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Wang X, Liao S, Zhang Z, Zhang J, Mei L, Li H. Hybridization, polyploidization, and morphological convergence make dozens of taxa into one chaotic genetic pool: a phylogenomic case of the Ficus erecta species complex (Moraceae). FRONTIERS IN PLANT SCIENCE 2024; 15:1354812. [PMID: 38595762 PMCID: PMC11002808 DOI: 10.3389/fpls.2024.1354812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/08/2024] [Indexed: 04/11/2024]
Abstract
The Ficus erecta complex, characterized by its morphological diversity and frequent interspecific overlap, shares pollinating fig wasps among several species. This attribute, coupled with its intricate phylogenetic relationships, establishes it as an exemplary model for studying speciation and evolutionary patterns. Extensive researches involving RADseq (Restriction-site associated DNA sequencing), complete chloroplast genome data, and flow cytometry methods were conducted, focusing on phylogenomic analysis, genetic structure, and ploidy detection within the complex. Significantly, the findings exposed a pronounced nuclear-cytoplasmic conflict. This evidence, together with genetic structure analysis, confirmed that hybridization within the complex is a frequent occurrence. The ploidy detection revealed widespread polyploidy, with certain species exhibiting multiple ploidy levels, including 2×, 3×, and 4×. Of particular note, only five species (F. abelii, F. erecta, F. formosana, F. tannoensis and F. vaccinioides) in the complex were proved to be monophyletic. Species such as F. gasparriniana, F. pandurata, and F. stenophylla were found to encompass multiple phylogenetically distinct lineages. This discovery, along with morphological comparisons, suggests a significant underestimation of species diversity within the complex. This study also identified F. tannoensis as an allopolyploid species originating from F. vaccinioide and F. erecta. Considering the integration of morphological, molecular systematics, and cytological evidences, it is proposed that the scope of the F. erecta complex should be expanded to the entire subsect. Frutescentiae. This would redefine the complex as a continuously evolving group comprising at least 33 taxa, characterized by blurred species boundaries, frequent hybridization and polyploidization, and ambiguous genetic differentiation.
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Affiliation(s)
- Xiaomei Wang
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuai Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - Zhen Zhang
- College of Architecture and Urban Planning, Tongji University, Shanghai, China
| | - Jianhang Zhang
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, China
| | - Li Mei
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Hongqing Li
- School of Life Sciences, East China Normal University, Shanghai, China
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Gardner EM, Bruun-Lund S, Niissalo M, Chantarasuwan B, Clement WL, Geri C, Harrison RD, Hipp AL, Holvoet M, Khew G, Kjellberg F, Liao S, Pederneiras LC, Peng YQ, Pereira JT, Phillipps Q, Ahmad Puad AS, Rasplus JY, Sang J, Schou SJ, Velautham E, Weiblen GD, Zerega NJC, Zhang Q, Zhang Z, Baraloto C, Rønsted N. Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs. Proc Natl Acad Sci U S A 2023; 120:e2222035120. [PMID: 37399402 PMCID: PMC10334730 DOI: 10.1073/pnas.2222035120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/11/2023] [Indexed: 07/05/2023] Open
Abstract
Studies investigating the evolution of flowering plants have long focused on isolating mechanisms such as pollinator specificity. Some recent studies have proposed a role for introgressive hybridization between species, recognizing that isolating processes such as pollinator specialization may not be complete barriers to hybridization. Occasional hybridization may therefore lead to distinct yet reproductively connected lineages. We investigate the balance between introgression and reproductive isolation in a diverse clade using a densely sampled phylogenomic study of fig trees (Ficus, Moraceae). Codiversification with specialized pollinating wasps (Agaonidae) is recognized as a major engine of fig diversity, leading to about 850 species. Nevertheless, some studies have focused on the importance of hybridization in Ficus, highlighting the consequences of pollinator sharing. Here, we employ dense taxon sampling (520 species) throughout Moraceae and 1,751 loci to investigate phylogenetic relationships and the prevalence of introgression among species throughout the history of Ficus. We present a well-resolved phylogenomic backbone for Ficus, providing a solid foundation for an updated classification. Our results paint a picture of phylogenetically stable evolution within lineages punctuated by occasional local introgression events likely mediated by local pollinator sharing, illustrated by clear cases of cytoplasmic introgression that have been nearly drowned out of the nuclear genome through subsequent lineage fidelity. The phylogenetic history of figs thus highlights that while hybridization is an important process in plant evolution, the mere ability of species to hybridize locally does not necessarily translate into ongoing introgression between distant lineages, particularly in the presence of obligate plant-pollinator relationships.
