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Sudmoon R, Kaewdaungdee S, Ho HX, Lee SY, Tanee T, Chaveerach A. The chloroplast genome sequences of Ipomoea alba and I. obscura (Convolvulaceae): genome comparison and phylogenetic analysis. Sci Rep 2024; 14:14078. [PMID: 38890502 PMCID: PMC11189557 DOI: 10.1038/s41598-024-64879-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Ipomoea species have diverse uses as ornamentals, food, and medicine. However, their genomic information is limited; I. alba and I. obscura were sequenced and assembled. Their chloroplast genomes were 161,353 bp and 159,691 bp, respectively. Both genomes exhibited a quadripartite structure, consisting of a pair of inverted repeat (IR) regions, which are separated by the large single-copy (LSC) and small single-copy (SSC) regions. The overall GC content was 37.5% for both genomes. A total of 104 and 93 simple sequence repeats, 50 large repeats, and 30 and 22 short tandem repeats were identified in the two chloroplast genomes, respectively. G and T were more preferred than C and A at the third base position based on the Parity Rule 2 plot analysis, and the neutrality plot revealed correlation coefficients of 0.126 and 0.105, indicating the influence of natural selection in shaping the codon usage bias in most protein-coding genes (CDS). Genome comparative analyses using 31 selected Ipomoea taxa from Thailand showed that their chloroplast genomes are rather conserved, but the presence of expansion or contraction of the IR region was identified in some of these Ipomoea taxa. A total of five highly divergent regions were identified, including the CDS genes accD, ndhA, and ndhF, as well as the intergenic spacer regions psbI-atpA and rpl32-ccsA. Phylogenetic analysis based on both the complete chloroplast genome sequence and CDS datasets of 31 Ipomoea taxa showed that I. alba is resolved as a group member for series (ser.) Quamoclit, which contains seven other taxa, including I. hederacea, I. imperati, I. indica, I. nil, I. purpurea, I. quamoclit, and I. × sloteri, while I. obscura is grouped with I. tiliifolia, both of which are under ser. Obscura, and is closely related to I. biflora of ser. Pes-tigridis. Divergence time estimation using the complete chloroplast genome sequence dataset indicated that the mean age of the divergence for Ipomoeeae, Argyreiinae, and Astripomoeinae, was approximately 29.99 Mya, 19.81 Mya, and 13.40 Mya, respectively. The node indicating the divergence of I. alba from the other members of Ipomoea was around 10.06 Mya, and the split between I. obscura and I. tiliifolia is thought to have happened around 17.13 Mya. The split between the I. obscura accessions from Thailand and Taiwan is thought to have taken place around 0.86 Mya.
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Affiliation(s)
| | - Sanit Kaewdaungdee
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Hao Xuan Ho
- Faculty of Health and Life Sciences, INTI International University, 71800, Nilai, Negeri Sembilan, Malaysia
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, 71800, Nilai, Negeri Sembilan, Malaysia.
| | - Tawatchai Tanee
- Faculty of Environment and Resource Studies, Mahasarakham University, Maha Sarakham, 44150, Thailand
| | - Arunrat Chaveerach
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand.
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Fehrer J, Bertrand YJK, Hartmann M, Caklová P, Josefiová J, Bräutigam S, Chrtek J. A Multigene Phylogeny of Native American Hawkweeds ( Hieracium Subgen. Chionoracium, Cichorieae, Asteraceae): Origin, Speciation Patterns, and Migration Routes. PLANTS (BASEL, SWITZERLAND) 2022; 11:2584. [PMID: 36235450 PMCID: PMC9571344 DOI: 10.3390/plants11192584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/24/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Native American hawkweeds are mainly mountainous species that are distributed all over the New World. They are severely understudied with respect to their origin, colonization of the vast distribution area, and species relationships. Here, we attempt to reconstruct the evolutionary history of the group by applying seven molecular markers (plastid, nuclear ribosomal and low-copy genes). Phylogenetic analyses revealed that Chionoracium is a subgenus of the mainly Eurasian genus Hieracium, which originated from eastern European hawkweeds about 1.58-2.24 million years ago. Plastid DNA suggested a single origin of all Chionoracium species. They colonized the New World via Beringia and formed several distinct lineages in North America. Via one Central American lineage, the group colonized South America and radiated into more than a hundred species within about 0.8 million years, long after the closure of the Isthmus of Panama and the most recent uplift of the Andes. Despite some incongruences shown by different markers, most of them revealed the same crown groups of closely related taxa, which were, however, largely in conflict with traditional sectional classifications. We provide a basic framework for further elucidation of speciation patterns. A thorough taxonomic revision of Hieracium subgen. Chionoracium is recommended.
