A Ring of Life

  • #26
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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]
 
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  • #27
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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.)
 
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  • #28
Buzz Bloom
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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
 
  • #29
Ygggdrasil
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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.
 
  • #30
Ygggdrasil
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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 occured 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.
 
  • #31
Buzz Bloom
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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
 
  • #32
Ygggdrasil
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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.
 
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  • #33
Buzz Bloom
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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
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:
For lab details, including a video of the 2011 Darwin Wallace Medal see:
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 [Broken]95.full
http://schaechter.asmblog.org/schaechter/2012/09/begetting-the-eukarya-an-un [Broken]expected-light.html
http://courses.missouristate.edu/chrisbarnhart/bio121/readings/Zimmer%20Orig [Broken]in%20of%20Eukaryotes.pdf
http://blogs.sciencemag.org/cgi-bin/mt/mt-search.cgi?tag=eocyte&IncludeBlogs [Broken]=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 [Broken]​

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:

Regards,
Buzz
 
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