1
|
Pacheco MA, Cepeda AS, Miller EA, Beckerman S, Oswald M, London E, Mateus-Pinilla NE, Escalante AA. A new long-read mitochondrial-genome protocol (PacBio HiFi) for haemosporidian parasites: a tool for population and biodiversity studies. Malar J 2024; 23:134. [PMID: 38704592 PMCID: PMC11069185 DOI: 10.1186/s12936-024-04961-8] [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: 02/26/2024] [Accepted: 04/24/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Studies on haemosporidian diversity, including origin of human malaria parasites, malaria's zoonotic dynamic, and regional biodiversity patterns, have used target gene approaches. However, current methods have a trade-off between scalability and data quality. Here, a long-read Next-Generation Sequencing protocol using PacBio HiFi is presented. The data processing is supported by a pipeline that uses machine-learning for analysing the reads. METHODS A set of primers was designed to target approximately 6 kb, almost the entire length of the haemosporidian mitochondrial genome. Amplicons from different samples were multiplexed in an SMRTbell® library preparation. A pipeline (HmtG-PacBio Pipeline) to process the reads is also provided; it integrates multiple sequence alignments, a machine-learning algorithm that uses modified variational autoencoders, and a clustering method to identify the mitochondrial haplotypes/species in a sample. Although 192 specimens could be studied simultaneously, a pilot experiment with 15 specimens is presented, including in silico experiments where multiple data combinations were tested. RESULTS The primers amplified various haemosporidian parasite genomes and yielded high-quality mt genome sequences. This new protocol allowed the detection and characterization of mixed infections and co-infections in the samples. The machine-learning approach converged into reproducible haplotypes with a low error rate, averaging 0.2% per read (minimum of 0.03% and maximum of 0.46%). The minimum recommended coverage per haplotype is 30X based on the detected error rates. The pipeline facilitates inspecting the data, including a local blast against a file of provided mitochondrial sequences that the researcher can customize. CONCLUSIONS This is not a diagnostic approach but a high-throughput method to study haemosporidian sequence assemblages and perform genotyping by targeting the mitochondrial genome. Accordingly, the methodology allowed for examining specimens with multiple infections and co-infections of different haemosporidian parasites. The pipeline enables data quality assessment and comparison of the haplotypes obtained to those from previous studies. Although a single locus approach, whole mitochondrial data provide high-quality information to characterize species pools of haemosporidian parasites.
Collapse
Affiliation(s)
- M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA.
| | - Axl S Cepeda
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA
| | - Erica A Miller
- University of Pennsylvania, Wildlife Futures Program, Kennett Square, Philadelphia, PA, 19348, USA
| | | | | | - Evan London
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Nohra E Mateus-Pinilla
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
- Illinois Natural History Survey-Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, 61802, USA
| | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, (SERC - 645), 1925 N. 12 St, Philadelphia, PA, 19122-1801, USA.
| |
Collapse
|
2
|
Pacheco MA, Escalante AA. Origin and diversity of malaria parasites and other Haemosporida. Trends Parasitol 2023; 39:501-516. [PMID: 37202254 DOI: 10.1016/j.pt.2023.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/17/2023] [Accepted: 04/23/2023] [Indexed: 05/20/2023]
Abstract
Symbionts, including parasites, are ubiquitous in all world ecosystems. Understanding the diversity of symbiont species addresses diverse questions, from the origin of infectious diseases to inferring processes shaping regional biotas. Here, we review the current approaches to studying Haemosporida's species diversity and evolutionary history. Despite the solid knowledge of species linked to diseases, such as the agents of human malaria, studies on haemosporidian phylogeny, diversity, ecology, and evolution are still limited. The available data, however, indicate that Haemosporida is an extraordinarily diverse and cosmopolitan clade of symbionts. Furthermore, this clade seems to have originated with their vertebrate hosts, particularly birds, as part of complex community level processes that we are still characterizing.
