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Cepeda AS, Mello B, Pacheco MA, Luo Z, Sullivan SA, Carlton JM, Escalante AA. The Genome of Plasmodium gonderi: Insights into the Evolution of Human Malaria Parasites. Genome Biol Evol 2024; 16:evae027. [PMID: 38376987 PMCID: PMC10901558 DOI: 10.1093/gbe/evae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/21/2023] [Accepted: 02/03/2024] [Indexed: 02/22/2024] Open
Abstract
Plasmodium species causing malaria in humans are not monophyletic, sharing common ancestors with nonhuman primate parasites. Plasmodium gonderi is one of the few known Plasmodium species infecting African old-world monkeys that are not found in apes. This study reports a de novo assembled P. gonderi genome with complete chromosomes. The P. gonderi genome shares codon usage, syntenic blocks, and other characteristics with the human parasites Plasmodium ovale s.l. and Plasmodium malariae, also of African origin, and the human parasite Plasmodium vivax and species found in nonhuman primates from Southeast Asia. Using phylogenetically aware methods, newly identified syntenic blocks were found enriched with conserved metabolic genes. Regions outside those blocks harbored genes encoding proteins involved in the vertebrate host-Plasmodium relationship undergoing faster evolution. Such genome architecture may have facilitated colonizing vertebrate hosts. Phylogenomic analyses estimated the common ancestor between P. vivax and an African ape parasite P. vivax-like, within the Asian nonhuman primates parasites clade. Time estimates incorporating P. gonderi placed the P. vivax and P. vivax-like common ancestor in the late Pleistocene, a time of active migration of hominids between Africa and Asia. Thus, phylogenomic and time-tree analyses are consistent with an Asian origin for P. vivax and an introduction of P. vivax-like into Africa. Unlike other studies, time estimates for the clade with Plasmodium falciparum, the most lethal human malaria parasite, coincide with their host species radiation, African hominids. Overall, the newly assembled genome presented here has the quality to support comparative genomic investigations in Plasmodium.
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Affiliation(s)
- Axl S Cepeda
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA
| | - Beatriz Mello
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA
| | - Zunping Luo
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Steven A Sullivan
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Jane M Carlton
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA
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Lamine I, Chahouri A, Moukrim A, Ait Alla A. The impact of climate change and pollution on trematode-bivalve dynamics. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106130. [PMID: 37625953 DOI: 10.1016/j.marenvres.2023.106130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
Coastal ecosystems and their marine populations are increasingly threatened by global environmental changes. Bivalves have emerged as crucial bioindicators within these ecosystems, offering valuable insights into biodiversity and overall ecosystem health. In particular, bivalves serve as hosts to trematode parasites, making them a focal point of study. Trematodes, with their life cycles intricately linked to external factors, provide excellent indicators of environmental changes and exhibit a unique ability to accumulate pollutants beyond ambient levels. Thus, they act as living sentinels, reflecting the ecological condition of their habitats. This paper presents a comprehensive review of recent research on the use of bivalve species as hosts for trematodes, examining the interactions between these organisms. The study also investigates the combined impact of trematode infections and other pollutants on bivalve molluscs. Trematode infections have multifaceted consequences for bivalve species, influencing various aspects of their physiology and behavior, including population-wide mortality. Furthermore, the coexistence of trematode infections and other sources of pollution compromises host resistance, disrupts parasite transmission, and reduces the abundance of intermediate hosts for complex-living parasites. The accumulation process of these parasites is influenced not only by external factors but also by host physiology. Consequently, the implications of climate change and environmental factors, such as temperature, salinity, and ocean acidification, are critical considerations. In summary, the intricate relationship between bivalves, trematode parasites, and their surrounding environment provides valuable insights into the health and sustainability of coastal ecosystems. A comprehensive understanding of these interactions, along with the influence of climate change and environmental parameters, is essential for effective management and conservation strategies aimed at preserving these delicate ecosystems and the diverse array of species that rely on them.
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Affiliation(s)
- Imane Lamine
- Laboratory of Aquatic Systems: Marine and Continental Ecosystems, Department of Biology, Faculty of Sciences, Ibn Zohr University, BP 8106, Agadir, Morocco.
| | - Abir Chahouri
- Laboratory of Aquatic Systems: Marine and Continental Ecosystems, Department of Biology, Faculty of Sciences, Ibn Zohr University, BP 8106, Agadir, Morocco
| | | | - Aicha Ait Alla
- Laboratory of Aquatic Systems: Marine and Continental Ecosystems, Department of Biology, Faculty of Sciences, Ibn Zohr University, BP 8106, Agadir, Morocco
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Abstract
African apes harbor at least twelve Plasmodium species, some of which have been a source of human infection. It is now well established that Plasmodium falciparum emerged following the transmission of a gorilla parasite, perhaps within the last 10,000 years, while Plasmodium vivax emerged earlier from a parasite lineage that infected humans and apes in Africa before the Duffy-negative mutation eliminated the parasite from humans there. Compared to their ape relatives, both human parasites have greatly reduced genetic diversity and an excess of nonsynonymous mutations, consistent with severe genetic bottlenecks followed by rapid population expansion. A putative new Plasmodium species widespread in chimpanzees, gorillas, and bonobos places the origin of Plasmodium malariae in Africa. Here, we review what is known about the origins and evolutionary history of all human-infective Plasmodium species, the time and circumstances of their emergence, and the diversity, host specificity, and zoonotic potential of their ape counterparts.
