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Phylogenetic analysis of neo-sex chromosome genes in Sylvioidea passerine birds

Zhang, Hongkai (2018) BION02 20172
Degree Projects in Biology
Popular Abstract
Sex matters!

It is natural to ask questions about where the species of this planet come from and how they become what they are. As a matter of fact, development of new species is in process all the time. Somebody named this process speciation. Like language which enables us to guess where the people might come from, some traits make it possible to recognize the individuals from the same population. This effect is important for new species to arise because hybridization between species is expected to fail (or at least be reduced) by a definition about species. It is well established that traits are mainly controlled by genes. A pair of chromosomes which is thought to have genes that control different traits between the sexes is given a... (More)
Sex matters!

It is natural to ask questions about where the species of this planet come from and how they become what they are. As a matter of fact, development of new species is in process all the time. Somebody named this process speciation. Like language which enables us to guess where the people might come from, some traits make it possible to recognize the individuals from the same population. This effect is important for new species to arise because hybridization between species is expected to fail (or at least be reduced) by a definition about species. It is well established that traits are mainly controlled by genes. A pair of chromosomes which is thought to have genes that control different traits between the sexes is given a special name, sex chromosomes. Of course, the sex chromosome is only meaningful in the lives that have different sexes, for example, humans. Birds also have a pair of sex chromosomes. However, unlike human, male birds have the same type of sex chromosomes called Z chromosomes. In female birds, there is a W chromosome besides the Z chromosome. Imagine what would become if the genes responsible for speciation are located on the sex chromosomes! Does it mean sex chromosomes could also account for the newly occurred species? Just as the adage goes “Rome wasn’t built in a day”, verifying the causality between genes and species is a long journey with numerous challenges and obstacles. Perhaps, searching for genes showing deviating patterns is a good way to start. This is the very purpose of my project.

The age of the Z and W chromosomes in birds is about 150 million years old. Such a long history is likely to cause one copy of the gene to disappear (usually the W in this case). Using genetic data from the sex chromosomes poses a great challenge because without the complete genetic data, the evolutionary relationships of them will be impossible to infer. Interestingly, researchers have discovered a pair of new sex chromosomes, so-called “neo-sex chromosomes”, in a bird superfamily called Sylvioidea. In my thesis, I used genetic data of five species from Sylvioidea, including Great reed warbler (Acrocephalus arundinaceus, GRW), Clamorous reed warbler (Acrocephalus stentoreus, CRW), Marsh warbler (Acrocephalus palustris, MW), Eurasian Blackcap (Sylvia atricapilla, BC) and Common Whitethroat (Sylvia communis, CW). GRW, CRW and MW form a genus called Acrocephalus, in contrast with BC and CW forming another one called Sylvia (Figure 1). The neo-sex chromosomes are regions of autosome which become connected with the sex
chromosome. What is so special about these neo-sex chromosomes is not only the young age (about 20-40 million years old), but also the relatively intact gene copies on both the Z and the W neo-sex chromosomes. The reason for this might be that the recombination between the gene copies on neo-Z and neo-W chromosomes has not become suppressed until recently. To infer the evolutionary relationships between the analysed subjects, I turn to the phylogenetic tree because it is straightforward to illustrate both the relationship and how many differences are there among them. Based on the phylogenetic trees, we can formulate speculations and hypotheses in the future.

To locate the genes that drive the speciation, the first thing I am curious about is when the gene copies on both neo-sex chromosomes show a sign of ceased recombination. If the timing of recombination cessation of any genes happens to be near the timing of speciation event, these genes have a possibility to contribute to speciation. To determine the timing of recombination, phylogenetic trees were built for several genes on the neo-Z and neo-W chromosomes. If the phylogenetic tree groups the gene copies according to the chromosome type (i.e. Z or W), we can tell that recombination of this gene stopped before the speciation of these species (Figure 2). Following this criterion, I analyzed 17 genes. Recombination of ten genes stopped before the speciation of Sylvioidea and the recombination of four genes stopped before the speciation of Acrocephalus and Sylvia. The other three genes exhibit phylogenetic trees that challenged the criterion of dating the recombination cessation, possibly because of the missing data on neo-W chromosomes, different timing of recombination cessation in different species, or mistakes in the process of the genetic data before building phylogenetic trees. Unexpectedly, after I ordered the phylogenetic trees of each gene according to the gene order on Zebra finch (Taeniopygia guttata) genome (a common reference genome in passerine birds), the genes with different phylogenetic patterns were scattered. This result led us to the suspicion that the actual gene order on these neo-sex chromosomes in Sylvioidea species has been rearranged.

Phylogenetic trees depict the evolutionary history. A phylogenetic tree differing from the other ones means a different evolutionary history than the average. Suppose we select a gene with different a phylogenetic signal from the others, we may increase our odds of finding genes that act during speciation. To complete this objective, I used the clustering analysis. Briefly speaking, it is a method of categorizing things, for example, we tend to categorize apples, bananas and pears into fruits. The things being categorized in my thesis are phylogenetic trees. Another important element when we categorize things is the reference or something we can compare to. Without objects like bikes and cars, fruit is a meaningless word, isn’t it? Here, I used the genetic data from autosomes to be something to compare with neo-sex chromosomes. The result of the clustering analysis grouped all the genetic data into four clusters. Almost all the autosomal genes and a large proportion of genetic data from neo-sex chromosomes fell into Cluster 1. Cluster 2, 3 and 4 had some genetic data from neo-sex chromosomes with unique phylogenetic trees. The statistical test proved the distribution of the genetic data in these 4 clusters to be associated with their chromosome types. With the cluster structure, we have chances to explore the underlying causes, and studying substitution rates could be a good start.

Phylogenetic trees are built on genetic data by likelihood algorithms, so it bears a certain risk of making mistakes. Analysing the genetic sequences themselves shall not be omitted. Here comes the third analysis of my thesis, that is, estimation of nonsynonymous substitution rates (dN) and synonymous substation rates (dS). dN calculates the rates of the change of nucleotides that can lead to the change of protein, but dS is the other way around. A summary of the results is that the genetic data on neo-sex chromosomes have signs of deviating from the autosomal genes, although the deviation is not prominent enough. In a way, the results support the idea of different selection pressures in females and males.

From these three analyses, I concluded that some genes on the neo-sex chromosomes have different evolutionary histories from the autosome, and this probably means that selection has been acting differently on them in females and males. Nonetheless, complications, such as some phylogenetic trees for which was difficult to determine the timing of recombination cessation, still hinder searching for genes for speciation, so next step would conduct additional analyses on the genes that showed different phylogenetic patterns from the autosomal genes.


Master’s Degree Project in Biology 45 credits 2018
Department of Biology, Lund University

Advisor: Bengt Hansson
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Zhang, Hongkai
supervisor
organization
course
BION02 20172
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8958655
date added to LUP
2018-09-13 14:02:27
date last changed
2018-09-13 14:02:27
@misc{8958655,
  author       = {Zhang, Hongkai},
  language     = {eng},
  note         = {Student Paper},
  title        = {Phylogenetic analysis of neo-sex chromosome genes in Sylvioidea passerine birds},
  year         = {2018},
}