Collapse
Affiliation(s)
- M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA.
| | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA.
| |
Collapse
|
3
|
Córdoba OH, Ferreira FC, Pacheco MA, Escalante AA, Braga ÉM. Plasmodium ouropretensis, n. sp., a new case of non-erythrocytic species within lizard malaria parasites. Parasitology 2021; 148:1467-1474. [PMID: 34099070 PMCID: PMC11010158 DOI: 10.1017/s0031182021000895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 11/07/2022]
Abstract
Delimiting and describing Plasmodium species in reptiles remains a pressing problem in Haemosporida taxonomy. The few morphological characters used can overlap, and the significance of some life-history traits is not fully understood. Morphologically identical lizard Plasmodium forms have been reported infecting different cell types (red and white blood cells) in the same host and have been considered the same species. An example is Plasmodium tropiduri tropiduri, a species known to infect erythrocytes, thrombocytes and lymphocyte-like cells. Here, both forms of P. t. tropiduri were analysed using light microscope-based morphological characteristics and phylogenetic inferences based on almost complete mitochondrial genomes of parasites naturally infecting lizards in southeastern Brazil. Although morphologically similar, two distinct phylogenetic lineages infecting erythrocytes and non-erythrocytic cells were found. The lineage found in the erythrocytes forms a monophyletic group with species from Colombia. However, the non-erythrocytic lineage shares a recent common ancestor with Plasmodium leucocytica, which infects leucocytes in lizards from the Caribbean islands. Here, Plasmodium ouropretensis n. sp. is described as a species that infects thrombocytes and lymphocyte-like cells.
Collapse
Affiliation(s)
- Oscar Hernandes Córdoba
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología, A.C. Xalapa, Veracruz, México
- Malaria Laboratory, Department of Parasitology, Universidade Federal de Minas Gerais, Belo Horizonte – MG, Brazil
| | - Francisco C. Ferreira
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
- Center for Vector Biology, Rutgers University, New Brunswick, NJ, USA
| | - M. Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA, USA
| | - Ananias A. Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA, USA
| | - Érika Martins Braga
- Malaria Laboratory, Department of Parasitology, Universidade Federal de Minas Gerais, Belo Horizonte – MG, Brazil
| |
Collapse
|
4
|
Oliveira L, Dias RJP, Rossi MF, D'Agosto M, Santos HA. Molecular diversity and coalescent species delimitation of avian haemosporidian parasites in an endemic bird species of South America. Parasitol Res 2020; 119:4033-4047. [PMID: 33030600 DOI: 10.1007/s00436-020-06908-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 09/27/2020] [Indexed: 12/18/2022]
Abstract
Haemoproteus spp. and Plasmodium spp. are blood parasites that occur in birds worldwide. Identifying the species within this group is complex, especially in wild birds that present low parasitemia when captured, making morphological identification very difficult. Thus, the use of alternative tools to identify species may be useful in the elucidation of the distribution of parasites that circulate in bird populations. The objectives of this study were to determine the prevalence and parasitemia of the genera Plasmodium and Haemoproteus in Tachyphonus coronatus in the Atlantic Forest, Brazil, and to evaluate the molecular diversity, geographic distribution, and specificity of these parasites based on coalescent species delimitation methods. Microscopic analysis, PCR, cyt b gene sequencing, phylogenetic analysis and coalescent species delimitation using single-locus algorithms were performed (Poisson tree process (PTP) and multi-rate Poisson tree process (MPTP) methods). The analyses were performed in 117 avian host individuals. The prevalence was 55.5% for Plasmodium and 1.7% for Haemoproteus, with a mean parasitemia of 0.06%. Twenty-five Plasmodium and two Haemoproteus lineages were recovered. The MPTP method recovered seven different evolutionarily significant units (ESUs) of Plasmodium and one of Haemoproteus, whereas PTP presented fourteen ESUs of Plasmodium and one of Haemoproteus. The MPTP was more consistent with current taxonomy, while PTP overestimated the number of lineages. These ESUs are widely distributed and have already been found in 22 orders of birds that, all together, inhabit every continent, except Antarctica. The computational methods of species delimitation proved to be effective in cases where the classification of Haemosporida based just on morphology is insufficient.
Collapse
Affiliation(s)
- Luísa Oliveira
- Department of Animal Parasitology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Seropédica, RJ, Brazil
| | - Roberto Júnio Pedroso Dias
- Department of Zoology (LabProto), Biological Sciences Institute, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil.,Laboratory of Protozoology (LabProto), Biological Sciences Institute, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Mariana F Rossi
- Department of Zoology (LabProto), Biological Sciences Institute, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil. .,Laboratory of Protozoology (LabProto), Biological Sciences Institute, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil.
