Transposable Elements May Be Extremely Helpful in Phylogenetics—But They’re Not Perfect

Transposable Elements May Be Extremely Helpful in Phylogenetics—But They’re Not Perfect

In the world of phylogenetics, where one is attempting to build an evolutionary tree for a set of species, there are certain elements in analysis that are considered “perfect”. These perfect elements are considered to be homoplasy free. That is, these elements have not evolved analogously. This is obviously helpful to phylogeneticists because it removes any unambiguity between species.

With that said, are transposable elements “perfect”? Han et al*. analyze the characteristics of transposable elements (TE) in avian genomes in order to find out. These TE are very rare yet accumulate rapidly enough for easy distinction between closely related species. In addition, the TE can have different orientations and types. For the most part, retrotransposons are the most common for TE analysis in phylogenetics.

Han et al. later go on to talk about how TE are, in fact, not completely free of homoplasy. There are two types of TEs: retrotransposons, which use a “copy-and-paste” mechanism, the second type uses “cut-and-paste”. And so they found there to be “hotspots” for transposable elements. These hotspots were found to be mutual through several avian genomes. Therefore, although, TE are distinct, they still lend themselves to homoplasy.

And so Han et al. found TE to be very useful as they are extremely prevalent in avian genomes and are distinct. However, they may not be the magical element that every phylogeneticist had hoped for. Still, further research into hotspots of TE may help us overcome the problem of homoplasy.  

_{*Han, et al. (2011) Are Transposable Element Insertions Homoplasy Free? An Examination Using the Avian Tree of Life. Systematic Biology 60: 1-12. doi: 10.1093/sysbio/sysq100.}

Evolution and natural selection across 10 bird species

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.

Künstner et al* performed brain transcriptome sequencing on 10 species of birds, with the intent of studying natural selection between bird species. All of the bird species were primarily tested against the coding sequences of the zebra finch (whose genome sequence was already available), as it appeared most comparable to the other species (the chicken was initially used as well, but was found to be less useful.) 

By studying the synonymous substitution rate (ds) in comparisons between the zebra finch and 10 bird species and estimating the mean ds for each chromosome, Künstner et al. reached the conclusion that small chromosomes have an elevated mutation rate. This suggests that small chromosomes, being more prone to “slightly deleterious mutations,” have less input in natural selection, supporting the Hill-Robertson effect. 

The Hill-Robertson effect is the idea that recombination of genes makes evolution go more quickly. In populations of fixed sides that are undergoing natural selection, genetic drift and gene mutations can slow evolution down. Suppose that there are two competing advantageous mutations, A and B. With recombination, organisms could have both A and B, making them stronger and more able to thrive. However, without recombination, a mutation would have to occur for both A and B to exist in the same organism. Waiting for this mutation could take a long time and delay evolution. 

Further study of chromosomal mutations suggested that the male mutation rate was at least twice that of the female rate, although the meaningfulness of the incidence was debatable. Künstner et al. tried to correct for statistical measurements they found to be misleading by more carefully analyzing the relationship between mean ds and mean ɷ (the sum of the rate of non-synonymous selection divided by ds.) 

Their analysis again supported the importance of chromosome size and the Hill-Robertson effect. 

*_{Kunstner et al (2010).  Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.Molecular Ecology 19: 266–276. doi: 10.1111/j.1365-294X.2009.04487.x}

Singing with Genes (Simmons)

Back in 2010, the fully sequenced genome of Taeniopygia guttata, the Zebra finch, was completed. It was the second bird, after the chicken, and the first of the passerines to have its genome completely sequenced. The Zebra finch, unlike the chicken, is a songbird, and, as a result, several studies focused on this characteristic’s relationship to its genomic sequence. In addition, the Zebra finch and other song birds communicate with “learned vocalizations,” which, so far, have only been observed in humans (Warren et al. 2010*). A research article published in Nature science journal by Warren et al. in 2010 provided an overview of the studies conducted by a research group from Washington University School of Medicine. The group highlights findings regarding the genome’s “active involvement” in neural processes involved in song behavior and communication (Warren et al. 2010). This includes their findings on how vocal communication has an effect on the expression of various genetic material, including microRNAs and transcription factors through having an effect on “gene regulatory networks” in the Zebra finch brain.

In Zebra finch culture, only the males sing, and, as a result, more fully develop the “song control nuclei” located in their forebrains. In addition, these increase in size and change in organization during the males’ juvenile stage, when they learn to sing, providing strong evidence for neural plasticity in songbirds (Warren et al. 2010*). The article also highlights how song behavior has been found to influence gene expression in songbirds. When learning songs, gene response changes in as quickly as the course of a day.

A Zebra Finch

In their studies, the research group used males, the homogametic sex with ZZ rather than ZW, in order to more thoroughly cover the Z chromosome. In addition, because the research group wanted to study the genes relevant to song behavior and brain development, they chose juvenile males and adult males in the study. The group used both “sequence alignment and fluorescent in situ hybridization” processes on the chromosomes of both the Zebra finches and chickens, the only other fully sequenced bird genome available at the time in order to explore questions regarding the species’ evolution. With regard to this, they found that both genomes lacked genes that encode for proteins involved in the creation of “vomeronasal receptors,” teeth, and breast milk. They also found that the Zebra finch genes for the development of major histocompatibility complex, involved in white blood cell function, are unusually dispersed across multiple chromosomes, in comparison to chicken and human MHC genes being more locally distributed. The article also addresses the controversy behind how birds balance Z chromosome expression in the homogametic sex, especially with regard to species that have a large difference between male and female appearance and behavior. The article suggests, that in most bird species, this could be linked to male hypermethylated RNA dosages, which, oddly, Zebra finches lack.

*_{Warren, et al. (2010) The Genome of a Song Bird. Nature 464: 757-762. dol:10.1038/nature08819}

Phylogenetic Analysis May be Misleading Due to Compositional Bias

Phylogenetic Analysis May be Misleading Due to Compositional Bias

In this paper, Foster et al* looked at DNA composition bias and how it adversely affects phylogenetic analysis. That is, phylogenetic analysis produces false results by grouping unrelated taxa. This has been shown to be the result of compositional bias i.e. AT/GC-rich components of the genome. With these biases, it is clear how errors would occur in phylogenetic analysis—they are being grouped together based on biased areas of the genome. For example, the nematode and honeybee were grouped together even though they are obviously biologically unrelated. They also mention how bias in the DNA can affect protein bias.

In their experiment, Foster et al performed phylogenetic analyses of the protein coding sequences from the mitochondria. The specie’s genes selected for analysis were known to have varying amounts of both DNA and amino acid composition bias and therefore, they are ideal for observation of the effect(s) of compositional bias.

Results revealed incorrect grouping of taxa with large compositional bias. Compositional bias couldn’t be the only factor, however, as the fruit fly is biologically more closely related to the honeybee than is the nematode and is slightly more AT-rich than the nematode. Foster et al speculate that this is due to strong amino acid bias—these are elements, which evolved independently and in a similar position in the genome.

In conclusion, Foster et al have shown that compositional bias can take away from the integrity of phylogenetic analysis. With this, we should keep in mind that we should be cautious when interpreting phylogenetic results. It is important to predetermine any compositional biases in your samples.

*^{Foster PG, Hickey DA (1999) Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. Journal of Molecular Evolution 48: 283–290. doi: 10.1007/pl00006471.}