1
|
Bromham L. Combining Molecular, Macroevolutionary, and Macroecological Perspectives on the Generation of Diversity. Cold Spring Harb Perspect Biol 2024; 16:a041453. [PMID: 38503506 PMCID: PMC11368193 DOI: 10.1101/cshperspect.a041453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Charles Darwin presented a unified process of diversification driven by the gradual accumulation of heritable variation. The growth in DNA databases and the increase in genomic sequencing, combined with advances in molecular phylogenetic analyses, gives us an opportunity to realize Darwin's vision, connecting the generation of variation to the diversification of lineages. The rate of molecular evolution is correlated with the rate of diversification across animals and plants, but the relationship between genome change and speciation is complex: Mutation rates evolve in response to life history and niche; substitution rates are influenced by mutation, selection, and population size; rates of acquisition of reproductive isolation vary between populations; and traits, niches, and distribution can influence diversification rates. The connection between mutation rate and diversification rate is one part of the complex and varied story of speciation, which has theoretical importance for understanding the generation of biodiversity and also practical impacts on the use of DNA to understand the dynamics of speciation over macroevolutionary timescales.
Collapse
Affiliation(s)
- Lindell Bromham
- Macroevolution and Macroecology, Research School of Biology, Australian National University, ACT 0200, Australia
| |
Collapse
|
2
|
Fiorini CF, de Camargo Smidt E, Lacey Knowles L, Leite Borba E. Hybridization boosters diversification in a Neotropical Bulbophyllum (Orchidaceae) group. Mol Phylogenet Evol 2023:107858. [PMID: 37329930 DOI: 10.1016/j.ympev.2023.107858] [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: 02/15/2023] [Revised: 06/06/2023] [Accepted: 06/10/2023] [Indexed: 06/19/2023]
Abstract
Genetic data shows that cryptic hybrids are more common than previously thought and that hybridization and introgression are widespread processes. Regardless, studies on hybridization are scarce for the highly speciose Bulbophyllum. The genus presents more than 2,200 species and many examples of recent radiations, in which hybridization is expected to be frequent. Currently, only four natural Bulbophyllum hybrids are recognized, all of them recently described based on morphological evidence. Here we test whether genomic evidence supports the hybrid status of two Neotropical Bulbophyllum species, while also evaluating the impact of this phenomenon on the genomes of the putative parental species. We also assess if there is evidence of hybridization among B. involutum and B. exaltatum, sister species that diverged recently. We leverage the power of next-generation sequence data, associated with model-based analysis for three systems putatively constituted by two parental species and one hybrid. All taxa belong to the Neotropical B. sect. Didactyle clade. We found evidence of hybridization in all studied systems. Despite the occurrence of hybridization, there are no signs of backcrossing. Because of the high propensity of hybridization across many taxa, the common occurrence of hybridization during the evolutionary history of B. sect. Didactyle means it is time to account for and examine its evolutionary role in these orchids.
Collapse
Affiliation(s)
- Cecilia F Fiorini
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil; Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
| | - Eric de Camargo Smidt
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, 81531-990, Brazil.
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109-1085, USA.
| | - Eduardo Leite Borba
- Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
| |
Collapse
|
3
|
Haerter CAG, Blanco DR, Traldi JB, Feldberg E, Margarido VP, Lui RL. Are scattered microsatellites weak chromosomal markers? Guided mapping reveals new insights into Trachelyopterus (Siluriformes: Auchenipteridae) diversity. PLoS One 2023; 18:e0285388. [PMID: 37310952 DOI: 10.1371/journal.pone.0285388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 04/22/2023] [Indexed: 06/15/2023] Open
Abstract
The scattered distribution pattern of microsatellites is a challenging problem in fish cytogenetics. This type of array hinders the identification of useful patterns and the comparison between species, often resulting in over-limited interpretations that only label it as "scattered" or "widely distributed". However, several studies have shown that the distribution pattern of microsatellites is non-random. Thus, here we tested whether a scattered microsatellite could have distinct distribution patterns on homeologous chromosomes of closely related species. The clustered sites of 18S and 5S rDNA, U2 snRNA and H3/H4 histone genes were used as a guide to compare the (GATA)n microsatellite distribution pattern on the homeologous chromosomes of six Trachelyopterus species: T. coriaceus and Trachelyopterus aff. galeatus from the Araguaia River basin; T. striatulus, T. galeatus and T. porosus from the Amazonas River basin; and Trachelyopterus aff. coriaceus from the Paraguay River basin. Most species had similar patterns of the (GATA)n microsatellite in the histone genes and 5S rDNA carriers. However, we have found a chromosomal polymorphism of the (GATA)n sequence in the 18S rDNA carriers of Trachelyopterus galeatus, which is in Hard-Weinberg equilibrium and possibly originated through amplification events; and a chromosome polymorphism in Trachelyopterus aff. galeatus, which combined with an inversion polymorphism of the U2 snRNA in the same chromosome pair resulted in six possible cytotypes, which are in Hardy-Weinberg disequilibrium. Therefore, comparing the distribution pattern on homeologous chromosomes across the species, using gene clusters as a guide to identify it, seems to be an effective way to further the analysis of scattered microsatellites in fish cytogenetics.
