1
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Bacon CD, Hill A. Hybridization in palms (Arecaceae). Ecol Evol 2024; 14:e70014. [PMID: 39011137 PMCID: PMC11246834 DOI: 10.1002/ece3.70014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024] Open
Abstract
Hybridization has significant evolutionary consequences across the Tree of Life. The process of hybridization has played a major role in plant evolution and has contributed to species richness and trait variation. Since morphological traits are partially a product of their environment, there may be a link between hybridization and ecology. Plant hybrid species richness is noted to be higher in harsh environments, and we explore this hypothesis with a keystone tropical plant lineage, palms (Arecaceae). Leveraging a recent literature review of naturally occurring palm hybrids, we developed a method to calculate hybrid frequency, and then tested if there is phylogenetic signal of hybrids using a phylogeny of all palms. Further, we used phylogenetic comparative methods to examine the interaction between hybrid frequency and presence in dry environments, on islands, and the species richness of genera. Phylogenetic generalized least squares models had stronger support than models of random association, indicating phylogenetic signal for the presence of hybrids in dry and island environments. However, all p-values were >.05 and therefore the correlation was poor between hybridization and the trait frequencies examined. Presence in particular environments are not strongly correlated to hybrid frequency, but phylogenetic signal suggests a role in its distribution in different habitats. Hybridization in palms is not evenly distributed across subfamilies, tribes, subtribes yet plays an important role in palm diversity, nonetheless. Increasing our understanding hybridization in this economically and culturally important plant family is essential, particularly since rates are projected to increase with climate change, reconfiguring the dynamics and distribution of biodiversity.
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Affiliation(s)
- Christine D. Bacon
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
- Gothenburg Global Biodiversity CentreGothenburgSweden
| | - Adrian Hill
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburgSweden
- Gothenburg Global Biodiversity CentreGothenburgSweden
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2
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Hernández F, Janzen T, Lavretsky P. simRestore: A decision-making tool for adaptive management of the native genetic status of wild populations. Mol Ecol Resour 2024; 24:e13892. [PMID: 37966172 DOI: 10.1111/1755-0998.13892] [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: 11/21/2022] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/16/2023]
Abstract
Anthropogenic hybridization, or higher and non-natural rates of gene flow directly and indirectly induced by human activities, is considered a significant threat to biodiversity. The primary concern for conservation is the potential for genomic extinction and loss of adaptiveness for native species due to the extensive introgression of non-native genes. To alleviate or reverse trends for such scenarios requires the direct integration of genomic data within a model framework for effective management. Towards this end, we developed the simRestore R program as a decision-making tool that integrates ecological and genomic information to simulate ancestry outcomes from optimized conservation strategies. In short, the program optimizes supplementation and removal strategies across generations until a set native genetic threshold is reached within the studied population. Importantly, in addition to helping with initial decision-making, simulations can be updated with the outcomes of ongoing efforts, allowing for the adaptive management of populations. After demonstrating functionality, we apply and optimize among actionable management strategies for the endangered Hawaiian duck for which the current primary threat is genetic extinction through ongoing anthropogenic hybridization with feral mallards. Simulations demonstrate that supplemental and removal efforts can be strategically tailored to move the genetic ancestry of Hawaii's hybrid populations towards Hawaiian duck without the need to completely start over. Further, we discuss ecological parameter sensitivity, including which factors are most important to ensure genetic outcomes (i.e. number of offspring). Finally, to facilitate use, the program is also available online as a Shiny Web application.
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Affiliation(s)
- Flor Hernández
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Thijs Janzen
- Department of Ecological Genomics, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
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3
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Tensen L, Fischer K. Evaluating hybrid speciation and swamping in wild carnivores with a decision-tree approach. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14197. [PMID: 37811741 DOI: 10.1111/cobi.14197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/12/2023] [Accepted: 06/28/2023] [Indexed: 10/10/2023]
Abstract
Hybridization is an important evolutionary force with a principal role in the origin of new species, known as hybrid speciation. However, ongoing hybridization can create hybrid swamping, in which parental genomes are completely lost. This can become a biodiversity threat if it involves species that have adapted to certain environmental conditions and occur nowhere else. Because conservation scientists commonly have a negative attitude toward hybrids, it is important to improve understanding of the influence of interspecific gene flow on the persistence of species. We reviewed the literature on species hybridization to build a list of all known cases in the order Carnivora. To examine the relative impact, we also noted level of introgression, whether fertile offspring were produced, and whether there was mention of negative or positive evolutionary effects (hybrid speciation and swamping). To evaluate the conservation implications of hybrids, we developed a decision-making tree with which to determine which actions should be taken to manage hybrid species. We found 53 hybrids involving 68 unique taxa, which is roughly 23% of all carnivore species. They mainly involved monophyletic (83%) and sympatric species (75%). For 2 species, the outcome of the assessment was to eliminate or restrict the hybrids: Ethiopian wolf (Canis simensis) and Scottish wildcat (Felis silvestris silvestris). Both species hybridize with their domestic conspecifics. For all other cases, we suggest hybrids be protected in the same manner as native species. We found no evidence of genomic extinction in Carnivora. To the contrary, some species appear to be of hybrid origin, such as the Asiatic black bear (Ursus thibetanus) and African golden wolf (Canis lupaster). Other positive outcomes of hybridization are novel genetic diversity, adaptation to extreme environments, and increased reproductive fitness. These outcomes are particularly valuable for counterbalancing genetic drift and enabling adaptive introgression in a human-dominated world.
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Affiliation(s)
- Laura Tensen
- Institute for Integrated Natural Sciences, Department of Zoology, University of Koblenz, Koblenz, Germany
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, Department of Zoology, University of Koblenz, Koblenz, Germany
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4
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Hill R, McMullan M. Recombination triggers fungal crop disease. Nat Ecol Evol 2023; 7:1961-1962. [PMID: 37945943 DOI: 10.1038/s41559-023-02132-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
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5
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White OW, Reyes-Betancort A, Carine MA, Chapman MA. Comparative transcriptomics and gene expression divergence associated with homoploid hybrid speciation in Argyranthemum. G3 (BETHESDA, MD.) 2023; 13:jkad158. [PMID: 37477910 PMCID: PMC10542503 DOI: 10.1093/g3journal/jkad158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 04/21/2023] [Accepted: 06/28/2023] [Indexed: 07/22/2023]
Abstract
Ecological isolation is increasingly thought to play an important role in speciation, especially for the origin and reproductive isolation of homoploid hybrid species. However, the extent to which divergent and/or transgressive gene expression changes are involved in speciation is not well studied. In this study, we employ comparative transcriptomics to investigate gene expression changes associated with the origin and evolution of two homoploid hybrid plant species, Argyranthemum sundingii and A. lemsii (Asteraceae). As there is no standard methodology for comparative transcriptomics, we examined five different pipelines for data assembly and analysing gene expression across the four species (two hybrid and two parental). We note biases and problems with all pipelines, and the approach used affected the biological interpretation of the data. Using the approach that we found to be optimal, we identify transcripts showing DE between the parental taxa and between the homoploid hybrid species and their parents; in several cases, putative functions of these DE transcripts have a plausible role in ecological adaptation and could be the cause or consequence of ecological speciation. Although independently derived, the homoploid hybrid species have converged on similar expression phenotypes, likely due to adaptation to similar habitats.
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Affiliation(s)
- Oliver W White
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | | | - Mark A Carine
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
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6
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Giesen A, Blanckenhorn WU, Schäfer MA, Shimizu KK, Shimizu-Inatsugi R, Misof B, Podsiadlowski L, Niehuis O, Lischer HEL, Aeschbacher S, Kapun M. Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species. Evol Biol 2023; 50:395-412. [PMID: 37854269 PMCID: PMC10579158 DOI: 10.1007/s11692-023-09612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The extent of interspecific gene flow and its consequences for the initiation, maintenance, and breakdown of species barriers in natural systems remain poorly understood. Interspecific gene flow by hybridization may weaken adaptive divergence, but can be overcome by selection against hybrids, which may ultimately promote reinforcement. An informative step towards understanding the role of gene flow during speciation is to describe patterns of past gene flow among extant species. We investigate signals of admixture between allopatric and sympatric populations of the two closely related European dung fly species Sepsis cynipsea and S. neocynipsea (Diptera: Sepsidae). Based on microsatellite genotypes, we first inferred a baseline demographic history using Approximate Bayesian Computation. We then used genomic data from pooled DNA of natural and laboratory populations to test for past interspecific gene flow based on allelic configurations discordant with the inferred population tree (ABBA-BABA test with D-statistic). Comparing the detected signals of gene flow with the contemporary geographic relationship among interspecific pairs of populations (sympatric vs. allopatric), we made two contrasting observations. At one site in the French Cevennes, we detected an excess of past interspecific gene flow, while at two sites in Switzerland we observed lower signals of past microsatellite genotypes gene flow among populations in sympatry compared to allopatric populations. These results suggest that the species boundaries between these two species depend on the past and/or present eco-geographic context in Europe, which indicates that there is no uniform link between contemporary geographic proximity and past interspecific gene flow in natural populations. Supplementary Information The online version contains supplementary material available at 10.1007/s11692-023-09612-5.
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Affiliation(s)
- Athene Giesen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wolf U. Blanckenhorn
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin A. Schäfer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | | | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, Freiburg, Germany
| | - Heidi E. L. Lischer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Kapun
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Division of Cell & Developmental Biology, Medical University of Vienna, Vienna, Austria
- Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
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7
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Wang D, Sun Y, Lei W, Zhu H, Wang J, Bi H, Feng S, Liu J, Ru D. Backcrossing to different parents produced two distinct hybrid species. Heredity (Edinb) 2023; 131:145-155. [PMID: 37264213 PMCID: PMC10382510 DOI: 10.1038/s41437-023-00630-9] [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: 09/29/2022] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
Repeated homoploid hybrid speciation (HHS) events with the same parental species have rarely been reported. In this study, we used population transcriptome data to test paraphyly and HHS events in the conifer Picea brachytyla. Our analyses revealed non-sister relationships for two lineages of P. brachytyla, with the southern lineage being placed within the re-circumscribed P. likiangensis species complex (PLSC) and P. brachytyla sensu stricto (s.s.) consisted solely of the northern lineage, forming a distinct clade that is paratactic to both the PLSC and P. wilsonii. Our phylogenetic and coalescent analyses suggested that P. brachytyla s.s. arose from HHS between the ancestor of the PLSC before its diversification and P. wilsonii through an intermediate hybrid lineage at an early stage and backcrossing to the ancestral PLSC. Additionally, P. purpurea shares the same parents and an extinct lineage with P. brachytyla s.s. but backcrossing to the other parent, P. wilsonii at a later stage. We reveal the first case that backcrossing to different parents of the same extinct hybrid lineage produced two different hybrid species. Our results highlight the existence of more reticulate evolution during species diversification in the spruce genus and more complex homoploid hybrid events than previously identified.
