloroplasts), and that ongoing HGT plays little role. From the abstract: "Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes."

From the body of the paper:

"Eukaryote gene evolution is resoundingly vertical..., with all supergroups, and eukaryotes as a group, passing the test as not significantly different from vertical, while the eukaryote-to-eukaryote LGT alternative ... is strongly rejected in all cases."

"While we do detect genome-specific candidate LGTs (cLGTs), namely eukaryotic singletons that show high similarity to prokaryotic genes, their frequency is approximately four to ten times lower than that of nuclear insertions of mitochondrial and chloroplast DNA... Thus, even on short timescales, the contribution of gene transfers from organelles is greater than that of cLGTs, whose numbers tend to decrease with updated genome annotations."

"Eukaryotes obtain novel gene families via gene and genome duplication, prokaryotes undergo LGT [lateral gene transfer]. Two episodes of gene influx—one from mitochondria and one from chloroplasts, followed by differential loss—account for the phylogeny and distribution of bacterial genes in eukaryotes."

 

[whois]

hmmmm . . .
We argue that HGT has occurred, and continues to occur, on a previously unsuspected scale in metazoans and is likely to have contributed to biochemical diversification during animal evolution.

Reports of HGT in animals are usually limited to the description of the transfer of only one or a few genes, making the extent of horizontal gene transfer in animals unclear. Examples include the transfer of fungal genes for carotenoid biosynthesis to the pea aphid, which results in a red pigmentation and is thought to be beneficial to the aphid [8] and the transfer of a cysteine synthase from a bacterium into the arthropod lineage (likely two independent transfers into a phytophagous mite ancestor and a lepidopteran ancestor), which allows the detoxification of cyanide produced by host plants [9].

In the human, however, there have been no follow-up studies since the original genome paper, and the true scale of HGT in humans, and metazoans generally, remains unclear.
To remedy this, we initially identified non-metazoan to metazoan HGT in multiple Drosophila, Caenohabditis and primate (including human) species. Due to the controversy surrounding the human studies [19-22], we then took our analysis a step further by comparing multiple closely related species and combining information on horizontally transferred (‘foreign’) genes found in more than one species in the group, thereby reducing mis-identification of HGT caused by spurious alignments. In this way, we identified up to hundreds of active foreign genes in animals, including humans, suggesting that HGT provides important contributions to metazoan evolution.

 

[sfs]

hmmmm . . .
We argue that HGT has occurred, and continues to occur, on a previously unsuspected scale in metazoans and is likely to have contributed to biochemical diversification during animal evolution.

Reports of HGT in animals are usually limited to the description of the transfer of only one or a few genes, making the extent of horizontal gene transfer in animals unclear. Examples include the transfer of fungal genes for carotenoid biosynthesis to the pea aphid, which results in a red pigmentation and is thought to be beneficial to the aphid [8] and the transfer of a cysteine synthase from a bacterium into the arthropod lineage (likely two independent transfers into a phytophagous mite ancestor and a lepidopteran ancestor), which allows the detoxification of cyanide produced by host plants [9].

In the human, however, there have been no follow-up studies since the original genome paper, and the true scale of HGT in humans, and metazoans generally, remains unclear.
To remedy this, we initially identified non-metazoan to metazoan HGT in multiple Drosophila, Caenohabditis and primate (including human) species. Due to the controversy surrounding the human studies [19-22], we then took our analysis a step further by comparing multiple closely related species and combining information on horizontally transferred (‘foreign’) genes found in more than one species in the group, thereby reducing mis-identification of HGT caused by spurious alignments. In this way, we identified up to hundreds of active foreign genes in animals, including humans, suggesting that HGT provides important contributions to metazoan evolution.

Right. That's the kind of analysis this paper is saying is mostly wrong.

 

[whois]

yes, i assume barbara went through a similar process with her transposon research.

 

[whois]

is there any reason to suppress HGT research or to deny it happens in animals, especially humans?
you be the judge:
On the other hand, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food.
-https://www.boundless.com/biology/textbooks/boundless-biology-textbook/phylogenies-and-the-history-of-life-20/perspectives-on-the-phylogenetic-tree-135/horizontal-gene-transfer-545-11754/

the above implies to me that GMO companies would have good reason to suppress this type of research.