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Affiliation(s)
- Paul M Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL, United Kingdom
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, EH9 3FL, United Kingdom
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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Reid MJC, Switzer WM, Alonso SK, Lowenberger CA, Schillaci MA. Evolutionary history of orangutan plasmodia revealed by phylogenetic analysis of complete mtDNA genomes and new biogeographical divergence dating calibration models. Am J Primatol 2021; 84:e23298. [PMID: 34227139 DOI: 10.1002/ajp.23298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/30/2021] [Accepted: 06/16/2021] [Indexed: 11/06/2022]
Abstract
During the past 15 years, researchers have shown a renewed interest in the study of the Plasmodium parasites that infect orangutans. Most recently, studies examined the phylogenetic relationships and divergence dates of these parasites in orangutans using complete mitochondrial DNA genomes. Questions regarding the dating of these parasites, however, remain. In the present study, we provide a new calibration model for dating the origins of Plasmodium parasites in orangutans using a modified date range for the origin of macaques in Asia. Our Bayesian phylogenetic analyses of complete Plasmodium sp. mitochondrial DNA genomes inferred two clades of plasmodia in orangutans (Pongo 1 and Pongo 2), and that these clades likely represent the previously identified species Plasmodium pitheci and Plasmodium silvaticum. However, we cannot identify which Pongo clade is representative of the morphologically described species. The most recent common ancestor of both Pongo sp. plasmodia, Plasmodium. hylobati, and Plasmodium. inui dates to 3-3.16 million years ago (mya) (95% highest posterior density [HPD]: 2.09-4.08 mya). The Pongo 1 parasite diversified 0.33-0.36 mya (95% HPD: 0.12-0.63), while the Pongo 2 parasite diversified 1.15-1.22 mya (95% HPD: 0.63-1.82 mya). It now seems likely that the monkey Plasmodium (P. inui) is the result of a host switch event from the Pongo 2 parasite to sympatric monkeys, or P. hylobati. Our new estimates for the divergence of orangutan malaria parasites, and subsequent diversification, are all several hundred thousand years later than previous Bayesian estimates.
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Affiliation(s)
- Michael J C Reid
- School of Interdisciplinary Studies, Durham College, Oshawa, Ontario, Canada.,Canadian Cameroon Ape Network, Toronto, Ontario, Canada
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Carl A Lowenberger
- Centre for Cell Biology, Development and Disease, Department of Biological Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael A Schillaci
- Department of Anthropology, University of Toronto Scarborough, Toronto, Ontario, Canada
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Hernández-Hernández T, Miller EC, Román-Palacios C, Wiens JJ. Speciation across the Tree of Life. Biol Rev Camb Philos Soc 2021; 96:1205-1242. [PMID: 33768723 DOI: 10.1111/brv.12698] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023]
Abstract
Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.
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Affiliation(s)
- Tania Hernández-Hernández
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A.,Catedrática CONACYT asignada a LANGEBIO-UGA Cinvestav, Libramiento Norte Carretera León Km 9.6, 36821, Irapuato, Guanajuato, Mexico
| | - Elizabeth C Miller
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
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Zerka A, Kaczmarek R, Czerwinski M, Jaskiewicz E. Plasmodium reichenowi EBA-140 merozoite ligand binds to glycophorin D on chimpanzee red blood cells, shedding new light on origins of Plasmodium falciparum. Parasit Vectors 2017; 10:554. [PMID: 29115972 PMCID: PMC5678783 DOI: 10.1186/s13071-017-2507-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/30/2017] [Indexed: 12/04/2022] Open
Abstract
Background All symptoms of malaria are caused by the intraerythrocytic proliferation of Plasmodium merozoites. Merozoites invade erythrocytes using multiple binding ligands that recognise specific surface receptors. It has been suggested that adaptation of Plasmodium parasites to infect specific hosts is driven by changes in genes encoding Plasmodium erythrocyte-binding ligands (EBL) and reticulocyte-binding ligands (RBL). Homologs of both EBL and RBL, including the EBA-140 merozoite ligand, have been identified in P. falciparum and P. reichenowi, which infect humans and chimpanzees, respectively. The P. falciparum EBA-140 was shown to bind human glycophorin C, a minor erythrocyte sialoglycoprotein. Until now, the erythrocyte receptor for the P. reichenowi EBA-140 remained unknown. Methods The baculovirus expression vector system was used to obtain the recombinant EBA-140 Region II, and flow cytometry and immunoblotting methods were applied to characterise its specificity. Results We showed that the chimpanzee glycophorin D is the receptor for the P. reichenowi EBA-140 ligand on chimpanzee red blood cells. Conclusions We propose that the development of glycophorin C specificity is spurred by the P. falciparum lineage. We speculate that the P. falciparum EBA-140 evolved to hijack GPC on human erythrocytes during divergence from its ape ancestor.
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Affiliation(s)
- Agata Zerka
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114, Wroclaw, Poland
| | - Radoslaw Kaczmarek
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114, Wroclaw, Poland
| | - Marcin Czerwinski
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114, Wroclaw, Poland.,Faculty of Physiotherapy and Physical Education, Opole University of Technology, 45-758, Opole, Poland
| | - Ewa Jaskiewicz
- Laboratory of Glycobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114, Wroclaw, Poland. .,Faculty of Biological Sciences, University of Zielona Góra, Szafrana 1, 65-516, Zielona Góra, Poland.