| | - Marta D'Agosto
- Department of Zoology (LabProto), Biological Sciences Institute, Federal University of Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Huarrisson A Santos
- Department of Epidemiology and Public Health, Veterinary Institute, Federal Rural University of Rio de Janeiro, Seropédica, RJ, Brazil
| |
Collapse
|
5
|
de Oliveira L, Cedrola F, Senra MVX, Scopel KKG, Martinele I, Tostes R, Dias RJP, D'Agosto M. Polymorphism evidence in Plasmodium (Haemamoeba) lutzi Lucena, 1939 (Apicomplexa, Haemosporida) isolated from Brazilian wild birds. Parasitol Int 2019; 70:70-76. [DOI: 10.1016/j.parint.2019.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 06/15/2018] [Accepted: 02/01/2019] [Indexed: 01/27/2023]
|
6
|
Malaria Infection is Lower in Invasive Anoles than Native Anoles in Central Florida, USA. J HERPETOL 2019. [DOI: 10.1670/18-056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
7
|
Galen SC, Nunes R, Sweet PR, Perkins SL. Integrating coalescent species delimitation with analysis of host specificity reveals extensive cryptic diversity despite minimal mitochondrial divergence in the malaria parasite genus Leucocytozoon. BMC Evol Biol 2018; 18:128. [PMID: 30165810 PMCID: PMC6117968 DOI: 10.1186/s12862-018-1242-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/15/2018] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Coalescent methods that use multi-locus sequence data are powerful tools for identifying putatively reproductively isolated lineages, though this approach has rarely been used for the study of microbial groups that are likely to harbor many unrecognized species. Among microbial symbionts, integrating genetic species delimitation methods with trait data that could indicate reproductive isolation, such as host specificity data, has rarely been used despite its potential to inform species limits. Here we test the ability of an integrative approach combining genetic and host specificity data to delimit species within the avian malaria parasite genus Leucocytozoon in central Alaska. RESULTS We sequenced seven nuclear loci for 69 Leucocytozoon samples and used multiple species delimitation methods (GMYC and BPP models), tested for differences in host infection patterns among putative species based on 406 individual infections, and characterized parasite morphology. We found that cryptic morphology has masked a highly diverse Leucocytozoon assemblage, with most species delimitation methods recovering support for at least 21 separate species that occur sympatrically and have divergent host infection patterns. Reproductive isolation among putative species appears to have evolved despite low mtDNA divergence, and in one instance two Leucocytozoon cytb haplotypes that differed by a single base pair (~ 0.2% divergence) were supported as separate species. However, there was no consistent association between mtDNA divergence and species limits. Among cytb haplotypes that differed by one to three base pairs we observed idiosyncratic patterns of nuclear and ecological divergence, with cytb haplotype pairs found to be either conspecific, reproductively isolated with no divergence in host specificity, or reproductively isolated with divergent patterns of host specialization. CONCLUSION Integrating multi-locus genetic species delimitation methods and non-traditional ecological data types such as host specificity provide a novel view of the diversity of avian malaria parasites that has been missed previously using morphology and mtDNA barcodes. Species delimitation methods show that Leucocytozoon is highly species-rich in Alaska, and the genus is likely to harbor extraordinary species-level diversity worldwide. Integrating genetic and ecological data will be an important approach for understanding the diversity and evolutionary history of microbial symbionts moving forward.
Collapse
Affiliation(s)
- Spencer C. Galen
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
| | - Renato Nunes
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
| | - Paul R. Sweet
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
| | - Susan L. Perkins
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024 USA
| |
Collapse
|
8
|
Pacheco MA, Cepeda AS, Bernotienė R, Lotta IA, Matta NE, Valkiūnas G, Escalante AA. Primers targeting mitochondrial genes of avian haemosporidians: PCR detection and differential DNA amplification of parasites belonging to different genera. Int J Parasitol 2018; 48:657-670. [PMID: 29625126 DOI: 10.1016/j.ijpara.2018.02.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/09/2018] [Accepted: 02/15/2018] [Indexed: 02/02/2023]
Abstract
Haemosporida is a diverse group of vector-borne parasitic protozoa, ubiquitous in terrestrial vertebrates worldwide. The renewed interest in their diversity has been driven by the extensive use of molecular methods targeting mitochondrial genes. Unfortunately, most studies target a 478 bp fragment of the cytochrome b (cytb) gene, which often cannot be used to separate lineages from different genera found in mixed infections that are common in wildlife. In this investigation, an alignment constructed with 114 mitochondrial genome sequences belonging to four genera (Leucocytozoon, Haemoproteus, Plasmodium and Hepatocystis) was used to design two different sets of primers targeting the cytb gene as well as the other two mitochondrial DNA genes: cytochrome c oxidase subunit 1 and cytochrome c oxidase subunit 3. The design of each pair of primers required consideration of different criteria, including a set for detection and another for differential amplification of DNA from parasites belonging to different avian haemosporidians. All pairs of primers were tested in three laboratories to assess their sensitivity and specificity under diverse practices and across isolates from different genera including single and natural mixed infections as well as experimental mixed infections. Overall, these primers exhibited high sensitivity regardless of the differences in laboratory practices, parasite species, and parasitemias. Furthermore, those primers designed to separate parasite genera showed high specificity, as confirmed by sequencing. In the case of cytb, a nested multiplex (single tube PCR) test was designed and successfully tested to differentially detect lineages of Plasmodium and Haemoproteus parasites by yielding amplicons with different sizes detectable in a standard agarose gel. To our knowledge, the designed assay is the first test for detection and differentiation of species belonging to these two genera in a single PCR. The experiments across laboratories provided recommendations that can be of use to those researchers seeking to standardise these or other primers to the specific needs of their field investigations.
