How Does Horizontal Gene Transfer Shape the Tree of Life?

[Ygggdrasil]

Since the time of Darwin, biologists have looked at the history of life as a tree showing how the common ancestor of all life gave rise to all extant species. However, as we have learned more about biology, we've found that organisms do not inherit genetic information from only their direct ancestors, but many organisms have also obtained genes through horizontal gene transfer, in which distantly related organism can swap genetic information.

Horizonal gene transfer has been important in many evolutionary events, including the evolution of eukaryotes, the domain of life that includes plants, animals, and all other multicellular life. Eukaryotes evolved from a type of archaea called an eocyte (whose name means "dawn cell") which took up a some bacteria through a process called endosymbiosis. Thus, eukaryotes are not a separate branch of the evolutionary tree, but rather the point at which two branches of the tree of life fuse together.

In a recent review discussing the evolution of eukaryotes, I found this figure that I'd like to share with you all. Instead of showing the typical evolutionary tree, the author draws the "tree" of life as a series of rings in order to highlight how eukaryotes (along with many other types of species) are the product of both horizontal and vertical gene transfer:

 

[atyy]

The diagram still shows only a single root of life. Do you have any thoughts on whether that may become a more nuanced concept, just as the notion of "tree of life"?

 

[Buzz Bloom]

I was unable to find "karyota" searching the internet. Apparently it is an alternate term for "eukaryote". Can anyone confirm this or explain a distinction?

 

[Ygggdrasil]

The diagram still shows only a single root of life. Do you have any thoughts on whether that may become a more nuanced concept, just as the notion of "tree of life"?

There is fairly strong evidence for a single root of life (i.e. that all extant life on Earth shares a common ancestor). There are many lines of evidence pointing to common descent, such as the conservation of ribosome structures, sequence and function between organisms, the universality of the genetic code, and the fact that all life uses primarily L-amino acids and D-sugars. An analysis of current genetic evidence also supports common descent.

There were very likely many independent origins of life, but only one of these independent lines has survived to the present day. However, it may be the case that the LUCA (last universal common ancestor) retained some elements of extinct lineages through horizontal gene transfer. Of course, there are still plenty of undiscovered species on Earth, so there is always the possibility of finding "alien" life, derived from an independent origin of life, hidden somewhere on Earth.

I was unable to find "karyota" searching the internet. Apparently it is an alternate term for "eukaryote". Can anyone confirm this or explain a distinction?

Karyota is a term that seems to have been defined by the author of the review article in which I found the figure:

The eocytes, formally the Eocyta (‘dawn cells'), and the eukaryotes are sister taxa within the eukaryotic informational gene flow as shown in the upper right part of figure 2. Together the eocytes, the eukaryotes and their last common ancestor form the taxonomic group known as the Karyota [38], or the karyotes informally.

The reference is to Simonson AB, Servin JA, Skophammer RG, Herbold CW, Rivera MC, Lake JA. 2005 Decoding the genomic tree of life. Proc. Natl Acad. Sci. USA 102, 6608–6613. (doi:10.1073/pnas.0501996102)

 

[Buzz Bloom]

Karyota is a term that seems to have been defined by the author of the review article in which I found the figure:

Hi Ygggdrasil:

Thanks for your reply to my question. Your cited article looks quite interesting.

Regards,
Buzz

 

[DiracPool]

There is fairly strong evidence for a single root of life (i.e. that all extant life on Earth shares a common ancestor). There are many lines of evidence pointing to common descent, such as the conservation of ribosome structures, sequence and function between organisms, the universality of the genetic code, and the fact that all life uses primarily L-amino acids and D-sugars. An analysis of current genetic evidence also supports common descent.

Another important factor is the conservation of neurotransmitters. I think most of the primary neurotransmitters such as the mono-amines (dopamine, serotonin, and norepinephrine) can be traced back and found in even the most ancient prokaryotes:

http://www.hindawi.com/journals/scientifica/2013/361073/

"To date, the majority of microbial endocrinology investigations have focused on the interaction of bacteria with stress-associated biochemicals, such as the catecholamine fight and flight hormones adrenaline, noradrenaline, and dopamine ."

 

[atyy]

There is fairly strong evidence for a single root of life (i.e. that all extant life on Earth shares a common ancestor). There are many lines of evidence pointing to common descent, such as the conservation of ribosome structures, sequence and function between organisms, the universality of the genetic code, and the fact that all life uses primarily L-amino acids and D-sugars. An analysis of current genetic evidence also supports common descent.