Collapse
Affiliation(s)
| | | | - Josiane Baccarin Traldi
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Brasil
| | | | - Vladimir Pavan Margarido
- Universidade Estadual do Oeste do Paraná, Centro de Ciências Biológicas e da Saúde, Cascavel, Paraná, Brasil
| | - Roberto Laridondo Lui
- Universidade Estadual do Oeste do Paraná, Centro de Ciências Biológicas e da Saúde, Cascavel, Paraná, Brasil
| |
Collapse
|
4
|
Gustafsson ALS, Gussarova G, Borgen L, Ikeda H, Antonelli A, Marie-Orleach L, Rieseberg LH, Brochmann C. Rapid evolution of post-zygotic reproductive isolation is widespread in Arctic plant lineages. ANNALS OF BOTANY 2022; 129:171-184. [PMID: 34643673 PMCID: PMC8796670 DOI: 10.1093/aob/mcab128] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/05/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS The Arctic tundra, with its extreme temperatures and short growing season, is evolutionarily young and harbours one of the most species-poor floras on Earth. Arctic species often show little phenotypic and genetic divergence across circumpolar ranges. However, strong intraspecific post-zygotic reproductive isolation (RI) in terms of hybrid sterility has frequently evolved within selfing Arctic species of the genus Draba. Here we assess whether incipient biological species are common in the Arctic flora. METHODS We conducted an extensive crossing experiment including six species representing four phylogenetically distant families collected across the circumpolar Arctic. We crossed conspecific parental populations representing different spatial scales, raised 740 F1 hybrids to maturity and measured fertility under laboratory conditions. We examined genetic divergence between populations for two of these species (Cardamine bellidifolia and Ranunculus pygmaeus). KEY RESULTS In five of the six species, we find extensive reduction in pollen fertility and seed set in F1 hybrids; 219 (46 %) of the 477 F1 hybrids generated between parents separated by ≥427 km had <20 % pollen fertility. Isolation with migration (IM) and *BEAST analyses of sequences of eight nuclear genes in C. bellidifolia suggests that reproductively isolated populations of this species diverged during, or even after, the last glaciation. Likewise, Arctic populations of R. pygmaeus were genetically very similar despite exhibiting strongly reduced fertility in crosses, suggesting that RI evolved recently also in this species. CONCLUSION We show that post-zygotic RI has developed multiple times within taxonomically recognized Arctic species belonging to several distantly related lineages, and that RI may have developed over just a few millennia. Rapid and widespread evolution of incipient biological species in the Arctic flora might be associated with frequent bottlenecks due to glacial cycles, and/or selfing mating systems, which are common in the harsh Arctic environment where pollinators are scarce.
Collapse
Affiliation(s)
| | - Galina Gussarova
- Natural History Museum, University of Oslo, Oslo, Norway
- Botany Department, Faculty of Biology and Soil Science, St Petersburg, Russia
- Tromsø University Museum, University of Tromsø, Tromsø, Norway
| | - Liv Borgen
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Hajime Ikeda
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Sweden
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Lucas Marie-Orleach
- Natural History Museum, University of Oslo, Oslo, Norway
- ECOBIO—Écosystèmes, Biodiversité, Évolution, Rennes, France
| | - Loren H Rieseberg
- Botany Department, University of British Columbia, Vancouver, Canada
| | | |
Collapse
|
5
|
Hörandl E. Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids. PLANTS (BASEL, SWITZERLAND) 2022; 11:204. [PMID: 35050093 PMCID: PMC8781807 DOI: 10.3390/plants11020204] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 05/08/2023]
Abstract
Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because of the complexity of processes and different evolutionary scenarios that do not fit with classical species concepts. Polyploid complexes are formed via combinations of allopolyploidy, autopolyploidy and homoploid hybridization with persisting sexual reproduction, resulting in many discrete lineages that have been classified as species. Polyploid complexes with facultative apomixis result in complicated net-work like clusters, or rarely in agamospecies. Various case studies illustrate the problems that apply to traditional species concepts to hybrids and polyploids. Conceptual progress can be made if lineage formation is accepted as an inevitable consequence of meiotic sex, which is established already in the first eukaryotes as a DNA restoration tool. The turnaround of the viewpoint that sex forms species as lineages helps to overcome traditional thinking of species as "units". Lineage formation and self-sustainability is the prerequisite for speciation and can also be applied to hybrids and polyploids. Species delimitation is aided by the improved recognition of lineages via various novel -omics methods, by understanding meiosis functions, and by recognizing functional phenotypes by considering morphological-physiological-ecological adaptations.
Collapse
Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Göttingen, Germany
| |
Collapse
|
6
|
Keivani M, Mehregan I, Albach DC. Evaluating morphological diversity among Plantago major L. populations and influence of ecological variables. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00711-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
7
|
Arida BL, Scopece G, Machado RM, Moraes AP, Forni-Martins E, Pinheiro F. Reproductive barriers and fertility of two neotropical orchid species and their natural hybrid. Evol Ecol 2021. [DOI: 10.1007/s10682-020-10095-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
8
|
Abdelaziz M, Muñoz-Pajares AJ, Berbel M, García-Muñoz A, Gómez JM, Perfectti F. Asymmetric Reproductive Barriers and Gene Flow Promote the Rise of a Stable Hybrid Zone in the Mediterranean High Mountain. FRONTIERS IN PLANT SCIENCE 2021; 12:687094. [PMID: 34512685 PMCID: PMC8424041 DOI: 10.3389/fpls.2021.687094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 07/15/2021] [Indexed: 05/13/2023]
Abstract
Hybrid zones have the potential to shed light on evolutionary processes driving adaptation and speciation. Secondary contact hybrid zones are particularly powerful natural systems for studying the interaction between divergent genomes to understand the mode and rate at which reproductive isolation accumulates during speciation. We have studied a total of 720 plants belonging to five populations from two Erysimum (Brassicaceae) species presenting a contact zone in the Sierra Nevada mountains (SE Spain). The plants were phenotyped in 2007 and 2017, and most of them were genotyped the first year using 10 microsatellite markers. Plants coming from natural populations were grown in a common garden to evaluate the reproductive barriers between both species by means of controlled crosses. All the plants used for the field and greenhouse study were characterized by measuring traits related to plant size and flower size. We estimated the genetic molecular variances, the genetic differentiation, and the genetic structure by means of the F-statistic and Bayesian inference. We also estimated the amount of recent gene flow between populations. We found a narrow unimodal hybrid zone where the hybrid genotypes appear to have been maintained by significant levels of a unidirectional gene flow coming from parental populations and from weak reproductive isolation between them. Hybrid plants exhibited intermediate or vigorous phenotypes depending on the analyzed trait. The phenotypic differences between the hybrid and the parental plants were highly coherent between the field and controlled cross experiments and through time. The highly coherent results obtained by combining field, experimental, and genetic data demonstrate the existence of a stable and narrow unimodal hybrid zone between Erysimum mediohispanicum and Erysimum nevadense at the high elevation of the Sierra Nevada mountains.
