@article {760,
	title = {Resolving the phylogeny of malaria parasites.},
	journal = {Proc Natl Acad Sci U S A},
	volume = {108},
	year = {2011},
	month = {2011 Aug 9},
	pages = {12973-4},
	keywords = {Animals, Evolution, Molecular, Malaria, Parasites},
	issn = {1091-6490},
	doi = {10.1073/pnas.1110141108},
	author = {Rich, Stephen M and Xu, Guang}
}
@article {775,
	title = {Progress in malaria research: the case for phylogenetics.},
	journal = {Adv Parasitol},
	volume = {54},
	year = {2003},
	month = {2003},
	pages = {255-80},
	abstract = {Malaria, from the Italian for "bad air", is a term used to describe a human disease caused by any of four parasites of the genus, Plasmodium. There are in fact over 200 described species of Plasmodium that parasitize reptiles, birds, and mammals, and may or may not cause disease in these various hosts. In this chapter, we highlight important evolutionary studies that have been undertaken to determine the relatedness among these species and their place in the taxonomic hierarchy. We begin by providing an overview of our present understanding of the phylum to which malaria parasites belong--Apicomplexa. The unique characteristics of these parasites reflect both their adaptation to the parasitic life style as well as some vestigial remnants of their pre-parasitic evolutionary past. Phylogenetic analyses provide the means for discerning the means by which these characteristics have come into existence. We next discuss the systematics of the genus Plasmodium. Morphology, genomic structure and content as well as host affiliation of these parasites are all traits that have been used for establishing taxonomic arrangements. Molecular phylogenetics has proven to be an invaluable tool in this regard and so we discuss the current phylogenetic picture of the genus as well as the correspondence among the various datasets (morphology, molecules, and host-preference). Lastly, we present a detailed account of our current understanding of the evolutionary past of the most deadly of the human malaria species--P. falciparum.},
	keywords = {Animals, Biomedical Research, Evolution, Molecular, Genome, Malaria, Phylogeny, Plasmodium},
	issn = {0065-308X},
	author = {Rich, Stephen M and Ayala, Francisco J}
}
@article {777,
	title = {Sequence diversity and evolution of the malaria vaccine candidate merozoite surface protein-1 (MSP-1) of Plasmodium falciparum.},
	journal = {Gene},
	volume = {304},
	year = {2003},
	month = {2003 Jan 30},
	pages = {65-75},
	abstract = {The merozoite surface protein-1 (MSP-1) of the malaria parasite Plasmodium falciparum is a major blood-stage antigen containing highly polymorphic tripeptide repeats in the domain known as block 2 and several non-repetitive domains that are essentially dimorphic. We have analyzed sequence variation in block 2 repeats and in non-repetitive block 17, as well as other polymorphisms within the MSP-1 gene, in clinical isolates of P. falciparum. Repeat haplotypes were defined as unique combinations of repeat motifs within block 2, whereas block 17 haplotypes were defined as unique combinations of single nucleotide replacements in this domain. A new block 17 haplotype, E-TNG-L, was found in one isolate from Vietnam. MSP-1 alleles, defined as unique combinations of haplotypes in blocks 2 and 17 and other polymorphisms within the molecule, were characterized in 60 isolates from hypoendemic Brazil and 37 isolates from mesoendemic Vietnam. Extensive diversity has been created in block 2 and elsewhere in the molecule, while maintaining significant linkage disequilibrium between polymorphisms across the non-telomeric MSP-1 locus separated by a map distance of more than 4 kb, suggesting that low meiotic recombination rates occur in both parasite populations. These results indicate a role for non-homologous recombination, such as strand-slippage mispairing during mitosis and gene conversion, in creating variation in a malarial antigen under strong diversifying selection.},
	keywords = {Alleles, Animals, Brazil, DNA, Protozoan, Evolution, Molecular, Genetic Variation, Haplotypes, Linkage Disequilibrium, Malaria Vaccines, Merozoite Surface Protein 1, Molecular Sequence Data, Plasmodium falciparum, Polymorphism, Single Nucleotide, Recombination, Genetic, Sequence Analysis, DNA, Tanzania, Thailand, Vietnam},
	issn = {0378-1119},
	author = {Ferreira, Marcelo U and Ribeiro, Weber L and Tonon, Angela P and Kawamoto, Fumihiko and Rich, Stephen M}
}
@article {780,
	title = {Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia.},
	journal = {Mol Biol Evol},
	volume = {19},
	year = {2002},
	month = {2002 May},
	pages = {619-30},
	abstract = {Mobile elements that use reverse transcriptase to make new copies of themselves are found in all major lineages of eukaryotes. The non-long terminal repeat (non-LTR) retrotransposons have been suggested to be the oldest of these eukaryotic elements. Phylogenetic analysis of non-LTR elements suggests that they have predominantly undergone vertical transmission, as opposed to the frequent horizontal transmissions found for other mobile elements. One prediction of this vertical model of inheritance is that the oldest lineages of eukaryotes should exclusively harbor the oldest lineages of non-LTR retrotransposons. Here we characterize the non-LTR retrotransposons present in one of the most primitive eukaryotes, the diplomonad Giardia lamblia. Two families of elements were detected in the WB isolate of G. lamblia currently being used for the genome sequencing project. These elements are clearly distinct from all other previously described non-LTR lineages. Phylogenetic analysis indicates that these Genie elements (for Giardia early non-LTR insertion element) are among the oldest known lineages of non-LTR elements consistent with strict vertical descent. Genie elements encode a single open reading frame with a carboxyl terminal endonuclease domain. Genie 1 is site specific, as seven to eight copies are present in a single tandem array of a 771-bp repeat near the telomere of one chromosome. The function of this repeat is not known. One additional, highly divergent, element within the Genie 1 lineage is not located in this tandem array but is near a second telomere. Four different telomere addition sites could be identified within or near the Genie elements on each of these chromosomes. The second lineage of non-LTR elements, Genie 2, is composed of about 10 degenerate copies. Genie 2 elements do not appear to be site specific in their insertion. An unusual aspect of Genie 2 is that all copies contain inverted repeats up to 172 bp in length.},
	keywords = {Animals, Base Sequence, DNA, Protozoan, Evolution, Molecular, Giardia lamblia, Long Interspersed Nucleotide Elements, Molecular Sequence Data, Open Reading Frames, Phylogeny, Repetitive Sequences, Nucleic Acid, Sequence Homology, Nucleic Acid, Telomere},
	issn = {0737-4038},
	author = {Burke, William D and Malik, Harmit S and Rich, Stephen M and Eickbush, Thomas H}
}