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Affiliation(s)
- Donglei Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Yongshuai Sun
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Weixiao Lei
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Hui Zhu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Ji Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Hao Bi
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China
| | - Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, Qinghai, China
| | - Jianquan Liu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China.
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
| | - Dafu Ru
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, PR China.
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
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8
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Kaskinova MD, Gaifullina LR, Saltykova ES. Haplotypes of the tRNAleu-COII mtDNA Region in Russian Apis mellifera Populations. Animals (Basel) 2023; 13:2394. [PMID: 37508171 PMCID: PMC10376158 DOI: 10.3390/ani13142394] [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: 05/02/2023] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 07/30/2023] Open
Abstract
Analysis of the mtDNA tRNAleu-COII locus is a widely used tool to establish belonging to a particular evolutionary lineage of Apis mellifera L. (lineages A, M, C, O, and Y). In Russia, most of the area was once inhabited by Apis mellifera mellifera from the M evolutionary lineage, but the introduction of bee subspecies from the southern regions of Russia (A. m. caucasica, A. m. carnica) and from abroad (A. m. carnica, A. m. ligustica) led to fragmentation of their native range. In this study, the results of assessing the haplotype number for the tRNAleu-COII locus of mtDNA in Russian Apis mellifera populations were presented. We analyzed 269 colonies from 19 regions of Russia. As a result, two evolutionary lineages were identified: the East European lineage C (26.4%) and the Northwestern European lineage M (73.6%). A total of 29 haplotypes were identified, 8 of them were already reported, and 21 were found to be novel. From the C lineage, haplotypes C1, C2, C2c, C2j, and C3 were predominant. All M lineage samples from Russia belong to the M17 and M4' haplogroups but have only minor variations in the form of nucleotide substitutions. An analysis of publications devoted to the tRNAleu-COII locus haplotypes, as well as an analysis of the available tRNAleu-COII sequences in GenBank, showed that there is still a problem with the haplotype nomenclature.
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Affiliation(s)
- Milyausha D Kaskinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Prospekt Oktyabrya 71, 450054 Ufa, Russia
| | - Luisa R Gaifullina
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Prospekt Oktyabrya 71, 450054 Ufa, Russia
| | - Elena S Saltykova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, Prospekt Oktyabrya 71, 450054 Ufa, Russia
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9
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Lopes F, Oliveira LR, Beux Y, Kessler A, Cárdenas-Alayza S, Majluf P, Páez-Rosas D, Chaves J, Crespo E, Brownell RL, Baylis AMM, Sepúlveda M, Franco-Trecu V, Loch C, Robertson BC, Peart CR, Wolf JBW, Bonatto SL. Genomic evidence for homoploid hybrid speciation in a marine mammal apex predator. SCIENCE ADVANCES 2023; 9:eadf6601. [PMID: 37134171 PMCID: PMC10156116 DOI: 10.1126/sciadv.adf6601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Hybridization is widespread and constitutes an important source of genetic variability and evolution. In animals, its role in generating novel and independent lineages (hybrid speciation) has been strongly debated, with only a few cases supported by genomic data. The South American fur seal (SAfs) Arctocephalus australis is a marine apex predator of Pacific and Atlantic waters, with a disjunct set of populations in Peru and Northern Chile [Peruvian fur seal (Pfs)] with controversial taxonomic status. We demonstrate, using complete genome and reduced representation sequencing, that the Pfs is a genetically distinct species with an admixed genome that originated from hybridization between the SAfs and the Galapagos fur seal (Arctocephalus galapagoensis) ~400,000 years ago. Our results strongly support the origin of Pfs by homoploid hybrid speciation over alternative introgression scenarios. This study highlights the role of hybridization in promoting species-level biodiversity in large vertebrates.
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Affiliation(s)
- Fernando Lopes
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
- Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, São Leopoldo, Brazil
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Larissa R Oliveira
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul (GEMARS), Torres, Brazil
| | - Yago Beux
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Amanda Kessler
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Susana Cárdenas-Alayza
- Centro para la Sostenibilidad Ambiental, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Patricia Majluf
- Centro para la Sostenibilidad Ambiental, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Diego Páez-Rosas
- Colegio de Ciencias Biológicas y Ambientales, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
- Dirección del Parque Nacional Galápagos, Oficina Técnica San Cristobal, Islas Galápagos, Ecuador
| | - Jaime Chaves
- Colegio de Ciencias Biológicas y Ambientales, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
- Galapagos Science Center, Puerto Baquerizo Moreno, Ecuador
- Department of Biology, San Francisco State University, 1800 Holloway Ave, San Francisco, CA, USA
| | - Enrique Crespo
- Laboratório de Mamíferos Marinos, CESIMAR - CCT CENPAT, CONICET, Puerto Madryn, Argentina
| | - Robert L Brownell
- Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA, USA
| | | | - Maritza Sepúlveda
- Centro de Investigación y Gestión de Recursos Naturales (CIGREN), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Valentina Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Carolina Loch
- Sir John Walsh Research Institute, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | | | - Claire R Peart
- Division of Evolutionary Biology, LMU Munich, München, Germany
| | - Jochen B W Wolf
- Division of Evolutionary Biology, LMU Munich, München, Germany
| | - Sandro L Bonatto
- Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
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10
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Jia Y, Liu ML, López-Pujol J, Jia RW, Kou YX, Yue M, Guan TX, Li ZH. The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis. Mol Phylogenet Evol 2023; 182:107736. [PMID: 36805473 DOI: 10.1016/j.ympev.2023.107736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.
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Affiliation(s)
- Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, Shaanxi, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Barcelona 08038, Catalonia, Spain; Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Rui-Wen Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yi-Xuan Kou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, Shaanxi, China
| | - Tian-Xia Guan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Key Laboratory of Hexi Corridor Resources Utilization of Gansu, College of Life Sciences and Engineering, Hexi University, Zhangye 734000, Gansu, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
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11
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Wei S, Zhang Q, Tang S, Liao W. Genetic and ecophysiological evidence that hybridization facilitated lineage diversification in yellow Camellia (Theaceae) species: a case study of natural hybridization between C. micrantha and C. flavida. BMC PLANT BIOLOGY 2023; 23:154. [PMID: 36944951 PMCID: PMC10031943 DOI: 10.1186/s12870-023-04164-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Hybridization is generally considered an important creative evolutionary force, yet this evolutionary process is still poorly characterized in karst plants. In this study, we focus on natural hybridization in yellow Camellia species, a group of habitat specialists confined to karst/non-karst habitats in southwestern China. RESULTS Based on population genome data obtain from double digest restriction-site associated DNA (ddRAD) sequencing, we found evidence for natural hybridization and introgression between C. micrantha and C. flavida, and specifically confirmed their hybrid population, C. "ptilosperma". Ecophysiological results suggested that extreme hydraulic traits were fixed in C. "ptilosperma", these being consistent with its distinct ecological niche, which lies outside its parental ranges. CONCLUSION The identified hybridization event is expected to have played a role in generating novel variation during, in which the hybrid population displays different phenological characteristics and novel ecophysiological traits associated with the colonization of a new niche in limestone karst.
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Affiliation(s)
- Sujuan Wei
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541004, China
| | - Qiwei Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541004, China
| | - Shaoqing Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, Guangxi Normal University, Guilin, 541004, China.
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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12
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Nali RC, Zamudio KR, Prado CPA. Hybridization despite elaborate courtship behavior and female choice in Neotropical tree frogs. Integr Zool 2023; 18:208-224. [PMID: 35041294 DOI: 10.1111/1749-4877.12628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanisms of hybridization can be elucidated by analyzing genotypes as well as phenotypes that could act as premating barriers, as the reproductive interactions among heterospecifics can alter the evolutionary history of species. In frogs, hybrids typically occur among species that reproduce explosively (in dense aggregations) with few opportunities for mate selection but are rare in species with elaborate courtship behaviors that may prevent erroneous mating. Using 21 microsatellite markers, we examined hybridization in the prolonged-breeding tree frogs Bokermannohyla ibitiguara and B. sazimai sampled within a contact zone in the Brazilian savanna (72 tadpoles; 74 adults). We also compared acoustic and morphological data. We confirmed both parental species genetically; STRUCTURE results confirmed 14 hybrids, 11 of which were second-generation according to NEWHYBRIDS, all with intermediate values of genetic dissimilarities compared to the parentals. Morphological and acoustic analyses revealed that hybrids showed variable but not necessarily intermediate phenotypes. Moreover, 2 hybrids exhibited call types different from parentals. The reproduction of B. ibitiguara involves territorial and aggressive males, elaborate courtships with acoustic and tactile stimuli, choosy females, and opportunistic strategies. Our study uncovers a rare case of viable hybridization among closely related frogs with such a combination of complex courtship behaviors and mate choice. We discuss the likely directionality and mechanisms behind this phenomenon, and highlight the importance of investigating hybridization even in species that show elaborate reproduction and female choice to advance our understanding of animal diversification.