Collapse
Affiliation(s)
- Mohamed Abdelaziz
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
- *Correspondence: Mohamed Abdelaziz
| | - A. Jesús Muñoz-Pajares
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
- Laboratório Associado, Plant Biology, Research Centre in Biodiversity and Genetic Resources, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade Do Porto, Campus Agrário de Vairão, Fornelo e Vairão, Portugal
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
| | - Modesto Berbel
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
| | - Ana García-Muñoz
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
| | - José M. Gómez
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
- Departamento de Ecología Funcional y Evolutiva, Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas, Almeria, Spain
| | - Francisco Perfectti
- Departamento de Genética, Facultad de Ciencias, Campus Fuentenueva, Universidad de Granada, Granada, Spain
- Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
| |
Collapse
|
9
|
Rodionov AV, Shneyer VS, Punina EO, Nosov NN, Gnutikov AA. The Law of Homologous Series in Variation for Systematics. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420110071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
10
|
Linan AG, Lowry PP, Miller AJ, Schatz GE, Sevathian JC, Edwards CE. RAD-sequencing reveals patterns of diversification and hybridization, and the accumulation of reproductive isolation in a clade of partially sympatric, tropical island trees. Mol Ecol 2020; 30:4520-4537. [PMID: 33210759 DOI: 10.1111/mec.15736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 12/31/2022]
Abstract
A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome-wide single nucleotide polymorphism data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are today largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression has occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now coexist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role that introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation.
Collapse
Affiliation(s)
- Alexander G Linan
- Department of Biology, Saint Louis University, St. Louis, MO, USA.,Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, USA
| | - Porter P Lowry
- Africa and Madagascar Program, Missouri Botanical Garden, St. Louis, MO, USA.,Institut de Systématique, Évolution et Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, Paris, France
| | - Allison J Miller
- Department of Biology, Saint Louis University, St. Louis, MO, USA.,Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - George E Schatz
- Africa and Madagascar Program, Missouri Botanical Garden, St. Louis, MO, USA
| | - Jean-Claude Sevathian
- Botanist, Sustainability Consultant and Landscape Care and Maintenance Service, Beau Bassin-Rose Hill, Mauritius
| | - Christine E Edwards
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, USA
| |
Collapse
|
11
|
Levin DA. Has the Polyploid Wave Ebbed? FRONTIERS IN PLANT SCIENCE 2020; 11:251. [PMID: 32211006 PMCID: PMC7077508 DOI: 10.3389/fpls.2020.00251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/18/2020] [Indexed: 05/13/2023]
Abstract
There was a wave of whole genome duplications (WGD) during and subsequent to the K-Pg interface, which was followed by an increase in the proportion of species that were polyploid. I consider why this wave of polyploid speciation has continued to rise through the divergent evolution of polyploid lineages, and through rounds of homoploid and heteroploid chromosomal change. I also consider why the polyploid speciation wave is likely to rise in the next millennium. I propose that the speed of polyploid genesis through ploidal increase and through diversification among polyploids likely will be greater than the speed of diploid speciation. The increase in polyploid diversity is expected to lag well behind episodes of WGD, owing to the very long period required for species diversification either by lineage splitting or additional rounds of polyploidy, in addition to the long period of genomic adjustment to higher ploidal levels in neopolyploids.
Collapse
Affiliation(s)
- Donald A. Levin
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States
| |
Collapse
|
12
|
Abstract
Interspecific hybridization is the process where closely related species mate and produce offspring with admixed genomes. The genomic revolution has shown that hybridization is common, and that it may represent an important source of novel variation. Although most interspecific hybrids are sterile or less fit than their parents, some may survive and reproduce, enabling the transfer of adaptive variants across the species boundary, and even result in the formation of novel evolutionary lineages. There are two main variants of hybrid species genomes: allopolyploid, which have one full chromosome set from each parent species, and homoploid, which are a mosaic of the parent species genomes with no increase in chromosome number. The establishment of hybrid species requires the development of reproductive isolation against parental species. Allopolyploid species often have strong intrinsic reproductive barriers due to differences in chromosome number, and homoploid hybrids can become reproductively isolated from the parent species through assortment of genetic incompatibilities. However, both types of hybrids can become further reproductively isolated, gaining extrinsic isolation barriers, by exploiting novel ecological niches, relative to their parents. Hybrids represent the merging of divergent genomes and thus face problems arising from incompatible combinations of genes. Thus hybrid genomes are highly dynamic and undergo rapid evolutionary change, including genome stabilization in which selection against incompatible combinations results in fixation of compatible ancestry block combinations within the hybrid species. The potential for rapid adaptation or speciation makes hybrid genomes a particularly exciting subject of in evolutionary biology. Here we summarize how introgressed alleles or hybrid species can establish and how the resulting hybrid genomes evolve.
