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Thawornwattana Y, Seixas F, Yang Z, Mallet J. Major patterns in the introgression history of Heliconius butterflies. eLife 2023; 12:RP90656. [PMID: 38108819 PMCID: PMC10727504 DOI: 10.7554/elife.90656] [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] [Indexed: 12/19/2023] Open
Abstract
Gene flow between species, although usually deleterious, is an important evolutionary process that can facilitate adaptation and lead to species diversification. It also makes estimation of species relationships difficult. Here, we use the full-likelihood multispecies coalescent (MSC) approach to estimate species phylogeny and major introgression events in Heliconius butterflies from whole-genome sequence data. We obtain a robust estimate of species branching order among major clades in the genus, including the 'melpomene-silvaniform' group, which shows extensive historical and ongoing gene flow. We obtain chromosome-level estimates of key parameters in the species phylogeny, including species divergence times, present-day and ancestral population sizes, as well as the direction, timing, and intensity of gene flow. Our analysis leads to a phylogeny with introgression events that differ from those obtained in previous studies. We find that Heliconius aoede most likely represents the earliest-branching lineage of the genus and that 'silvaniform' species are paraphyletic within the melpomene-silvaniform group. Our phylogeny provides new, parsimonious histories for the origins of key traits in Heliconius, including pollen feeding and an inversion involved in wing pattern mimicry. Our results demonstrate the power and feasibility of the full-likelihood MSC approach for estimating species phylogeny and key population parameters despite extensive gene flow. The methods used here should be useful for analysis of other difficult species groups with high rates of introgression.
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Affiliation(s)
| | - Fernando Seixas
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College LondonLondonUnited Kingdom
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
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2
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Odero JO, Nambunga IH, Wangrawa DW, Badolo A, Weetman D, Koekemoer LL, Ferguson HM, Okumu FO, Baldini F. Advances in the genetic characterization of the malaria vector, Anopheles funestus, and implications for improved surveillance and control. Malar J 2023; 22:230. [PMID: 37553665 PMCID: PMC10410966 DOI: 10.1186/s12936-023-04662-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
Anopheles mosquitoes present a major public health challenge in sub-Saharan Africa; notably, as vectors of malaria that kill over half a million people annually. In parts of the east and southern Africa region, one species in the Funestus group, Anopheles funestus, has established itself as an exceptionally dominant vector in some areas, it is responsible for more than 90% of all malaria transmission events. However, compared to other malaria vectors, the species is far less studied, partly due to difficulties in laboratory colonization and the unresolved aspects of its taxonomy and systematics. Control of An. funestus is also increasingly difficult because it has developed widespread resistance to public health insecticides. Fortunately, recent advances in molecular techniques are enabling greater insights into species identity, gene flow patterns, population structure, and the spread of resistance in mosquitoes. These advances and their potential applications are reviewed with a focus on four research themes relevant to the biology and control of An. funestus in Africa, namely: (i) the taxonomic characterization of different vector species within the Funestus group and their role in malaria transmission; (ii) insecticide resistance profile; (iii) population genetic diversity and gene flow, and (iv) applications of genetic technologies for surveillance and control. The research gaps and opportunities identified in this review will provide a basis for improving the surveillance and control of An. funestus and malaria transmission in Africa.
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Affiliation(s)
- Joel O Odero
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania.
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Ismail H Nambunga
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania
| | - Dimitri W Wangrawa
- Laboratoire d'Entomologie Fondamentale et Appliquée, Université Joseph ZEBRO, Ouagadougou, Burkina Faso
| | - Athanase Badolo
- Laboratoire d'Entomologie Fondamentale et Appliquée, Université Joseph ZEBRO, Ouagadougou, Burkina Faso
| | - David Weetman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Lizette L Koekemoer
- Wits Research Institute for Malaria, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Emerging Zoonotic Parasitic Diseases, Vector Control Reference Laboratory, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Heather M Ferguson
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fredros O Okumu
- Environmental Health and Ecological Sciences Department, Ifakara Health Institute, Ifakara, Tanzania
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- School of Public Health, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- School of Life Science and Biotechnology, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Francesco Baldini
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK.
