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The Genetics of Colour Polymorphism

Evans, Alice (2013) BION34 20131
Degree Projects in Biology
Abstract
Abstract

Understanding the genetic basis of phenotypic traits is of fundamental importance in evolutionary and conservation biology. A genetic colour polymorphism occurs when more than one clearly distinct, heritable colour phenotype exists within a randomly mating population. Female limited genetic colour polymorphisms are widespread in Odonates and provide excellent study systems to further understand the genetic architecture and inheritance of colour genes and the evolutionary processes maintaining morph frequencies. This project describes the first steps in analysing the first ever damselfly genome, to establish a bioinformatical method and to look for basic patterns between pooled genomic data of the three female colour morphs of... (More)
Abstract

Understanding the genetic basis of phenotypic traits is of fundamental importance in evolutionary and conservation biology. A genetic colour polymorphism occurs when more than one clearly distinct, heritable colour phenotype exists within a randomly mating population. Female limited genetic colour polymorphisms are widespread in Odonates and provide excellent study systems to further understand the genetic architecture and inheritance of colour genes and the evolutionary processes maintaining morph frequencies. This project describes the first steps in analysing the first ever damselfly genome, to establish a bioinformatical method and to look for basic patterns between pooled genomic data of the three female colour morphs of Ischnura elegans. (Less)
Abstract
Popular science summary

Genetic colour polymorphisms (the occurrence of two or more heritable colour morphs in the same habitat, within a randomly mating population) are widespread in nature. Whether evolving through natural selection or sexual selection, or whether to aid in e.g. camouflage or mate-selection; genetic colour polymorphisms provide a fascinating study system from which to gain insights into the processes of evolution, genetics and ecology

Using the blue-tailed damselfly Ischnura elegans as a model organism, this report explores the first steps in the genetic analysis of the first ever sequenced damselfly genome. The goal was to analyse the differences between the three female colour morphs that occur in I. elegans.... (More)
Popular science summary

Genetic colour polymorphisms (the occurrence of two or more heritable colour morphs in the same habitat, within a randomly mating population) are widespread in nature. Whether evolving through natural selection or sexual selection, or whether to aid in e.g. camouflage or mate-selection; genetic colour polymorphisms provide a fascinating study system from which to gain insights into the processes of evolution, genetics and ecology

Using the blue-tailed damselfly Ischnura elegans as a model organism, this report explores the first steps in the genetic analysis of the first ever sequenced damselfly genome. The goal was to analyse the differences between the three female colour morphs that occur in I. elegans. Very little genetic information is known about damselflies and dragonflies (Odonates), which are one of the most ancient insect lineages.

Ischnura elegans exhibits a female-limited genetic colour polymorphism, in which there is the androchrome morph (male-like, blue colouration), infuscans morph (female-like, green colouration) and infuscans-obsoleta morph (female-like brown-green colouration). Mating comes at a fitness cost for females, as copulation times are long. When one morph is most common, this morph receives more mating harassment, and so becomes under a selective disadvantage. These three morphs therefore fluctuate in frequency within the population, and so are subsequently under what is known as ‘negative-frequency dependent selection’ from male mating harassment.

I tested a bioinformatical method to search for basic patterns between pooled genomic data of the three female colour morphs which may have indicated a gene region associated with colour polymorphism. Roughly 4 billion reads (short known sequences of DNA) were mapped to a roughly 1 billion base pair reference genome, and the genetic differences then observed. The programme Bowtie2 was used to run a large scale sequence alignment (mapping the 4 billion reads to the reference genome) and the programme Popoolation2 was used to search for single nucleotide polymorphisms (SNPs) and population differentiation measured by the fixation index (FST).

I found no clear evidence for a gene region associated with colour, as all of the SNPs with the highest FST values were none-significant according to the Fisher’s Exact Test. This could be due to the quality of the reference genome, which was composed of 217,286 scaffolds (sections of DNA which the reference genome is split into) which preferably should be a much lower number. This could also be due to sampling variance or sequencing error. I did find a significant difference between the total number of SNPs within each morph, but no significant difference in average allele frequency, and no significant BLAST (basic local alignment search tool) hits.

Further genetic studies of Odonates for comparison, and a better reference genome may shed light on this phenomenon in the future.

Advisor: Maren Wellenreuther
Master´s Degree Project 45 credits in Molecular Ecology 2013
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Evans, Alice
supervisor
organization
course
BION34 20131
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
4092200
date added to LUP
2013-10-16 12:03:44
date last changed
2013-10-17 13:15:01
@misc{4092200,
  abstract     = {Popular science summary

Genetic colour polymorphisms (the occurrence of two or more heritable colour morphs in the same habitat, within a randomly mating population) are widespread in nature. Whether evolving through natural selection or sexual selection, or whether to aid in e.g. camouflage or mate-selection; genetic colour polymorphisms provide a fascinating study system from which to gain insights into the processes of evolution, genetics and ecology 

Using the blue-tailed damselfly Ischnura elegans as a model organism, this report explores the first steps in the genetic analysis of the first ever sequenced damselfly genome. The goal was to analyse the differences between the three female colour morphs that occur in I. elegans. Very little genetic information is known about damselflies and dragonflies (Odonates), which are one of the most ancient insect lineages.

Ischnura elegans exhibits a female-limited genetic colour polymorphism, in which there is the androchrome morph (male-like, blue colouration), infuscans morph (female-like, green colouration) and infuscans-obsoleta morph (female-like brown-green colouration). Mating comes at a fitness cost for females, as copulation times are long. When one morph is most common, this morph receives more mating harassment, and so becomes under a selective disadvantage. These three morphs therefore fluctuate in frequency within the population, and so are subsequently under what is known as ‘negative-frequency dependent selection’ from male mating harassment.

I tested a bioinformatical method to search for basic patterns between pooled genomic data of the three female colour morphs which may have indicated a gene region associated with colour polymorphism. Roughly 4 billion reads (short known sequences of DNA) were mapped to a roughly 1 billion base pair reference genome, and the genetic differences then observed. The programme Bowtie2 was used to run a large scale sequence alignment (mapping the 4 billion reads to the reference genome) and the programme Popoolation2 was used to search for single nucleotide polymorphisms (SNPs) and population differentiation measured by the fixation index (FST).

I found no clear evidence for a gene region associated with colour, as all of the SNPs with the highest FST values were none-significant according to the Fisher’s Exact Test. This could be due to the quality of the reference genome, which was composed of 217,286 scaffolds (sections of DNA which the reference genome is split into) which preferably should be a much lower number. This could also be due to sampling variance or sequencing error. I did find a significant difference between the total number of SNPs within each morph, but no significant difference in average allele frequency, and no significant BLAST (basic local alignment search tool) hits.

Further genetic studies of Odonates for comparison, and a better reference genome may shed light on this phenomenon in the future. 

Advisor: Maren Wellenreuther
Master´s Degree Project 45 credits in Molecular Ecology 2013
Department of Biology, Lund University},
  author       = {Evans, Alice},
  language     = {eng},
  note         = {Student Paper},
  title        = {The Genetics of Colour Polymorphism},
  year         = {2013},
}