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Affiliation(s)
- Renato C Nali
- Programa de Pós-Graduação em Ecologia, Evolução e Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA.,Department of Integrative Biology, University of Texas, Austin, Texas, USA
| | - Cynthia P A Prado
- Programa de Pós-Graduação em Ecologia, Evolução e Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil.,Departamento de Morfologia e Fisiologia Animal, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, São Paulo, Brazil
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13
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MacPherson N, Champion CP, Weir LK, Dalziel AC. Reproductive isolating mechanisms contributing to asymmetric hybridization in Killifishes (Fundulus spp.). J Evol Biol 2023; 36:605-621. [PMID: 36636892 DOI: 10.1111/jeb.14148] [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: 06/03/2022] [Revised: 10/27/2022] [Accepted: 11/26/2022] [Indexed: 01/14/2023]
Abstract
When species hybridize, one F1 hybrid cross type often predominates. Such asymmetry can arise from differences in a variety of reproductive barriers, but the relative roles and concordance of pre-mating, post-mating prezygotic, and post-zygotic barriers in producing these biases in natural animal populations have not been widely investigated. Here, we study a population of predominantly F1 hybrids between two killifish species (Fundulus heteroclitus and F. diaphanus) in which >95% of F1 hybrids have F. diaphanus mothers and F. heteroclitus fathers (D♀ × H♂). To determine why F. heteroclitus × F. diaphanus F1 hybrids (H♀ × D♂) are so rare, we tested for asymmetry in pre-mating reproductive barriers (female preference and male aggression) at a common salinity (10 ppt) and post-mating, pre-zygotic (fertilization success) and post-zygotic (embryonic development time and hatching success) reproductive barriers at a range of ecologically relevant salinities (0, 5, 10, and 15 ppt). We found that F. heteroclitus females preferred conspecific males, whereas F. diaphanus females did not, matching the observed cross bias in the wild. Naturally rare H♀ × D♂ crosses also had lower fertilization success than all other cross types, and a lower hatching success than the prevalent D♀ × H♂ crosses at the salinity found in the hybrid zone centre (10 ppt). Furthermore, the naturally predominant D♀ × H♂ crosses had a higher hatching success than F. diaphanus crosses at 10 ppt, which may further increase their relative abundance. The present study suggests that a combination of incomplete mating, post-mating pre-zygotic and post-zygotic reproductive isolating mechanisms act in concert to produce hybrid asymmetry in this system.
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Affiliation(s)
- Nathalie MacPherson
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Chloe P Champion
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Laura K Weir
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Anne C Dalziel
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
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14
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Noguerales V, Ortego J. Genomic evidence of speciation by fusion in a recent radiation of grasshoppers. Evolution 2022; 76:2618-2633. [PMID: 35695020 PMCID: PMC9796961 DOI: 10.1111/evo.14508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/22/2022] [Accepted: 04/02/2022] [Indexed: 01/22/2023]
Abstract
Postdivergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). Although neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between the sister taxa C. binotatus (that exclusively feeds on scrub legumes) and C. saulcyi (that only feeds on gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirm that C. s. algoaldensis represents an independently evolving lineage and support the ancient hybrid origin of this taxon (about 1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate their long-term persistence through geographic isolation from parental forms in topographically complex landscapes.
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Affiliation(s)
- Víctor Noguerales
- Department of Biological SciencesUniversity of CyprusNicosia1678Cyprus,Island Ecology and Evolution GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de La Laguna38206Spain
| | - Joaquín Ortego
- Department of Integrative EcologyEstación Biológica de Doñana (EBD‐CSIC)Sevilla41092Spain
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15
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Introduced, Mixed, and Peripheral: Conservation of Mitochondrial-DNA Lineages in the Wild Boar (Sus scrofa L.) Population in the Urals. DIVERSITY 2022. [DOI: 10.3390/d14110916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Translocations and introductions are important events that allow organisms to overcome natural barriers. The genetic background of colonization success and genetic consequences of the establishment of populations in new environments are of great interest for predicting species’ colonization success. The wild boar has been introduced into many parts of the world. We analyzed sequences of the mitochondrial-DNA control region in the wild boars introduced into the Ural region and compared them with sequences from founder populations (from Europe, the Caucasus, Central Asia, and the Far East). We found that the introduced population has high genetic diversity. Haplotypes from all the major phylogenetic clades were detected in the analyzed group of the animals from the Urals. In this group, no haplotypes identical to Far Eastern sequences were detectable despite a large number of founders from that region. The contribution of lineages originating from Eastern Europe was greater than expected from the proportions (%) of European and Asian animals in the founder populations. This is the first study on the genetic diversity and structure of a wild boar population of mixed origin at the northern periphery of this species’ geographical range.
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16
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Knytl M, Forsythe A, Kalous L. A Fish of Multiple Faces, Which Show Us Enigmatic and Incredible Phenomena in Nature: Biology and Cytogenetics of the Genus Carassius. Int J Mol Sci 2022; 23:8095. [PMID: 35897665 PMCID: PMC9330404 DOI: 10.3390/ijms23158095] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022] Open
Abstract
Sexual vs. asexual reproduction-unisexual vs. bisexual populations-diploid vs. polyploid biotypes-genetic vs. environmental sex determination: all these natural phenomena are associated with the genus of teleost fish, Carassius. This review places emphasis on two Carassius entities with completely different biological characteristics: one globally widespread and invasive Carassius gibelio, and the other C. carassius with a decreasing trend of natural occurrence. Comprehensive biological and cytogenetic knowledge of both entities, including the physical interactions between them, can help to balance the advantages of highly invasive and disadvantages of threatened species. For example, the benefits of a wide-ranged colonization can lead to the extinction of native species or be compensated by parasitic enemies and lead to equilibrium. This review emphasizes the comprehensive biology and cytogenetic knowledge and the importance of the Carassius genus as one of the most useful experimental vertebrate models for evolutionary biology and genetics. Secondly, the review points out that effective molecular cytogenetics should be used for the identification of various species, ploidy levels, and hybrids. The proposed investigation of these hallmark characteristics in Carassius may be applied in conservation efforts to sustain threatened populations in their native ranges. Furthermore, the review focuses on the consequences of the co-occurrence of native and non-native species and outlines future perspectives of Carassius research.
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Affiliation(s)
- Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Adrian Forsythe
- Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, 75236 Uppsala, Sweden;
| | - Lukáš Kalous
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 16521 Prague, Czech Republic;
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17
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Zhou J, Yang Y, Lv Y, Pu Q, Li J, Zhang Y, Deng X, Wang M, Wang J, Tao D. Interspecific Hybridization Is an Important Driving Force for Origin and Diversification of Asian Cultivated Rice Oryza sativa L. FRONTIERS IN PLANT SCIENCE 2022; 13:932737. [PMID: 35845644 PMCID: PMC9280345 DOI: 10.3389/fpls.2022.932737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
As one of the most important crops, Asian cultivated rice has evolved into a complex group including several subgroups adapting various eco-climate-systems around the globe. Here, we pictured a comprehensive view of its original domestication, divergences, and the origin of different subgroups by integrating agriculture, archeology, genetics, nuclear, and cytoplasm genome results. Then, it was highlighted that interspecific hybridization-introgression has played important role in improving the genetic diversity and adaptation of Oryza sativa during its evolution process. Natural hybridization-introgression led to the origin of indica, aus, and basmatic subgroups, which adapted to changing cultivated environments, and produced feral weedy rice coexisting and competing with cultivars under production management. Artificial interspecific hybridization-introgression gained several breakthroughs in rice breeding, such as developing three-line hybrid rice, new rice for Africa (NERICA), and some important pest and disease resistance genes in rice genetic improvement, contributing to the stable increase of rice production to meet the expanding human population. We proposed a series to exploit the virtues of hybridization-introgression in the genetic improvement of Asian cultivated rice. But some key issues such as reproductive barriers especially hybrid sterility should be investigated further, which are conducive to gene exchange between cultivated rice and its relatives, and even is beneficial to exploiting interspecific hybrid vigor. New technologies help introduce favorable genes from distant wild species to Asian cultivated rice, such as transgenic and genome editing systems. Rising introgression lines in a wider range with multi-donor benefits allele mining, understanding genetic network of rice growth and development, yield formation, and environmental adaptation. Then, integration of new tools and interspecific hybridization can be a future direction to develop more usable breeding populations which can make Asian cultivated rice more resilient to the changing climate and world.
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Affiliation(s)
- Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ying Yang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yonggang Lv
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Qiuhong Pu
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jing Li
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yu Zhang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xianneng Deng
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Min Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Jie Wang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
- Institute of Plant Resources, Yunnan University, Kunming, China
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
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18
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Chao YS, Ebihara A, Chiou WL, Tsai JM, Huang YW, Ranker TA. Reticulate evolution in the Pteris fauriei group (Pteridaceae). Sci Rep 2022; 12:9145. [PMID: 35650209 PMCID: PMC9159987 DOI: 10.1038/s41598-022-11390-7] [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] [Received: 08/17/2021] [Accepted: 04/14/2022] [Indexed: 11/10/2022] Open
Abstract
The Pteris fauriei group (Pteridaceae) has a wide distribution in Eastern Asia and includes 18 species with similar but varied morphology. We collected more than 300 specimens of the P. fauriei group and determined ploidy by flow cytometry and inferred phylogenies by molecular analyses of chloroplast and nuclear DNA markers. Our results reveal a complicated reticulate evolution, consisting of seven parental taxa and 58 hybrids. The large number of hybrid taxa have added significant morphological complexity to the group leading to difficult taxonomic issues. The hybrids generally had broader ranges and more populations than their parental taxa. Genetic combination of different pairs of parental species created divergent phenotypes of hybrids, exhibited by both morphological characteristics and ecological fidelities. Niche novelty could facilitate hybrid speciation. Apogamy is common in this group and potentially contributes to the sustainability of the whole group. We propose that frequent hybridizations among members of the P. fauriei group generate and maintain genetic diversity, via novel genetic combinations, niche differentiation, and apogamy.
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Affiliation(s)
- Yi-Shan Chao
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100, Shih-Chuan 1st Rd., Kaohsiung, 80708, Taiwan.
