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A Big Problem for Common Descent: Hundreds of "Active 'Foreign' Genes" Don't Fit the Standard Evolutionary Phylogeny

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A new paper in Genome Biology, "Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes," reports the discovery of many genes that do not fit the standard evolutionary phylogeny. Science Daily states:

Many animals, including humans, acquired essential 'foreign' genes from microorganisms co-habiting their environment in ancient times, according to research published in the open access journal Genome Biology. The study challenges conventional views that animal evolution relies solely on genes passed down through ancestral lines, suggesting that, at least in some lineages, the process is still ongoing.

The transfer of genes between organisms living in the same environment is known as horizontal gene transfer (HGT). It is well known in single-celled organisms and thought to be an important process that explains how quickly bacteria evolve, for example, resistance to antibiotics.

Whenever you hear "horizontal gene transfer" invoked in a context like this, what that really means is that biologists have uncovered genetic data sharply at variance with the standard evolutionary phylogenetic tree. So just how prevalent is "horizontal gene transfer" are genes that don't fit the standard evolutionary phylogeny? According to the Science Daily piece, they're very prevalent:
Lead author Alastair Crisp from the University of Cambridge, UK, said: "This is the first study to show how widely horizontal gene transfer (HGT) occurs in animals, including humans, giving rise to tens or hundreds of active 'foreign' genes. Surprisingly, far from being a rare occurrence, it appears that HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing, meaning that we may need to re-evaluate how we think about evolution."

Essentially, they take a gene, sequence it, and then try to match the gene to other species thought to be closely related. If the gene doesn't align with genes from closely related species, they assume it's of "foreign origin." They presume that this means there was horizontal gene transfer. However, in reality all the raw data really shows is a gene that appears in a location entirely incongruent with what we'd expect from common descent. Science Daily again:

The researchers studied the genomes of 12 species of Drosophila or fruit fly, four species of nematode worm, and 10 species of primate, including humans. They calculated how well each of their genes aligns to similar genes in other species to estimate how likely they were to be foreign in origin. By comparing with other groups of species, they were able to estimate how long ago the genes were likely to have been acquired.
Indeed, using these methods "they confirmed 17 previously reported genes acquired from HGT, and identified 128 additional foreign genes in the human genome that have not previously been reported." These "foreign genes in the human genome" had all kinds of functions:
Some of those genes were involved in lipid metabolism, including the breakdown of fatty acids and the formation of glycolipids. Others were involved in immune responses, including the inflammatory response, immune cell signalling, and antimicrobial responses, while further gene categories include amino-acid metabolism, protein modification and antioxidant activities.
The technical paper tries to explain this data through HGT:
The acquisition of genes from an organism other than a direct ancestor (that is, horizontal gene transfer (HGT) also called lateral gene transfer) is well known in bacteria and unicellular eukaryotes, where it plays an important role in evolution, with recent estimates suggesting that on average 81% of prokaryotic genes have been involved in HGT at some point. However, relatively few cases have been documented in multicellular organisms.

(Alastair Crisp, Chiara Boschetti, Malcolm Perry, Alan Tunnacliffe, Gos Micklem, "Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes," Genome Biology, 16 (1) (2015).)

But what does it mean to "document" HGT in a multicellular organism? For them, again, it simply means finding a gene that contradicts the phylogeny. They don't actually demonstrate that the gene arose by HGT. They just find a gene that seems more similar to one in another very different type of organism (like bacteria, protists, or fungi) than to more closely related organisms. Then they assume it got there by HGT.

Under their evolutionary mindset, such severe phylogenetic conflict is not taken as evidence that something is wrong with the hypothesis of common ancestry. Rather, it is taken as evidence of HGT. An article in Philosophical Transactions of the Royal Society B admits this reasoning explicitly:

In the phylogenetic approach, each instance of topological discordance between a gene tree and a trusted reference tree is taken as a prima facie instance of LGT. Discordance can be found throughout the entire range of nodal depths within these trees, from recent (genera, species) to older, presumably reflecting a commerce in genetic material that has been ongoing since pre-genomic times (Woese 2000). Viewed in this way, every genome has LGT in its ancestry.

(Mark A. Ragan and Robert G. Beiko, "Lateral genetic transfer: open issues," Philosophical Transactions of the Royal Society B, 364 (2009): 2241-2251.)

Indeed, UC Davis microbiologist and molecular systematist Jonathan Eisen critiqued this paper, noting:
Many researchers show evidence that is consistent with the occurence of HGT (which they did here) but few actually explicitly test alternative hypotheses such as gene loss, bad alignments, convergence, divergence, contamination, random noise, and more. I think their work is certainly interesting, but they just have not tested all of these alternatives.
In addition to the options Eisen lists, another possible alternative hypothesis is that this evidence simply reflects the fact that common descent is not correct. In any case, as Prof. Eisen correctly points out, the authors of the study just assume that phylogenetically incongruent data reflects HGT, not considering other possible alternative explanations.

The Genome Biology paper concludes:

Although observed rates of acquisition of horizontally transferred genes in eukaryotes are generally lower than in prokaryotes, it appears that, far from being a rare occurrence, HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing in most lineages. Between tens and hundreds of foreign genes are expressed in all the animals we surveyed, including humans.
Certainly the authors mean what they say, but this statement can also be understood in a very different manner. They say "HGT" or "foreign genes," but at base all that really means is "genes that conflict with the phylogeny." Taken that way, the case against common descent is compelling.

Image: � vitstudio / Dollar Photo Club.