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Affiliation(s)
- Judith Fehrer
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
| | - Yann J. K. Bertrand
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
| | - Matthias Hartmann
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
- Department of Geobotany & Botanical Garden, Institute of Biology, Martin Luther University Halle-Wittenberg, 06108 Halle (Saale), Germany
- Thünen Institute of Biodiversity, Bundesallee 65, 38116 Braunschweig, Germany
| | - Petra Caklová
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
| | - Jiřina Josefiová
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
| | | | - Jindřich Chrtek
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, 12801 Prague, Czech Republic
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Simões ARG, Eserman LA, Zuntini AR, Chatrou LW, Utteridge TMA, Maurin O, Rokni S, Roy S, Forest F, Baker WJ, Stefanović S. A Bird's Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data. FRONTIERS IN PLANT SCIENCE 2022; 13:889988. [PMID: 35909765 PMCID: PMC9331175 DOI: 10.3389/fpls.2022.889988] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Convolvulaceae is a family of c. 2,000 species, distributed across 60 currently recognized genera. It includes species of high economic importance, such as the crop sweet potato (Ipomoea batatas L.), the ornamental morning glories (Ipomoea L.), bindweeds (Convolvulus L.), and dodders, the parasitic vines (Cuscuta L.). Earlier phylogenetic studies, based predominantly on chloroplast markers or a single nuclear region, have provided a framework for systematic studies of the family, but uncertainty remains at the level of the relationships among subfamilies, tribes, and genera, hindering evolutionary inferences and taxonomic advances. One of the enduring enigmas has been the relationship of Cuscuta to the rest of Convolvulaceae. Other examples of unresolved issues include the monophyly and relationships within Merremieae, the "bifid-style" clade (Dicranostyloideae), as well as the relative positions of Erycibe Roxb. and Cardiochlamyeae. In this study, we explore a large dataset of nuclear genes generated using Angiosperms353 kit, as a contribution to resolving some of these remaining phylogenetic uncertainties within Convolvulaceae. For the first time, a strongly supported backbone of the family is provided. Cuscuta is confirmed to belong within family Convolvulaceae. "Merremieae," in their former tribal circumscription, are recovered as non-monophyletic, with the unexpected placement of Distimake Raf. as sister to the clade that contains Ipomoeeae and Decalobanthus Ooststr., and Convolvuleae nested within the remaining "Merremieae." The monophyly of Dicranostyloideae, including Jacquemontia Choisy, is strongly supported, albeit novel relationships between genera are hypothesized, challenging the current tribal delimitation. The exact placements of Erycibe and Cuscuta remain uncertain, requiring further investigation. Our study explores the benefits and limitations of increasing sequence data in resolving higher-level relationships within Convolvulaceae, and highlights the need for expanded taxonomic sampling, to facilitate a much-needed revised classification of the family.