There were very likely many independent origins of life, but only one of these independent lines has survived to the present day. However, it may be the case that the LUCA (last universal common ancestor) retained some elements of extinct lineages through horizontal gene transfer. Of course, there are still plenty of undiscovered species on Earth, so there is always the possibility of finding "alien" life, derived from an independent origin of life, hidden somewhere on Earth.

Thanks, I was wondering whether the many independent origins was still plausible after the Theobald paper. It's interesting that you still think it likely. If there was extensive horizontal gene transfer among the independent origins, then in a way, rather than saying only one origin has survived, presumably one could also say that many independent origins have survived? (For simplicity, let's assume current genetic evidence and no discoveries of still surviving "alien" life.) Of course, that's a continuum of possibilities, but is it still open whether we are "closer" (in some appropriate sense) to one end of the continuum than the other (single origin survived vs all origins survived). Theobald seems to leave both possibilities open, but doesn't indicate their relative likelihoods: "If life began multiple times, UCA requires a ‘bottleneck’ in evolution in which descendants of only one of the independent origins have survived exclusively until the present (and the rest have become extinct), or, multiple populations with independent, separate origins convergently gained the ability to exchange essential genetic material (in effect, to become one species). All of the models examined here are compatible with multiple origins in both the above schemes, and therefore the tests reported here are designed to discriminate specifically between UCA and multiple ancestry, rather than between single and multiple origins of life."

 

[mfb]

Independent of the option of multiple origins, LUCA lead to the extinction of everything else (apart from possible horizontal gene transfer) related to it. It is at least plausible that it could have lead to the extinction of different origins of life as well. Something like the genetic code and its current translation to amino acids could have been such a powerful development that other life didn't have a chance.

 

[atyy]

Independent of the option of multiple origins, LUCA lead to the extinction of everything else (apart from possible horizontal gene transfer) related to it. It is at least plausible that it could have lead to the extinction of different origins of life as well. Something like
the genetic code and its current translation to amino acids could have been such a powerful development that other life didn't have a chance.

I guess one should distinguish two different ideas of "lines". One of these is the idea of the lineage in the "Darwinian" sense (it's a bad term, but let's just use it as convenient name, I borrow it from similar usage in the Woese article below like "Darwinian threshold"), the other is the other of lines that can be traced from "independent origins". It does indeed seem that once the idea of a Darwinian line is possible, then all known life comes from a single Darwinian line.

But was there a time before the first Darwinian line had formed, but after multiple independent origins, in which eg. that the genetic code had not yet settled down, and was itself evolving? Eg. what is the status of ideas like

http://www.ncbi.nlm.nih.gov/pubmed/19117371
Koonin and Novozhilov, Origin and evolution of the genetic code: the universal enigma.

http://www.pnas.org/content/99/13/8742
Woese, On the Evolution of Cells

 

[Ygggdrasil]

Thanks, I was wondering whether the many independent origins was still plausible after the Theobald paper. It's interesting that you still think it likely. If there was extensive horizontal gene transfer among the independent origins, then in a way, rather than saying only one origin has survived, presumably one could also say that many independent origins have survived? (For simplicity, let's assume current genetic evidence and no discoveries of still surviving "alien" life.) Of course, that's a continuum of possibilities, but is it still open whether we are "closer" (in some appropriate sense) to one end of the continuum than the other (single origin survived vs all origins survived). Theobald seems to leave both possibilities open, but doesn't indicate their relative likelihoods: "If life began multiple times, UCA requires a ‘bottleneck’ in evolution in which descendants of only one of the independent origins have survived exclusively until the present (and the rest have become extinct), or, multiple populations with independent, separate origins convergently gained the ability to exchange essential genetic material (in effect, to become one species). All of the models examined here are compatible with multiple origins in both the above schemes, and therefore the tests reported here are designed to discriminate specifically between UCA and multiple ancestry, rather than between single and multiple origins of life."

I'd agree that the http://www.nature.com/nature/journal/v465/n7295/full/nature09014.html cannot rule out the possibility that other independent lineages of life arose but have gone extinct. It's unclear whether horizontal gene transfer could occur between independent lineages as they may have had very different ways of encoding genetic information (for example, it's hard to imagine how information could transfer between organisms with different genetic codes). One could imagine a scenario, however, where maybe one form of life led to the abundance of L-amino acids and the current LUCA evolved in such an environment, eventually outcompeting all other forms of life. Here, the preference for L-amino acids originated not with the LUCA, but with other, independent forms of life predating the LUCA.