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7
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De Nys H, Löhrich T, Wu D, Calvignac-Spencer S, Leendertz F. Wild African great apes as natural hosts of malaria parasites: current knowledge and research perspectives. Primate Biol 2017; 4:47-59. [PMID: 32110692 PMCID: PMC7041518 DOI: 10.5194/pb-4-47-2017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 02/24/2017] [Indexed: 11/24/2022] Open
Abstract
Humans and African great apes (AGAs) are naturally infected with several species of closely related malaria parasites. The need to understand the origins of human malaria as well as the risk of zoonotic transmissions and emergence of new malaria strains in human populations has markedly encouraged research on great ape Plasmodium parasites. Progress in the use of non-invasive methods has rendered investigations into wild ape populations possible. Present knowledge is mainly focused on parasite diversity and phylogeny, with still large gaps to fill on malaria parasite ecology. Understanding what malaria infection means in terms of great ape health is also an important, but challenging avenue of research and has been subject to relatively few research efforts so far. This paper reviews current knowledge on African great ape malaria and identifies gaps and future research perspectives.
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Affiliation(s)
- Hélène Marie De Nys
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- current address: UMI 233, Institut de Recherche pour le Développement (IRD), INSERM U1175, and University of Montpellier, Montpellier, France
| | - Therese Löhrich
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Doris Wu
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | | | - Fabian Hubertus Leendertz
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
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8
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Silva JC, Egan A, Arze C, Spouge JL, Harris DG. A new method for estimating species age supports the coexistence of malaria parasites and their Mammalian hosts. Mol Biol Evol 2015; 32:1354-64. [PMID: 25589738 PMCID: PMC4408405 DOI: 10.1093/molbev/msv005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Species in the genus Plasmodium cause malaria in humans and infect a variety of mammals and other vertebrates. Currently, estimated ages for several mammalian Plasmodium parasites differ by as much as one order of magnitude, an inaccuracy that frustrates reliable estimation of evolutionary rates of disease-related traits. We developed a novel statistical approach to dating the relative age of evolutionary lineages, based on Total Least Squares regression. We validated this lineage dating approach by applying it to the genus Drosophila. Using data from the Drosophila 12 Genomes project, our approach accurately reconstructs the age of well-established Drosophila clades, including the speciation event that led to the subgenera Drosophila and Sophophora, and age of the melanogaster species subgroup. We applied this approach to hundreds of loci from seven mammalian Plasmodium species. We demonstrate the existence of a molecular clock specific to individual Plasmodium proteins, and estimate the relative age of mammalian-infecting Plasmodium. These analyses indicate that: 1) the split between the human parasite Plasmodium vivax and P. knowlesi, from Old World monkeys, occurred 6.1 times earlier than that between P. falciparum and P. reichenowi, parasites of humans and chimpanzees, respectively; and 2) mammalian Plasmodium parasites originated 22 times earlier than the split between P. falciparum and P. reichenowi. Calibrating the absolute divergence times for Plasmodium with eukaryotic substitution rates, we show that the split between P. falciparum and P. reichenowi occurred 3.0-5.5 Ma, and that mammalian Plasmodium parasites originated over 64 Ma. Our results indicate that mammalian-infecting Plasmodium evolved contemporaneously with their hosts, with little evidence for parasite host-switching on an evolutionary scale, and provide a solid timeframe within which to place the evolution of new Plasmodium species.
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Affiliation(s)
- Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine Department of Microbiology and Immunology, University of Maryland School of Medicine
| | - Amy Egan
- Institute for Genome Sciences, University of Maryland School of Medicine
| | - Cesar Arze
- Institute for Genome Sciences, University of Maryland School of Medicine
| | - John L Spouge
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | - David G Harris
- Department of Applied Mathematics and Statistics, University of Maryland, College Park
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9
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Coevolutionary patterns and diversification of avian malaria parasites in African sunbirds (Family Nectariniidae). Parasitology 2014; 142:635-47. [DOI: 10.1017/s0031182014001681] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
SUMMARYThe coevolutionary relationships between avian malaria parasites and their hosts influence the host specificity, geographical distribution and pathogenicity of these parasites. However, to understand fine scale coevolutionary host–parasite relationships, robust and widespread sampling from closely related hosts is needed. We thus sought to explore the coevolutionary history of avianPlasmodiumand the widespread African sunbirds, family Nectariniidae. These birds are distributed throughout Africa and occupy a variety of habitats. Considering the role that habitat plays in influencing host-specificity and the role that host-specificity plays in coevolutionary relationships, African sunbirds provide an exceptional model system to study the processes that govern the distribution and diversity of avian malaria. Here we evaluated the coevolutionary histories using a multi-gene phylogeny for Nectariniidae and avianPlasmodiumfound in Nectariniidae. We then assessed the host–parasite biogeography and the structuring of parasite assemblages. We recoveredPlasmodiumlineages concurrently in East, West, South and Island regions of Africa. However, severalPlasmodiumlineages were recovered exclusively within one respective region, despite being found in widely distributed hosts. In addition, we inferred the biogeographic history of these parasites and provide evidence supporting a model of biotic diversification in avianPlasmodiumof African sunbirds.