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, 4-1-1, Amakubo, Tsukuba-shi, Ibaraki, 305-0005, Japan
| | - Wen-Liang Chiou
- Taiwan Forestry Research Institute, 53 Nan-Hai Rd., Taipei, 100051, Taiwan
| | - Jer-Min Tsai
- Department of Information and Communication, Kun Shan University, 195, Kunda Rd., Tainan, 710303, Taiwan
| | - Yu-Wen Huang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100, Shih-Chuan 1st Rd., Kaohsiung, 80708, Taiwan
| | - Tom A Ranker
- University of Hawai'i at Mānoa, School of Life Sciences, Honolulu, HI, 96822, USA
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Vučić T, Ivanović A, Ajduković M, Bajler N, Cvijanović M. The Reproductive Success of Triturus ivanbureschi × T. macedonicus F1 Hybrid Females (Amphibia: Salamandridae). Animals (Basel) 2022; 12:ani12040443. [PMID: 35203151 PMCID: PMC8868055 DOI: 10.3390/ani12040443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Two moderately related large-bodied newt species endemic to the Balkan Peninsula, the Balkan crested newt (Triturus ivanbureschi) and the Macedonian crested newt (T. macedonicus), coexist and hybridize in central Serbia. Many generations of mutual hybrid crossings and backcrossings with parental species shaped the genetic composition of hybrid populations. Natural populations have admixed nuclear DNA (nuDNA) of parental species and T. ivanbureschi mitochondrial DNA (mtDNA), which is usually maternally inherited. The mechanisms that direct gene flow and shape the first generations of hybrids could explain the formation of hybrid zones and their maintenance in nature. We followed and compared life history traits related to reproduction of the first generation of reciprocal hybrids obtained by experimental crossing. Our results suggested that possible incompatibilities between mitochondrial and nuclear genomes, which could lead to the exclusion of T. macedonicus mtDNA in natural populations, most likely act at later stages of development or subsequent hybrid generations. Results from this study add to the growing knowledge of Triturus hybrid biology and ecology, which is the baseline for conservation programs necessary to protect these highly endangered amphibians. Abstract Two large-bodied newt species, Triturus ivanbureschi and T. macedonicus, hybridize in nature across the Balkan Peninsula. Consequences of hybridization upon secondary contact of two species include species displacement and asymmetrical introgression of T. ivanbureschi mtDNA. We set an experimental reciprocal cross of parental species and obtained two genotypes of F1 hybrids (with T. ivanbureschi or T. macedonicus mtDNA). When hybrids attained sexual maturity, they were engaged in mutual crossings and backcrossing with parental species. We followed reproductive traits over two successive years. Our main aim was to explore the reproductive success of F1 females carrying different parental mtDNA. Additionally, we tested for differences in reproductive success within female genotypes depending on the crossing with various male genotypes (hybrids or parental species). Both female genotypes had similar oviposition periods, number of laid eggs and hatched larvae but different body and egg sizes. Overall reproductive success (percentage of egg-laying females and viability of embryos) was similar for both genotypes. The type of crossing led to some differences in reproductive success within female genotypes. The obtained results suggest that processes that led to exclusion of T. macedonicus mtDNA in natural populations may be related to the survival at postembryonic stages of F2 generation or reproductive barriers that emerged in subsequent hybrid generations.
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Affiliation(s)
- Tijana Vučić
- Faculty of Biology, Institute of Zoology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (A.I.); (N.B.)
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia;
- Correspondence: (T.V.); (M.C.)
| | - Ana Ivanović
- Faculty of Biology, Institute of Zoology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (A.I.); (N.B.)
| | - Maja Ajduković
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia;
| | - Nikola Bajler
- Faculty of Biology, Institute of Zoology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (A.I.); (N.B.)
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia;
| | - Milena Cvijanović
- Department of Evolutionary Biology, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia;
- Correspondence: (T.V.); (M.C.)
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20
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Bugarčić M, Ivanović A, Cvijanović M, Vučić T. Consequences of hybridization on life history and growth in postmetamorphic Triturus macedonicus. AMPHIBIA-REPTILIA 2022. [DOI: 10.1163/15685381-bja10082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
The Macedonian crested newt T. macedonicus forms a complex hybrid zone with the Balkan crested newt T. ivanbureschi in the central part of the Balkan Peninsula. In this study, we compared life history parameters (sex ratio, survival rate and age of sexual maturation) and growth parameters (body length and mass) of T. macedonicus and T. macedonicus × T. ivanbureschi hybrids over the first three postmetamorphic years. Survival rates were high and similar for both genotypes. Sexual dimorphism in body size (length and mass) was evident at the beginning of the third postmetamorphic year, after the first breeding year, for both T. macedonicus and hybrids. We did not find clear and consistent difference in any of the analysed traits suggesting that hybridization with T. ivabureschi does not affect postmetamorphic growth and survival of T. macedonicus.
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Affiliation(s)
- Marko Bugarčić
- University of Belgrade, Faculty of Biology, Institute of Zoology, 11000 Belgrade, Serbia
| | - Ana Ivanović
- University of Belgrade, Faculty of Biology, Institute of Zoology, 11000 Belgrade, Serbia
| | - Milena Cvijanović
- University of Belgrade, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, Department of Evolutionary Biology, 11000 Belgrade, Serbia
| | - Tijana Vučić
- University of Belgrade, Faculty of Biology, Institute of Zoology, 11000 Belgrade, Serbia
- University of Belgrade, Institute for Biological Research “Siniša Stanković”, National Institute of the Republic of Serbia, Department of Evolutionary Biology, 11000 Belgrade, Serbia
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21
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Chen C, Zheng Z, Wu D, Tan L, Yang C, Liu S, Lu J, Cheng Y, Sha L, Wang Y, Kang H, Fan X, Zhou Y, Zhang C, Zhang H. Morphological, cytological, and molecular evidences for natural hybridization between Roegneria stricta and Roegneria turczaninovii (Triticeae: Poaceae). Ecol Evol 2022; 12:e8517. [PMID: 35136562 PMCID: PMC8809439 DOI: 10.1002/ece3.8517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 11/26/2021] [Accepted: 12/16/2021] [Indexed: 12/05/2022] Open
Abstract
Some plants with low fertility are morphologically intermediate between Roegneria stricta and Roegneria turczaninovii, and were suspected to be natural hybrids between these species. In this study, karyotype analysis showed that natural hybrids and their putative parents were tetraploids (2n = 4x = 28). Meiotic pairing in natural hybrids is more irregular than its putative parents. Results of genomic in situ hybridization and fluorescence in situ hybridization indicate that natural hybrids contain the same genome as their putative parents. The nuclear gene DNA meiotic recombinase 1 (DMC1) and the chloroplast gene rps16 of natural hybrids and their putative parents were analyzed for evidence of hybridization. The results from molecular data supported by morphology and cytology demonstrated that the plants represent natural hybrids between R. stricta and R. turczaninovii. The study is important for understanding species evolution in the genus since it demonstrates for the first time the existence of populations of natural homoploid hybrids in Roegneria. The study also reports for the first time that the composition of the genomic formula of R. turczaninovii is StY, confirming that the current taxonomic status is correct.
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Affiliation(s)
- Chen Chen
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Zilue Zheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Dandan Wu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Lu Tan
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
| | - Cairong Yang
- College of Chemistry and Life SciencesChengdu Normal UniversityChengduChina
| | - Songqing Liu
- College of Chemistry and Life SciencesChengdu Normal UniversityChengduChina
| | - Jiale Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yiran Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Yi Wang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Houyang Kang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Xing Fan
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | - Yonghong Zhou
- Triticeae Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
| | | | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaSichuan Agricultural UniversityChengduChina
- College of Grassland Science and TechnologySichuan Agricultural UniversityChengduChina
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22
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Suvorov A, Scornavacca C, Fujimoto MS, Bodily P, Clement M, Crandall KA, Whiting MF, Schrider DR, Bybee SM. Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies. Syst Biol 2021; 71:526-546. [PMID: 34324671 PMCID: PMC9017697 DOI: 10.1093/sysbio/syab063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Introgression is an important biological process affecting at least 10% of the extant species in the animal kingdom. Introgression significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically "intermediate" species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression.
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Affiliation(s)
- Anton Suvorov
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Celine Scornavacca
- Institut des Sciences de l'Evolution Université de Montpellier, CNRS, IRD, EPHE CC 064, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - M Stanley Fujimoto
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Paul Bodily
- Department of Computer Science, Idaho State University, Pocatello, ID, United States
| | - Mark Clement
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
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23
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Lu Z, Sun Y, Li Y, Yang Y, Wang G, Liu J. Species delimitation and hybridization history of a hazel species complex. ANNALS OF BOTANY 2021; 127:875-886. [PMID: 33564860 PMCID: PMC8225278 DOI: 10.1093/aob/mcab015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/03/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS Hybridization increases species adaptation and biodiversity but also obscures species boundaries. In this study, species delimitation and hybridization history were examined within one Chinese hazel species complex (Corylus chinensis-Corylus fargesii). Two species including four varieties have already been described for this complex, with overlapping distributions. METHODS A total of 322 trees from 44 populations of these four varieties across their ranges were sampled for morphological and molecular analyses. Climatic datasets based on 108 geographical locations were used to evaluate their niche differentiations. Flowering phenology was also observed for two co-occurring species or varieties. KEY RESULTS Four statistically different phenotypic clusters were revealed, but these clusters were highly inconsistent with the traditional taxonomic groups. All the clusters showed statistically distinct niches, with complete or partial geographical isolation. Only two clusters displayed a distributional overlap, but they had distinct flowering phenologies at the site where they co-occurred. Population-level evidence based on the genotypes of ten simple sequence repeat loci supported four phenotypic clusters. In addition, one cluster was shown to have an admixed genetic composition derived from the other three clusters through repeated historical hybridizations. CONCLUSIONS Based on our new evidence, it is better to treat the four clusters identified here as four independent species. One of them was shown to have an admixed genetic composition derived from the other three through repeated historical hybridizations. This study highlights the importance of applying integrative and statistical methods to infer species delimitations and hybridization history. Such a protocol should be adopted widely for future taxonomic studies.
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Affiliation(s)
- Zhiqiang Lu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Yongshuai Sun
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Gaini Wang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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24
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Lorenzoni M, Carosi A, Quadroni S, De Santis V, Vanetti I, Delmastro GB, Zaccara S. Cryptic diversity within endemic Italian barbels: revalidation and description of new Barbus species (Teleostei: Cyprinidae). JOURNAL OF FISH BIOLOGY 2021; 98:1433-1449. [PMID: 33486760 DOI: 10.1111/jfb.14688] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Two fluviolacustrine lineages (SI1 Barbus and SI2 Barbus) of the Barbus genus have been recently detected in the Apulia-Campania ichthyogeographic district (southern Italy). The aim of this study was to determine the taxonomic status of these lineages by comparing them with the two already-established Italian fluviolacustrine species Barbus plebejus and Barbus tyberinus through a more in-depth molecular and morphological investigation. Genetic analyses were performed on both mitochondrial (cytochrome b) and nuclear (growth hormone paralog 2) DNA markers, and morphological analyses were carried out on specific age classes and purebred populations. Molecular analyses detected four evolutionary lineages at the mitochondrial level, whereas the nuclear data set highlighted the strict evolutionary relation between B. plebejus sensu stricto and the new lineages, converged in the B. plebejus complex clade. The morphological analyses allowed us to discriminate SI1 Barbus and SI2 Barbus from both B. plebejus and B. tyberinus. The new taxa could be discriminated by the greatest maximum body height and the longest pre-orbital distance, respectively. Both the new lineages have longer ventral and pectoral fins than B. plebejus and B. tyberinus, a larger caudal fin than B. tyberinus and a lower number of scales along the lateral line than B. plebejus. Both molecular and morphological results suggested the two southern Italian lineages could be considered as distinct endemic species: the formal description of the new species Barbus samniticus sp. nov. (i.e., SI1 Barbus) and the revalidation of Barbus fucini Costa, 1853 (i.e., SI2 Barbus) were thus proposed, and, for both species, molecular and morphological diagnosis were provided.