 

[juvenissun]

A major paper appeared in Nature three days ago, reassessing evidence for horizontal gene transfer from bacteria to eukaryotes and between eukaryotes; the paper is here (behind paywall). The authors' conclusion is that eukaryotes have acquired bacterial genes predominantly through genes transferred from endosymbionts (mitochondria and chloroplasts), and that ongoing HGT plays little role. From the abstract: "Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes."

From the body of the paper:

"Eukaryote gene evolution is resoundingly vertical..., with all supergroups, and eukaryotes as a group, passing the test as not significantly different from vertical, while the eukaryote-to-eukaryote LGT alternative ... is strongly rejected in all cases."

"While we do detect genome-specific candidate LGTs (cLGTs), namely eukaryotic singletons that show high similarity to prokaryotic genes, their frequency is approximately four to ten times lower than that of nuclear insertions of mitochondrial and chloroplast DNA... Thus, even on short timescales, the contribution of gene transfers from organelles is greater than that of cLGTs, whose numbers tend to decrease with updated genome annotations."

"Eukaryotes obtain novel gene families via gene and genome duplication, prokaryotes undergo LGT [lateral gene transfer]. Two episodes of gene influx—one from mitochondria and one from chloroplasts, followed by differential loss—account for the phylogeny and distribution of bacterial genes in eukaryotes."

Does this one give any implication to the creation/evolution problem?
Easy, I just want to know any possible implication to you. No evidence is needed.

 

[The Cadet]

is there any reason to suppress HGT research

I think this is possibly one of the least productive ways to look at new scientific research that runs contrary to existing research. I'm in over my depth on this one, I just felt the need to point this out. Research is research is research. This isn't suppressing HGT. It's simply attempting to reevaluate what we know.

 

[whois]

I think this is possibly one of the least productive ways to look at new scientific research that runs contrary to existing research. I'm in over my depth on this one, I just felt the need to point this out. Research is research is research. This isn't suppressing HGT. It's simply attempting to reevaluate what we know.

only because you don't want to believe it.
it's a sad but true fact, money and lobbyists talk when it comes to science.
and it's this very thing that MUST be kept in the open, for everyone to see.
i would imagine the very same thing happened to barbara, her evidence was suppressed, even maybe other "evidence" stated it was wrong.
this sort of thing happens the cadet, you need to accept it.

 

[lasthero]

only because you don't want to believe it.
it's a sad but true fact, money and lobbyists talk when it comes to science.
and it's this very thing that MUST be kept in the open, for everyone to see.
i would imagine the very same thing happened to barbara, her evidence was suppressed, even maybe other "evidence" stated it was wrong.
this sort of thing happens the cadet, you need to accept it.

Why would anyone be lobbying and spending money to surprise this? Who? You never really answered your own question.

 

[whois]

Why would anyone be lobbying and spending money to surprise this? Who?

i gave one possibility in post 5 for HGT.
as far as barbara is concerned, there is little doubt her research, and her, was ridiculed, even to the point where she quit publishing.
i would guess her research didn't fit into the darwinist paradigm, so they tried to bury it.
there's your "peer review" for ya.

 

[sfs]

is there any reason to suppress HGT research or to deny it happens in animals, especially humans?
you be the judge:
On the other hand, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food.
-https://www.boundless.com/biology/textbooks/boundless-biology-textbook/phylogenies-and-the-history-of-life-20/perspectives-on-the-phylogenetic-tree-135/horizontal-gene-transfer-545-11754/

the above implies to me that GMO companies would have good reason to suppress this type of research.

1) I cannot imagine how the above would provide the slightest motivation for GMO companies to suppress this type of research.
2) GMO companies have nothing to do with funding the vast majority of genomics research, anyway. Almost all of it is funded by the government.
3) "A valid hypothesis once faced opposition, therefore my idea is true because it faces opposition" is not a very persuasive argument.
4) There is, in fact, not the slightest opposition to funding or reporting HGT research. The Human Genome Project paper, which was written by a who's who of leaders in genomics research, claimed to have strong evidence for a substantial amount of HGT in the human lineage. That claim was ultimately rejected, not because it was unfashionable or because it threatened corporate interests, but because it was wrong. It's turns out to be quite easy to find spurious evidence for HGT. That's why many geneticists are quite skeptical about HGT claims: they may well be wrong. Even so, extensive HGT in bacteria is now universally accepted. All it took was strong evidence.