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10
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Perkins SL. Malaria's many mates: past, present, and future of the systematics of the order Haemosporida. J Parasitol 2013; 100:11-25. [PMID: 24059436 DOI: 10.1645/13-362.1] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Malaria has been one of the most important diseases of humans throughout history and continues to be a major public health concern. The 5 species of Plasmodium that cause the disease in humans are part of the order Haemosporida, a diverse group of parasites that all have heteroxenous life cycles, alternating between a vertebrate host and a free-flying, blood-feeding dipteran vector. Traditionally, the identification and taxonomy of these parasites relied heavily on life-history characteristics, basic morphological features, and the host species infected. However, molecular approaches to resolving the phylogeny of the group have sometimes challenged many of these traditional hypotheses. One of the greatest debates has concerned the origin of the most virulent of the human-infecting parasites, Plasmodium falciparum, with early results suggesting a close relationship with an avian parasite. Subsequent phylogenetic studies placed it firmly within the mammalian clade instead, but the avian origin hypothesis has been revived with recent genome-based analyses. The rooting of the tree of Haemosporida has also been inconsistent, and the various topologies that result certainly affect our interpretation of the history of the group. There is clearly a pressing need to obtain a much more complete degree of taxon sampling of haemosporidians, as well as a greater number of characters before confidence can be placed in any hypothesis regarding the evolutionary history of the order. There are numerous challenges moving forward, particularly for generating complete genome sequences of avian and saurian parasites.
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Affiliation(s)
- Susan L Perkins
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024
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11
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Bensch S, Hellgren O, Križanauskienė A, Palinauskas V, Valkiūnas G, Outlaw D, Ricklefs RE. How can we determine the molecular clock of malaria parasites? Trends Parasitol 2013; 29:363-9. [DOI: 10.1016/j.pt.2013.03.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 03/25/2013] [Accepted: 03/27/2013] [Indexed: 01/02/2023]
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12
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Diversity, host switching and evolution of Plasmodium vivax infecting African great apes. Proc Natl Acad Sci U S A 2013; 110:8123-8. [PMID: 23637341 DOI: 10.1073/pnas.1306004110] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Plasmodium vivax is considered to be absent from Central and West Africa because of the protective effect of Duffy negativity. However, there are reports of persons returning from these areas infected with this parasite and observations suggesting the existence of transmission. Among the possible explanations for this apparent paradox, the existence of a zoonotic reservoir has been proposed. May great apes be this reservoir? We analyze the mitochondrial and nuclear genetic diversity of P. vivax parasites isolated from great apes in Africa and compare it to parasites isolated from travelers returning from these regions of Africa, as well as to human isolates distributed all over the world. We show that the P. vivax sequences from parasites of great apes form a clade genetically distinct from the parasites circulating in humans. We show that this clade's parasites can be infectious to humans by describing the case of a traveler returning from the Central African Republic infected with one of them. The relationship between this P. vivax clade in great apes and the human isolates is discussed.
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13
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Sundararaman SA, Liu W, Keele BF, Learn GH, Bittinger K, Mouacha F, Ahuka-Mundeke S, Manske M, Sherrill-Mix S, Li Y, Malenke JA, Delaporte E, Laurent C, Mpoudi Ngole E, Kwiatkowski DP, Shaw GM, Rayner JC, Peeters M, Sharp PM, Bushman FD, Hahn BH. Plasmodium falciparum-like parasites infecting wild apes in southern Cameroon do not represent a recurrent source of human malaria. Proc Natl Acad Sci U S A 2013; 110:7020-5. [PMID: 23569255 PMCID: PMC3637760 DOI: 10.1073/pnas.1305201110] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Wild-living chimpanzees and gorillas harbor a multitude of Plasmodium species, including six of the subgenus Laverania, one of which served as the progenitor of Plasmodium falciparum. Despite the magnitude of this reservoir, it is unknown whether apes represent a source of human infections. Here, we used Plasmodium species-specific PCR, single-genome amplification, and 454 sequencing to screen humans from remote areas of southern Cameroon for ape Laverania infections. Among 1,402 blood samples, we found 1,000 to be Plasmodium mitochondrial DNA (mtDNA) positive, all of which contained human parasites as determined by sequencing and/or restriction enzyme digestion. To exclude low-abundance infections, we subjected 514 of these samples to 454 sequencing, targeting a region of the mtDNA genome that distinguishes ape from human Laverania species. Using algorithms specifically developed to differentiate rare Plasmodium variants from 454-sequencing error, we identified single and mixed-species infections with P. falciparum, Plasmodium malariae, and/or Plasmodium ovale. However, none of the human samples contained ape Laverania parasites, including the gorilla precursor of P. falciparum. To characterize further the diversity of P. falciparum in Cameroon, we used single-genome amplification to amplify 3.4-kb mtDNA fragments from 229 infected humans. Phylogenetic analysis identified 62 new variants, all of which clustered with extant P. falciparum, providing further evidence that P. falciparum emerged following a single gorilla-to-human transmission. Thus, unlike Plasmodium knowlesi-infected macaques in southeast Asia, African apes harboring Laverania parasites do not seem to serve as a recurrent source of human malaria, a finding of import to ongoing control and eradication measures.