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Affiliation(s)
- Massimo Lorenzoni
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Perugia, Italy
| | - Antonella Carosi
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, Perugia, Italy
| | - Silvia Quadroni
- Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Vanessa De Santis
- Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Isabella Vanetti
- Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | | | - Serena Zaccara
- Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
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25
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Caputo B, Pichler V, Bottà G, De Marco C, Hubbart C, Perugini E, Pinto J, Rockett KA, Miles A, Della Torre A. Novel genotyping approaches to easily detect genomic admixture between the major Afrotropical malaria vector species, Anopheles coluzzii and An. gambiae. Mol Ecol Resour 2021; 21:1504-1516. [PMID: 33590707 PMCID: PMC8252489 DOI: 10.1111/1755-0998.13359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 02/05/2021] [Accepted: 02/11/2021] [Indexed: 11/28/2022]
Abstract
The two most efficient and most recently radiated Afrotropical vectors of human malaria - Anopheles coluzzii and An. gambiae - are identified by single-locus diagnostic PCR assays based on species-specific markers in a 4 Mb region on chromosome-X centromere. Inherently, these diagnostic assays cannot detect interspecific autosomal admixture shown to be extensive at the westernmost and easternmost extremes of the species range. The main aim of this study was to develop novel, easy-to-implement tools for genotyping An. coluzzii and An. gambiae-specific ancestral informative markers (AIMs) identified from the Anopheles gambiae 1000 genomes (Ag1000G) project. First, we took advantage of this large set of data in order to develop a multilocus approach to genotype 26 AIMs on all chromosome arms valid across the species range. Second, we tested the multilocus assay on samples from Guinea Bissau, The Gambia and Senegal, three countries spanning the westernmost hybridization zone, where conventional species diagnostic is problematic due to the putative presence of a novel "hybrid form". The multilocus assay was able to capture patterns of admixture reflecting those revealed by the whole set of AIMs and provided new original data on interspecific admixture in the region. Third, we developed an easy-to-use, cost-effective PCR approach for genotyping two AIMs on chromosome-3 among those included in the multilocus approach, opening the possibility for advanced identification of species and of admixed specimens during routine large scale entomological surveys, particularly, but not exclusively, at the extremes of the range, where WGS data highlighted unexpected autosomal admixture.
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Affiliation(s)
- Beniamino Caputo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
| | - Verena Pichler
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
| | - Giordano Bottà
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy.,Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford, UK
| | - Carlo De Marco
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
| | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford, UK
| | - Eleonora Perugini
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
| | - Joao Pinto
- Global Health & Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford, UK
| | - Alistair Miles
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,MRC Centre for Genomics and Global Health, University of Oxford, Oxford, UK
| | - Alessandra Della Torre
- Dipartimento di Sanità Pubblica e Malattie Infettive, Istituto Pasteur Italia-Fondazione Cenci-Bolognetti, Università di Roma "Sapienza", Rome, Italy
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26
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Fabritzek AG, Griebeler EM, Kadereit JW. Hybridization, ecogeographical displacement and the emergence of new lineages - A genotyping-by-sequencing and ecological niche and species distribution modelling study of Sempervivum tectorum L. (Houseleek). J Evol Biol 2021; 34:830-844. [PMID: 33714223 DOI: 10.1111/jeb.13784] [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: 11/02/2020] [Revised: 01/18/2021] [Accepted: 03/03/2021] [Indexed: 11/28/2022]
Abstract
Ecogeographical displacement of homoploid hybrid lineages from their parents is well documented and considered an important mechanism to achieve reproductive isolation. In this study, we investigated the origin of the flowering plant species Sempervivum tectorum in the Massif Central (France) through homoploid hybridization between lineages of the species from the Rhine Gorge area (Germany) and the Pyrenees (France). We used genotyping-by-sequencing genetic data as evidence for the hybrid origin of the Massif Central lineage, and WorldClim climatic data and soil pH and soil temperature data collected by us for ecological niche and species distribution modelling. We could show that the Massif Central lineage shows hybrid admixture and that the niche of this lineage is significantly different from those of the parental lineages. In comparison with the parental niches, different variables of the niche of the hybrid lineage are intermediate, parental-combined or extreme. The different niche of the Massif Central populations thus can plausibly be interpreted as hybridization-derived. Our species distribution modelling for the Last Glacial Maximum and Mid-Holocene showed that the potential distribution of the hybrid lineage at the likely time of its origin in the Quaternary possibly was parapatric in relation to the largely sympatric distributions of the parental lineages. We hypothesize that reproductive isolation of the hybrid lineage from the parental lineages resulted from the segregation of distribution ranges by a differential response of the three lineages to a warming climate.
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Affiliation(s)
- Armin G Fabritzek
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Eva Maria Griebeler
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Joachim W Kadereit
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
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27
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Fu PC, Twyford AD, Sun SS, Wang HY, Xia MZ, Tan CX, Zhou XJ, Chen SL. Recurrent hybridization underlies the evolution of novelty in Gentiana (Gentianaceae) in the Qinghai-Tibetan Plateau. AOB PLANTS 2021; 13:plaa068. [PMID: 33510891 PMCID: PMC7821390 DOI: 10.1093/aobpla/plaa068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 11/30/2020] [Indexed: 05/31/2023]
Abstract
The Qinghai-Tibetan Plateau (QTP) and adjacent areas are centres of diversity for several alpine groups. Although it is known that the QTP acted as a source area for diversification of the alpine genus Gentiana, the evolutionary processes underlying diversity in this genus, especially the formation of narrow endemics, are still poorly understood. Hybridization has been proposed as a driver of plant endemism in the QTP but few cases have been documented with genetic data. Here, we describe a new endemic species in Gentiana section Cruciata as G. hoae sp. nov., and explore its evolutionary history with complete plastid genomes and nuclear ribosomal internal transcribed spacer sequence data. Genetic divergence within G. hoae ~3 million years ago was followed by postglacial expansion on the QTP, suggesting Pleistocene glaciations as a key factor shaping the population history of G. hoae. Furthermore, a mismatch between plastid and nuclear data suggest that G. hoae participated in historical hybridization, while population sequencing show this species continues to hybridize with the co-occurring congener G. straminea in three locations. Our results indicate that hybridization may be a common process in the evolution of Gentiana and may be widespread among recently diverged taxa of the QTP.
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Affiliation(s)
- Peng-Cheng Fu
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Shan-Shan Sun
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Hong-Yu Wang
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Ming-Ze Xia
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Cheng-Xi Tan
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Xiao-Jun Zhou
- School of Life Science, Luoyang Normal University, Luoyang, P.R. China
| | - Shi-Long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, P.R. China
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28
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Wilches R, Beluch WH, McConnell E, Tautz D, Chan YF. Independent evolution toward larger body size in the distinctive Faroe Island mice. G3-GENES GENOMES GENETICS 2021; 11:6062402. [PMID: 33561246 PMCID: PMC8022703 DOI: 10.1093/g3journal/jkaa051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/10/2020] [Indexed: 11/29/2022]
Abstract
Most phenotypic traits in nature involve the collective action of many genes. Traits that evolve repeatedly are particularly useful for understanding how selection may act on changing trait values. In mice, large body size has evolved repeatedly on islands and under artificial selection in the laboratory. Identifying the loci and genes involved in this process may shed light on the evolution of complex, polygenic traits. Here, we have mapped the genetic basis of body size variation by making a genetic cross between mice from the Faroe Islands, which are among the largest and most distinctive natural populations of mice in the world, and a laboratory mouse strain selected for small body size, SM/J. Using this F2 intercross of 841 animals, we have identified 111 loci controlling various aspects of body size, weight and growth hormone levels. By comparing against other studies, including the use of a joint meta-analysis, we found that the loci involved in the evolution of large size in the Faroese mice were largely independent from those of a different island population or other laboratory strains. We hypothesize that colonization bottleneck, historical hybridization, or the redundancy between multiple loci have resulted in the Faroese mice achieving an outwardly similar phenotype through a distinct evolutionary path.
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Affiliation(s)
- Ricardo Wilches
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - William H Beluch
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
| | - Ellen McConnell
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, 24306 Plön, Germany
| | - Diethard Tautz
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, 24306 Plön, Germany
| | - Yingguang Frank Chan
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tübingen, Germany
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29
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Nevado B, Harris SA, Beaumont MA, Hiscock SJ. Rapid homoploid hybrid speciation in British gardens: The origin of Oxford ragwort (
Senecio squalidus
). Mol Ecol 2020; 29:4221-4233. [DOI: 10.1111/mec.15630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 01/17/2023]
Affiliation(s)
- Bruno Nevado
- Department of Plant Sciences University of Oxford Oxford UK
| | | | | | - Simon J. Hiscock
- Department of Plant Sciences University of Oxford Oxford UK
- Oxford Botanic Garden and Arboretum Oxford UK
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30
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Pärssinen V, Hulthén K, Brönmark C, Skov C, Brodersen J, Baktoft H, Chapman BB, Hansson LA, Nilsson PA. Maladaptive migration behaviour in hybrids links to predator-mediated ecological selection. J Anim Ecol 2020; 89:2596-2604. [PMID: 32745243 PMCID: PMC7692921 DOI: 10.1111/1365-2656.13308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/24/2020] [Indexed: 12/22/2022]
Abstract
Different migratory species have evolved distinct migratory characteristics that improve fitness in their particular ecological niches. However, when such species hybridize, migratory traits from parental species can combine maladaptively and cause hybrids to fall between parental fitness peaks, with potential consequences for hybrid viability and species integrity. Here, we take advantage of a natural cross‐breeding incident to study migratory behaviour in naturally occurring hybrids as well as in their parental species and explore links between migratory traits and predation risk. To achieve this, we used electronic tags and passive telemetry to record detailed individual migration patterns (timing and number of migratory trips) in two common freshwater fish species, roach Rutilus rutilus, common bream Abramis brama as well as their hybrids. Next, we scanned for tags regurgitated by a key avian predator (great cormorant Phalacrocorax carbo) at nearby roosting sites, allowing us to directly link migratory behaviour to predation risk in the wild. We found that hybrid individuals showed a higher number of short, multi‐trip movements between lake and stream habitats as compared to both parental species. The mean date of first lake departure differed between bream and roach by more than 10 days, while hybrids departed in two distinct peaks that overlapped with the parental species' averages. Moreover, the probability of cormorant predation increased with multi‐trip movement frequency across species and was higher for hybrids. Our data provide novel insights into hybrid viability, with links to predator‐mediated ecological selection. Increased exposure to predators via maladaptive migratory behaviour reduces hybrid survival and can thereby reinforce species integrity.