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3
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Yurchenko AA, Naumenko AN, Artemov GN, Karagodin DA, Hodge JM, Velichevskaya AI, Kokhanenko AA, Bondarenko SM, Abai MR, Kamali M, Gordeev MI, Moskaev AV, Caputo B, Aghayan SA, Baricheva EM, Stegniy VN, Sharakhova MV, Sharakhov IV. Phylogenomics revealed migration routes and adaptive radiation timing of Holarctic malaria mosquito species of the Maculipennis Group. BMC Biol 2023; 21:63. [PMID: 37032389 PMCID: PMC10084679 DOI: 10.1186/s12915-023-01538-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/08/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Phylogenetic analyses of closely related species of mosquitoes are important for better understanding the evolution of traits contributing to transmission of vector-borne diseases. Six out of 41 dominant malaria vectors of the genus Anopheles in the world belong to the Maculipennis Group, which is subdivided into two Nearctic subgroups (Freeborni and Quadrimaculatus) and one Palearctic (Maculipennis) subgroup. Although previous studies considered the Nearctic subgroups as ancestral, details about their relationship with the Palearctic subgroup, and their migration times and routes from North America to Eurasia remain controversial. The Palearctic species An. beklemishevi is currently included in the Nearctic Quadrimaculatus subgroup adding to the uncertainties in mosquito systematics. RESULTS To reconstruct historic relationships in the Maculipennis Group, we conducted a phylogenomic analysis of 11 Palearctic and 2 Nearctic species based on sequences of 1271 orthologous genes. The analysis indicated that the Palearctic species An. beklemishevi clusters together with other Eurasian species and represents a basal lineage among them. Also, An. beklemishevi is related more closely to An. freeborni, which inhabits the Western United States, rather than to An. quadrimaculatus, a species from the Eastern United States. The time-calibrated tree suggests a migration of mosquitoes in the Maculipennis Group from North America to Eurasia about 20-25 million years ago through the Bering Land Bridge. A Hybridcheck analysis demonstrated highly significant signatures of introgression events between allopatric species An. labranchiae and An. beklemishevi. The analysis also identified ancestral introgression events between An. sacharovi and its Nearctic relative An. freeborni despite their current geographic isolation. The reconstructed phylogeny suggests that vector competence and the ability to enter complete diapause during winter evolved independently in different lineages of the Maculipennis Group. CONCLUSIONS Our phylogenomic analyses reveal migration routes and adaptive radiation timing of Holarctic malaria vectors and strongly support the inclusion of An. beklemishevi into the Maculipennis Subgroup. Detailed knowledge of the evolutionary history of the Maculipennis Subgroup provides a framework for examining the genomic changes related to ecological adaptation and susceptibility to human pathogens. These genomic variations may inform researchers about similar changes in the future providing insights into the patterns of disease transmission in Eurasia.
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Affiliation(s)
- Andrey A Yurchenko
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- Kurchatov Genomics Center, the Federal Research Center, Institute of Cytology and Genetics, Novosibirsk, Russia
- Current Address: INSERM U981, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Anastasia N Naumenko
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Gleb N Artemov
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Dmitry A Karagodin
- Laboratory of Cell Differentiation Mechanisms, the Federal Research Center, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - James M Hodge
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Alena I Velichevskaya
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Alina A Kokhanenko
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Semen M Bondarenko
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Mohammad R Abai
- Department of Medical Entomology and Vector Control, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Kamali
- Department of Medical Entomology and Parasitology, Tarbiat Modares University, Tehran, Iran
| | - Mikhail I Gordeev
- Department of General Biology and Ecology, State University of Education, Mytishchi, Russia
| | - Anton V Moskaev
- Department of General Biology and Ecology, State University of Education, Mytishchi, Russia
| | - Beniamino Caputo
- Dipartimento Di Sanità Pubblica E Malattie Infettive, Università Sapienza, Rome, Italy
| | - Sargis A Aghayan
- Scientific Center of Zoology and Hydroecology, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
- Department of Zoology, Yerevan State University, Yerevan, Armenia
| | - Elina M Baricheva
- Laboratory of Cell Differentiation Mechanisms, the Federal Research Center, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Vladimir N Stegniy
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Maria V Sharakhova
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- Laboratory of Cell Differentiation Mechanisms, the Federal Research Center, Institute of Cytology and Genetics, Novosibirsk, Russia.
| | - Igor V Sharakhov
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- Department of Genetics and Cell Biology and the Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia.
