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Whole mitochondrial genome phylogeny of a community of Haemoproteus parasites - evolutionary patterns of host specificity and transmission

Duc, Mélanie (2019) BION03 20182
Degree Projects in Biology
Abstract
Whole mitochondrial genome sequences have the potential to clarify avian haemosporidian phylogenies and evolution. In this study, we sequenced mitochondrial genomes from isolates of 26 genetic lineages of avian haemosporidian parasites of the genus Haemoproteus (subgenus Parahaemoproteus) with a nested long-range PCR protocol and next-generation sequencing. We identified more mixed infections than expected based on Sanger sequencing of the mitochondrial gene cytochrome b, which is typically used for bar-coding these parasites. The phylogeny obtained was robust, but seven of 37 nodes still had bootstrap values under 50 %. A clade of “pale-staining” parasites previously identified with cytochrome b sequences was supported in this analysis... (More)
Whole mitochondrial genome sequences have the potential to clarify avian haemosporidian phylogenies and evolution. In this study, we sequenced mitochondrial genomes from isolates of 26 genetic lineages of avian haemosporidian parasites of the genus Haemoproteus (subgenus Parahaemoproteus) with a nested long-range PCR protocol and next-generation sequencing. We identified more mixed infections than expected based on Sanger sequencing of the mitochondrial gene cytochrome b, which is typically used for bar-coding these parasites. The phylogeny obtained was robust, but seven of 37 nodes still had bootstrap values under 50 %. A clade of “pale-staining” parasites previously identified with cytochrome b sequences was supported in this analysis and the relationships between morphological species corresponded with previous studies. The GC content was higher in the non-protein coding parts of the mitochondrial genome (i.e., parts coding mainly for rRNA) than in the protein coding parts. The host and parasite phylogenies were more congruent in topology than expected by chance, but the relative contributions of cospeciation and host shifting to the evolutionary history of this clade of parasites remain to be determined. Indexes of the host specificity of the parasites (i.e., the diversity of host species a parasite lineage can infect) were sensitive to rare infections. By considering the index results in parallel with the number of host species each parasite infected, the parasites present in the local community seemed to be more specialists than generalists, apart from the Haemoproteus majoris clade which is mainly generalized. However, there was no phylogenetic signal in host specificity across the parasite phylogeny, possibly suggesting that host specificity changes do not depend on the phylogeny or that the local sampling does not have all the lineages in this clade of parasites, diluting the phylogenetic signal. (Less)
Popular Abstract
Who do I infect? By bird parasites.

Humans have malaria, so do birds. But they are infected by different species of parasites. Birds are infected by three kinds (genera) of blood parasites (Haemosporidians: Plasmodium, Haemoproteus and Leucocytozoon). I studied how Haemoproteus parasites spread among bird species.

Evolution is one of the key concepts in Biology, which in parasites needs several factors to be considered. A good sample size is needed in order to not miss the interactions between the parasites and the hosts (here birds). But it is also important to have a robust phylogeny for both the parasites and the hosts. By studying a local community, we look closer to what has happened and is happening between the species, as... (More)
Who do I infect? By bird parasites.

Humans have malaria, so do birds. But they are infected by different species of parasites. Birds are infected by three kinds (genera) of blood parasites (Haemosporidians: Plasmodium, Haemoproteus and Leucocytozoon). I studied how Haemoproteus parasites spread among bird species.

Evolution is one of the key concepts in Biology, which in parasites needs several factors to be considered. A good sample size is needed in order to not miss the interactions between the parasites and the hosts (here birds). But it is also important to have a robust phylogeny for both the parasites and the hosts. By studying a local community, we look closer to what has happened and is happening between the species, as parasites are different in how they vary in host specificity.

How we studied and identified parasites?
Blood samples were collected from birds at the Lake Krankesjön, South Sweden. Out of the blood, Haemoproteus parasites DNA was extracted to produce sequences for building a robust parasite phylogeny. To confirm the identity of the lineages (different versions of a gene which are likely to represent different species) we used a global database (MalAvi), which gather information about all studies that have been done on avian haemosporidian parasites. Mixed infections (more than one parasite species per sample) were identified by analyzing the DNA sequences.

A tree of parasites
A phylogeny shows the relationships among the different species. The closer two species are in a phylogeny, the more related they are. My phylogeny improved the resolution and support of the links in the parasite phylogeny (the higher it is, the more likely the link between the species is).
Using this new phylogenetic tree, I investigated the parasites and the hosts. I found that some of the parasites and hosts have evolved together. Those parasites were mainly generalists. Generalist parasites can infect more than one bird species; while parasites that are specialists only infect one or very few species of birds. In Krankesjön, the parasites seemed to be mainly specialists, with some generalists spread across the phylogeny. But there was no statistical support when looking at closely related parasites having the same host specificity.

Application of the study
Birds are easy to study and can provide a good size of sample for studies. The results obtained by studying them improve our knowledge on blood parasites and can also be applied to studies of malaria in humans.

Master’s Degree Project in Biology 60 credits 2019
Department of Biology, Lund University

Advisor: Bensch Staffan. Co-advisor: Ellis Vincenzo
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Duc, Mélanie
supervisor
organization
course
BION03 20182
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
8989827
date added to LUP
2019-07-03 15:42:50
date last changed
2019-07-03 15:42:50
@misc{8989827,
  abstract     = {Whole mitochondrial genome sequences have the potential to clarify avian haemosporidian phylogenies and evolution. In this study, we sequenced mitochondrial genomes from isolates of 26 genetic lineages of avian haemosporidian parasites of the genus Haemoproteus (subgenus Parahaemoproteus) with a nested long-range PCR protocol and next-generation sequencing. We identified more mixed infections than expected based on Sanger sequencing of the mitochondrial gene cytochrome b, which is typically used for bar-coding these parasites. The phylogeny obtained was robust, but seven of 37 nodes still had bootstrap values under 50 %. A clade of “pale-staining” parasites previously identified with cytochrome b sequences was supported in this analysis and the relationships between morphological species corresponded with previous studies. The GC content was higher in the non-protein coding parts of the mitochondrial genome (i.e., parts coding mainly for rRNA) than in the protein coding parts. The host and parasite phylogenies were more congruent in topology than expected by chance, but the relative contributions of cospeciation and host shifting to the evolutionary history of this clade of parasites remain to be determined. Indexes of the host specificity of the parasites (i.e., the diversity of host species a parasite lineage can infect) were sensitive to rare infections. By considering the index results in parallel with the number of host species each parasite infected, the parasites present in the local community seemed to be more specialists than generalists, apart from the Haemoproteus majoris clade which is mainly generalized. However, there was no phylogenetic signal in host specificity across the parasite phylogeny, possibly suggesting that host specificity changes do not depend on the phylogeny or that the local sampling does not have all the lineages in this clade of parasites, diluting the phylogenetic signal.},
  author       = {Duc, Mélanie},
  language     = {eng},
  note         = {Student Paper},
  title        = {Whole mitochondrial genome phylogeny of a community of Haemoproteus parasites - evolutionary patterns of host specificity and transmission},
  year         = {2019},
}