It's difficult to estimate the likelihood of whether there were multiple origins of life on Earth. One could argue that for life to have evolved, abiogenesis must not be an extremely improbable event, which would suggest that life could have arisen multiple times. However, it could also be the case that the first "type" of life to arise could have been very successful and filled all the niches on Earth, precluding further abiogenesis events. It is likely a difficult question to answer as evidence would be very difficult to find.

But was there a time before the first Darwinian line had formed, but after multiple independent origins, in which eg. that the genetic code had not yet settled down, and was itself evolving? Eg. what is the status of ideas like

http://www.ncbi.nlm.nih.gov/pubmed/19117371
Koonin and Novozhilov, Origin and evolution of the genetic code: the universal enigma.

http://www.pnas.org/content/99/13/8742
Woese, On the Evolution of Cells

Given that the genetic code is "one in a million," that is it seems optimized to be robust against mutation and error, it's almost certain that there was a point during which organisms with different genetic codes were competing against each other (these organisms, however, would likely have shared a common ancestor as they would have all been derived from the ancestor of the ribosome).

With regard to Woese's points about HGT, differences in genetic code would seem to limit the opportunities for HGT prior to the establishment of the genetic code. Indeed, even in today's world with a (very near) universal genetic code, many other factors constrain HGT:

Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer (HGT) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. HGT among prokaryotes is not random, however. Some genes (informational genes) are more difficult to transfer than others (operational genes). Furthermore, environmental, metabolic, and genetic differences among organisms restrict HGT, so that prokaryotes preferentially share genes with other prokaryotes having properties in common, including genome size, genome G+C composition, carbon utilization, oxygen utilization/sensitivity, and temperature optima, further complicating attempts to reconstruct the tree of life.

Simonson AB, Servin JA, Skophammer RG, Herbold CW, Rivera MC, Lake JA. 2005 Decoding the genomic tree of life. Proc. Natl Acad. Sci. USA 102, 6608–6613. (doi:10.1073/pnas.0501996102)

 

[jerromyjon]

It's difficult to estimate the likelihood of whether there were multiple origins of life on Earth.

That's the tough part I believe. Perhaps multiple rings overlap, each ring containing not only genetic signatures but environmental repercussions which might have effected other rings...

As the rings of a tree, the core had only mud to grow from and each successive ring has the previous rings machinery and residual environment to evolve from.

 

[Torbjorn_L]

When the average rate of vertical gene transfer is 1/day (say) and the average rate of horizontal gene transfer is 1/4 billion years - at a ratio of 10^-12 - is it really useful to describe the resulting web as a set of "rings"? It is rather a fuzzy tree, as rRNA phylogenies show.

As an example, the evolution of eukaryotes seems to have involved very little genetic inheritance from the first parasitic, later endosymbiont Rickettsiale. [ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110685 ] The "eocyta" tree is wrong too, I think, eukaryotes split from within still living archaea, as a sister lineage to Lokiarchaea. [ http://www.nature.com/nature/journal/v521/n7551/abs/nature14447.html ]

"There were very likely many independent origins of life, but only one of these independent lines has survived to the present day."

Raup's and Valentine's model is quirky, if one assumes a single origin it gives back a probability of 1 for monophyly (as it should) but the life/death context drops out. It doesn't seem to have anything to say on the UCA lineage.

Do we also think there were many endosymbiont analogies to the eukaryotes, but only one survivor? I have a feeling we are missing something. Life seems to got started as soon as the conditions allowed (oceans before 4.3 Ga bp http://www.minsocam.org/msa/ammin/toc/2015/open_access/AM100P1355.pdf , first dated lineage splits before 4.2 Ga bp http://www.timetree.org/search/pairwise/2/2157? , first fossils before 4.1 Ga bp http://www.pnas.org/content/early/2015/10/14/1517557112.full.pdf), same for eukaryotes after the GOE. Yet in both cases we don't see any signs of extinct competitors. Ecological lock in effects?

 

[Monsterboy]

Thus, eukaryotes are not a separate branch of the evolutionary tree, but rather the point at which two branches of the tree of life fuse together.