Collapse
Affiliation(s)
- M Andreína Pacheco
- Department of Biology/Institute for Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122, USA.
| | - Axl S Cepeda
- Universidad Nacional de Colombia, Sede Bogotá-Facultad de Ciencias, Departamento de Biología, Grupo de Investigación Caracterización genética e inmunología, Carrera 30 No. 45-03, Bogotá 111321, Colombia
| | - Rasa Bernotienė
- Nature Research Centre, Akademijos 2, LT-08412 Vilnius, Lithuania
| | - Ingrid A Lotta
- Universidad Nacional de Colombia, Sede Bogotá-Facultad de Ciencias, Departamento de Biología, Grupo de Investigación Caracterización genética e inmunología, Carrera 30 No. 45-03, Bogotá 111321, Colombia
| | - Nubia E Matta
- Universidad Nacional de Colombia, Sede Bogotá-Facultad de Ciencias, Departamento de Biología, Grupo de Investigación Caracterización genética e inmunología, Carrera 30 No. 45-03, Bogotá 111321, Colombia
| | | | - Ananias A Escalante
- Department of Biology/Institute for Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122, USA.
| |
Collapse
|
9
|
Plasmodium parasites in reptiles from the Colombia Orinoco-Amazon basin: a re-description of Plasmodium kentropyxi Lainson R, Landau I, Paperna I, 2001 and Plasmodium carmelinoi Lainson R, Franco CM, da Matta R, 2010. Parasitol Res 2018. [PMID: 29516213 DOI: 10.1007/s00436-018-5815-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Colombia is a megadiverse country with about 600 species of reptiles; however, there are few studies on species of hemoparasites found in this taxonomic group. Here, we document the presence of Plasmodium spp. in four species of reptiles from the northern part of the Orinoco-Amazon region in Colombia. Individuals analyzed in this study were captured in localities between 200 and 500 m altitude, in the department of Guaviare. Each sample was screened for haemosporidian parasites by using morphology and a nested polymerase chain reaction (PCR) protocol that targets the mitochondrial cytochrome b (cytb) gene. Four morphotypes of the genus Plasmodium were found; two of these species are re-described using morphological and molecular data (cytb). For the other two morphotypes, it was not possible to assign a described species. Among those, Plasmodium screened one species was only detected by microscopy. Considering the potential species diversity, it is possible that commonly used primers may not detect all species, reinforcing the importance of using microscopy in haematozoa surveys. There was no correspondence between the morphological traits associated with the subgenera and the phylogenetic relationships that we found in our analyses. Additionally, we found an expansion in the geographical distribution of these two species, and a new host for P. kentropyxi, demonstrating that studies of tropical herpetofauna and their parasites deserve more attention.
