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Speciation and hybridization in European crows - inference of selection and demography using RAD-sequencing data

Keehnen, Naomi (2013) BIOP34 20122
Degree Projects in Biology
Abstract
Abstract

The hooded crow (Corvus corone cornix) and carrion crow (Corvus corone corone) differ in plumage colouration, ecological characteristics, and have almost completely allopatric distribution ranges. However, the two (sub)species do meet and interbreed in the European crow hybrid zone. The classification of these two crow-types is debated heavily, since no genetic difference has been found when using traditional DNA markers. Restriction-site Associated DNA sequencing (RAD-seq) produces a large amount of sequences, by fragmenting genomes with restriction enzymes and high-throughput sequencing. RAD-seq results in thousands of informative RAD-tags with detectable Single Nucleotide Polymorphisms (SNPs), which can be used to find... (More)
Abstract

The hooded crow (Corvus corone cornix) and carrion crow (Corvus corone corone) differ in plumage colouration, ecological characteristics, and have almost completely allopatric distribution ranges. However, the two (sub)species do meet and interbreed in the European crow hybrid zone. The classification of these two crow-types is debated heavily, since no genetic difference has been found when using traditional DNA markers. Restriction-site Associated DNA sequencing (RAD-seq) produces a large amount of sequences, by fragmenting genomes with restriction enzymes and high-throughput sequencing. RAD-seq results in thousands of informative RAD-tags with detectable Single Nucleotide Polymorphisms (SNPs), which can be used to find genetic differences and population structures. This study RAD-sequenced thirty-four samples, which were collected from within the Danish-German hybrid zone and Skåne (Sweden). The individuals were scored based on morphology and were classified as either pure hooded (N= 15), pure carrion (N=12) or hybrid (N=7). A total of 127,493 loci were produced, with 69,085 loci containing SNPs. The overall genetic differentiation between the two crow-types was low (Fst =0.001). However, 319 RAD-tags were found to differ significantly between the two crow types. Population structure analysis separates the two crow-types based on these loci, with hybrids being intermediates at these loci. These results support the classification of hooded and carrion crow as subspecies. Furthermore, the differentiating loci show potential as candidate loci for the plumage polymorphism. (Less)
Abstract
Popular science summary

The classification of the European Crow

Species status is a highly discussed topic as species classification can be challenging. Several species concepts have been formulated to standardize classifications. These species concept help with taxonomy, however many species remain problematic to classify, especially if interbreeding occurs.

The hooded crow (Corvus corone cornix) and carrion crow (Corvus corone corone) differ in plumage colouration, certain ecological characteristics, and have almost completely separate distribution ranges. However, the two (sub)species meet and interbreed in the European crow hybrid zone. The classification of these two crow-types is debated heavily, since no genetic... (More)
Popular science summary

The classification of the European Crow

Species status is a highly discussed topic as species classification can be challenging. Several species concepts have been formulated to standardize classifications. These species concept help with taxonomy, however many species remain problematic to classify, especially if interbreeding occurs.

The hooded crow (Corvus corone cornix) and carrion crow (Corvus corone corone) differ in plumage colouration, certain ecological characteristics, and have almost completely separate distribution ranges. However, the two (sub)species meet and interbreed in the European crow hybrid zone. The classification of these two crow-types is debated heavily, since no genetic differences have been found when using traditional DNA markers. To solve the question if these two crow-types are different species or not, and if their morphological difference has a genetic basis new DNA techniques are needed.

One of these new techniques is called Restriction-site Associated DNA sequencing (RAD-seq), and produces large amounts of DNA sequences. Genomes are fragmented with restriction enzymes and high-throughput sequencing produces a larger database than traditional DNA sequencing techniques can. RAD-seq results in thousands of informative sequences (RAD-tags) with detectable Single Nucleotide Polymorphisms (SNPs). A SNP is a DNA sequence variation occurring when a single nucleotide- A, T, C or G - differs between individuals. These SNPs can then be used to find genetic differences and population structures.

In total thirty-four samples were RAD-sequenced, the samples were collected from within the Danish-German hybrid zone and Skåne (Sweden). The individuals were scored based on morphology and were classified as either pure hooded (n= 15), pure carrion (n=12) or hybrid (n=7). A total of 127,493 loci were produced, with 69,085 loci containing SNPs. The overall genetic differentiation between the two crow-types was low (Fst =0.001). However, 319 RAD-tags were found to differ significantly between the two crow types. Population structure analysis separates the two crow-types based on these loci, with hybrids being intermediates at these loci.

These results support the classification of hooded and carrion crow as subspecies of the European crow. Furthermore, the differentiating loci show potential as candidate loci for the plumage polymorphism, more research is needed to single out the loci responsible for this colour difference between the two crow-types.


Advisor: Bengt Hansson
Degree project 60 credits in Molecular Ecology, 2013
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Keehnen, Naomi
supervisor
organization
course
BIOP34 20122
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
4153281
date added to LUP
2013-11-14 10:35:27
date last changed
2013-11-14 10:35:27
@misc{4153281,
  abstract     = {Popular science summary

The classification of the European Crow

Species status is a highly discussed topic as species classification can be challenging. Several species concepts have been formulated to standardize classifications. These species concept help with taxonomy, however many species remain problematic to classify, especially if interbreeding occurs. 

The hooded crow (Corvus corone cornix) and carrion crow (Corvus corone corone) differ in plumage colouration, certain ecological characteristics, and have almost completely separate distribution ranges. However, the two (sub)species meet and interbreed in the European crow hybrid zone. The classification of these two crow-types is debated heavily, since no genetic differences have been found when using traditional DNA markers. To solve the question if these two crow-types are different species or not, and if their morphological difference has a genetic basis new DNA techniques are needed. 

One of these new techniques is called Restriction-site Associated DNA sequencing (RAD-seq), and produces large amounts of DNA sequences. Genomes are fragmented with restriction enzymes and high-throughput sequencing produces a larger database than traditional DNA sequencing techniques can. RAD-seq results in thousands of informative sequences (RAD-tags) with detectable Single Nucleotide Polymorphisms (SNPs). A SNP is a DNA sequence variation occurring when a single nucleotide- A, T, C or G - differs between individuals. These SNPs can then be used to find genetic differences and population structures. 

In total thirty-four samples were RAD-sequenced, the samples were collected from within the Danish-German hybrid zone and Skåne (Sweden). The individuals were scored based on morphology and were classified as either pure hooded (n= 15), pure carrion (n=12) or hybrid (n=7). A total of 127,493 loci were produced, with 69,085 loci containing SNPs. The overall genetic differentiation between the two crow-types was low (Fst =0.001). However, 319 RAD-tags were found to differ significantly between the two crow types. Population structure analysis separates the two crow-types based on these loci, with hybrids being intermediates at these loci. 

These results support the classification of hooded and carrion crow as subspecies of the European crow. Furthermore, the differentiating loci show potential as candidate loci for the plumage polymorphism, more research is needed to single out the loci responsible for this colour difference between the two crow-types.


Advisor: Bengt Hansson
Degree project 60 credits in Molecular Ecology, 2013
Department of Biology, Lund University},
  author       = {Keehnen, Naomi},
  language     = {eng},
  note         = {Student Paper},
  title        = {Speciation and hybridization in European crows - inference of selection and demography using RAD-sequencing data},
  year         = {2013},
}