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Affiliation(s)
- Varpu Pärssinen
- Department of Biology - Aquatic Ecology, Lund University, Lund, Sweden
| | - Kaj Hulthén
- Department of Biology - Aquatic Ecology, Lund University, Lund, Sweden
| | - Christer Brönmark
- Department of Biology - Aquatic Ecology, Lund University, Lund, Sweden
| | - Christian Skov
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), Silkeborg, Denmark
| | - Jakob Brodersen
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Department of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Henrik Baktoft
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), Silkeborg, Denmark
| | - Ben B Chapman
- Division of Evolution and Genomics, School of Biological Sciences, University of Manchester, Manchester, UK
| | | | - Per Anders Nilsson
- Department of Biology - Aquatic Ecology, Lund University, Lund, Sweden.,Department of Environmental and Life Sciences - Biology, Karlstad University, Karlstad, Sweden
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31
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Zhou Z, Feng C, Liu X, Liu S. 3nLcn2, a teleost lipocalin 2 that possesses antimicrobial activity and inhibits bacterial infection in triploid crucian carp. FISH & SHELLFISH IMMUNOLOGY 2020; 102:47-55. [PMID: 32283247 DOI: 10.1016/j.fsi.2020.04.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/25/2020] [Accepted: 04/05/2020] [Indexed: 06/11/2023]
Abstract
Lipocalin 2 (Lcn2) has been identified in mammals, however, the in vivo function of fish Lcn2 is essentially unknown. Triploid crucian carp (3n = 150) of red crucian carp (female, 2n = 100) and allotetraploid (male, 4n = 200) shows better resistance to pathogenic infections. To elucidate the antimicrobial mechanism of triploid crucian carp, we examined the function of a novel Lcn2 from triploid crucian carp (3nLcn2). 3nLcn2 is 183 residues in length and contains a conserved lipocalin domain. Quantitative real time reverse transcription PCR (qRT-PCR) analysis showed that 3nLcn2 expression occurred in multiple tissues and was upregulated by bacterial infection in a time-dependent manner. We found that purified recombinant 3nLcn2 (r3nLcn2) exerted bactericidal activity to Aeromonas hydrophila and Escherichia coli. qRT-PCR detected increased expression of pro-inflammatory cytokines and tight junctions in fish with 3nLcn2 overexpression. Fish administered with 3nLcn2 exhibited enhanced intestinal barrier and resistance against bacterial infection. These results provide the first evidence that 3nLcn2 is a functional lipocalin with antimicrobial activity and plays a positive role in the immune defense during bacterial infection.
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Affiliation(s)
- Zejun Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Chen Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xiaofeng Liu
- Department of Nutrition, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
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32
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Costa GC, Schlupp I. Placing the hybrid origin of the asexual Amazon molly (Poecilia formosa) based on historical climate data. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Asexual hybrids are important model organisms for addressing questions in evolution and ecology, especially for understanding the role of hybridization in speciation. They are rare in nature and several hypotheses have been suggested to explain this. We use an asexual fish, the Amazon molly (Poecilia formosa), to establish the area in which it was formed via hybridization 125 000 years ago. Using species distribution models and climate models for the Last Interglacial (LIG) we found that model projections to the LIG show a similar map to the present climate model and parental species potentially overlapped in a relatively small area near Tampico, Mexico. This makes P. formosa one of a few hybrid species for which we know the parental species, the time of hybridization, and likely the place of hybridization. Based on the small area of overlap, our data is in agreement with the idea that asexual hybrids may be rare not because they are evolutionary dead ends but are formed rarely.
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Affiliation(s)
- Gabriel C Costa
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL, USA
| | - Ingo Schlupp
- Department of Biology, University of Oklahoma, Norman, OK, USA
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33
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Zhang Z, Bendixsen DP, Janzen T, Nolte AW, Greig D, Stelkens R. Recombining Your Way Out of Trouble: The Genetic Architecture of Hybrid Fitness under Environmental Stress. Mol Biol Evol 2020; 37:167-182. [PMID: 31518427 PMCID: PMC6984367 DOI: 10.1093/molbev/msz211] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hybridization between species can either promote or impede adaptation. But we know very little about the genetic basis of hybrid fitness, especially in nondomesticated organisms, and when populations are facing environmental stress. We made genetically variable F2 hybrid populations from two divergent Saccharomyces yeast species. We exposed populations to ten toxins and sequenced the most resilient hybrids on low coverage using ddRADseq to investigate four aspects of their genomes: 1) hybridity, 2) interspecific heterozygosity, 3) epistasis (positive or negative associations between nonhomologous chromosomes), and 4) ploidy. We used linear mixed-effect models and simulations to measure to which extent hybrid genome composition was contingent on the environment. Genomes grown in different environments varied in every aspect of hybridness measured, revealing strong genotype–environment interactions. We also found selection against heterozygosity or directional selection for one of the parental alleles, with larger fitness of genomes carrying more homozygous allelic combinations in an otherwise hybrid genomic background. In addition, individual chromosomes and chromosomal interactions showed significant species biases and pervasive aneuploidies. Against our expectations, we observed multiple beneficial, opposite-species chromosome associations, confirmed by epistasis- and selection-free computer simulations, which is surprising given the large divergence of parental genomes (∼15%). Together, these results suggest that successful, stress-resilient hybrid genomes can be assembled from the best features of both parents without paying high costs of negative epistasis. This illustrates the importance of measuring genetic trait architecture in an environmental context when determining the evolutionary potential of genetically diverse hybrid populations.
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Affiliation(s)
- Zebin Zhang
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Devin P Bendixsen
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Thijs Janzen
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Arne W Nolte
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Duncan Greig
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Max Planck Institute for Evolutionary Biology, Plön, Germany
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Aubier TG, Kokko H, Joron M. Coevolution of male and female mate choice can destabilize reproductive isolation. Nat Commun 2019; 10:5122. [PMID: 31719522 PMCID: PMC6851176 DOI: 10.1038/s41467-019-12860-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/17/2019] [Indexed: 11/09/2022] Open
Abstract
Sexual interactions play an important role in the evolution of reproductive isolation, with important consequences for speciation. Theoretical studies have focused on the evolution of mate preferences in each sex separately. However, mounting empirical evidence suggests that premating isolation often involves mutual mate choice. Here, using a population genetic model, we investigate how female and male mate choice coevolve under a phenotype matching rule and how this affects reproductive isolation. We show that the evolution of female preferences increases the mating success of males with reciprocal preferences, favouring mutual mate choice. However, the evolution of male preferences weakens indirect selection on female preferences and, with weak genetic drift, the coevolution of female and male mate choice leads to periodic episodes of random mating with increased hybridization (deterministic 'preference cycling' triggered by stochasticity). Thus, counterintuitively, the process of establishing premating isolation proves rather fragile if both male and female mate choice contribute to assortative mating.
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Affiliation(s)
- Thomas G Aubier
- Centre d'Ecologie Fonctionnelle et Evolutive, CEFE - UMR 5175 - CNRS, Université de Montpellier, EPHE, Université Paul Valéry, 1919 route de Mende, F-34293, Montpellier 5, France.
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, CEFE - UMR 5175 - CNRS, Université de Montpellier, EPHE, Université Paul Valéry, 1919 route de Mende, F-34293, Montpellier 5, France.
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35
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Päckert M, Ait Belkacem A, Wolfgramm H, Gast O, Canal D, Giacalone G, Lo Valvo M, Vamberger M, Wink M, Martens J, Stuckas H. Genetic admixture despite ecological segregation in a North African sparrow hybrid zone (Aves, Passeriformes, Passer domesticus × Passer hispaniolensis). Ecol Evol 2019; 9:12710-12726. [PMID: 31788209 PMCID: PMC6875665 DOI: 10.1002/ece3.5744] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 11/29/2022] Open
Abstract
Under different environmental conditions, hybridization between the same species might result in different patterns of genetic admixture. Particularly, species pairs with large distribution ranges and long evolutionary history may have experienced several independent hybridization events over time in different zones of overlap. In birds, the diverse hybrid populations of the house sparrow (Passer domesticus) and the Spanish sparrow (Passer hispaniolensis) provide a striking example. Throughout their range of sympatry, these two species do not regularly interbreed; however, a stabilized hybrid form (Passer italiae) exists on the Italian Peninsula and on several Mediterranean islands. The spatial distribution pattern on the Eurasian continent strongly contrasts the situation in North Africa, where house sparrows and Spanish sparrows occur in close vicinity of phenotypically intermediate populations across a broad mosaic hybrid zone. In this study, we investigate patterns of divergence and admixture among the two parental species, stabilized and nonstabilized hybrid populations in Italy and Algeria based on a mitochondrial marker, a sex chromosomal marker, and 12 microsatellite loci. In Algeria, despite strong spatial and temporal separation of urban early-breeding house sparrows and hybrids and rural late-breeding Spanish sparrows, we found strong genetic admixture of mitochondrial and nuclear markers across all study populations and phenotypes. That pattern of admixture in the North African hybrid zone is strikingly different from i) the Iberian area of sympatry where we observed only weak asymmetrical introgression of Spanish sparrow nuclear alleles into local house sparrow populations and ii) the very homogenous Italian sparrow population where the mitogenome of one parent (P. domesticus) and the Z-chromosomal marker of the other parent (P. hispaniolensis) are fixed. The North African sparrow hybrids provide a further example of enhanced hybridization along with recent urbanization and anthropogenic land-use changes in a mosaic landscape.