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4
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Small ST, Costantini C, Sagnon N, Guelbeogo MW, Emrich SJ, Kern AD, Fontaine MC, Besansky NJ. Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito. Proc Natl Acad Sci U S A 2023; 120:e2219835120. [PMID: 36881629 PMCID: PMC10089221 DOI: 10.1073/pnas.2219835120] [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: 11/26/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Species distributed across heterogeneous environments often evolve locally adapted ecotypes, but understanding of the genetic mechanisms involved in their formation and maintenance in the face of gene flow is incomplete. In Burkina Faso, the major African malaria mosquito Anopheles funestus comprises two strictly sympatric and morphologically indistinguishable yet karyotypically differentiated forms reported to differ in ecology and behavior. However, knowledge of the genetic basis and environmental determinants of An. funestus diversification was impeded by lack of modern genomic resources. Here, we applied deep whole-genome sequencing and analysis to test the hypothesis that these two forms are ecotypes differentially adapted to breeding in natural swamps versus irrigated rice fields. We demonstrate genome-wide differentiation despite extensive microsympatry, synchronicity, and ongoing hybridization. Demographic inference supports a split only ~1,300 y ago, closely following the massive expansion of domesticated African rice cultivation ~1,850 y ago. Regions of highest divergence, concentrated in chromosomal inversions, were under selection during lineage splitting, consistent with local adaptation. The origin of nearly all variations implicated in adaptation, including chromosomal inversions, substantially predates the ecotype split, suggesting that rapid adaptation was fueled mainly by standing genetic variation. Sharp inversion frequency differences likely facilitated adaptive divergence between ecotypes by suppressing recombination between opposing chromosomal orientations of the two ecotypes, while permitting free recombination within the structurally monomorphic rice ecotype. Our results align with growing evidence from diverse taxa that rapid ecological diversification can arise from evolutionarily old structural genetic variants that modify genetic recombination.
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Affiliation(s)
- Scott T. Small
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Carlo Costantini
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
- Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC), Université de Montpellier, CNRS 5290, Institute of Research for Development (IRD) 224, F-34394Montpellier, France
| | - N’Fale Sagnon
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
| | - Moussa W. Guelbeogo
- Centre National de Recherche et Formation sur le Paludisme, Ouagadougou01 BP 2208, Burkina Faso
| | - Scott J. Emrich
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN46556
| | - Andrew D. Kern
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR97403
| | - Michael C. Fontaine
- Infectious Diseases and Vectors: Ecology, Genetics, Evolution and Control (MIVEGEC), Université de Montpellier, CNRS 5290, Institute of Research for Development (IRD) 224, F-34394Montpellier, France
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AGGroningen, The Netherlands
| | - Nora J. Besansky
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN46556
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5
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Gene drive in species complexes: defining target organisms. Trends Biotechnol 2023; 41:154-164. [PMID: 35868886 DOI: 10.1016/j.tibtech.2022.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/17/2022] [Accepted: 06/27/2022] [Indexed: 01/24/2023]
Abstract
Engineered gene drives, which bias their own inheritance to increase in frequency in target populations, are being developed to control mosquito malaria vectors. Such mosquitoes can belong to complexes of both vector and nonvector species that can produce fertile interspecific hybrids, making vertical gene drive transfer (VGDT) to sibling species biologically plausible. While VGDT to other vectors could positively impact human health protection goals, VGDT to nonvectors might challenge biodiversity ones. Therefore, environmental risk assessment of gene drive use in species complexes invites more nuanced considerations of target organisms and nontarget organisms than for transgenes not intended to increase in frequency in target populations. Incorporating the concept of target species complexes offers more flexibility when assessing potential impacts from VGDT.
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6
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Yusuf LH, Tyukmaeva V, Hoikkala A, Ritchie MG. Divergence and introgression among the virilis group of Drosophila. Evol Lett 2022; 6:537-551. [PMID: 36579165 PMCID: PMC9783487 DOI: 10.1002/evl3.301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 09/23/2022] [Accepted: 10/12/2022] [Indexed: 12/03/2022] Open
Abstract
Speciation with gene flow is now widely regarded as common. However, the frequency of introgression between recently diverged species and the evolutionary consequences of gene flow are still poorly understood. The virilis group of Drosophila contains 12 species that are geographically widespread and show varying levels of prezygotic and postzygotic isolation. Here, we use de novo genome assemblies and whole-genome sequencing data to resolve phylogenetic relationships and describe patterns of introgression and divergence across the group. We suggest that the virilis group consists of three, rather than the traditional two, subgroups. Some genes undergoing rapid sequence divergence across the group were involved in chemical communication and desiccation tolerance, and may be related to the evolution of sexual isolation and adaptation. We found evidence of pervasive phylogenetic discordance caused by ancient introgression events between distant lineages within the group, and more recent gene flow between closely related species. When assessing patterns of genome-wide divergence in species pairs across the group, we found no consistent genomic evidence of a disproportionate role for the X chromosome as has been found in other systems. Our results show how ancient and recent introgressions confuse phylogenetic reconstruction, but may play an important role during early radiation of a group.