Collapse
Affiliation(s)
- Anna Runemark
- Department of Biology, Lund University, Lund, Sweden
- * E-mail:
| | - Mario Vallejo-Marin
- Biological and Environmental Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Joana I. Meier
- St John's College, Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
13
|
Levin DA. Plant speciation in the age of climate change. ANNALS OF BOTANY 2019; 124:769-775. [PMID: 31250895 PMCID: PMC6868396 DOI: 10.1093/aob/mcz108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/25/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Species diversity is likely to undergo a sharp decline in the next century. Perhaps as many as 33 % of all plant species may expire as a result of climate change. All parts of the globe will be impacted, and all groups of organisms will be affected. Hundreds of species throughout the world have already experienced local extinction. PERSPECTIVES While thousands of species may become extinct in the next century and beyond, species formation will still occur. I consider which modes of plant species formation are likely to prevail in the next 500 years. I argue that speciation primarily will involve mechanisms that produce reproductively isolated lineages within less (often much less) than 100 generations. I will not especially consider the human element in promoting species formation, because it will continue and because the conclusions presented here are unaffected by it. The impact of climate change may be much more severe and widespread. CONCLUSIONS The most common modes of speciation likely to be operative in the next 500 years ostensibly will be auto- and allopolyploidy. Polyploid species or the antecedents thereof can arise within two generations. Moreover, polyploids often have broader ecological tolerances, and are likely to be more invasive than are their diploid relatives. Polyploid species may themselves spawn additional higher level polyploids either through crosses with diploid species or between pre-existing polyploids. The percentage of polyploid species is likely to exceed 50 % within the next 500 years vs. 35 % today. The stabilized hybrid derivatives (homoploid hybrid speciation) could emerge within a hundred generations after species contact, as could speciation involving chromosomal rearrangements (and perhaps number), but the number of such events is likely to be low. Speciation involving lineage splitting will be infrequent because the formation of substantive pre- and post-zygotic barriers typically takes many thousands of years.
Collapse
Affiliation(s)
- Donald A Levin
- Department of Integrative Biology, University of Texas, Austin, USA
| |
Collapse
|
14
|
Nevado B, Contreras-Ortiz N, Hughes C, Filatov DA. Pleistocene glacial cycles drive isolation, gene flow and speciation in the high-elevation Andes. THE NEW PHYTOLOGIST 2018; 219:779-793. [PMID: 29862512 DOI: 10.1111/nph.15243] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/30/2018] [Indexed: 05/10/2023]
Abstract
Mountain ranges are amongst the most species-rich habitats, with many large and rapid evolutionary radiations. The tempo and mode of diversification in these systems are key unanswered questions in evolutionary biology. Here we study the Andean Lupinus radiation to understand the processes driving very rapid diversification in montane systems. We use genomic and transcriptomic data of multiple species and populations, and apply phylogenomic and demographic analyses to test whether diversification proceeded without interspecific gene flow - as expected if Andean orogeny and geographic isolation were the main drivers of diversification - or if diversification was accompanied by gene flow, in which case other processes were probably involved. We uncover several episodes of gene flow between species, including very recent events likely to have been prompted by changes in habitat connectivity during Pleistocene glacial cycles. Furthermore, we find that gene flow between species was heterogeneously distributed across the genome. We argue that exceptionally fast diversification of Andean Lupinus was partly a result of Late Pleistocene glacial cycles, with associated cycles of expansion and contraction driving geographic isolation or secondary contact of species. Furthermore, heterogeneous gene flow across the genome suggests a role for selection and ecological speciation in rapid diversification in this system.
Collapse
Affiliation(s)
- Bruno Nevado
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Natalia Contreras-Ortiz
- Laboratorio de Botánica y Sistemática, Departamento de Ciencias Biológicas, Universidad de los Andes, Apartado Aéreo, 4976, Bogotá, Colombia
- Jardín Botánico de Bogotá 'José Celestino Mutis', Avenida Calle 63 No. 68-95, Bogotá DC, Colombia
| | - Colin Hughes
- Department of Systematic & Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| |
Collapse
|
15
|
Levin DA, Soltis DE. Factors promoting polyploid persistence and diversification and limiting diploid speciation during the K-Pg interlude. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:1-7. [PMID: 29107221 DOI: 10.1016/j.pbi.2017.09.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 05/14/2023]
Abstract
The large wave of polyploidization following the Cretaceous-Paleogene (K-Pg) mass extinction has been explained by enhanced polyploid persistence arising from adaptive properties of the polyploids themselves, as well as an increase in unreduced gamete production and diploid hybridization. We propose that the demise of diploids afforded opportunities for polyploid establishment and expansion into novel habitats. Augmented polyploid gene pools from diploid and polyploid relatives, in association with their multiple and independent origins (of both autopolyploids and allopolyploids), facilitated their subsequent diversification. Their ability to recruit genetic variation from their diploid relatives or from products of recurrent origins sharing their genome(s) ostensibly contributed to polyploid persistence. Concomitantly, we propose that the number of congeneric diploid species dramatically contracted disproportionally to polyploids during the K-Pg interval (i.e. a diploid trough), resulting in a reduction in the rate of diploid speciation. Accordingly, the preponderance of neopolyploids was likely autopolyploids.