I read that Neanderthals and Humans interbred in Europe ,so is this another case of two branches fusing together ?although this was due to sexual reproduction and not HGT.

 

[Ygggdrasil]

When the average rate of vertical gene transfer is 1/day (say) and the average rate of horizontal gene transfer is 1/4 billion years - at a ratio of 10^-12 - is it really useful to describe the resulting web as a set of "rings"? It is rather a fuzzy tree, as rRNA phylogenies show.

Where do you get these rate estimate? Anyway, while HGT may be more infrequent than vertical transmission, if HGT produces organisms with increased fitness (as in the case of the events that produced eukaryotes), it can have a big impact on evolution. Also, rRNAs are primarily transmitted vertically, so rRNA phylogenies won't show HGT. It's only when you compare the phylogenies from looking at rRNAs with the phylogenies of other genes that you see evidence of HGT.

As an example, the evolution of eukaryotes seems to have involved very little genetic inheritance from the first parasitic, later endosymbiont Rickettsiale. [ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110685 ]

If you're talking about the Rickettsiale that eventually became the mitochondrion, there was extensive HGT between that organism and eukaryotes. From the paper you cite, "Starting with 427,186 genes from 30 eukaryotic genomes representing a broad range of phylogenetic diversity, we identified 4,459 genes belonging to 394 families as mitochondria-derived nuclear genes." In other words, they identified >4,000 genes residing in the nucleus of all eukaryotes that were originally derived from alphaproteobacteria. However, other than the genes received from the endosymbiotic bacteria that became the chloroplasts and mitochondria, HGT between prokaryotes and eukaryotes is more limited (http://rstb.royalsocietypublishing.org/content/370/1678/20140324d).

The "eocyta" tree is wrong too, I think, eukaryotes split from within still living archaea, as a sister lineage to Lokiarchaea. [ http://www.nature.com/nature/journal/v521/n7551/abs/nature14447.html ]

No, the lokiarchaea finding confirms the eocyte hypothesis. From the paper you cite: "[The eukaryotic] lineage might either descend from a common ancestor shared with Archaea (following Woese’s classical three-domains-of-life treehttp://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref5), or have emerged from within the archaeal domain (so-called archaeal host or eocyte-like scenarioshttp://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref1, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref14, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref15, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref16, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref17). Recent phylogenetic analyses of universal protein data sets have provided increasing support for models in which eukaryotes emerge as sister to or from within the archaeal ‘TACK’ superphylumhttp://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref18, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref19, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref20, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref21, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref22, a clade originally comprising the archaeal phyla Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeotahttp://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref23. [...]Here we describe the discovery of a new archaeal lineage related to the TACK superphylum that represents the nearest relative of eukaryotes in phylogenomic analyses, and intriguingly, its genome encodes many eukaryote-specific features, providing a unique insight in the emergence of cellular complexity in eukaryotes." In other words, Lokiarchaea represent a close relative of the the hypothesized eocyte archaeum that eventually became eukaryotes.

 

[Ygggdrasil]

I read that Neanderthals and Humans interbred in Europe ,so is this another case of two branches fusing together ?although this was due to sexual reproduction and not HGT.

That's certainly a possibility. Biologists have observed examples of despeciation—species disappearing due to hybridization with related species. A recent example was observed with Darwin's finches in the Gallapagos, where it seems one species of finch may have gone "extinct" though interbreeding with other species:
http://www.nature.com/nature/journal/v507/n7491/full/507178b.html
http://www.nature.com/scitable/blog/accumulating-glitches/speciation_in_reverse

 

[jerromyjon]

There is also a recent article I read regarding a much more lucrative mRNA from the father's sperm which can cause immediate genetic benefits in the offspring... There is monstrous amount of genetic information we really don't know much about yet... we certainly need a more dynamic system to get a handle on it all.

 

[Pythagorean]

Re: Tobjorn's rate argument.

There may be times in early evolutionary history when horizontal transfer and endosymbiosis were significant determinants of evolutionary path, does that really have to do with rate or is it more to do with chance and environmental context?

But I agree with Yggg that it's important to know where those rates come from to really know what you're saying.

 

[Chronos]

Viruses are the grand masters of genetic manipulation, so it should come as no surprise they play a significant role in the gene pool. It is a likely explanation for why the plague was so virulent in the middle ages.