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Affiliation(s)
- Sesh A. Sundararaman
- Departments of Medicine and
- Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Brandon F. Keele
- The AIDS and Cancer Virus Program, Science Applications International Corporation–Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | | | - Kyle Bittinger
- Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Fatima Mouacha
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement and University of Montpellier 1, 34394 Montpellier, France
| | - Steve Ahuka-Mundeke
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement and University of Montpellier 1, 34394 Montpellier, France
| | - Magnus Manske
- Sanger Institute Malaria Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Scott Sherrill-Mix
- Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | | | | | - Eric Delaporte
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement and University of Montpellier 1, 34394 Montpellier, France
| | - Christian Laurent
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement and University of Montpellier 1, 34394 Montpellier, France
| | - Eitel Mpoudi Ngole
- Centre de Recherches pour les Maladies Emergents et Ré-émergents and Institut de Recherches Médicales et d'Etudes des Plantes Médicinales, BP 906, Yaoundé, Cameroon; and
| | - Dominic P. Kwiatkowski
- Sanger Institute Malaria Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - George M. Shaw
- Departments of Medicine and
- Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Julian C. Rayner
- Sanger Institute Malaria Programme, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Martine Peeters
- Unité Mixte Internationale 233, Institut de Recherche pour le Développement and University of Montpellier 1, 34394 Montpellier, France
| | - Paul M. Sharp
- Institute of Evolutionary Biology and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Frederic D. Bushman
- Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Beatrice H. Hahn
- Departments of Medicine and
- Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Putaporntip C, Hughes AL, Jongwutiwes S. Low level of sequence diversity at merozoite surface protein-1 locus of Plasmodium ovale curtisi and P. ovale wallikeri from Thai isolates. PLoS One 2013; 8:e58962. [PMID: 23536840 PMCID: PMC3594193 DOI: 10.1371/journal.pone.0058962] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 02/08/2013] [Indexed: 12/04/2022] Open
Abstract
Background The merozoite surface protein-1 (MSP-1) is a candidate target for the development of blood stage vaccines against malaria. Polymorphism in MSP-1 can be useful as a genetic marker for strain differentiation in malarial parasites. Although sequence diversity in the MSP-1 locus has been extensively analyzed in field isolates of Plasmodium falciparum and P. vivax, the extent of variation in its homologues in P. ovale curtisi and P. ovale wallikeri, remains unknown. Methodology/Principal Findings Analysis of the mitochondrial cytochrome b sequences of 10 P. ovale isolates from symptomatic malaria patients from diverse endemic areas of Thailand revealed co-existence of P. ovale curtisi (n = 5) and P. ovale wallikeri (n = 5). Direct sequencing of the PCR-amplified products encompassing the entire coding region of MSP-1 of P. ovale curtisi (PocMSP-1) and P. ovale wallikeri (PowMSP-1) has identified 3 imperfect repeated segments in the former and one in the latter. Most amino acid differences between these proteins were located in the interspecies variable domains of malarial MSP-1. Synonymous nucleotide diversity (πS) exceeded nonsynonymous nucleotide diversity (πN) for both PocMSP-1 and PowMSP-1, albeit at a non-significant level. However, when MSP-1 of both these species was considered together, πS was significantly greater than πN (p<0.0001), suggesting that purifying selection has shaped diversity at this locus prior to speciation. Phylogenetic analysis based on conserved domains has placed PocMSP-1 and PowMSP-1 in a distinct bifurcating branch that probably diverged from each other around 4.5 million years ago. Conclusion/Significance The MSP-1 sequences support that P. ovale curtisi and P. ovale wallikeri are distinct species. Both species are sympatric in Thailand. The low level of sequence diversity in PocMSP-1 and PowMSP-1 among Thai isolates could stem from persistent low prevalence of these species, limiting the chance of outcrossing at this locus.
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Affiliation(s)
- Chaturong Putaporntip
- Molecular Biology of Malaria and Opportunistic Parasites Research Unit, Department of Parasitology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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15
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Yalcindag E, Elguero E, Arnathau C, Durand P, Akiana J, Anderson TJ, Aubouy A, Balloux F, Besnard P, Bogreau H, Carnevale P, D'Alessandro U, Fontenille D, Gamboa D, Jombart T, Le Mire J, Leroy E, Maestre A, Mayxay M, Ménard D, Musset L, Newton PN, Nkoghé D, Noya O, Ollomo B, Rogier C, Veron V, Wide A, Zakeri S, Carme B, Legrand E, Chevillon C, Ayala FJ, Renaud F, Prugnolle F. Multiple independent introductions of Plasmodium falciparum in South America. Proc Natl Acad Sci U S A 2012; 109:511-6. [PMID: 22203975 PMCID: PMC3258587 DOI: 10.1073/pnas.1119058109] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The origin of Plasmodium falciparum in South America is controversial. Some studies suggest a recent introduction during the European colonizations and the transatlantic slave trade. Other evidence--archeological and genetic--suggests a much older origin. We collected and analyzed P. falciparum isolates from different regions of the world, encompassing the distribution range of the parasite, including populations from sub-Saharan Africa, the Middle East, Southeast Asia, and South America. Analyses of microsatellite and SNP polymorphisms show that the populations of P. falciparum in South America are subdivided in two main genetic clusters (northern and southern). Phylogenetic analyses, as well as Approximate Bayesian Computation methods suggest independent introductions of the two clusters from African sources. Our estimates of divergence time between the South American populations and their likely sources favor a likely introduction from Africa during the transatlantic slave trade.