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Affiliation(s)
- Martin Päckert
- Senckenberg Naturhistorische Sammlungen Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System ResearchDresdenGermany
| | - Abdelkrim Ait Belkacem
- Laboratoire d'Exploration et de Valorisation des Écosystèmes SteppiquesFaculté des Sciences de la nature et de la vieUniversité de DjelfaDjelfaAlgeria
| | - Hannes Wolfgramm
- Senckenberg Naturhistorische Sammlungen Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System ResearchDresdenGermany
| | - Oliver Gast
- Institute of Vertebrate Biology Brno & Masaryk University BrnoBrnoCzech Republic
| | - David Canal
- Department of Evolutionary EcologyEstación Biológica de Doñana—CSICSevilleSpain
- Centro para el Estudio y Conservación de las Aves Rapaces en Argentina (CECARA‐UNLPam) & Instituto de las Ciencias de la Tierra y Ambientales de La Pampa (INCITAP)Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Santa RosaArgentina
| | | | - Mario Lo Valvo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e FarmaceuticheUniversità degli Studi di PalermoPalermoItaly
| | - Melita Vamberger
- Senckenberg Naturhistorische Sammlungen Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System ResearchDresdenGermany
| | - Michael Wink
- Department of BiologyInstitute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityHeidelbergGermany
| | - Jochen Martens
- Institute of Organismic and Molecular EvolutionJohannes Gutenberg UniversityMainzGermany
| | - Heiko Stuckas
- Senckenberg Naturhistorische Sammlungen Dresden, Senckenberg|Leibniz Institution for Biodiversity and Earth System ResearchDresdenGermany
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Gallone B, Steensels J, Mertens S, Dzialo MC, Gordon JL, Wauters R, Theßeling FA, Bellinazzo F, Saels V, Herrera-Malaver B, Prahl T, White C, Hutzler M, Meußdoerffer F, Malcorps P, Souffriau B, Daenen L, Baele G, Maere S, Verstrepen KJ. Interspecific hybridization facilitates niche adaptation in beer yeast. Nat Ecol Evol 2019; 3:1562-1575. [PMID: 31636425 DOI: 10.1038/s41559-019-0997-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 09/02/2019] [Indexed: 11/09/2022]
Abstract
Hybridization between species often leads to non-viable or infertile offspring, yet examples of evolutionarily successful interspecific hybrids have been reported in all kingdoms of life. However, many questions on the ecological circumstances and evolutionary aftermath of interspecific hybridization remain unanswered. In this study, we sequenced and phenotyped a large set of interspecific yeast hybrids isolated from brewing environments to uncover the influence of interspecific hybridization in yeast adaptation and domestication. Our analyses demonstrate that several hybrids between Saccharomyces species originated and diversified in industrial environments by combining key traits of each parental species. Furthermore, posthybridization evolution within each hybrid lineage reflects subspecialization and adaptation to specific beer styles, a process that was accompanied by extensive chimerization between subgenomes. Our results reveal how interspecific hybridization provides an important evolutionary route that allows swift adaptation to novel environments.
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Affiliation(s)
- Brigida Gallone
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jan Steensels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Stijn Mertens
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Maria C Dzialo
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Jonathan L Gordon
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Ruben Wauters
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Florian A Theßeling
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Francesca Bellinazzo
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Veerle Saels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | - Beatriz Herrera-Malaver
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium.,Leuven Institute for Beer Research, Leuven, Belgium
| | | | | | - Mathias Hutzler
- Research Center Weihenstephan for Brewing and Food Quality, TU München, Freising, Germany
| | - Franz Meußdoerffer
- Research Center Weihenstephan for Brewing and Food Quality, TU München, Freising, Germany
| | | | | | | | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Steven Maere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, Ghent, Belgium.
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium. .,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Leuven, Belgium. .,Leuven Institute for Beer Research, Leuven, Belgium.
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37
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Marques DA, Meier JI, Seehausen O. A Combinatorial View on Speciation and Adaptive Radiation. Trends Ecol Evol 2019; 34:531-544. [DOI: 10.1016/j.tree.2019.02.008] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 02/07/2019] [Accepted: 02/13/2019] [Indexed: 01/28/2023]
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38
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Barker AM, Adams DH, Driggers WB, Frazier BS, Portnoy DS. Hybridization between sympatric hammerhead sharks in the western North Atlantic Ocean. Biol Lett 2019; 15:20190004. [PMID: 30940019 DOI: 10.1098/rsbl.2019.0004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hybridization between closely related species has been documented across a wide range of taxa but has not been well studied in elasmobranchs. Hammerhead sharks have drawn global conservation concern because they experience some of the highest mortality rates among sharks when interacting with fisheries. Here we report on the detection of hybrids between the globally distributed scalloped hammerhead ( Sphyrna lewini) and recently described Carolina hammerhead ( S. gilberti) which are only known from the western Atlantic Ocean. Using a genomics approach, 10 first-generation hybrids and 15-17 backcrosses were detected from 554 individuals. The identification of backcrosses demonstrates hybrids are viable, and all backcrosses but one involved a scalloped hammerhead. All hybrids but one possessed Carolina hammerhead mtDNA, indicating sex-biased gene flow between species. Repeated hybridization and backcrossing with scalloped hammerheads could lead to the loss of endemic Carolina hammerheads.
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Affiliation(s)
- Amanda M Barker
- 1 Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi , Corpus Christi, TX , USA
| | - Douglas H Adams
- 2 Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute , Melbourne, FL , USA
| | - William B Driggers
- 3 Southeast Fisheries Science Center, National Marine Fisheries Service, NOAA , Pascagoula, MS , USA
| | - Bryan S Frazier
- 4 South Carolina Department of Natural Resources , Charleston, SC , USA
| | - David S Portnoy
- 1 Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University-Corpus Christi , Corpus Christi, TX , USA
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39
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Abstract
Introgression is emerging as an important source of novel genetic variation, alongside standing variation and mutation. It is adaptive when such introgressed alleles are maintained by natural selection. Recently, there has been an explosion in the number of studies on adaptive introgression. In this review, we take a plant perspective centred on four lines of evidence: (i) introgression, (ii) selection, (iii) phenotype and (iv) fitness. While advances in genomics have contributed to our understanding of introgression and porous species boundaries (task 1), and the detection of signatures of selection in introgression (task 2), the investigation of adaptive introgression critically requires links to phenotypic variation and fitness (tasks 3 and 4). We also discuss the conservation implications of adaptive introgression in the face of climate change. Adaptive introgression is particularly important in rapidly changing environments, when standing genetic variation and mutation alone may only offer limited potential for adaptation. We conclude that clarifying the magnitude and fitness effects of introgression with improved statistical techniques, coupled with phenotypic evidence, has great potential for conservation and management efforts.
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Affiliation(s)
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, Canada
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40
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MacGuigan DJ, Near TJ. Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae). Syst Biol 2019; 68:329-346. [PMID: 30395332 DOI: 10.1093/sysbio/syy074] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/29/2018] [Indexed: 12/17/2022] Open
Abstract
Evolutionary history is typically portrayed as a branching phylogenetic tree, yet not all evolution proceeds in a purely bifurcating manner. Introgressive hybridization is one process that results in reticulate evolution. Most known examples of genome-wide introgression occur among closely related species with relatively recent common ancestry; however, we present evidence for ancient hybridization and genome-wide introgression between major stem lineages of darters, a species-rich clade of North American freshwater fishes. Previous attempts to resolve the relationships of darters have been confounded by the uncertain phylogenetic resolution of the lineage Allohistium. In this study, we investigate the phylogenomics of darters, specifically the relationships of Allohistium, through analyses of approximately 30,000 RADseq loci sampled from 112 species. Our phylogenetic inferences are based on traditional approaches in combination with strategies that accommodate reticulate evolution. These analyses result in a novel phylogenetic hypothesis for darters that includes ancient introgression between Allohistium and other two major darter lineages, minimally occurring 20 million years ago. Darters offer a compelling case for the necessity of incorporating phylogenetic networks in reconstructing the evolutionary history of diversification in species-rich lineages. We anticipate that the growing wealth of genomic data for clades of non-model organisms will reveal more examples of ancient hybridization, eventually requiring a re-evaluation of how evolutionary history is visualized and utilized in macroevolutonary investigations.
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Affiliation(s)
- Daniel J MacGuigan
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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41
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Bauer T, Feldmeier S, Krehenwinkel H, Wieczorrek C, Reiser N, Breitling R. Steatoda nobilis, a false widow on the rise: a synthesis of past and current distribution trends. NEOBIOTA 2019. [DOI: 10.3897/neobiota.42.31582] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Noble False Widow, Steatodanobilis (Thorell, 1875) (Araneae, Theridiidae), is, due to its relatively large size and potential medical importance, one of the most notable invasive spider species worldwide. Probably originating from the Canary Islands and Madeira, the species is well established in Western Europe and large parts of the Mediterranean area and has spread recently into California and South America, while Central European populations were not known until 2011.
We report on long-time observations that reveal that at least two flourishing populations in Germany (Cologne) have been present for over five years, while in Ecuador one population has been observed between 2014 and 2018 and several other records were made in other parts of the country. Data obtained from the British Spider Recording Scheme demonstrate that the species moved significantly northwards since the report of the first populations in the very South of England, after several decades of relative stasis. The sudden northward expansion highly correlates with a massive rise in press coverage of the species.
In the Americas, S.nobilis is currently known from four countries (USA, Chile, Ecuador, Colombia), and available DNA barcoding data obtained for specimens from this area suggest that multiple introductions occurred within each country. Using ecological niche modeling, we identified suitable climate regions for the species and discuss possible reasons for its current spread. We propose that seaside cities and villages with a temperate oceanic or Mediterranean climate are especially favourable potential habitats for S.nobilis and will face the highest colonization pressure in the future, while tropical upland regions with temperate climates are also vulnerable to invasion by S.nobilis.