Collapse
Affiliation(s)
- Donald A Levin
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32608, USA
| |
Collapse
|
16
|
Meleshko O, Stenøien HK, Speed JDM, Flatberg KI, Kyrkjeeide MO, Hassel K. Is interspecific gene flow and speciation in peatmosses ( Sphagnum) constrained by phylogenetic relationship and life-history traits? LINDBERGIA 2018. [DOI: 10.25227/linbg.01107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Olena Meleshko
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | - Hans K. Stenøien
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | - James D. M. Speed
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | - Kjell I. Flatberg
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| | | | - Kristian Hassel
- O. Meleshko , H. K. Stenøien, J. D. M. Speed, K, I. Flatberg and K. Hassel, NTNU University Museum, Norwegian Univ. of Science and Technology, NO-7491 Trondheim, Norway
| |
Collapse
|
17
|
Zhan Z, Nwafor CC, Hou Z, Gong J, Zhu B, Jiang Y, Zhou Y, Wu J, Piao Z, Tong Y, Liu C, Zhang C. Cytological and morphological analysis of hybrids between Brassicoraphanus, and Brassica napus for introgression of clubroot resistant trait into Brassica napus L. PLoS One 2017; 12:e0177470. [PMID: 28505203 PMCID: PMC5432170 DOI: 10.1371/journal.pone.0177470] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 04/27/2017] [Indexed: 11/29/2022] Open
Abstract
Interspecific hybridization is a powerful tool for improvement of crop species, it has the potential to broaden the genetic base and create new plant forms for breeding programs. Synthetic allopolyploid is a widely-used model for the study of genetic recombination and fixed heterosis in Brassica. In Brassica napus breeding, identification and introgression of new sources of clubroot resistance trait from wild or related species into it by hybridization is a long-term crop management strategy for clubroot disease. Radish (Raphanus sativus L.) is a close relative of the Brassica and most radish accessions are immune to the clubroot disease. A synthesized allotetraploid Brassicoraphanus (RRCC, 2n = 36) between R. sativus cv. HQ-04 (2n = 18, RR) and Brassica oleracea var. alboglabra (L.H Bailey) (2n = 18, CC) proved resistant of multiple clubroot disease pathogen P. brassicae. To predict the possibility to transfer the clubroot resistance trait from the RR subgenome of allotetraploid Brassicoraphanus (RRCC, 2n = 36) into Brassica napus (AACC, 2n = 38), we analyzed the frequency of chromosome pairings in the F1 hybrids produced from a cross between B. napus cv. HS5 and the allotetraploid, characterize the genomic composition of some backcrossed progeny (BC1) using GISH, BAC-FISH and AFLP techniques. The level of intergenomic pairing between A and R genomes in the F1 hybrid was high, allosyndetic bivalents formed in 73.53% PMCs indicative of significant level of homeologous recombination between two genomes and high probability of incorporating chromosomal segments/genes from R-genome into A/C-genomes. The BC1 plants inherited variant extra R chromosomes or fragments from allotetraploid as revealed by GISH and AFLP analysis. 13.51% BC2 individuals were resistant to clubroot disease, and several resistance lines had high pollen fertility, Overall, the genetic material presented in this work represents a potential new genetic resource for practical use in breeding B. napus clubroot resistant cultivars.
Collapse
Affiliation(s)
- Zongxiang Zhan
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chinedu Charles Nwafor
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhaoke Hou
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianfang Gong
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bin Zhu
- College of Life Science, Guizhou Normal University, Guiyang, China
| | - Yingfen Jiang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yongming Zhou
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiangsheng Wu
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhongyun Piao
- Department of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yue Tong
- Yichang Academy of Agriculture Science, Yichang, China
| | - Chao Liu
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chunyu Zhang
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
| |
Collapse
|
18
|
Levin DA, Scarpino SV. On the young age of intraspecific herbaceous taxa. THE NEW PHYTOLOGIST 2017; 213:1513-1520. [PMID: 27726173 DOI: 10.1111/nph.14224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Dated phylogenies rarely include the divergence times of sister intraspecific taxa, and when they do little is said about this subject. We show that over 90% of the intraspecific plant taxa found in a literature search are estimated to be 5 million yr old or younger, with only 4% of taxa estimated to be over 10 million yr old or older. A Bayesian analysis of intraspecific taxon ages indicates that indeed these taxa are expected to be < 10 million yr old. This result for the young age of intraspecific taxa is consistent with the earlier observation that post-pollination reproductive barriers develop between 5 and 10 million yr after lineage splitting, thus leading to species formation. If lineages have not graduated to the species level of divergence by 10 million yr or so, they are likely to have gone extinct by that time as a result of narrow geographical distributions, narrow niche breadths, and relatively small numbers across populations.
Collapse
Affiliation(s)
- Donald A Levin
- Department of Integrative Biology, University of Texas, Austin, TX 78713, USA
| | - Samuel V Scarpino
- Department of Mathematics & Statistics, University of Vermont, Burlington, VT 05401, USA
- Complex Systems Center, University of Vermont, Burlington, VT 05401, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| |
Collapse
|
19
|
Favre A, Widmer A, Karrenberg S. Differential adaptation drives ecological speciation in campions (Silene): evidence from a multi-site transplant experiment. THE NEW PHYTOLOGIST 2017; 213:1487-1499. [PMID: 27775172 DOI: 10.1111/nph.14202] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
In order to investigate the role of differential adaptation for the evolution of reproductive barriers, we conducted a multi-site transplant experiment with the dioecious sister species Silene dioica and S. latifolia and their hybrids. Crosses within species as well as reciprocal first-generation (F1 ) and second-generation (F2 ) interspecific hybrids were transplanted into six sites, three within each species' habitat. Survival and flowering were recorded over 4 yr. At all transplant sites, the local species outperformed the foreign species, reciprocal F1 hybrids performed intermediately and F2 hybrids underperformed in comparison to F1 hybrids (hybrid breakdown). Females generally had slightly higher cumulative fitness than males in both within- and between-species crosses and we thus found little evidence for Haldane's rule acting on field performance. The strength of selection against F1 and F2 hybrids as well as hybrid breakdown increased with increasing strength of habitat adaptation (i.e. the relative fitness difference between the local and the foreign species) across sites. Our results suggest that differential habitat adaptation led to ecologically dependent post-zygotic reproductive barriers and drives divergence and speciation in this Silene system.