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Affiliation(s)
- Erhan Yalcindag
- Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle, Unité Mixte de Recherche 5290-224, Centre National de la Recherche Scientifique-Institut de Recherche pour le Développement-Université de Montpellier I-Université de Montpellier II, 34394 Montpellier Cedex 5, France
| | - Eric Elguero
- Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle, Unité Mixte de Recherche 5290-224, Centre National de la Recherche Scientifique-Institut de Recherche pour le Développement-Université de Montpellier I-Université de Montpellier II, 34394 Montpellier Cedex 5, France
| | - Céline Arnathau
- Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle, Unité Mixte de Recherche 5290-224, Centre National de la Recherche Scientifique-Institut de Recherche pour le Développement-Université de Montpellier I-Université de Montpellier II, 34394 Montpellier Cedex 5, France
| | - Patrick Durand
- Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle, Unité Mixte de Recherche 5290-224, Centre National de la Recherche Scientifique-Institut de Recherche pour le Développement-Université de Montpellier I-Université de Montpellier II, 34394 Montpellier Cedex 5, France
| | - Jean Akiana
- Service Epidémiologie Moléculaire et Parasitaire, Département de la Médecine Préventive et des Essais Cliniques, Laboratoire National de Santé Publique, Brazzaville, 1 Kinshasa, Republic of the Congo
| | - Timothy J. Anderson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX 78245
| | - Agnes Aubouy
- Institut de Recherche pour le Développement–Unité Mixte de Recherche 152, Université Paul Sabatier, 31062 Toulouse, France
| | - François Balloux
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College, London W2 1PG, United Kingdom
| | - Patrick Besnard
- Malaria Control Program, Société Nationale de Métallurgie (Sonamet), Lobito, Angola
| | - Hervé Bogreau
- Institute for Biomedical Research of the French Army and Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes–Unité Mixte de Recherche 6236, Allée du Médecin Colonel Jamot, Marseille, Cedex 07, France
| | - Pierre Carnevale
- Institut de Recherche pour le Développement, 34394 Montpellier, France
| | - Umberto D'Alessandro
- Department of Parasitology, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Didier Fontenille
- Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle, Unité Mixte de Recherche 5290-224, Centre National de la Recherche Scientifique-Institut de Recherche pour le Développement-Université de Montpellier I-Université de Montpellier II, 34394 Montpellier Cedex 5, France
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, AP 4314, Lima 100, Peru
| | - Thibaut Jombart
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College, London W2 1PG, United Kingdom
| | - Jacques Le Mire
- Malaria Control Program, Société Nationale de Métallurgie (Sonamet), Lobito, Angola
| | - Eric Leroy
- Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle, Unité Mixte de Recherche 5290-224, Centre National de la Recherche Scientifique-Institut de Recherche pour le Développement-Université de Montpellier I-Université de Montpellier II, 34394 Montpellier Cedex 5, France
- Unité Emergence des Pathologies Virales, Unité Mixte de Recherche 190, Institut de Recherche pour le Développement, Université de la Méditerranée, Centre International de Recherche médicale de Franceville BP 769 Franceville, Gabon
| | - Amanda Maestre
- Grupo Salud y Comunidad, Facultad de Medicina, Universidad de Antioquía, Medellín, Colombia
| | - Mayfong Mayxay
- Wellcome Trust–Mahosot Hospital–Oxford Tropical Medicine Research Collaboration, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Didier Ménard
- Molecular Epidemiology Unit, Pasteur Institute of Cambodia, 12152 Phnom Penh, Cambodia
| | - Lise Musset
- Parasitology Unit, Institut Pasteur de Guyane, BP6010, 97306 Cayenne Cedex, French Guiana
| | - Paul N. Newton
- Wellcome Trust–Mahosot Hospital–Oxford Tropical Medicine Research Collaboration, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Dieudonné Nkoghé
- Unité Emergence des Pathologies Virales, Unité Mixte de Recherche 190, Institut de Recherche pour le Développement, Université de la Méditerranée, Centre International de Recherche médicale de Franceville BP 769 Franceville, Gabon
| | - Oscar Noya
- Centro para Estudios Sobre Malaria, Instituto de Altos Estudios en Salud “Dr. Arnoldo Gabaldón”, Ministerio del Poder Popular para la Salud and Instituto de Medicina Tropical, Universidad Central de Venezuela, 2101 Maracay, Caracas, Venezuela
| | - Benjamin Ollomo
- Unité Emergence des Pathologies Virales, Unité Mixte de Recherche 190, Institut de Recherche pour le Développement, Université de la Méditerranée, Centre International de Recherche médicale de Franceville BP 769 Franceville, Gabon
| | - Christophe Rogier
- Institute for Biomedical Research of the French Army and Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes–Unité Mixte de Recherche 6236, Allée du Médecin Colonel Jamot, Marseille, Cedex 07, France
| | - Vincent Veron
- Centre d'Investigation Clinique Epidémiologie Clinique Antilles, Guyane 802, Cayenne General Hospital, 97306 Cayenne, French Guiana
| | - Albina Wide
- Centro para Estudios Sobre Malaria, Instituto de Altos Estudios en Salud “Dr. Arnoldo Gabaldón”, Ministerio del Poder Popular para la Salud and Instituto de Medicina Tropical, Universidad Central de Venezuela, 2101 Maracay, Caracas, Venezuela
| | - Sedigheh Zakeri
- Malaria and Vector Research Group, Biotechnology Research Center, Pasteur Institute of Iran, 13164 Tehran, Iran; and