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42
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Dennenmoser S, Sedlazeck FJ, Schatz MC, Altmüller J, Zytnicki M, Nolte AW. Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish. Mol Ecol 2019; 28:1491-1505. [DOI: 10.1111/mec.14969] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/15/2018] [Accepted: 10/23/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Stefan Dennenmoser
- Institute for Biology and Environmental Sciences Carl von Ossietzky University Oldenburg Oldenburg Germany
| | | | - Michael C. Schatz
- Cold Spring Harbor Laboratory Cold Spring Harbor New York
- Departments of Computer Science and Biology Johns Hopkins University Baltimore Maryland
| | - Janine Altmüller
- Cologne Center for Genomics, and Institute of Human Genetics University of Cologne Cologne Germany
| | | | - Arne W. Nolte
- Institute for Biology and Environmental Sciences Carl von Ossietzky University Oldenburg Oldenburg Germany
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43
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Ottenburghs J. Exploring the hybrid speciation continuum in birds. Ecol Evol 2018; 8:13027-13034. [PMID: 30619602 PMCID: PMC6308868 DOI: 10.1002/ece3.4558] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 01/03/2023] Open
Abstract
Hybridization is increasingly recognized as a creative evolutionary force contributing to adaptation and speciation. Homoploid hybrid speciation-the process in which hybridization results in a stable, fertile, and reproductively isolated hybrid lineage where there is no change in ploidy-has been documented in several taxa. Hybridization can directly contribute to reproductive isolation or reinforce it at a later stage. Alternatively, hybridization might not be related to the evolution of reproductive isolation. To account for these different scenarios, I propose to discriminate between two types of hybrid speciation: type I where reproductive isolation is a direct consequence of hybridization and type II where it is the by-product of other processes. I illustrate the applicability of this classification scheme with avian examples. To my knowledge, seven hybrid bird species have been proposed: Italian sparrow, Audubon's warbler, Genovesa mockingbird, Hawaiian duck, red-breasted goose, golden-crowned manakin, and a recent lineage of Darwin's finches on the island of Daphne Major ("Big Bird"). All studies provide convincing evidence for hybridization, but do not always confidently discriminate between scenarios of hybrid speciation and recurrent introgressive hybridization. The build-up of reproductive isolation between the hybrid species and their parental taxa is mainly driven by premating isolation mechanisms and comparable to classical speciation events. One hybrid species can be classified as type I ("Big Bird") while three species constitute type II hybrid species (Italian sparrow, Audubon's warbler, and golden-crowned manakin). The diversity in hybrid bird species across a range of divergence times also provides an excellent opportunity to study the evolution of hybrid genomes in terms of genome stabilization and adaptation.
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Affiliation(s)
- Jente Ottenburghs
- Resource Ecology GroupWageningen UniversityWageningenThe Netherlands
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44
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White OW, Reyes-Betancort A, Chapman MA, Carine MA. Independent homoploid hybrid speciation events in the Macaronesian endemic genus Argyranthemum. Mol Ecol 2018; 27:4856-4874. [DOI: 10.1111/mec.14889] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/29/2018] [Accepted: 09/26/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Oliver W. White
- Algae, Fungi and Plants Division; Department of Life Sciences; The Natural History Museum; London UK
- Biological Sciences; University of Southampton; Southampton UK
| | | | - Mark A. Chapman
- Biological Sciences; University of Southampton; Southampton UK
| | - Mark A. Carine
- Algae, Fungi and Plants Division; Department of Life Sciences; The Natural History Museum; London UK
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45
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Pacheco-Sierra G, Vázquez-Domínguez E, Pérez-Alquicira J, Suárez-Atilano M, Domínguez-Laso J. Ancestral Hybridization Yields Evolutionary Distinct Hybrids Lineages and Species Boundaries in Crocodiles, Posing Unique Conservation Conundrums. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00138] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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46
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Vreven EJWMN, Musschoot T, Decru E, Wamuini Lunkayilakio S, Obiero K, Cerwenka AF, Schliewen UK. The complex origins of mouth polymorphism in the Labeobarbus (Cypriniformes: Cyprinidae) of the Inkisi River basin (Lower Congo, DRC, Africa): insights from an integrative approach. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Emmanuel J W M N Vreven
- Vertebrate Section, Ichthyology, Royal Museum for Central Africa, RMCA, Leuvensesteenweg, Tervuren, Belgium
- KU Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Charles Deberiotstraat, Leuven, Belgium
| | - Tobias Musschoot
- Vertebrate Section, Ichthyology, Royal Museum for Central Africa, RMCA, Leuvensesteenweg, Tervuren, Belgium
| | - Eva Decru
- Vertebrate Section, Ichthyology, Royal Museum for Central Africa, RMCA, Leuvensesteenweg, Tervuren, Belgium
- KU Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Charles Deberiotstraat, Leuven, Belgium
| | | | - Kevin Obiero
- Kenya Marine and Fisheries Research Institute, Lake Turkana Research Station, Lodwar, Kenya
| | - Alexander F Cerwenka
- SNSB Bavarian Natural History Collections, Bavarian State Collection of Zoology, Department of Ichthyology, Münchhausenstrasse, München, Germany
| | - Ulrich K Schliewen
- SNSB Bavarian Natural History Collections, Bavarian State Collection of Zoology, Department of Ichthyology, Münchhausenstrasse, München, Germany
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47
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Feurtey A, Stukenbrock EH. Interspecific Gene Exchange as a Driver of Adaptive Evolution in Fungi. Annu Rev Microbiol 2018; 72:377-398. [DOI: 10.1146/annurev-micro-090817-062753] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Throughout evolutionary history in the kingdom Fungi, taxa have exchanged genetic information among species, as revealed in particular by analyses of genome sequences. In fungi, hybridization can occur by sexual mating or by fusion of vegetative structures giving rise to new species or leaving traces of introgression in the genome. Furthermore, gene exchange can occur by horizontal gene transfer between species and can even include organisms outside the kingdom Fungi. In several cases, interspecific gene exchange has been instrumental in rapid adaptive evolution of fungal species and has notably played a role in the emergence of new pathogens. Here we summarize mechanisms and examples of gene exchange in fungi with a particular focus on the genomic context. We emphasize the need for and potential of applying population genetic approaches to better understand the processes and the impact of interspecific gene exchange in rapid adaptive evolution and species diversification. The broad occurrence of gene exchange among fungal species challenges our species concepts in the kingdom Fungi.
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Affiliation(s)
- Alice Feurtey
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;,
| | - Eva H. Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;,
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
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Giesen A, Schäfer MA, Blanckenhorn WU. Geographic patterns of postzygotic isolation between two closely related widespread dung fly species (Sepsis cynipseaandSepsis neocynipsea; Diptera: Sepsidae). J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Athene Giesen
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Martin A. Schäfer
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Wolf U. Blanckenhorn
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
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Wang GD, Zhang BL, Zhou WW, Li YX, Jin JQ, Shao Y, Yang HC, Liu YH, Yan F, Chen HM, Jin L, Gao F, Zhang Y, Li H, Mao B, Murphy RW, Wake DB, Zhang YP, Che J. Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri. Proc Natl Acad Sci U S A 2018; 115:E5056-E5065. [PMID: 29760079 PMCID: PMC5984489 DOI: 10.1073/pnas.1716257115] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Tibetan frogs, Nanorana parkeri, are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome. Selection accounts for 579 broadly scattered, highly divergent regions (HDRs) of the genome, which involve 365 genes. These genes fall into 51 gene ontology (GO) functional classes, 14 of which are likely to be important in driving reproductive isolation. GO enrichment analyses of E reveal many overrepresented functional categories associated with adaptation to high elevations, including blood circulation, response to hypoxia, and UV radiation. Four genes, including DNAJC8 in the brain, TNNC1 and ADORA1 in the heart, and LAMB3 in the lung, differ in levels of expression between low- and high-elevation populations. High-altitude adaptation plays an important role in maintaining and driving continuing divergence and reproductive isolation. Use of total genomes enabled recognition of selection and adaptation in and between populations, as well as documentation of evolution along a stepped cline toward speciation.
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Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, 05282 Nay Pyi Taw, Myanmar
| | - Yong-Xin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - He-Chuan Yang
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Yan-Hu Liu
- Laboratory for Conservation and Utilization of Bio-Resources & Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hong-Man Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Li Jin
- Key Laboratory of Freshwater Fish Reproduction and Development of the Ministry of Education and Key Laboratory of Aquatic Science of Chongqing, Southwest University School of Life Sciences, Chongqing 400715, China
| | - Feng Gao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yaoguang Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development of the Ministry of Education and Key Laboratory of Aquatic Science of Chongqing, Southwest University School of Life Sciences, Chongqing 400715, China
| | - Haipeng Li
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada M5S 2C6
| | - David B Wake
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720-3160
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, 05282 Nay Pyi Taw, Myanmar
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Janzen T, Nolte AW, Traulsen A. The breakdown of genomic ancestry blocks in hybrid lineages given a finite number of recombination sites. Evolution 2018; 72:735-750. [PMID: 29411878 PMCID: PMC5947311 DOI: 10.1111/evo.13436] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 01/16/2018] [Indexed: 01/03/2023]
Abstract
When a lineage originates from hybridization genomic blocks of contiguous ancestry from different ancestors are fragmented through genetic recombination. The resulting blocks are delineated by so called junctions, which accumulate with every generation that passes. Modeling the accumulation of ancestry block junctions can elucidate processes and timeframes of genomic admixture. Previous models have not addressed ancestry block dynamics for chromosomes that consist of a finite number of recombination sites. However, genomic data typically consist of informative markers that are interspersed with fragments for which no ancestry information is available. Hence, repeated recombination events may occur between markers, effectively removing existing junctions. Here, we present an analytical treatment of the dynamics of the mean number of junctions over time, taking into account the number of recombination sites per chromosome, population size, genetic map length, and the frequency of the ancestral species in the founding hybrid swarm. We describe the expected number of junctions using equidistant molecular markers and estimate the number of junctions using random markers. This extended theory of junctions thus reflects properties of empirical data and can serve to study the genomic patterns following admixture.
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Affiliation(s)
- Thijs Janzen
- Carl von Ossietzky UniversityCarl‐von‐Ossietzky‐Str. 9‐1126111OldenburgGermany
- Max‐Planck‐Institute for Evolutionary BiologyAugust‐Thienemann‐Straße 224306PlönGermany
| | - Arne W. Nolte
- Carl von Ossietzky UniversityCarl‐von‐Ossietzky‐Str. 9‐1126111OldenburgGermany
| | - Arne Traulsen
- Max‐Planck‐Institute for Evolutionary BiologyAugust‐Thienemann‐Straße 224306PlönGermany
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