Collapse
Affiliation(s)
- Adrien Favre
- Plant Ecological Genetics, ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zurich, Switzerland
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, University of Leipzig, Johannisallee 21-23, 04103, Leipzig, Germany
| | - Alex Widmer
- Plant Ecological Genetics, ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zurich, Switzerland
| | - Sophie Karrenberg
- Plant Ecological Genetics, ETH Zurich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zurich, Switzerland
- Department of Ecology and Genetics, Plant Ecology and Evolution, Uppsala University, Norbyvägen 18 D, 752 36, Uppsala, Sweden
| |
Collapse
|
20
|
Zhan SH, Drori M, Goldberg EE, Otto SP, Mayrose I. Phylogenetic evidence for cladogenetic polyploidization in land plants. AMERICAN JOURNAL OF BOTANY 2016; 103:1252-1258. [PMID: 27466054 DOI: 10.3732/ajb.1600108] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/12/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Polyploidization is a common and recurring phenomenon in plants and is often thought to be a mechanism of "instant speciation". Whether polyploidization is associated with the formation of new species (cladogenesis) or simply occurs over time within a lineage (anagenesis), however, has never been assessed systematically. METHODS We tested this hypothesis using phylogenetic and karyotypic information from 235 plant genera (mostly angiosperms). We first constructed a large database of combined sequence and chromosome number data sets using an automated procedure. We then applied likelihood models (ClaSSE) that estimate the degree of synchronization between polyploidization and speciation events in maximum likelihood and Bayesian frameworks. KEY RESULTS Our maximum likelihood analysis indicated that 35 genera supported a model that includes cladogenetic transitions over a model with only anagenetic transitions, whereas three genera supported a model that incorporates anagenetic transitions over one with only cladogenetic transitions. Furthermore, the Bayesian analysis supported a preponderance of cladogenetic change in four genera but did not support a preponderance of anagenetic change in any genus. CONCLUSIONS Overall, these phylogenetic analyses provide the first broad confirmation that polyploidization is temporally associated with speciation events, suggesting that it is indeed a major speciation mechanism in plants, at least in some genera.
Collapse
Affiliation(s)
- Shing H Zhan
- Department of Zoology, 4200-6270 University Boulevard, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
| | - Michal Drori
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, P. O. Box 39040, Tel Aviv 69978, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution, & Behavior, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, Minnesota 55108 USA
| | - Sarah P Otto
- Department of Zoology, 4200-6270 University Boulevard, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, P. O. Box 39040, Tel Aviv 69978, Israel
| |
Collapse
|
21
|
Barker MS, Husband BC, Pires JC. Spreading Winge and flying high: The evolutionary importance of polyploidy after a century of study. AMERICAN JOURNAL OF BOTANY 2016; 103:1139-45. [PMID: 27480249 DOI: 10.3732/ajb.1600272] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 05/10/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 USA
| |
Collapse
|
22
|
Evans DL, Joshi SV. Complete chloroplast genomes of Saccharum spontaneum, Saccharum officinarum and Miscanthus floridulus (Panicoideae: Andropogoneae) reveal the plastid view on sugarcane origins. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1197336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Dyfed Lloyd Evans
- South African Sugarcane Research Institute, 170 Flanders Drive, Private Bag X02, Mount Edgecombe, Durban, 4300, South Africa
- School of Life Sciences, College of Agriculture, Engineering and Science, University of Kwa-Zulu Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Shailesh Vinay Joshi
- South African Sugarcane Research Institute, 170 Flanders Drive, Private Bag X02, Mount Edgecombe, Durban, 4300, South Africa
- School of Life Sciences, College of Agriculture, Engineering and Science, University of Kwa-Zulu Natal, Private Bag X54001, Durban, 4000, South Africa
| |
Collapse
|
23
|
Payseur BA, Rieseberg LH. A genomic perspective on hybridization and speciation. Mol Ecol 2016; 25:2337-60. [PMID: 26836441 PMCID: PMC4915564 DOI: 10.1111/mec.13557] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022]
Abstract
Hybridization among diverging lineages is common in nature. Genomic data provide a special opportunity to characterize the history of hybridization and the genetic basis of speciation. We review existing methods and empirical studies to identify recent advances in the genomics of hybridization, as well as issues that need to be addressed. Notable progress has been made in the development of methods for detecting hybridization and inferring individual ancestries. However, few approaches reconstruct the magnitude and timing of gene flow, estimate the fitness of hybrids or incorporate knowledge of recombination rate. Empirical studies indicate that the genomic consequences of hybridization are complex, including a highly heterogeneous landscape of differentiation. Inferred characteristics of hybridization differ substantially among species groups. Loci showing unusual patterns - which may contribute to reproductive barriers - are usually scattered throughout the genome, with potential enrichment in sex chromosomes and regions of reduced recombination. We caution against the growing trend of interpreting genomic variation in summary statistics across genomes as evidence of differential gene flow. We argue that converting genomic patterns into useful inferences about hybridization will ultimately require models and methods that directly incorporate key ingredients of speciation, including the dynamic nature of gene flow, selection acting in hybrid populations and recombination rate variation.
Collapse
Affiliation(s)
- Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|
24
|
Barker MS, Arrigo N, Baniaga AE, Li Z, Levin DA. On the relative abundance of autopolyploids and allopolyploids. THE NEW PHYTOLOGIST 2016; 210:391-8. [PMID: 26439879 DOI: 10.1111/nph.13698] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Nils Arrigo
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- Department of Ecology and Evolution, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Anthony E Baniaga
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Donald A Levin
- Section of Integrative Biology, University of Texas, Austin, TX, 78713, USA
| |
Collapse
|
25
|
Michalski SG, Durka W. Separation in flowering time contributes to the maintenance of sympatric cryptic plant lineages. Ecol Evol 2015; 5:2172-84. [PMID: 26078854 PMCID: PMC4461419 DOI: 10.1002/ece3.1481] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 03/18/2015] [Accepted: 03/23/2015] [Indexed: 01/08/2023] Open
Abstract
Sympatric cryptic lineages are a challenge for the understanding of species coexistence and lineage diversification as well as for management, conservation, and utilization of plant genetic resources. In higher plants studies providing insights into the mechanisms creating and maintaining sympatric cryptic lineages are rare. Here, using microsatellites and chloroplast sequence data, morphometric analyses, and phenological observations, we ask whether sympatrically coexisting lineages in the common wetland plant Juncus effusus are ecologically differentiated and reproductively isolated. Our results show two genetically highly differentiated, homoploid lineages within J. effusus that are morphologically cryptic and have similar preference for soil moisture content. However, flowering time differed significantly between the lineages contributing to reproductive isolation and the maintenance of these lineages. Furthermore, the later flowering lineage suffered less from predispersal seed predation by a Coleophora moth species. Still, we detected viable and reproducing hybrids between both lineages and the earlier flowering lineage and J. conglomeratus, a coexisting close relative. Flowering time differentiation between the lineages can be explained by neutral divergence alone and together with a lack of postzygotic isolation mechanisms; the sympatric coexistence of these lineages is most likely the result of an allopatric origin with secondary contact.