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Affiliation(s)
| | - Lauren A. Eserman
- Conservation & Research Department, Atlanta Botanical Garden, Atlanta, GA, United States
| | | | - Lars W. Chatrou
- Systematic and Evolutionary Botany Lab, University of Ghent, Ghent, Belgium
| | | | | | - Saba Rokni
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
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Laux M, Oliveira RRM, Vasconcelos S, Pires ES, Lima TGL, Pastore M, Nunes GL, Alves R, Oliveira G. New plastomes of eight Ipomoea species and four putative hybrids from Eastern Amazon. PLoS One 2022; 17:e0265449. [PMID: 35298523 PMCID: PMC8929602 DOI: 10.1371/journal.pone.0265449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/01/2022] [Indexed: 11/18/2022] Open
Abstract
Ipomoea is a large pantropical genus globally distributed, which importance goes beyond the economic value as food resources or ornamental crops. This highly diverse genus has been the focus of a great number of studies, enriching the plant genomics knowledge, and challenging the plant evolution models. In the Carajás mountain range, located in Eastern Amazon, the savannah-like ferruginous ecosystem known as canga harbors highly specialized plant and animal populations, and Ipomoea is substantially representative in such restrictive habitat. Thus, to provide genetic data and insights into whole plastome phylogenetic relationships among key Ipomoea species from Eastern Amazon with little to none previously available data, we present the complete plastome sequences of twelve lineages of the genus, including the canga microendemic I. cavalcantei, the closely related I. marabaensis, and their putative hybrids. The twelve plastomes presented similar gene content as most publicly available Ipomoea plastomes, although the putative hybrids were correctly placed as closely related to the two parental species. The cavalcantei-marabaensis group was consistently grouped between phylogenetic methods. The closer relationship of the I. carnea plastome with the cavalcantei-marabaensis group, as well as the branch formed by I. quamoclit, I. asarifolia and I. maurandioides, were probably a consequence of insufficient taxonomic representativity, instead of true genetic closeness, reinforcing the importance of new plastome assemblies to resolve inconsistencies and boost statistical confidence, especially the case for South American clades of Ipomoea. The search for k-mers presenting high dispersion among the frequency distributions pointed to highly variable coding and intergenic regions, which may potentially contribute to the genetic diversity observed at species level. Our results contribute to the resolution of uncertain clades within Ipomoea and future phylogenomic studies, bringing unprecedented results to Ipomoea species with restricted distribution, such as I. cavalcantei.
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Affiliation(s)
| | - Renato R. M. Oliveira
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa Interunidades de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | - Mayara Pastore
- Programa de Pós-Graduação em Botânica Tropical, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
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Beaulieu WT, Panaccione DG, Quach QN, Smoot KL, Clay K. Diversification of ergot alkaloids and heritable fungal symbionts in morning glories. Commun Biol 2021; 4:1362. [PMID: 34873267 PMCID: PMC8648897 DOI: 10.1038/s42003-021-02870-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/08/2021] [Indexed: 11/12/2022] Open
Abstract
Heritable microorganisms play critical roles in life cycles of many macro-organisms but their prevalence and functional roles are unknown for most plants. Bioactive ergot alkaloids produced by heritable Periglandula fungi occur in some morning glories (Convolvulaceae), similar to ergot alkaloids in grasses infected with related fungi. Ergot alkaloids have been of longstanding interest given their toxic effects, psychoactive properties, and medical applications. Here we show that ergot alkaloids are concentrated in four morning glory clades exhibiting differences in alkaloid profiles and are more prevalent in species with larger seeds than those with smaller seeds. Further, we found a phylogenetically-independent, positive correlation between seed mass and alkaloid concentrations in symbiotic species. Our findings suggest that heritable symbiosis has diversified among particular clades by vertical transmission through seeds combined with host speciation, and that ergot alkaloids are particularly beneficial to species with larger seeds. Our results are consistent with the defensive symbiosis hypothesis where bioactive ergot alkaloids from Periglandula symbionts protect seeds and seedlings from natural enemies, and provide a framework for exploring microbial chemistry in other plant-microbe interactions.
