The frequency of splicing errors reflects the balance between selection and drift

Splice variants are very common in eukaryotes. We know that it's possible to detect dozens of different splice variants for each gene with multiple introns. In the past, these variants were thought to be examples of differential regulation by alternative spicing but we now know that most of them are due to splicing errors. Most of the variants have been removed from the sequence databases but many remain and they are annotated as examples of alternative splicing, which implies that they have a biological function.

I have blogged about splice variants many times, noting that alternative splicing is a very real phenomenon but it's probably restricted to just a small percentage of genes. Most of splice variants that remain in the databases are probably due to splicing errors. They are junk RNA [The persistent myth of alternative splicing].

The ongoing controversy over the origin of splice variants is beginning to attract attention in the scientific literature although it's fair to say that most scientists are still unaware of the controversy. They continue to believe that abundant alternative splicing is a real phenomenon and they don't realize that the data is more compatible with abundant splicing errors.

Some molecular evolution labs have become interested in the controversy and have devised tests of the two possibilities. I draw your attention to a paper that was published 18 months ago.

Are multiple transcription start sites functional or mistakes?

If you look in the various databases you'll see that most human genes have multiple transcription start sites. The evidence for the existence of these variants is solid—they exist—but it's not clear whether the minor start sites are truly functional or whether they are just due to mistakes in transcription initiation. They are included in the databases because annotators are unable to distinguish between these possibilities.

Let's look at the entry for the human triosephosphate isomerase gene (TPI1; Gene ID 7167).

The correct mRNA is NM_0003655, third from the top. (Trust me on this!). The three other variants have different transcription start sites: two of them are upstream and one is downstream of the major site. Are these variants functional or are they simply transcription initiation errors? This is the same problem that we dealt with when we looked at splice variants. In that case I concluded that most splice variants are due to splicing errors and true alternative splicing is rare.

What is the dominant view of junk DNA?

I think that about 90% of our genome is junk and I know lots of other scientists who feel the same way. I'm pretty sure that this view is not shared by the majority of scientists but I don't know whether they are convinced that most of our genome is functional or whether they just think the question is unanswerable at the present time. I suspect that the latter view is more common but I'd like to hear your opinion.

Yeast loses its introns

Baker’s yeast (Saccharomyces cerevisiae) is one of the best studied eukaryotes. Its genome is just slightly larger than the largest bacterial genome and it was the first eukaryotic genome to be sequenced (Mewes at al., 1997). It has about 7000 genes in total and 6,604 of these genes are protein-coding genes but only 280 of these genes contain introns.¹ The rest have lost their introns over the course of several hundred million years of evolution (Hooks et al., 2014).

We know that introns have been lost in yeast because the genes of related species have lots of introns. The common ancestor of all fungi undoubtedly had genes with multiple introns because the available evidence indicates that introns invaded eukarotic genes very early in the evolution of eukaryotes. The fact that most introns have been purged from the yeast genome suggests that introns are not essential for gene function. In other words, introns are mostly junk.²

What happens when twins get their DNA tested?

The Canadian Broadcastng Company (CBC) has a TV show called Marketplace that promotes itself as an advocate of consumers' rights. It has a history of testing the claims of advertisers and usually shows that these claims are misleading or false. Here's what they say on their website.

On air since 1972, Marketplace is Canada’s consumer watchdog. We get the goods to help you shop smarter and protect yourself from slick scams and misleading marketing claims. We investigate the products and services we all use every day and push companies and government for answers. And we expose the truth on stories that matter to you and your family.

Most popular Sandwalk posts of 2018

Blogging was light last year because I was busy with other things and because the popularity of blogs is declining rapidly. The most popular post, based on the number of views, garnered only 9229 views, which is more than the most popular post of 2017 but only half as much as the most popular post of 2016. The post with the most comments (53) has almost 10X fewer comments than posts from a few years ago but that's partly because more people are commenting on Facebook and because I'm restricting blog comments in various ways.

On the accuracy of Ancestry.com DNA predictions

I'm very impressed with the DNA test administered by Ancestry.com. They report that I have over 600 fourth cousins or closer but I have confirmed some even more distant relationships. See below for the most distant relationship that the DNA tests reveal.

In the vast majority of cases the people who share DNA markers with me have no family tree that's on Ancestry.com so it's impossible to say for sure whether we are related. There are often clues based on who else shares our haplotypes but unless the person reveals their name and some of their ancestors that's all I can do. I usually contact those people who could hep me sort out some unknown relationships but I rarely get a reply.

Most popular Sandwalk posts of 2017

I was looking at some of my posts from the past few years and wondered which ones were the most popular. I had previously identified the most popular post of 2016 but not the most popular ones from 2017 so here they are.

The one with the most views (7481) is a link to a video by Michio Kaku who tells us that humans have stopped evolving [Another physicist teaches us about evolution].

The one with the most comments (259) is a post about my attempts to teach a creationist about glycolysis and evolution [Trying to educate a creationist (Otangelo Grasso)].

The post that I'm most proud of is: Historical evolution is determined by chance events

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My DNA story

This is the latest update from Ancestry.com. Their algorithms are getting better and better. This corresponds very closely to what I know of my ancestors.

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Alternative splicing in the nematode C. elegans

The importance of alternative splicing is highly controversial. In the case of humans, the competing views are: (a) more than 90% of human protein-coding genes are alternatively spliced to produce multiple protein isoforms, and (b) less than 10% of human genes are alternatively spliced and most of the splice variants detected are due to splicing errors.