Collapse
Affiliation(s)
- Stefan G Michalski
- Department of Community Ecology (BZF), Helmholtz Centre for Environmental Research UFZ Theodor-Lieser-Strasse 4, Halle, D-06120, Germany
| | - Walter Durka
- Department of Community Ecology (BZF), Helmholtz Centre for Environmental Research UFZ Theodor-Lieser-Strasse 4, Halle, D-06120, Germany
| |
Collapse
|
26
|
Larcombe MJ, Holland B, Steane DA, Jones RC, Nicolle D, Vaillancourt RE, Potts BM. Patterns of Reproductive Isolation inEucalyptus—A Phylogenetic Perspective. Mol Biol Evol 2015; 32:1833-46. [DOI: 10.1093/molbev/msv063] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
|
27
|
Chu P, Liu H, Yang Q, Wang Y, Yan G, Guan R. An RNA-seq transcriptome analysis of floral buds of an interspecific Brassica hybrid between B. carinata and B. napus. PLANT REPRODUCTION 2014; 27:225-237. [PMID: 25398253 DOI: 10.1007/s00497-014-0253-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/03/2014] [Indexed: 06/04/2023]
Abstract
Interspecific hybridizations promote gene transfer between species and play an important role in plant speciation and crop improvement. However, hybrid sterility that commonly found in the first generation of hybrids hinders the utilization of interspecific hybridization. The combination of divergent parental genomes can create extensive transcriptome variations, and to determine these gene expression alterations and their effects on hybrids, an interspecific Brassica hybrid of B. carinata × B. napus was generated. Scanning electron microscopy analysis indicated that some of the hybrid pollen grains were irregular in shape and exhibited abnormal exine patterns compared with those from the parents. Using the Illumina HiSeq 2000 platform, 39,598, 32,403 and 42,208 genes were identified in flower buds of B. carinata cv. W29, B. napus cv. Zhongshuang 11 and their hybrids, respectively. The differentially expressed genes were significantly enriched in pollen wall assembly, pollen exine formation, pollen development, pollen tube growth, pollination, gene transcription, macromolecule methylation and translation, which might be associated with impaired fertility in the F1 hybrid. These results will shed light on the mechanisms underlying the low fertility of the interspecific hybrids and expand our knowledge of interspecific hybridization.
Collapse
Affiliation(s)
- Pu Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | | | | | | | | | | |
Collapse
|
28
|
Stathos A, Fishman L. Chromosomal rearrangements directly cause underdominant F1pollen sterility inMimulus lewisii-Mimulus cardinalishybrids. Evolution 2014; 68:3109-19. [DOI: 10.1111/evo.12503] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 07/17/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Angela Stathos
- Division of Biological Sciences; University of Montana; Missoula Montana 59812
| | - Lila Fishman
- Division of Biological Sciences; University of Montana; Missoula Montana 59812
| |
Collapse
|
29
|
Lima TG. Higher levels of sex chromosome heteromorphism are associated with markedly stronger reproductive isolation. Nat Commun 2014; 5:4743. [DOI: 10.1038/ncomms5743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/21/2014] [Indexed: 01/08/2023] Open
|
30
|
Etienne RS, Morlon H, Lambert A. Estimating the duration of speciation from phylogenies. Evolution 2014; 68:2430-40. [PMID: 24758256 PMCID: PMC4262007 DOI: 10.1111/evo.12433] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 03/27/2014] [Indexed: 01/27/2023]
Abstract
Speciation is not instantaneous but takes time. The protracted birth–death diversification model incorporates this fact and predicts the often observed slowdown of lineage accumulation toward the present. The mathematical complexity of the protracted speciation model has barred estimation of its parameters until recently a method to compute the likelihood of phylogenetic branching times under this model was outlined (Lambert et al. 2014). Here, we implement this method and study using simulated phylogenies of extant species how well we can estimate the model parameters (rate of initiation of speciation, rate of extinction of incipient and good species, and rate of completion of speciation) as well as the duration of speciation, which is a combination of the aforementioned parameters. We illustrate our approach by applying it to a primate phylogeny. The simulations show that phylogenies often do not contain enough information to provide unbiased estimates of the speciation-initiation rate and the extinction rate, but the duration of speciation can be estimated without much bias. The estimate of the duration of speciation for the primate clade is consistent with literature estimates. We conclude that phylogenies combined with the protracted speciation model provide a promising way to estimate the duration of speciation.