Collapse
|
10
|
Miller MA, Kinsella JM, Snow RW, Hayes MM, Falk BG, Reed RN, Mazzotti FJ, Guyer C, Romagosa CM. Parasite spillover: indirect effects of invasive Burmese pythons. Ecol Evol 2018; 8:830-840. [PMID: 29375757 PMCID: PMC5773325 DOI: 10.1002/ece3.3557] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/28/2017] [Accepted: 10/08/2017] [Indexed: 11/12/2022] Open
Abstract
Identification of the origin of parasites of nonindigenous species (NIS) can be complex. NIS may introduce parasites from their native range and acquire parasites from within their invaded range. Determination of whether parasites are non-native or native can be complicated when parasite genera occur within both the NIS' native range and its introduced range. We explored potential for spillover and spillback of lung parasites infecting Burmese pythons (Python bivittatus) in their invasive range (Florida). We collected 498 indigenous snakes of 26 species and 805 Burmese pythons during 2004-2016 and examined them for lung parasites. We used morphology to identify three genera of pentastome parasites, Raillietiella, a cosmopolitan form, and Porocephalus and Kiricephalus, both New World forms. We sequenced these parasites at one mitochondrial and one nuclear locus and showed that each genus is represented by a single species, R. orientalis, P. crotali, and K. coarctatus. Pythons are host to R. orientalis and P. crotali, but not K. coarctatus; native snakes are host to all three species. Sequence data show that pythons introduced R. orientalis to North America, where this parasite now infects native snakes. Additionally, our data suggest that pythons are competent hosts to P. crotali, a widespread parasite native to North and South America that was previously hypothesized to infect only viperid snakes. Our results indicate invasive Burmese pythons have affected parasite-host dynamics of native snakes in ways that are consistent with parasite spillover and demonstrate the potential for indirect effects during invasions. Additionally, we show that pythons have acquired a parasite native to their introduced range, which is the initial condition necessary for parasite spillback.
Collapse
Affiliation(s)
| | | | - Ray W. Snow
- Everglades National ParkNational Park ServiceHomesteadFLUSA
| | | | - Bryan G. Falk
- Fort Collins Science CenterU.S. Geological SurveyFort CollinsCOUSA
| | - Robert N. Reed
- Fort Collins Science CenterU.S. Geological SurveyFort CollinsCOUSA
| | - Frank J. Mazzotti
- Department of Wildlife Ecology and ConservationFt. Lauderdale Research and Education CenterUniversity of FloridaFt. LauderdaleFLUSA
| | - Craig Guyer
- Department of Biological SciencesAuburn UniversityAuburnALUSA
| | - Christina M. Romagosa
- Department of Wildlife Ecology and ConservationUniversity of FloridaGainesvilleFLUSA
| |
Collapse
|
11
|
Florio AM, Raxworthy CJ. A Phylogeographic Assessment of the Malagasy Giant Chameleons (Furcifer verrucosus and Furcifer oustaleti). PLoS One 2016; 11:e0154144. [PMID: 27257819 PMCID: PMC4892496 DOI: 10.1371/journal.pone.0154144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 04/08/2016] [Indexed: 01/27/2023] Open
Abstract
The Malagasy giant chameleons (Furcifer oustaleti and Furcifer verrucosus) are sister species that are both broadly distributed in Madagascar, and also endemic to the island. These species are also morphologically similar and, because of this, have been frequently misidentified in the field. Previous studies have suggested that cryptic species are nested within this chameleon group, and two subspecies have been described in F. verrucosus. In this study, we utilized a phylogeographic approach to assess genetic diversification within these chameleons. This was accomplished by (1) identifying clades within each species supported by both mitochondrial and nuclear DNA, (2) assessing divergence times between clades, and (3) testing for niche divergence or conservatism. We found that both F. oustaleti and F. verrucosus could be readily identified based on genetic data, and within each species, there are two well-supported clades. However, divergence times are not contemporary and spatial patterns are not congruent. Diversification within F. verrucosus occurred during the Plio-Pleistocene, and there is evidence for niche divergence between a southwestern and southeastern clade, in a region of Madagascar that shows no obvious landscape barriers to dispersal. Diversification in F. oustaleti occurred earlier in the Pliocene or Miocene, and niche conservatism is supported with two genetically distinct clades separated at the Sofia River in northwestern Madagascar. Divergence within F. verrucosus is most consistent with patterns expected from ecologically mediated speciation, whereas divergence in F. oustaleti most strongly matches the patterns expected from the riverine barrier hypothesis.