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Affiliation(s)
- Wesley T Beaulieu
- Department of Biology, Indiana University, Bloomington, IN, USA
- Jaeb Center for Health Research, Tampa, FL, USA
| | - Daniel G Panaccione
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Quynh N Quach
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
| | - Katy L Smoot
- Division of Plant & Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Keith Clay
- Department of Biology, Indiana University, Bloomington, IN, USA.
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA.
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Barba-Montoya J, Tao Q, Kumar S. Assessing rapid relaxed-clock methods for phylogenomic dating. Genome Biol Evol 2021; 13:6423996. [PMID: 34751377 PMCID: PMC8633771 DOI: 10.1093/gbe/evab251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
Rapid relaxed-clock dating methods are frequently applied to analyze phylogenomic data sets containing hundreds to thousands of sequences because of their accuracy and computational efficiency. However, the relative performance of different rapid dating methods is yet to be compared on the same data sets, and, thus, the power and pitfalls of selecting among these approaches remain unclear. We compared the accuracy, bias, and coverage probabilities of RelTime, treePL, and least-squares dating time estimates by applying them to analyze computer-simulated data sets in which evolutionary rates varied extensively among branches in the phylogeny. RelTime estimates were consistently more accurate than the other two, particularly when evolutionary rates were autocorrelated or shifted convergently among lineages. The 95% confidence intervals (CIs) around RelTime dates showed appropriate coverage probabilities (95% on average), but other methods produced rather low coverage probabilities because of overly narrow CIs of time estimates. Overall, RelTime appears to be a more efficient method for estimating divergence times for large phylogenies.
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Affiliation(s)
- Jose Barba-Montoya
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Department of Biology, Temple University, Philadelphia, PA, USA
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Department of Biology, Temple University, Philadelphia, PA, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Department of Biology, Temple University, Philadelphia, PA, USA.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
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Carruthers T, Scotland RW. The implications of interrelated assumptions on estimates of divergence times and rates of diversification. Syst Biol 2021; 70:1181-1199. [PMID: 33760070 DOI: 10.1093/sysbio/syab021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 11/15/2022] Open
Abstract
Phylogenies are increasingly being used as a basis to provide insight into macroevolutionary history. Here, we use simulation experiments and empirical analyses to evaluate methods that use phylogenies as a basis to make estimates of divergence times and rates of diversification. This is the first study to present a comprehensive assessment of the key variables that underpin analyses in this field - including substitution rates, speciation rates, and extinction, plus character sampling and taxon sampling. We show that in unrealistically simplistic cases (where substitution rates and speciation rates are constant, and where there is no extinction), increased character and taxon sampling lead to more accurate and precise parameter estimates. By contrast, in more complex but realistic cases (where substitution rates, speciation rates, and extinction rates vary), gains in accuracy and precision from increased character and taxon sampling are far more limited. The lack of accuracy and precision even occurs when using methods that are designed to account for more complex cases, such as relaxed clocks, fossil calibrations, and models that allow speciation rates and extinction rates to vary. The problem also persists when analysing genomic scale datasets. These results suggest two interrelated problems that occur when the processes that generated the data are more complex. First, methodological assumptions are more likely to be violated. Second, limitations in the information content of the data become more important.