In addition to this fundamental difference in how to interpret the data, there's a controversy over the meaning and significance of abundant alternative splicing, assuming that it exists. The consensus view among the workers in the field is that alternative splicing is ubiquitous and it explains why humans are so complex when they have only the same number of genes as "lower" species like the nematode C. elegans. This was the view expressed by Gil Ast in a 2005 Scientific American article on "The Alternative Genome."

The persistent myth of alternative splicing

I'm convinced that widespread alternative splicing does not occur in humans or in any other species. It's true that the phenomenon exists but it's restricted to a small number of genes—probably fewer than 1000 genes in humans. Most of the unusual transcripts detected by modern technology are rare and unstable, which is consistent with the idea that they are due to splicing errors. Genome annotators have rejected almost all of those transcripts.

You can see links to my numerous posts on this topic at: Alternative splicing and the gene concept and Are splice variants functional or noise?.

The textbook view of alternative splicing

As most of you know, I'm interested in the problem of alternative splicing. I believe that the number of splice variants that have been detected is perfectly consistent with the known rate of splicing errors and that there's no significant evidence to support the claim that alternative splicing leading to the production of biologically relevant protein variants is widespread. In fact, there's plenty of evidence for the opposite view; namely, splicing errors (lack of conservation, low abundance, improbable protein predictions, inability to detect the predicted proteins).

My preferred explanation is definitely the minority view. What puzzles me is not the fact that the majority is wrong () but the fact that they completely ignore any other explanation of the data and consider the case for abundant alternative splicing to be settled.

Deflated egos and the G-value paradox

The Deflated Ego Problem refers to the fact that many scientists were very disappointed to learn we had less than 30,000 genes. Those scientists were expecting that the human genome would contain many more genes in line with their belief that humans must be genetically more complex than the "lower" animals. They should have known better since knowledgeable experts were predicting fewer than 30,000 genes and these same experts knew that humans don't need many more genes than other animals [see: Revisiting the deflated ego problem].

Disappointed scientists don't use the term "deflated ego;" instead they refer to their problem as the G-value paradox. This makes it seem like a real problem instead of just a mistaken view of evolution.

Michael Behe's third book

I'm looking forward to Michael Behe's third book, which is due to be published in February. As most of you probably know, Michael Behe is a biochemist and a former professor at Lehigh University in Scranton, Pennsylvania, USA. He's also a senior fellow at the Discovery Institute’s Center for Science & Culture—the most prominent organization pushing Intelligent Design Creationism.

This will be Behe's third book. The first one was Darwin's Black Box (1996) where he argued against evolution by suggesting that some cellular complexes (e.g. bacterial flagella) are irreducibly complex and could not possibly have evolved by natural means. His second book was The Edge of Evolution (2007) where the theme was that there are limits to evolution preventing it from accomplishing significant beneficial changes.

Latest Tango in Halifax

I've known Yana Eglit for many years. She frequently posts comments on this blog but you won't recognize her name because she uses a pseudonym.¹ Yana is a graduate student in the lab of Alastair Simpson at Dalhousie University in Halifax, Nova Scotia, Canada. A few years ago she saw some strange organisms dancing in a Petri dish.²

The microorganisms belong to the group Hemimastigophora. Yana found them in a clump of dirt she picked up while hiking near Halifax. They named the species Hemimastix kukwesjijk. The group only contains a few other species.

Hemimastigophora is one of those protist groups that have been difficult to classify and difficult to place relative to other protists. It's traditionally been given the status of a phylum but its position in the eukaryotic tree was ambiguous.

The Simpson lab, in a collaboration with Andrew Roger's group, sequenced a number of genes (transcripts) from H. kukwesjijk and another species that they recently identified (Spirenema). The datasets contained samples of about 300 genes of each species. Trees constructed with this dataset place the Hemimastigophora near the base of the eukrayotic tree as a sister group to Diaphoretices. The work was published in a recent issue of Nature (Lax, Egrit, et al., 2018).

The details of eukaryotic taxonomy and the various subdivisions needn't concern us but the important take-home lesson is that there are a huge number of protists forming diverse groups that separated more than a billion years ago. The authors claim that Hemimastigophora deserves supra-kingdom status equivalent to the other supra-kingdoms shown in the figure (modified from Figure 4 of the paper).

The root of the eukaryotic tree is controversial. It could be at positions a, b, or c, shown in the figure. According to the authors, position a is the most favored these days. Regardless of where the root is actually placed, the new positioning of Hemimastigophora adds a lot of information to the deepest parts of the eukaryotic tree and brings us closer to identifying the most primitive features of the eukaryotic cell.

I wonder how many other strange species can be found in Canadian dirt?

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Photo Credit: The photo of Yana Eglit at her microscope is from the Dalhousie University press office [Hidden in plain sight: Dal evolutionary biologists uncover a new branch on the Tree of Life]

1. Which she might accidentally reveal if she responds to this post!

2. The fact they were "dancing" gave me an excuse to use a corny title that refers to one of our favorite TV shows, "Last Tango in Halifax."

Lax, G., Eglit, Y., Eme, L., Bertrand, E. M., Roger, A. J., and Simpson, A. G. B. (2018) Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes. Nature. (in press) [doi: 10.1038/s41586-018-0708-8]