 

[hagar]

I was unable to find "karyota" searching the internet. Apparently it is an alternate term for "eukaryote". Can anyone confirm this or explain a distinction?

A general term for nucleated cells, as opposed to akaryota, or non-nucleated cells

 

[Greg Bernhardt]

Where does fungai fit into this model?

 

[Ygggdrasil]

Viruses are the grand masters of genetic manipulation, so it should come as no surprise they play a significant role in the gene pool. It is a likely explanation for why the plague was so virulent in the middle ages.

Where exactly viruses fit in the picture is still a question researchers are working on. There are some hypotheses that the recently discovered "giant viruses" could be modern remnants of the origin of life, though this hypothesis is controversial (and probably wrong).

Where does fungai fit into this model?

Fungi are eukaryotes that are a sister kingdom to animals. In terms of the main kingdoms of eukaryotes that we think of—plants, animals, and fungi—animals and fungi are more closely related to each other than they are to plants. Here's a nice figure illustrating the evolutionary relationships among eukaryotes:

Animals and fungi are both classified together in the purple branch as opisthokonta. (img source)

 

[hagar]

Where does fungai fit into this model?

Bernardino Fungai (1460–1516) was an Italian painter. :-)

 

[AgentSmith]

I'm not a biologist, much less an evolutionary biologist, but if there were multiple lines of origins, wouldn't there be some empirical evidence of this, even fossil microbiota?
Or something a little "alien" in Archean DNA? If there is no empirical evidence, then this is speculation, albeit very interesting.

 

[Buzz Bloom]

If there is no empirical evidence, then this is speculation

Hi AgentSmith:

There seems to be some empirical evidence, but I do not have the research skill to locate many. Here is one from 2014:

http://gbe.oxfordjournals.org/content/6/3/474​

that I was able to track down.

The link to the review article from 2014

http://rstb.royalsocietypublishing.org/content/370/1678/20140321​

in post #1 of this thread also has a large list of references.

Regards,
Buzz

 

[Torbjorn_L]

Where do you get these rate estimate?

My reference library is in shambles as I write this, but I think it was an old estimate of Koonin. I found a paper of him saying much the same thing based on paralog acquitions/displacements, i.e. on average ~ 100 % of genes have undergone a HGT event during 4 billion years. [ http://www.ncbi.nlm.nih.gov/books/NBK2228/ ; Table 4.]

And of course we have Theobald's result that VGT is much more important than HGT. [ file:///C:/Users/Medborgarskolan/Downloads/Theobald_2010_Nature_all.pdf ]

Anyway, while HGT may be more infrequent than vertical transmission, if HGT produces organisms with increased fitness (as in the case of the events that produced eukaryotes), it can have a big impact on evolution. Also, rRNAs are primarily transmitted vertically, so rRNA phylogenies won't show HGT. It's only when you compare the phylogenies from looking at rRNAs with the phylogenies of other genes that you see evidence of HGT.

Agreed, HGT has been important, say in mitochondria or the viral genes that enables some mammals to have a tight placenta/fetus implantation.

But for establishing organismal lineages, their overall "identity", as opposed to gene lineages, their traits, we are interested in rRNA. Theobald's result is then relevant.

No, the lokiarchaea finding confirms the eocyte hypothesis. From the paper you cite: "[The eukaryotic] lineage might either descend from a common ancestor shared with Archaea (following Woese’s classical three-domains-of-life tree5), or have emerged from within the archaeal domain (so-called archaeal host or eocyte-like scenarios1, 14, 15, 16, 17). Recent phylogenetic analyses of universal protein data sets have provided increasing support for models in which eukaryotes emerge as sister to or from within the archaeal ‘TACK’ superphylum18, 19, 20, 21, 22, a clade originally comprising the archaeal phyla Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota23. [...]Here we describe the discovery of a new archaeal lineage related to the TACK superphylum that represents the nearest relative of eukaryotes in phylogenomic analyses, and intriguingly, its genome encodes many eukaryote-specific features, providing a unique insight in the emergence of cellular complexity in eukaryotes." In other words, Lokiarchaea represent a close relative of the the hypothesized eocyte archaeum that eventually became eukaryotes.

Agreed, I didn't object to the eocyte theory.

I objected to the topological description inherent in the diagram, supposedly derived from "eukaryotes are not a separate branch of the evolutionary tree, but rather the point at which two branches of the tree of life fuse together."