 

[whois]

1) I cannot imagine how the above would provide the slightest motivation for GMO companies to suppress this type of research.
2) GMO companies have nothing to do with funding the vast majority of genomics research, anyway. Almost all of it is funded by the government.
3) "A valid hypothesis once faced opposition, therefore my idea is true because it faces opposition" is not a very persuasive argument.
4) There is, in fact, not the slightest opposition to funding or reporting HGT research. The Human Genome Project paper, which was written by a who's who of leaders in genomics research, claimed to have strong evidence for a substantial amount of HGT in the human lineage. That claim was ultimately rejected, not because it was unfashionable or because it threatened corporate interests, but because it was wrong. It's turns out to be quite easy to find spurious evidence for HGT. That's why many geneticists are quite skeptical about HGT claims: they may well be wrong. Even so, extensive HGT in bacteria is now universally accepted. All it took was strong evidence.

i honestly believe this post of yours was made in desperation, without the slightest regard to what you are saying.
unbelievable.

 

[USincognito]

i honestly believe this post of yours was made in desperation, without the slightest regard to what you are saying.
unbelievable.

 

[whois]

scripts and flash are blocked from my browser.

 

[lasthero]

i honestly believe this post of yours was made in desperation, without the slightest regard to what you are saying.
unbelievable.

I honestly believe this post of yours was made in desperation, without the slightest regard to what you are saying.

Unbelievable.

 

[sfs]

Does this one give any implication to the creation/evolution problem?
Easy, I just want to know any possible implication to you. No evidence is needed.

It has no implication for me. Either with or without horizontal gene transfer, common descent is simply a fact about the history of life on Earth. I introduced the paper because HGT keeps being raised by poster "whois". Why exactly is unclear to me, since I don't recall ever seeing the poster explain its relevance to creationism or the validity of evolution.

 

[sfs]

I note that the authors of this paper promote thoroughly non-Darwinian mechanisms, mechanisms that were not dreamed of by the founders of the Modern Synthesis. They accept widespread HGT among prokaryotes, and large scale transfer of bacterial genes into eukaryotes through endosymbiosis. And yet somehow the tottering edifice of Darwinian evolution has failed to collapse.

 

[Willtor]

It has no implication for me. Either with or without horizontal gene transfer, common descent is simply a fact about the history of life on Earth. I introduced the paper because HGT keeps being raised by poster "whois". Why exactly is unclear to me, since I don't recall ever seeing the poster explain its relevance to creationism or the validity of evolution.

Yeah, it's worth repeating that HGT is already observed in prokaryotes. If it were discovered that it happened between eukaryotes, too, that would be _really_ surprising, but it doesn't change anything in this subforum.

 

[DogmaHunter]

i gave one possibility in post 5 for HGT.
as far as barbara is concerned, there is little doubt her research, and her, was ridiculed, even to the point where she quit publishing.
i would guess her research didn't fit into the darwinist paradigm, so they tried to bury it.
there's your "peer review" for ya.

Yes, yes.... "they" and "them" are the evil overlords of any and all publications in science and it's a conspiracy.... A conspiracy I tell you!!!

I always knew "they" were upto something!!!

 

[Shemjaza]

It has no implication for me. Either with or without horizontal gene transfer, common descent is simply a fact about the history of life on Earth. I introduced the paper because HGT keeps being raised by poster "whois". Why exactly is unclear to me, since I don't recall ever seeing the poster explain its relevance to creationism or the validity of evolution.

whois isn't a garden variety creationist. I think he has a "Universe is eternal, life is eternal" kind of belief system.

(I mean no offense if I've misread you @whois this is just the impression I've gleaned from your references. I would very much appreciate you being more open about your beliefs as the HGT and Koonin references have not been creating productive or interesting threads or discussions.)