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Affiliation(s)
- Tom Carruthers
- Royal Botanic Gardens Kew, Richmond, London, TW9 3AE, United Kingdom
| | - Robert W Scotland
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom
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Deanna R, Wilf P, Gandolfo MA. New physaloid fruit-fossil species from early Eocene South America. AMERICAN JOURNAL OF BOTANY 2020; 107:1749-1762. [PMID: 33247843 DOI: 10.1002/ajb2.1565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/19/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Solanaceae is a scientifically and economically important angiosperm family with a minimal fossil record and an intriguing early evolutionary history. Here, we report a newly discovered fossil lantern fruit with a suite of features characteristic of Physalideae within Solanaceae. The fossil comes from the early Eocene Laguna del Hunco site (ca. 52 Ma) in Chubut, Argentina, which previously yielded the only other physaloid fruit fossil, Physalis infinemundi. METHODS The fruit morphology and calyx venation pattern of the new fossil were compared with P. infinemundi and extant species of Solanaceae. RESULTS Physalis hunickenii sp. nov. is clearly distinct from P. infinemundi in its fruiting calyx with wider primary veins, longer and thinner lobes, and especially in its venation pattern with high density, transverse tertiary veins; these features support its placement in a new species. In comparison with extant physaloid genera, the calyx venation pattern and other diagnostic traits reinforce placement of the new fossil, like P. infinemundi, within the tribe Physalideae of Solanaceae. CONCLUSIONS Both species of fossil nightshades from Laguna del Hunco represent crown-group Solanaceae but are older than all prior age estimates of the family. Although at least 20 transoceanic dispersals have been proposed as the driver of range expansion of Solanaceae, the Patagonian fossils push back the diversification of the family to Gondwanan times. Thus, overland dispersal across Gondwana is now a likely scenario for at least some biogeographic patterns, in light of the ancient trans-Antarctic land connections between South America and Australia.
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Affiliation(s)
- Rocío Deanna
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), CC 495, Córdoba, 5000, Argentina
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias Químicas (FCQ, UNC), Medina Allende s.n., Córdoba, 5000, Argentina
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80305, USA
| | - Peter Wilf
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Maria A Gandolfo
- L.H. Bailey Hortorium, Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, USA
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Ostevik KL, Rifkin JL, Xia H, Rausher MD. Morning glory species co-occurrence is associated with asymmetrically decreased and cascading reproductive isolation. Evol Lett 2020; 5:75-85. [PMID: 33552537 PMCID: PMC7857285 DOI: 10.1002/evl3.205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/04/2020] [Accepted: 10/19/2020] [Indexed: 01/25/2023] Open
Abstract
Hybridization between species can affect the strength of the reproductive barriers that separate those species. Two extensions of this effect are (1) the expectation that asymmetric hybridization or gene flow will have asymmetric effects on reproductive barrier strength and (2) the expectation that local hybridization will affect only local reproductive barrier strength and could therefore alter within‐species compatibility. We tested these hypotheses in a pair of morning glory species that exhibit asymmetric gene flow from highly selfing Ipomoea lacunosa into mixed‐mating Ipomoea cordatotriloba in regions where they co‐occur. Because of the direction of this gene flow, we predicted that reproductive barrier strength would be more strongly affected in I. cordatotriloba than I. lacunosa. We also predicted that changes to reproductive barriers in sympatric I. cordatotriloba populations would affect compatibility with allopatric populations of that species. We tested these predictions by measuring the strength of a reproductive barrier to seed set across the species’ ranges. Consistent with our first prediction, we found that sympatric and allopatric I. lacunosa produce the same number of seeds in crosses with I. cordatotriloba, whereas crosses between sympatric I. cordatotriloba and I. lacunosa are more successful than crosses between allopatric I. cordatotriloba and I. lacunosa. This difference in compatibility appears to reflect an asymmetric decrease in the strength of the barrier to seed set in sympatric I. cordatotriloba, which could be caused by I. lacunosa alleles that have introgressed into I. cordatotriloba. We further demonstrated that changes to sympatric I. cordatotriloba have decreased its ability to produce seeds with allopatric populations of the same species, in line with our second prediction. Thus, in a manner analogous to cascade reinforcement, we suggest that introgression associated with hybridization not only influences between‐species isolation but can also contribute to isolation within a species.
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Affiliation(s)
- Kate L Ostevik
- Department of Biology Duke University Durham North Carolina 27708
| | - Joanna L Rifkin
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON M5S 3B2 Canada
| | - Hanhan Xia
- College of Horticulture and Landscape Architecture Zhongkai University of Agriculture and Engineering Guangzhou 510225 China
| | - Mark D Rausher
- Department of Biology Duke University Durham North Carolina 27708
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