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Transcriptome analysis to elucidate the radiation of endemic finches (Nesospiza acunhae) on the islands of Tristan da Cunha

Klincke, Franziska (2014) BINP31 20132
Degree Projects in Bioinformatics
Abstract
Abstract

There is adaptive radiation of endemic finches on the islands of Tristan da Cunha. On each of two of the islands a small-billed and a large-billed subspecies have evolved independently. In this study we analysed the transcriptome of the finch Nesospiza acunhae of Inaccessible Island with the use of RNA-seq reads. The rapid improvement in nextgeneration sequencing technologies as well as the software used to analyse this data, makes it possible to get insight into transcriptomes of non-model organisms like these finches. First a de novo gene prediction was carried out. Next, a de novo transcriptome assembly was performed and in a later step these transcripts were annotated using BLAST and Pfam searches. Next, transcripts of the... (More)
Abstract

There is adaptive radiation of endemic finches on the islands of Tristan da Cunha. On each of two of the islands a small-billed and a large-billed subspecies have evolved independently. In this study we analysed the transcriptome of the finch Nesospiza acunhae of Inaccessible Island with the use of RNA-seq reads. The rapid improvement in nextgeneration sequencing technologies as well as the software used to analyse this data, makes it possible to get insight into transcriptomes of non-model organisms like these finches. First a de novo gene prediction was carried out. Next, a de novo transcriptome assembly was performed and in a later step these transcripts were annotated using BLAST and Pfam searches. Next, transcripts of the small-billed and large-billed subspecies of N. acunhae were compared in order to identify variation in sequences both between individuals and between the two subspecies. Only few differences between the two subspecies could be confidently identified due to low sequencing depth. These variations in transcripts might be involved in the differences in beak size and shape between the two subspecies and with this give insight into adaptive speciation (Less)
Popular Abstract
Multiplying birds

Already Charles Darwin studied evolution with the help of finches from the Galápagos islands. He was interested in why there are finches with different beak sizes and shapes. Darwin’s work helped us to understand how new species emerge and others cease to exist.

In this project we follow the lead of Darwin and study another group of finches with different beak sizes. In particular, we study two variants of the same species, one with a small and the other with a large beak. We are using genetic methods that were not available at the time Darwin lived.
First, we study their genome, which is all the genetic material found in a cell. In the genome we identify genes, the genetic material in the genome that produces... (More)
Multiplying birds

Already Charles Darwin studied evolution with the help of finches from the Galápagos islands. He was interested in why there are finches with different beak sizes and shapes. Darwin’s work helped us to understand how new species emerge and others cease to exist.

In this project we follow the lead of Darwin and study another group of finches with different beak sizes. In particular, we study two variants of the same species, one with a small and the other with a large beak. We are using genetic methods that were not available at the time Darwin lived.
First, we study their genome, which is all the genetic material found in a cell. In the genome we identify genes, the genetic material in the genome that produces proteins. Additionally, we identify genes that are also found in other bird species.
Second, we study their transcriptome, the set of transcripts that come from genes at a particular
time. In the transcriptome we identify many transcripts that are also found in other birds.
Next, we compare the transcripts between the two variants and identify differences in those
transcripts. These differences might contribute to the differences in the beak size. If so they are also involved in multiplying the birds, meaning to make two (variants) out of one (species).

Not only do these findings help to understand the evolution of the studied finches, but also do they add to understanding evolution in general.

Advisor: Björn Canbäck
Master´s Degree Project 45 credits in Bioinformatics 2014
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Klincke, Franziska
supervisor
organization
course
BINP31 20132
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
4519660
date added to LUP
2014-06-26 17:14:38
date last changed
2014-06-26 17:14:38
@misc{4519660,
  abstract     = {{Abstract

There is adaptive radiation of endemic finches on the islands of Tristan da Cunha. On each of two of the islands a small-billed and a large-billed subspecies have evolved independently. In this study we analysed the transcriptome of the finch Nesospiza acunhae of Inaccessible Island with the use of RNA-seq reads. The rapid improvement in nextgeneration sequencing technologies as well as the software used to analyse this data, makes it possible to get insight into transcriptomes of non-model organisms like these finches. First a de novo gene prediction was carried out. Next, a de novo transcriptome assembly was performed and in a later step these transcripts were annotated using BLAST and Pfam searches. Next, transcripts of the small-billed and large-billed subspecies of N. acunhae were compared in order to identify variation in sequences both between individuals and between the two subspecies. Only few differences between the two subspecies could be confidently identified due to low sequencing depth. These variations in transcripts might be involved in the differences in beak size and shape between the two subspecies and with this give insight into adaptive speciation}},
  author       = {{Klincke, Franziska}},
  language     = {{eng}},
  note         = {{Student Paper}},
  title        = {{Transcriptome analysis to elucidate the radiation of endemic finches (Nesospiza acunhae) on the islands of Tristan da Cunha}},
  year         = {{2014}},
}