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Affiliation(s)
- Leeban H. Yusuf
- Centre for Biological Diversity, School of BiologyUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom
| | - Venera Tyukmaeva
- Centre for Biological Diversity, School of BiologyUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom,Department of Evolution, Ecology and BehaviourUniversity of LiverpoolLiverpoolL69 7ZBUnited Kingdom
| | - Anneli Hoikkala
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskylä40014Finland
| | - Michael G. Ritchie
- Centre for Biological Diversity, School of BiologyUniversity of St AndrewsSt AndrewsKY16 9THUnited Kingdom
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7
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Gloria-Soria A. Special Collection: Highlights of Medical, Urban and Veterinary Entomology. Highlights in Medical Entomology, 2021. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:1853-1860. [PMID: 36197947 DOI: 10.1093/jme/tjac063] [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: 03/14/2022] [Indexed: 06/16/2023]
Abstract
Life remained far from normal as we completed the first year of the Covid-19 pandemic and entered a second year. Despite the challenges faced worldwide, together we continue to move the field of Medical Entomology forward. Here, I reflect on parallels between control of Covid-19 and vector-borne disease control, discuss the advantages and caveats of using new genotyping technologies for the study of invasive species, and proceed to highlight papers that were published between 2020 and 2021 with a focus on those related to mosquito surveillance and population genetics of mosquito vectors.
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Affiliation(s)
- A Gloria-Soria
- Department of Environmental Sciences, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, CT 06511, USA
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
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8
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Dagilis AJ, Peede D, Coughlan JM, Jofre GI, D'Agostino ERR, Mavengere H, Tate AD, Matute DR. A need for standardized reporting of introgression: Insights from studies across eukaryotes. Evol Lett 2022; 6:344-357. [PMID: 36254258 PMCID: PMC9554761 DOI: 10.1002/evl3.294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/04/2022] [Accepted: 06/12/2022] [Indexed: 01/04/2023] Open
Abstract
With the rise of affordable next-generation sequencing technology, introgression-or the exchange of genetic materials between taxa-has become widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment of the frequency of introgression across eukaryotes in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by examining patterns of introgression across eukaryotes. We collated a single statistic, Patterson's D, which can be used as a test for introgression across 123 studies to further assess how taxonomic group, divergence time, and sequencing technology influence reports of introgression. Overall, introgression has mostly been measured in plants and vertebrates, with less attention given to the rest of the Eukaryotes. We find that the most frequently used metrics to detect introgression are difficult to compare across studies and even more so across biological systems due to differences in study effort, reporting standards, and methodology. Nonetheless, our analyses reveal several intriguing patterns, including the observation that differences in sequencing technologies may bias values of Patterson's D and that introgression may differ throughout the course of the speciation process. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities and highlight important areas of future research that can be better assessed once this unified approach is met.
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Affiliation(s)
| | - David Peede
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology, Evolution, and Organismal BiologyBrown UniversityProvidenceRIUSA
- Center for Computational Molecular BiologyBrown UniversityProvidenceRIUSA
| | - Jenn M. Coughlan
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Gaston I. Jofre
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
| | - Emmanuel R. R. D'Agostino
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
| | - Heidi Mavengere
- Biology DepartmentUniversity of North CarolinaChapel HillNCUSA
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9
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Abstract
Some of the most striking polymorphisms in nature are regulated by “supergenes,” which are clusters of tightly linked genes that coordinately control complex phenotypes. Here, we study the evolutionary history of a supergene regulating colony social organization in fire ants. We show that the three inversions constituting the social supergene emerged sequentially during the separation of the ancestral lineages of Solenopsis invicta and Solenopsis richteri. Once completely assembled in S. richteri, the supergene introgressed into multiple closely related species despite recent hybridization being uncommon between several of the species. These findings provide a rare and striking example of how introgression can lead to the rapid spread of a novel variant controlling complex traits. Supergenes are clusters of tightly linked genes that jointly produce complex phenotypes. Although widespread in nature, how such genomic elements are formed and how they spread are in most cases unclear. In the fire ant Solenopsis invicta and closely related species, a “social supergene controls whether a colony maintains one or multiple queens. Here, we show that the three inversions constituting the Social b (Sb) supergene emerged sequentially during the separation of the ancestral lineages of S. invicta and Solenopsis richteri. The two first inversions arose in the ancestral population of both species, while the third one arose in the S. richteri lineage. Once completely assembled in the S. richteri lineage, the supergene first introgressed into S. invicta, and from there into the other species of the socially polymorphic group of South American fire ant species. Surprisingly, the introgression of this large and important genomic element occurred despite recent hybridization being uncommon between several of the species. These results highlight how supergenes can readily move across species boundaries, possibly because of fitness benefits they provide and/or expression of selfish properties favoring their transmission.