Since we can identify a "host" from a sister lineage to Lokiarchaea, we reject that there is an identity loss during fusion. We track the rRNA and the coding sequences. Lokiarchaea had 5381 CDS @ 92 % coverage, so perhaps 5850 genes. That means the composite lineage has ~ 4459/5850 or ~ 40 % bacterial core genes at the stem.

The phylogenetic web topology is still well approximated by a tree.
[ http://www.nature.com/nature/journal/v521/n7551/fig_tab/nature14522_F1.html ]

 

[Torbjorn_L]

I read that Neanderthals and Humans interbred in Europe ,so is this another case of two branches fusing together ?although this was due to sexual reproduction and not HGT.

That's certainly a possibility. Biologists have observed examples of despeciation—species disappearing due to hybridization with related species. A recent example was observed with Darwin's finches in the Gallapagos, where it seems one species of finch may have gone "extinct" though interbreeding with other species:
http://www.nature.com/nature/journal/v507/n7491/full/507178b.html
http://www.nature.com/scitable/blog/accumulating-glitches/speciation_in_reverse

I like what paleanthropologist John Hawks and speciation specialist Jerry Coyne writes on this. They agree that anatomically modern humans, Neanderthals and Denisovans are subspecies, so we are today a hardy hybrid rather than a puerile purebred. [From the recent sequencing of 4 kyrs old african we can now see that there was a backflow from west Asia of agrarians ~ 6 kyrs ago all the way sub-south Sahara, bringing back Neanderthal genes to almost every living african.]

"So what about “modern” H. sapiens, Neandertals, and Denisovans? Clearly they hybridized, and some of the hybrids were fertile, for traces of Denisovan and Neandertal genes remain in our genomes. On this basis, anthropologist John Hawks deems Neandertals, modern humans, and Denisovans members of the same species; Gibbons quotes him as saying “They mated with each other. We’ll call them the same species.” (I hope by “mating” he means “mated and produced fertile offspring”.)

But a little bit of gene flow isn’t enough to convince most of us that these groups were conspecific. On that basis, the Darwin’s finches would be deemed conspecific, but nobody does that. The question is whether that gene flow reflected lack of opportunity for mating (in which case they might be the same species), or pervasive hybridization (between, say, modern humans and Neandertals) but only weak viability or fertility of the “hybrids” (in which case they’d be different species). We will probably never know the answer to this.

Does this make the species status of these three groups purely arbitrary? I don’t think so. What we can do is get a “yardstick” by seeing whether other species of primates that were separated for as long as Neandertals, Denisovans, and modern humans—roughly half a million years—have evolved into reproductively isolated groups. I’m not sure what the answer is (it’s probably sitting there somewhere in the literature), but I’d guess that they wouldn’t be separate species, especially because humans have much longer generation times than other primates and so would speciate even more slowly. If it were my call, I’d agree with Hawks (but for somewhat different reasons), calling Neandertals, Denisovans, and modern humans all members of Homo sapiens.

But as for the hobbits, H. floresiensis, I’d stick with calling them a different species. They diverged from modern H. sapiens much further in the past, although they may have been contemporaneous with us."

[ https://whyevolutionistrue.wordpress.com/2011/01/28/how-many-species-of-humans-were-contemporaries/ ; my bold]

 

[Torbjorn_L]

Where exactly viruses fit in the picture is still a question researchers are working on. There are some hypotheses that the recently discovered "giant viruses" could be modern remnants of the origin of life, though this hypothesis is controversial (and probably wrong).

A more alluring hypothesis is that the main lineages of viruses have ancestors in stem lineages to cellular life. I.e. +ssRNA, retrovirus and some dsDNA virus could have split off from the stem of our RNA/protein -> DNA/protein cellular universal ancestor lineage, predicting our shared genetic code. They would split off from successive evolutionary stages - RNA/protein, RNA/DNA/protein and DNA/protein - and be among our best evidence for early evolution. [It is one of Koonin's papers I think. As noted before, I don't have my refrence library integrated right now.]

Similarly giant viruses could be among, and informative of, the eukaryote stem lineages. They have our aminoacyl tRNA synthases, but they lack any mitochondrial derived genes IIRC. [Unsubstantiated memory, can't check, YMMV.] As per above they ought to have a 40/60 mix if they split off after the mitochondrial endosymbiosis.