Collapse
Affiliation(s)
- Rampal S Etienne
- Community and Conservation Ecology Group, Centre for Ecological and Evolutionary Studies, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands.
| | | | | |
Collapse
|
31
|
Interspecific crossing and genetic mapping reveal intrinsic genomic incompatibility between two Senecio species that form a hybrid zone on Mount Etna, Sicily. Heredity (Edinb) 2014; 113:195-204. [PMID: 24595365 DOI: 10.1038/hdy.2014.14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 01/24/2014] [Accepted: 01/27/2014] [Indexed: 01/27/2023] Open
Abstract
Studies of hybridizing species can reveal much about the genetic basis and maintenance of species divergence in the face of gene flow. Here we report a genetic segregation and linkage analysis conducted on F2 progeny of a reciprocal cross between Senecio aethnensis and S. chrysanthemifolius that form a hybrid zone on Mount Etna, Sicily, aimed at determining the genetic basis of intrinsic hybrid barriers between them. Significant transmission ratio distortion (TRD) was detected at 34 (∼27%) of 127 marker loci located in nine distinct clusters across seven of the ten linkage groups detected, indicating genomic incompatibility between the species. TRD at these loci could not be attributed entirely to post-zygotic selective loss of F2 individuals that failed to germinate or flower (16.7%). At four loci tests indicated that pre-zygotic events, such as meiotic drive in F1 parents or gametophytic selection, contributed to TRD. Additional tests revealed that cytonuclear incompatibility contributed to TRD at five loci, Bateson-Dobzhansky-Muller (BDM) incompatibilities involving epistatic interactions between loci contributed to TRD at four loci, and underdominance (heterozygote disadvantage) was a possible cause of TRD at one locus. Major chromosomal rearrangements were probably not a cause of interspecific incompatibility at the scale that could be examined with current map marker density. Intrinsic genomic incompatibility between S. aethnensis and S. chrysanthemifolius revealed by TRD across multiple genomic regions in early-generation hybrids is likely to impact the genetic structure of the natural hybrid zone on Mount Etna by limiting introgression and promoting divergence across the genome.
Collapse
|
32
|
Abstract
BACKGROUND Our understanding of the processes and dynamics of allopolyploid speciation, the long-term consequences of ploidal change, and the genetic and chromosomal changes in new emerged allopolyploids has substantially increased during the past few decades. Yet we remain uncertain about the time since lineage divergence when two taxa are capable of spawning such entities. Indeed, the matter has seemed intractable. Knowledge of the window of opportunity for allopolyploid production is very important because it provides temporal insight into a key evolutionary process, and a temporal reference against which other modes of speciation may be measured. SCOPE This Viewpoint paper reviews and integrates published information on the crossability of herbaceous species and the fertility of their hybrids in relation to species' divergence times. Despite limitations in methodology and sampling, the estimated times to hybrid sterility are somewhat congruent across disparate lineages. Whereas the waiting time for hybrid sterility is roughly 4-5 million years, the waiting time for cross-incompatibility is roughly 8-10 million years, sometimes considerably more. Strict allopolyploids may be formed in the intervening time window. The progenitors of several allopolyploids diverged between 4 and 6 million years before allopolyploid synthesis, as expected. This is the first study to propose a general temporal framework for strict allopolyploidy. This Viewpoint paper hopefully will stimulate interest in studying the tempo of speciation and the tempo of reproductive isolation in general.
Collapse
|
33
|
Tayalé A, Parisod C. Natural pathways to polyploidy in plants and consequences for genome reorganization. Cytogenet Genome Res 2013; 140:79-96. [PMID: 23751271 DOI: 10.1159/000351318] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The last decade highlighted polyploidy as a rampant evolutionary process that triggers drastic genome reorganization, but much remains to be understood about their causes and consequences in both autopolyploids and allopolyploids. Here, we provide an overview of the current knowledge on the pathways leading to different types of polyploids and patterns of polyploidy-induced genome restructuring and functional changes in plants. Available evidence leads to a tentative 'diverge, merge and diverge' model supporting polyploid speciation and stressing patterns of divergence between diploid progenitors as a suitable predictor of polyploid genome reorganization. The merging of genomes at the origin of a polyploid lineage may indeed reveal different kinds of incompatibilities (chromosomal, genic and transposable elements) that have accumulated in diverging progenitors and reduce the fitness of nascent polyploids. Accordingly, successful polyploids have to overcome these incompatibilities through non-Mendelian mechanisms, fostering polyploid genome reorganization in association with the establishment of new lineages. See also sister article focusing on animals by Collares-Pereira et al., in this themed issue.
Collapse
Affiliation(s)
- A Tayalé
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | | |
Collapse
|
34
|
Goodwillie C, Ness JM. Interactions of hybridization and mating systems: a case study in Leptosiphon (Polemoniaceae). AMERICAN JOURNAL OF BOTANY 2013; 100:1002-1013. [PMID: 23507735 DOI: 10.3732/ajb.1200616] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY The roles of hybridization and mating systems in the evolution of angiosperms have been well studied, but less work has focused on their interactions. Self-incompatible and self-compatible species often show asymmetry in heterospecific pollen rejection. Self-fertilization can preempt ovules before opportunities for hybridization. In turn, hybridization might affect mating system evolution through selection for selfing to avoid production of low fitness hybrids. • METHODS AFLP and morphological analyses were used to test for hybrids in a contact zone between species with contrasting breeding systems. Crossing experiments examined the relative contributions to reproductive isolation of pollen-pistil interactions, timing of self-fertilization, and F1 viability and fertility. A diallel cross of siblings tested for an association between heterospecific incompatibility and S-genotype in the self-incompatible species. • KEY RESULTS A low frequency of hybrids was detected in the contact zone. Pollen-pistil interactions were partially consistent with the SI × SC rule; some individuals of the self-incompatible species rejected heterospecific pollen, whereas the self-compatible species was fully receptive to it. In the selfing species, individuals with early selfing produced fewer hybrid progeny than did those with delayed self-compatibility when heterospecific pollen was applied after self-pollen. Viability of F1s was high but fertility was low. Variability in heterospecific pollen rejection was not related to S-genotype. • CONCLUSIONS Both self-fertilization and self-incompatibility are associated with limits to hybridization at this site. The strong effect of timing of selfing on production of low fitness F1s suggests that hybridization might select for early selfing in this population.
Collapse
Affiliation(s)
- Carol Goodwillie
- Department of Biology, East Carolina University, Mailstop 551, Greenville, NC 27858, USA.
| | | |
Collapse
|