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10
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Harris AJ, Foley NM, Williams TL, Murphy WJ. Tree House Explorer: A Novel Genome Browser for Phylogenomics. Mol Biol Evol 2022; 39:msac130. [PMID: 35700217 PMCID: PMC9246335 DOI: 10.1093/molbev/msac130] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/09/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. THEx allows users to visualize genome-wide variation in evolutionary histories and genetic divergence on a chromosome-by-chromosome basis, with continuous sliding window comparisons to gene annotations (GFF/GTF), recombination rates, and other user-specified, highly customizable feature annotations. THEx provides a new platform for interactive phylogenomic data visualization to analyze and interpret the diverse evolutionary histories woven throughout genomes. Hosted on Conda, THEx integrates seamlessly into new or pre-existing workflows.
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Affiliation(s)
- Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Tiffani L Williams
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
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11
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Dittberner H, Tellier A, de Meaux J. Approximate Bayesian computation untangles signatures of contemporary and historical hybridization between two endangered species. Mol Biol Evol 2022; 39:6516021. [PMID: 35084503 PMCID: PMC8826969 DOI: 10.1093/molbev/msac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Contemporary gene flow, when resumed after a period of isolation, can have crucial consequences for endangered species, as it can both increase the supply of adaptive alleles and erode local adaptation. Determining the history of gene flow and thus the importance of contemporary hybridization, however, is notoriously difficult. Here, we focus on two endangered plant species, Arabis nemorensis and A. sagittata, which hybridize naturally in a sympatric population located on the banks of the Rhine. Using reduced genome sequencing, we determined the phylogeography of the two taxa but report only a unique sympatric population. Molecular variation in chloroplast DNA indicated that A. sagittata is the principal receiver of gene flow. Applying classical D-statistics and its derivatives to whole-genome data of 35 accessions, we detect gene flow not only in the sympatric population but also among allopatric populations. Using an Approximate Bayesian computation approach, we identify the model that best describes the history of gene flow between these taxa. This model shows that low levels of gene flow have persisted long after speciation. Around 10 000 years ago, gene flow stopped and a period of complete isolation began. Eventually, a hotspot of contemporary hybridization was formed in the unique sympatric population. Occasional sympatry may have helped protect these lineages from extinction in spite of their extremely low diversity.
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Affiliation(s)
- Hannes Dittberner
- Institute of Plant Sciences,University of Cologne, Zülpicher str. 47b, Germany
| | - Aurelien Tellier
- Department of Life Science Systems, Technical University of Munich, Freising, Germany
| | - Juliette de Meaux
- Institute of Plant Sciences,University of Cologne, Zülpicher str. 47b, Germany
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12
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Korlević P, McAlister E, Mayho M, Makunin A, Flicek P, Lawniczak MKN. A Minimally Morphologically Destructive Approach for DNA Retrieval and Whole-Genome Shotgun Sequencing of Pinned Historic Dipteran Vector Species. Genome Biol Evol 2021; 13:evab226. [PMID: 34599327 PMCID: PMC8536546 DOI: 10.1093/gbe/evab226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2021] [Indexed: 01/08/2023] Open
Abstract
Museum collections contain enormous quantities of insect specimens collected over the past century, covering a period of increased and varied insecticide usage. These historic collections are therefore incredibly valuable as genomic snapshots of organisms before, during, and after exposure to novel selective pressures. However, these samples come with their own challenges compared with present-day collections, as they are fragile and retrievable DNA is low yield and fragmented. In this article, we tested several DNA extraction procedures across pinned historic Diptera specimens from four disease vector genera: Anopheles, Aedes, Culex, and Glossina. We identify an approach that minimizes morphological damage while maximizing DNA retrieval for Illumina library preparation and sequencing that can accommodate the fragmented and low yield nature of historic DNA. We identify several key points in retrieving sufficient DNA while keeping morphological damage to a minimum: an initial rehydration step, a short incubation without agitation in a modified low salt Proteinase K buffer (referred to as "lysis buffer C" throughout), and critical point drying of samples post-extraction to prevent tissue collapse caused by air drying. The suggested method presented here provides a solid foundation for exploring the genomes and morphology of historic Diptera collections.