The above would still imply parasitic simplification, an extreme one some cases. Very timely, here is a new record holder:

"Not only has the parasitic micro jellyfish evolved a stripped-down body plan of just a few cells, but via data generated at the KU Medical Center's Genome Sequencing Facility researchers also found the myxozoan genome was drastically simplified.

"These were 20 to 40 times smaller than average jellyfish genomes," Cartwright said. "It's one of the smallest animal genomes ever reported. It only has about 20 million base pairs, whereas the average Cnidarian has over 300 million. These are tiny little genomes by comparison.""

""Their biology was well-known, but not their evolutionary origins," she said. "They're microscopic, only a few cells measuring 10 to 20 microns. Some people originally thought they were single-celled organisms. But when their DNA was sequenced, researchers started to surmise they were animals—just really weird ones."

Indeed, Cartwright said traits scientists understood as vital for animal development are absent in Myxozoa.

"Hox genes are one example, which are important to development of all animals, and these lack them," she said."

[ http://phys.org/news/2015-11-sequence-genomes-parasite-micro-jellyfish.html#jCp ; my bold]

If 0.5 - 1 Gyrs of parasite evolution can reduce a genome 20 - 40 times, reducing an early UCA sister lineage of 1000 - 4000 genes to a handful is doable over 4 Gyrs. (Admittedly I am extrapolating from an eukaryote genome with lots of junk to a prokaryote derived lineage with none.)

 

[Buzz Bloom]

I’d stick with calling them a different species.

Hi Torbjorn:

Can you cite a reference with a contemporary definition of animal species. I seem to remember from undergraduate biology many decades ago that the definition is different that that used for plant species. I also understand from more recent readings that in phylogenetic analyses, the "species" concept has been replaced by "clade".

Regards,
Buzz

 

[Ygggdrasil]

I objected to the topological description inherent in the diagram, supposedly derived from "eukaryotes are not a separate branch of the evolutionary tree, but rather the point at which two branches of the tree of life fuse together."

Since we can identify a "host" from a sister lineage to Lokiarchaea, we reject that there is an identity loss during fusion. We track the rRNA and the coding sequences. Lokiarchaea had 5381 CDS @ 92 % coverage, so perhaps 5850 genes. That means the composite lineage has ~ 4459/5850 or ~ 40 % bacterial core genes at the stem.

The phylogenetic web topology is still well approximated by a tree.
[ http://www.nature.com/nature/journal/v521/n7551/fig_tab/nature14522_F1.html ]

By the same logic, we can identify the bacterium that eventually became the mitochondrion as an alphaproteobacterium of the SAR11 clade similar to the present day Rickettsiales. While one might think the host in the endosymbiosis would provide most of the defining characteristics of the resulting eukaryotes, eukaryotic genomes are best described as a fusion of two classes of genes: informational genes (those that control the central dogma of transcription, translation and replication) from archaea and operational genes (those that control metabolism) from bacteria. In many eukaryotes, like yeast, many more genes in these eukaryotes (75%) more closely resemble their bacterial homologues than their archaeal homologues.

At this point, biologists primarily draw trees because that's what we're used to seeing, and it's much more computationally difficult to account for HGT in evolutionary studies than to rely on models that consider only VGT. A tree approximates evolutionary history on Earth quite well, but in order to capture many important events in evolution, we need to stop looking only at the trees and see the broader forest of events occurring in evolution.

 

[Ygggdrasil]

My reference library is in shambles as I write this, but I think it was an old estimate of Koonin. I found a paper of him saying much the same thing based on paralog acquitions/displacements, i.e. on average ~ 100 % of genes have undergone a HGT event during 4 billion years. [ http://www.ncbi.nlm.nih.gov/books/NBK2228/ ; Table 4.]

I don't think the point of that sentence was to say that the rate of HGT is 1 per 4 billion years, but rather to say that every gene has been affected by HGT. Using this data as a rate estimate entails other problems, such as genes undergoing multiple HGT events per those 4 billion years would not be accounted for, and the fact that some genes are much more likely to undergo HGT than others, so the rate estimate is skewed toward the rate at which the slowest genes undergo HGT.

Since we're citing Koonin, he has written that "comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution." (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588523/)(emphasis mine) directly in opposition to many of your points.