Collapse
Affiliation(s)
- Antonia M. Florio
- Department of Herpetology, American Museum of Natural History, New York, NY, United States of America
| | - Christopher J. Raxworthy
- Department of Herpetology, American Museum of Natural History, New York, NY, United States of America
| |
Collapse
|
12
|
Diverse sampling of East African haemosporidians reveals chiropteran origin of malaria parasites in primates and rodents. Mol Phylogenet Evol 2016; 99:7-15. [DOI: 10.1016/j.ympev.2016.03.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 03/03/2016] [Accepted: 03/06/2016] [Indexed: 11/19/2022]
|
13
|
Falk BG, Glor RE, Perkins SL. Clonal reproduction shapes evolution in the lizard malaria parasite Plasmodium floridense. Evolution 2015; 69:1584-1596. [PMID: 25959003 DOI: 10.1111/evo.12683] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 04/15/2015] [Indexed: 11/28/2022]
Abstract
The preponderant clonal evolution hypothesis (PCE) predicts that frequent clonal reproduction (sex between two clones) in many pathogens capable of sexual recombination results in strong linkage disequilibrium and the presence of discrete genetic subdivisions characterized by occasional gene flow. We expand on the PCE and predict that higher rates of clonal reproduction will result in: (1) morphologically cryptic species that exhibit (2) low within-species variation and (3) recent between-species divergence. We tested these predictions in the Caribbean lizard malaria parasite Plasmodium floridense using 63 single-infection samples in lizards collected from across the parasite's range, and sequenced them at two mitochondrial, one apicoplast, and five nuclear genes. We identified 11 provisionally cryptic species within P. floridense, each of which exhibits low intraspecific variation and recent divergence times between species (some diverged approximately 110,000 years ago). Our results are consistent with the hypothesis that clonal reproduction can profoundly affect diversification of species capable of sexual recombination, and suggest that clonal reproduction may have led to a large number of unrecognized pathogen species. The factors that may influence the rates of clonal reproduction among pathogens are unclear, and we discuss how prevalence and virulence may relate to clonal reproduction.
Collapse
Affiliation(s)
- Bryan G Falk
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024.,U.S. Geological Survey, Daniel Beard Center, Everglades National Park, 40001 SR 9336, Homestead, Florida, 33034
| | - Richard E Glor
- Department of Ecology and Evolutionary Biology and Biodiversity Institute and Natural History Museum, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045
| | - Susan L Perkins
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York, 10024
| |
Collapse
|
14
|
González AD, Lotta IA, García LF, Moncada LI, Matta NE. Avian haemosporidians from Neotropical highlands: Evidence from morphological and molecular data. Parasitol Int 2015; 64:48-59. [PMID: 25638289 DOI: 10.1016/j.parint.2015.01.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 01/07/2015] [Accepted: 01/16/2015] [Indexed: 11/18/2022]
Abstract
Avian haemosporidian parasites have been scarcely studied in the Neotropical highlands despite the high avian diversity reported and the uniqueness of these ecosystems. The aims of this study were to examine Haemoproteus and Plasmodium diversity based on morphological and molecular data, as well as to explore the concordance between these two approaches, when identifying species. We sampled 1487 birds belonging to 166 species, in localities of the Colombian Andean region at elevations ranging from 2100 to 4000 m above sea level. Here, we report twelve morphological parasite species, of which five are undescribed. Thirty parasite cytochrome b lineages are reported, 17 of which for the first time. We provide morphological information and illustrations, as well as, cytochrome b lineages for six morphospecies: Haemoproteus columbae, Haemoproteus witti, Haemoproteus coatneyi, Haemoproteus vireonis, Plasmodium lutzi, and Plasmodium unalis. This is the first report to provide a linkage between morphology and a molecular lineage for H. witti. Cytochrome b gene proved to be useful for species determination as DNA barcoding. Differences in parasite composition between lowlands and highlands in Colombia suggest a replacement of avian Plasmodium fauna. Parasite lineages restricted to either Colombian resident or Nearctic migratory birds were found; but a single lineage common in both has not been recorded in Nearctic non-migratory birds. We generated valuable information by using both morphological and molecular data representing competent host-parasite relationships which are based on observation of gametocytes in circulation; and increased the taxon sampling of avian haemosporidian.
Collapse
Affiliation(s)
- Angie D González
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá Carrera 30 No 45-03, Bogotá, Colombia.
| | - Ingrid A Lotta
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá Carrera 30 No 45-03, Bogotá, Colombia.
| | - Luis F García
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá Carrera 30 No 45-03, Bogotá, Colombia.
| | - Ligia I Moncada
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Sede Bogotá, Carrera 30 No 45-03, Bogotá, Colombia.
| | - Nubia E Matta
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá Carrera 30 No 45-03, Bogotá, Colombia.
| |
Collapse
|
15
|
Culleton RL, Abkallo HM. Malaria parasite genetics: doing something useful. Parasitol Int 2014; 64:244-53. [PMID: 25073068 DOI: 10.1016/j.parint.2014.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 07/11/2014] [Indexed: 01/15/2023]
Abstract
Genetics has informed almost every aspect of the study of malaria parasites, and remains a key component of much of the research that aims to reduce the burden of the disease they cause. We describe the history of genetic studies of malaria parasites and give an overview of the utility of the discipline to malariology.