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Affiliation(s)
- Petra Korlević
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Erica McAlister
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Matthew Mayho
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alex Makunin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mara K N Lawniczak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Ndiaye E, Ould Mohamed Salem Boukhary A, Diallo M, Diallo D, Labbo R, Boussès P, Le Goff G, Robert V. [Mosquitoes, Distribution and Specific Richness in Eight Countries of Africa: Cape Verde, Mauritania, Senegal, Gambia, Mali, Burkina Faso, Niger and Chad]. MEDECINE TROPICALE ET SANTE INTERNATIONALE 2021; 1:mtsibulletin.2021.109. [PMID: 35586589 PMCID: PMC9022770 DOI: 10.48327/mtsibulletin.2021.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/25/2021] [Indexed: 11/14/2022]
Abstract
Mosquitoes (Diptera, Culicidae) form a family of insects of considerable public health importance. Mention of their presence/absence was tackled in the literature and by specialized websites for eight African countries: Cape Verde, Mauritania, Senegal, Gambia, Mali, Burkina Faso, Niger and Chad. In total, 216 species have been recorded belonging to 13 genera: Anopheles (48 species), Aedeomyia (2), Aedes (62), Coquillettidia (6), Culex (54), Culiseta (1), Eretmapodites (7), Ficalbia (3), Lutzia (1), Mansonia (2), Mimomyia (7), Toxorhynchites (4) and Uranotaenia (19). The presence of these species in the study area is certain except for three species whose presence is doubtful. This specific richness represents 6% of the world's richness. The countries with the highest specific richness are Burkina Faso (162 species), Senegal (143) and Mali (110); the country with the lowest richness is Cape Verde (11). This richness is lower in the north in hyper-arid climate and higher in the south in sub-humid climate. Chad is the least well inventoried country. All species are considered native, with the exception of Ae. (Stegomyia ) albopictus (the Asian tiger mosquito) introduced in 2016 into Mali and possibly Ae. (Ochlerotatus ) caspius into Mauritania and Ae. (Stg. ) aegypti introduced into Nouakchott, Mauritania. This synthesis of the knowledge may be useful for vector control, public health, and future research.
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Affiliation(s)
- E.H. Ndiaye
- Pôle de zoologie médicale, Institut Pasteur de Dakar, B.P. 220, Dakar, Sénégal
| | - A. Ould Mohamed Salem Boukhary
- Université de Nouakchott Al-Aasriya, Unité de recherche génomes et milieux (jeune équipe associée à l'IRD), Laboratoire environnement, santé et société LE2S, BP 880, Nouakchott, Mauritanie; Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, Marseille, France
| | - M. Diallo
- Pôle de zoologie médicale, Institut Pasteur de Dakar, B.P. 220, Dakar, Sénégal
| | - D. Diallo
- Pôle de zoologie médicale, Institut Pasteur de Dakar, B.P. 220, Dakar, Sénégal
| | - R. Labbo
- Centre de recherche médicale et sanitaire (CERMES), BP 10887, Niamey, Niger
| | - P. Boussès
- Unité MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - G. Le Goff
- Unité MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France
| | - V. Robert
- Unité MIVEGEC, Université de Montpellier, IRD, CNRS, Montpellier, France,*
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14
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Profile of Nora J. Besansky. Proc Natl Acad Sci U S A 2021; 118:2101734118. [PMID: 33627410 DOI: 10.1073/pnas.2101734118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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15
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Hoffman JE, Ciubotariu II, Simubali L, Mudenda T, Moss WJ, Carpi G, Norris DE, Stevenson JC. Phylogenetic Complexity of Morphologically Identified Anopheles squamosus in Southern Zambia. INSECTS 2021; 12:insects12020146. [PMID: 33567609 PMCID: PMC7915044 DOI: 10.3390/insects12020146] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022]
Abstract