| | - Bernard Carme
- Centre d'Investigation Clinique Epidémiologie Clinique Antilles, Guyane 802, Cayenne General Hospital, 97306 Cayenne, French Guiana
| | - Eric Legrand
- Parasitology Unit, Institut Pasteur de Guyane, BP6010, 97306 Cayenne Cedex, French Guiana
| | - Christine Chevillon
- Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle, Unité Mixte de Recherche 5290-224, Centre National de la Recherche Scientifique-Institut de Recherche pour le Développement-Université de Montpellier I-Université de Montpellier II, 34394 Montpellier Cedex 5, France
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
| | - François Renaud
- Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle, Unité Mixte de Recherche 5290-224, Centre National de la Recherche Scientifique-Institut de Recherche pour le Développement-Université de Montpellier I-Université de Montpellier II, 34394 Montpellier Cedex 5, France
| | - Franck Prugnolle
- Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle, Unité Mixte de Recherche 5290-224, Centre National de la Recherche Scientifique-Institut de Recherche pour le Développement-Université de Montpellier I-Université de Montpellier II, 34394 Montpellier Cedex 5, France
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Panneerselvam P, Bawankar P, Kulkarni S, Patankar S. In Silico Prediction of Evolutionarily Conserved GC-Rich Elements Associated with Antigenic Proteins of Plasmodium falciparum. Evol Bioinform Online 2011; 7:235-55. [PMID: 22375094 PMCID: PMC3283219 DOI: 10.4137/ebo.s8162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The Plasmodium falciparum genome being AT-rich, the presence of GC-rich regions suggests functional significance. Evolution imposes selection pressure to retain functionally important coding and regulatory elements. Hence searching for evolutionarily conserved GC-rich, intergenic regions in an AT-rich genome will help in discovering new coding regions and regulatory elements. We have used elevated GC content in intergenic regions coupled with sequence conservation against P. reichenowi, which is evolutionarily closely related to P. falciparum to identify potential sequences of functional importance. Interestingly, ~30% of the GC-rich, conserved sequences were associated with antigenic proteins encoded by var and rifin genes. The majority of sequences identified in the 5′ UTR of var genes are represented by short expressed sequence tags (ESTs) in cDNA libraries signifying that they are transcribed in the parasite. Additionally, 19 sequences were located in the 3′ UTR of rifins and 4 also have overlapping ESTs. Further analysis showed that several sequences associated with var genes have the capacity to encode small peptides. A previous report has shown that upstream peptides can regulate the expression of var genes hence we propose that these conserved GC-rich sequences may play roles in regulation of gene expression.
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Affiliation(s)
- Porkodi Panneerselvam
- Centre for Biotechnology, Anna University, Sardar Patel Road, Guindy, Chennai 600025, India
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17
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Pacheco MA, Battistuzzi FU, Junge RE, Cornejo OE, Williams CV, Landau I, Rabetafika L, Snounou G, Jones-Engel L, Escalante AA. Timing the origin of human malarias: the lemur puzzle. BMC Evol Biol 2011; 11:299. [PMID: 21992100 PMCID: PMC3228831 DOI: 10.1186/1471-2148-11-299] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 10/12/2011] [Indexed: 01/14/2023] Open
Abstract
Background Timing the origin of human malarias has been a focus of great interest. Previous studies on the mitochondrial genome concluded that Plasmodium in primates, including those parasitic to humans, radiated relatively recently during a process where host switches were common. Those investigations, however, assumed constant rate of evolution and tightly bound (fixed) calibration points based on host fossils or host distribution. We investigate the effect of such assumptions using different molecular dating methods. We include parasites from Lemuroidea since their distribution provides an external validation to time estimates allowing us to disregard scenarios that cannot explain their introduction in Madagascar. Results We reject the assumption that the Plasmodium mitochondrial genome, as a unit or each gene separately, evolves at a constant rate. Our analyses show that Lemuroidea parasites are a monophyletic group that shares a common ancestor with all Catarrhini malarias except those related to P. falciparum. However, we found no evidence that this group of parasites branched with their hosts early in the evolution of primates. We applied relaxed clock methods and different calibrations points to explore the origin of primate malarias including those found in African apes. We showed that previous studies likely underestimated the origin of malarial parasites in primates. Conclusions The use of fossils from the host as absolute calibration and the assumption of a strict clock likely underestimate time when performing molecular dating analyses on malarial parasites. Indeed, by exploring different calibration points, we found that the time for the radiation of primate parasites may have taken place in the Eocene, a time consistent with the radiation of African anthropoids. The radiation of the four human parasite lineages was part of such events. The time frame estimated in this investigation, together with our phylogenetic analyses, made plausible a scenario where gorillas and humans acquired malaria from a Pan lineage.