Collapse
Affiliation(s)
- Richard L Culleton
- Malaria Unit, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.
| | - Hussein M Abkallo
- Malaria Unit, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| |
Collapse
|
16
|
Paranjpe DA, Medina D, Nielsen E, Cooper RD, Paranjpe SA, Sinervo B. Does Thermal Ecology Influence Dynamics of Side-Blotched Lizards and Their Micro-Parasites? Integr Comp Biol 2014; 54:108-17. [DOI: 10.1093/icb/icu069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
17
|
Species limits in avian malaria parasites (Haemosporida): how to move forward in the molecular era. Parasitology 2014; 141:1223-32. [PMID: 24813385 DOI: 10.1017/s0031182014000560] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Delimiting species of malaria parasites (Haemosporida) has become increasingly problematic as new lineages of parasites are identified solely by molecular information, particularly mitochondrial cytochrome b sequence data. In this review, we highlight some of the issues, both historical and contemporary, that have hindered the development of objective criteria to diagnose, delimit and define species of haemosporidians. Defining species is not the focal interest of most researchers, most of whom merely wish to determine whether lineages identified in their samples match those of other researchers, and if so, where and in which host species. Rather than revisiting all the issues with respect to delimiting and naming species, we instead focus on finding a practical near-term resolution to the 'species problem' that utilizes the community's largest resource: mitochondrial cytochrome b DNA sequences. We recommend a standardized procedure to 'tag' these sequences, based on per cent sequence similarity, that will allow researchers to directly assess the novelty, known hosts and geographic distribution of avian malaria parasite lineages.
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Falk BG, Perkins SL. Host specificity shapes population structure of pinworm parasites in Caribbean reptiles. Mol Ecol 2013; 22:4576-90. [DOI: 10.1111/mec.12410] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Bryan G. Falk
- Division of Invertebrate Zoology; Sackler Institute for Comparative Genomics; American Museum of Natural History; Central Park West at 79 Street New York NY 10024 USA
| | - Susan L. Perkins
- Division of Invertebrate Zoology; Sackler Institute for Comparative Genomics; American Museum of Natural History; Central Park West at 79 Street New York NY 10024 USA
| |
Collapse
|
20
|
Jorge F, Perera A, Carretero MA, James Harris D, Roca V. Cryptic species unveiled: the case of the nematode Spauligodon atlanticus. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fátima Jorge
- CIBIO-UP; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da; Universidade do Porto; Porto Portugal
| | - Ana Perera
- CIBIO-UP; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | - Miguel A. Carretero
- CIBIO-UP; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | - D. James Harris
- CIBIO-UP; Centro de Investigação em Biodiversidade e Recursos Genéticos; Universidade do Porto; Vairão Portugal
| | - Vicente Roca
- Departament de Zoologia; Facultat de Ciències Biològiques; Universitat de València; València Spain
| |
Collapse
|
21
|
Orkun Ö, Güven E. A new species of Haemoproteus from a tortoise (Testudo graeca) in Turkey, with remarks on molecular phylogenetic and morphological analysis. J Parasitol 2012; 99:112-7. [PMID: 22924909 DOI: 10.1645/ge-3100.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Haemoproteus anatolicum n. sp. was identified in the tortoise Testudo graeca. The new species is described based on the morphology of its blood stages and a segment of the mitochondrial cytochrome b gene, which can be used for molecular identification and diagnosis. Chelonian haemoproteids recorded in the past were defined solely on the basis of their morphological characteristics. The chelonian haemoproteid we describe as a new species has a close genetic relationship to lizard haemoproteids, i.e., Haemoproteus ptyodactylii and Haemoproteus kopki. The new species description provides significant new information for little-known chelonian haemoproteids.
Collapse
Affiliation(s)
- Ömer Orkun
- Department of Parasitology, Faculty of Veterinary Medicine, Ankara University, Ankara 06110, Turkey.
| | | |
Collapse
|