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Evolution of Major Histocompatibility Complex (MHC) Genes in Songbirds

Angelidou, Georgia (2015) BINP32 20142
Degree Projects in Bioinformatics
Abstract
The major histocompatibility complex (MHC) is a membrane protein group of central importance in the immune system. It is divided into two main classes, class I and class II. The MHCs are highly polymorphic which is believed to be indication of trans-species polymorphism (TSP). There is TSP when an allele is maintained in two species through a speciation event. The songbirds that I study here belong to the Passerida group, I focus only on MHC class I exon 3 which encodes the peptide binding region of the MHC protein. At the beginning a database was constructed to store all the information from the di_erent species and a web site was created for easier access to the information. The database has 32 species that belong to the group Passerida... (More)
The major histocompatibility complex (MHC) is a membrane protein group of central importance in the immune system. It is divided into two main classes, class I and class II. The MHCs are highly polymorphic which is believed to be indication of trans-species polymorphism (TSP). There is TSP when an allele is maintained in two species through a speciation event. The songbirds that I study here belong to the Passerida group, I focus only on MHC class I exon 3 which encodes the peptide binding region of the MHC protein. At the beginning a database was constructed to store all the information from the di_erent species and a web site was created for easier access to the information. The database has 32 species that belong to the group Passerida and all of them were used for checking if there is a TSP. There are some older studies which have found a TSP 6-7 million years ago (MYA)and my aim was to see if I could _nd a TSP even older than that. I checked for TSP in three di_erent ways by: a) creating a MHC tree using only ten random sequences per species, b) creating three subtrees on species with most recent common ancestors 22-30 MYA and c) checking for identical sequences between the species. The species that were sharing identical sequence also showed TSP in the MHC random tree and all of them are diverged until seven MYA. Another interesting results is that there are some TSP which are going back to two speciation events one was 20 MY. The most recent relationship that we found was three MYA between Passer domesticus and Passer hispaniolensis and the oldest one was 28 MYA between Carpodacus erythrinus, Haemorhous mexicanus and Thraupis episcopus. (Less)
Popular Abstract
Genes older than 28 million years

When new species emerge also their genes become increasingly diverged. Some genes contain information about protein structure and in general it is easy to identify the species that a gene belongs to.

But is this always true?
Studies have found that humans and chimpanzees share genes, hence these are older than 5 million years. Such genes make it impossible to identify which species they belong to. Do the genes come from human or from chimpanzee? The similarity origins from the most recent common ancestor and after the species separated they remain almost the same. This phenomenon is called trans-species polymorphism (TSP). When the species separate from their common ancestor is called a speciation... (More)
Genes older than 28 million years

When new species emerge also their genes become increasingly diverged. Some genes contain information about protein structure and in general it is easy to identify the species that a gene belongs to.

But is this always true?
Studies have found that humans and chimpanzees share genes, hence these are older than 5 million years. Such genes make it impossible to identify which species they belong to. Do the genes come from human or from chimpanzee? The similarity origins from the most recent common ancestor and after the species separated they remain almost the same. This phenomenon is called trans-species polymorphism (TSP). When the species separate from their common ancestor is called a speciation event. More specifically the genes that I investigated were the ones that contain information about proteins that play main roles in the immune system and are called major histocompatibility complex genes (MHC). More studies based on these genes showed that other species also have similar MHC genes. Two of these species are warbler which belong to the songbirds.

How much further back in time can we find similar genes?
To investigate this, information from 34 songbird species were gathered from various locations in Europe. To be able to use the data, all information were organized into tables and later a web site was created so the user can have an easy and more friendly access to the information.
The phylogenetic trees were created only after all the information was collected. First a species tree was created to see when the species diverged. Then four different MHC trees were created which demonstrates how the genes are connected with each other. More specifically it shows how they group together and how they group with genes from other species. When they are grouped with other species means that it is difficult to identify to which species they belong and indicates TSP.

Genes can be 28 million years old.
The results revealed MHC genes that are older than 28 million years. Also there are occasions where genes went through two speciation events as we can see in the figure (orange and blue boxes) and are still similar between the species. Species that were separated more recently have also identical genes like the one in blue color in the figure.


Supervisor: Björn Canbäck and Helena Westerdahl
Master's Degree Project in Bioinformatics, 60 credits 2015
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Angelidou, Georgia
supervisor
organization
course
BINP32 20142
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
5464889
date added to LUP
2015-06-04 15:16:26
date last changed
2015-06-04 15:16:26
@misc{5464889,
  abstract     = {The major histocompatibility complex (MHC) is a membrane protein group of central importance in the immune system. It is divided into two main classes, class I and class II. The MHCs are highly polymorphic which is believed to be indication of trans-species polymorphism (TSP). There is TSP when an allele is maintained in two species through a speciation event. The songbirds that I study here belong to the Passerida group, I focus only on MHC class I exon 3 which encodes the peptide binding region of the MHC protein. At the beginning a database was constructed to store all the information from the di_erent species and a web site was created for easier access to the information. The database has 32 species that belong to the group Passerida and all of them were used for checking if there is a TSP. There are some older studies which have found a TSP 6-7 million years ago (MYA)and my aim was to see if I could _nd a TSP even older than that. I checked for TSP in three di_erent ways by: a) creating a MHC tree using only ten random sequences per species, b) creating three subtrees on species with most recent common ancestors 22-30 MYA and c) checking for identical sequences between the species. The species that were sharing identical sequence also showed TSP in the MHC random tree and all of them are diverged until seven MYA. Another interesting results is that there are some TSP which are going back to two speciation events one was 20 MY. The most recent relationship that we found was three MYA between Passer domesticus and Passer hispaniolensis and the oldest one was 28 MYA between Carpodacus erythrinus, Haemorhous mexicanus and Thraupis episcopus.},
  author       = {Angelidou, Georgia},
  language     = {eng},
  note         = {Student Paper},
  title        = {Evolution of Major Histocompatibility Complex (MHC) Genes in Songbirds},
  year         = {2015},
}