Despite dramatic reductions in malaria cases in the catchment area of Macha Hospital, Choma District, Southern Province in Zambia, prevalence has remained near 1-2% by RDT for the past several years. To investigate residual malaria transmission in the area, this study focuses on the relative abundance, foraging behavior, and phylogenetic relationships of Anopheles squamosus specimens. In 2011, higher than expected rates of anthropophily were observed among "zoophilic" An. squamosus, a species that had sporadically been found to contain Plasmodium falciparum sporozoites. The importance of An. squamosus in the region was reaffirmed in 2016 when P. falciparum sporozoites were detected in numerous An. squamosus specimens. This study analyzed Centers for Disease Control (CDC) light trap collections of adult mosquitoes from two collection schemes: one performed as part of a reactive-test-and-treat program and the second performed along a geographical transect. Morphological identification, molecular verification of anopheline species, and blood meal source were determined on individual samples. Data from these collections supported earlier studies demonstrating An. squamosus to be primarily exophagic and zoophilic, allowing them to evade current control measures. The phylogenetic relationships generated from the specimens in this study illustrate the existence of well supported clade structure among An. squamosus specimens, which further emphasizes the importance of molecular identification of vectors. The primarily exophagic behavior of An. squamosus in these collections also highlights that indoor vector control strategies will not be sufficient for elimination of malaria in southern Zambia.
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Affiliation(s)
- Jordan E. Hoffman
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA;
| | - Ilinca I. Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (I.I.C.); (G.C.)
| | | | - Twig Mudenda
- Macha Research Trust, Choma, Zambia; (L.S.); (T.M.); (J.C.S.)
| | - William J. Moss
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA;
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (I.I.C.); (G.C.)
| | - Douglas E. Norris
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Correspondence: ; Tel.: +1-410-614-2710
| | - Jennifer C. Stevenson
- Macha Research Trust, Choma, Zambia; (L.S.); (T.M.); (J.C.S.)
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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Lukindu M, Love RR, Guelbeogo MW, Small ST, Stephens MT, Campbell NR, Sagnon N, Costantini C, Besansky NJ. High-Throughput Genotyping of Common Chromosomal Inversions in the Afrotropical Malaria Mosquito Anopheles Funestus. INSECTS 2020; 11:E693. [PMID: 33065978 PMCID: PMC7650614 DOI: 10.3390/insects11100693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022]
Abstract
Polymorphic chromosomal inversions have been implicated in local adaptation. In anopheline mosquitoes, inversions also contribute to epidemiologically relevant phenotypes such as resting behavior. Progress in understanding these phenotypes and their mechanistic basis has been hindered because the only available method for inversion genotyping relies on traditional cytogenetic karyotyping, a rate-limiting and technically difficult approach that is possible only for the fraction of the adult female population at the correct gonotrophic stage. Here, we focus on an understudied malaria vector of major importance in sub-Saharan Africa, Anopheles funestus. We ascertain and validate tag single nucleotide polymorphisms (SNPs) using high throughput molecular assays that allow rapid inversion genotyping of the three most common An. funestus inversions at scale, overcoming the cytogenetic karyotyping barrier. These same inversions are the only available markers for distinguishing two An. funestus ecotypes that differ in indoor resting behavior, Folonzo and Kiribina. Our new inversion genotyping tools will facilitate studies of ecotypic differentiation in An. funestus and provide a means to improve our understanding of the roles of Folonzo and Kiribina in malaria transmission.
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Affiliation(s)
- Martin Lukindu
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA; (M.L.); (R.R.L.); (S.T.S.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | - R. Rebecca Love
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA; (M.L.); (R.R.L.); (S.T.S.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | - Moussa W. Guelbeogo
- Centre National de Recherche et Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso; (M.W.G.); (N.S.); (C.C.)
| | - Scott T. Small
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA; (M.L.); (R.R.L.); (S.T.S.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | - Melissa T. Stephens
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | | | - N’Fale Sagnon
- Centre National de Recherche et Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso; (M.W.G.); (N.S.); (C.C.)
| | - Carlo Costantini
- Centre National de Recherche et Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso; (M.W.G.); (N.S.); (C.C.)
- 5 MIVEGEC, University of Montpellier, CNRS 5290, IRD 224, F-34394 Montpellier, France
| | - Nora J. Besansky
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA; (M.L.); (R.R.L.); (S.T.S.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
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