The article, and the one you cite, give various examples of where HGT has occurred fairly rapidly (e.g. in the spread of antibiotic resistance). For example, he cites work on pathogenic E. coli strains and writes: "The now classic comparative genomic analysis of the enterohemorrhagic O157: H7 strain and the laboratory K12 strain of Eschersichia coli has shown that the pathogenic strain contained 1387 extra genes distributed between several strain-specific clusters (pathogenicity islands) of widely different sizes (166). Thus, up to 30% of the genes in the pathogenic strain seem to have been acquired via a relatively recent HGT. A further, detailed analysis of individual lineages of E. coli O157: H7 has demonstrated continuous HGT, apparently, contributing to the differential virulence of these isolates (167)." (emphasis mine) Thus, HGT can occur rapidly and contributes significantly to evolutionary novelty, driving phenotypic and genotypic changes in organisms, pushing evolution forward.

 

[Buzz Bloom]

In a recent review discussing the evolution of eukaryotes, I found this figure that I'd like to share with you all.

Hi @Ygggdrasil:

I have been trying to absorb the new organization shown in the figure in post #1, but I am having difficulty understanding the evolutionary lineage categories corresponding to the colors: white, orange, yellow, blue, green, and red. I get that purple represents the eukaryotes, but for the other six colors I can not find any correspnding named lineages. Can you help me?

Regards,
Buzz

 

[Ygggdrasil]

Hi @Ygggdrasil:

I have been trying to absorb the new organization shown in the figure in post #1, but I am having difficulty understanding the evolutionary lineage categories corresponding to the colors: white, orange, yellow, blue, green, and red. I get that purple represents the eukaryotes, but for the other six colors I can not find any correspnding named lineages. Can you help me?

Regards,
Buzz

That's a good question. From what I can tell, the author does not really elaborate on this in the article. I don't know enough about bacterial and archaeal evolution to answer, so if you're really interested, perhaps its worth contacting the author of the article for more information.

 

[Buzz Bloom]

Hi @Ygggdrasil:

I received permission form Prof. James Lake to post some references about this topic. He also requested that the figures from the original link

http://rstb.royalsocietypublishing.org/content/370/1678/20140321​

should be cited as being from:

Lake, JA, 2015 Eukaryotic Origins, Phil. Trans. R. Soc. B, 370, 20140321. http://dx.doi.org/10.1098/rstb.2014.0321, Vol 370, Issue 1678, 26 September 2015.​

Also, the original link should be cited as

James Lake
Distinguished Prof. MCDBiology and Human Genetics
UCLA
For our latest review on the eocyte (or two domains tree) see the recent review: Eukaryotic Origins, James A. Lake, Accepted 5 May 2015
Philosophical Transactions R. Soc. B, 370, 20140321,
http//dx.doi.org/10.1098/rstb.2014.0321.​

Here are some other references on this topic.

Latest reviews and results supporting the Eocyte tree:

http://www.npr.org/blogs/health/201...may-help-explain-how-single-cells-became-usll​

For lab details, including a video of the 2011 Darwin Wallace Medal see:

http://www.mcdb.ucla.edu/Research/Lake/
​

See additional reviews and results supporting the Eocyte Hypothesis:

http://phenomena.nationalgeographic.com/2012/12/20/redrawing-the-tree-of-life/
http://rspb.royalsocietypublishing.org/content/early/2012/10/18/rspb.2012.17 95.full
http://schaechter.asmblog.org/schaechter/2012/09/begetting-the-eukarya-an-un expected-light.html
http://courses.missouristate.edu/chrisbarnhart/bio121/readings/Zimmer%20Orig in%20of%20Eukaryotes.pdf
http://blogs.sciencemag.org/cgi-bin/mt/mt-search.cgi?tag=eocyte&IncludeBlogs =7
http://rstb.royalsocietypublishing.org/content/364/1527/2197.full.pdf
http://www.pnas.org/content/105/51/20049.full
http://www.yale.edu/ochman/Papers/Ochman_EnvMicro2009aop.pdf​

Regarding the colors in the original figure, he wrote the following:

The major pathways mentioned are photosynthesis – in green – which flows all the way to to the Plants at the top.
Phototrophy, a type of pre-photosynthesis, is shown in yellow and then it evolves into photosynthesis (again the green flow).
And last, the magenta flow goes into the eocytes (the dawn cells) and into the nucleus that is present in all eukaryotes.
These are labeled in the figure at the following url:

http://rstb.royalsocietypublishing.org/content/370/1678/20140321​

Regards,
Buzz