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Affiliation(s)
- M Andreína Pacheco
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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18
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Blanquart S, Gascuel O. Mitochondrial genes support a common origin of rodent malaria parasites and Plasmodium falciparum's relatives infecting great apes. BMC Evol Biol 2011; 11:70. [PMID: 21406081 PMCID: PMC3070646 DOI: 10.1186/1471-2148-11-70] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 03/15/2011] [Indexed: 11/16/2022] Open
Abstract
Background Plasmodium falciparum is responsible for the most acute form of human malaria. Most recent studies demonstrate that it belongs to a monophyletic lineage specialized in the infection of great ape hosts. Several other Plasmodium species cause human malaria. They all belong to another distinct lineage of parasites which infect a wider range of primate species. All known mammalian malaria parasites appear to be monophyletic. Their clade includes the two previous distinct lineages of parasites of primates and great apes, one lineage of rodent parasites, and presumably Hepatocystis species. Plasmodium falciparum and great ape parasites are commonly thought to be the sister-group of all other mammal-infecting malaria parasites. However, some studies supported contradictory origins and found parasites of great apes to be closer to those of rodents, or to those of other primates. Results To distinguish between these mutually exclusive hypotheses on the origin of Plasmodium falciparum and its great ape infecting relatives, we performed a comprehensive phylogenetic analysis based on a data set of three mitochondrial genes from 33 to 84 malaria parasites. We showed that malarial mitochondrial genes have evolved slowly and are compositionally homogeneous. We estimated their phylogenetic relationships using Bayesian and maximum-likelihood methods. Inferred trees were checked for their robustness to the (i) site selection, (ii) assumptions of various probabilistic models, and (iii) taxon sampling. Our results robustly support a common ancestry of rodent parasites and Plasmodium falciparum's relatives infecting great apes. Conclusions Our results refute the most common view of the origin of great ape malaria parasites, and instead demonstrate the robustness of a less well-established phylogenetic hypothesis, under which Plasmodium falciparum and its relatives infecting great apes are closely related to rodent parasites. This study sheds light on the evolutionary history of Plasmodium falciparum, a major issue for human health.
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Affiliation(s)
- Samuel Blanquart
- Méthodes et Algorithmes pour la Bioinformatique, LIRMM, UMR 5506, CNRS-Université de Montpellier 2, Montpellier, France.
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19
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Prugnolle F, Durand P, Ollomo B, Duval L, Ariey F, Arnathau C, Gonzalez JP, Leroy E, Renaud F. A fresh look at the origin of Plasmodium falciparum, the most malignant malaria agent. PLoS Pathog 2011; 7:e1001283. [PMID: 21383971 PMCID: PMC3044689 DOI: 10.1371/journal.ppat.1001283] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
From which host did the most malignant human malaria come: birds, primates, or rodents? When did the transfer occur? Over the last half century, these have been some of the questions up for debate about the origin of Plasmodium falciparum, the most common and deadliest human malaria parasite, which is responsible for at least one million deaths every year. Recent findings bring elements in favor of a transfer from great apes, but are these evidences really solid? What are the grey areas that remain to be clarified? Here, we examine in depth these new elements and discuss how they modify our perception of the origin and evolution of P. falciparum. We also discuss the perspectives these new discoveries open.
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Affiliation(s)
- Franck Prugnolle
- Laboratoire MIVEGEC (UM1-CNRS-IRD), Montpellier, France
- * E-mail: (FP); (PD); (FR)
| | - Patrick Durand
- Laboratoire MIVEGEC (UM1-CNRS-IRD), Montpellier, France
- * E-mail: (FP); (PD); (FR)
| | - Benjamin Ollomo
- Unité de Parasitologie Médicale, Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Linda Duval
- Laboratoire MIVEGEC (UM1-CNRS-IRD), Montpellier, France
- Unité de Parasitologie Médicale, Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Frédéric Ariey
- Unité de Parasitologie Médicale, Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | | | - Jean-Paul Gonzalez
- Unité de Recherche en Ecologie de la Santé, Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Eric Leroy
- Laboratoire MIVEGEC (UM1-CNRS-IRD), Montpellier, France
- Unité des Maladies Virales Emergentes, Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - François Renaud
- Laboratoire MIVEGEC (UM1-CNRS-IRD), Montpellier, France
- * E-mail: (FP); (PD); (FR)
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Abstract
OBJECTIVE The evolutionary history of human malaria parasites (genus Plasmodium) has long been a subject of speculation and controversy. The complete genome sequences of the two most widespread human malaria parasites, P. falciparum and P. vivax, and of the monkey parasite P. knowlesi are now available, together with the draft genomes of the chimpanzee parasite P. reichenowi, three rodent parasites, P. yoelii yoelli, P. berghei and P. chabaudi chabaudi, and one avian parasite, P. gallinaceum. METHODS We present here an analysis of 45 orthologous gene sequences across the eight species that resolves the relationships of major Plasmodium lineages, and provides the first comprehensive dating of the age of those groups. RESULTS Our analyses support the hypothesis that the last common ancestor of P. falciparum and the chimpanzee parasite P. reichenowi occurred around the time of the human-chimpanzee divergence. P. falciparum infections of African apes are most likely derived from humans and not the other way around. On the other hand, P. vivax, split from the monkey parasite P. knowlesi in the much more distant past, during the time that encompasses the separation of the Great Apes and Old World Monkeys. CONCLUSION The results support an ancient association between malaria parasites and their primate hosts, including humans.
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