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Affiliation(s)
- Elliot M. Gardner
- International Center for Tropical Botany at the Kampong, Institute of Environment, Florida International University, Miami, FL33133
- National Tropical Botanical Garden, Kalāheo, HI96741
- Singapore Botanic Gardens, National Parks Board, 259569, Singapore
| | - Sam Bruun-Lund
- Natural History Museum of Denmark, University of Copenhagen, 1123Copenhagen, Denmark
| | - Matti Niissalo
- Singapore Botanic Gardens, National Parks Board, 259569, Singapore
| | - Bhanumas Chantarasuwan
- Thailand National History Museum, National Science Museum, Klong Luang, Pathum Thani12120, Thailand
| | - Wendy L. Clement
- Department of Biology, The College of New Jersey, Ewing, NJ08618
| | - Connie Geri
- Sarawak Forestry Corporation, 93250Kuching, Sarawak, Malaysia
| | | | | | - Maxime Holvoet
- Natural History Museum of Denmark, University of Copenhagen, 1123Copenhagen, Denmark
| | - Gillian Khew
- Singapore Botanic Gardens, National Parks Board, 259569, Singapore
| | - Finn Kjellberg
- CEFE, CNRS, Université de Montpellier, EPHE, IRD, 34090Montpellier, France
| | - Shuai Liao
- The Morton Arboretum, Lisle, IL60532
- South China Botanical Garden, Chinese Academy of Sciences, 510650Guangzhou, China
- School of Life Sciences, East China Normal University, 200241Shanghai, China
| | - Leandro Cardoso Pederneiras
- Instituto de Pesquisa do Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, 22460-030Rio de Janeiro–RJ, Brazil
| | - Yan-Qiong Peng
- Chinese Academy of Sciences, Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, 666303Mengla, China
| | - Joan T. Pereira
- Sabah Forest Research Centre, Sabah Forestry Department, 90175Sandakan, Sabah, Malaysia
| | | | - Aida Shafreena Ahmad Puad
- Faculty of Agriculture & Applied Sciences, i-CATS University College, 93350Kuching, Sarawak, Malaysia
| | - Jean-Yves Rasplus
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, 34988Montpellier, France
| | - Julia Sang
- Sarawak Forest Department, 34988Kuching, Sarawak, Malaysia
| | - Sverre Juul Schou
- Natural History Museum of Denmark, University of Copenhagen, 1123Copenhagen, Denmark
| | - Elango Velautham
- Singapore Botanic Gardens, National Parks Board, 259569, Singapore
| | - George D. Weiblen
- Bell Museum, University of Minnesota, St. Paul, MN55113
- Department of Plant Biology, University of Minnesota, St. Paul, MN55108
| | - Nyree J. C. Zerega
- Plant Biology and Conservation, Northwestern University, Evanston, IL60208
- Negaunee Institute for Plant Conservation and Action, Chicago Botanic Garden, Glencoe, IL60022
| | - Qian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093Beijing, China
| | - Zhen Zhang
- School of Life Sciences, East China Normal University, 200241Shanghai, China
| | - Christopher Baraloto
- International Center for Tropical Botany at the Kampong, Institute of Environment, Florida International University, Miami, FL33133
| | - Nina Rønsted
- National Tropical Botanical Garden, Kalāheo, HI96741
- Natural History Museum of Denmark, University of Copenhagen, 1123Copenhagen, Denmark
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Satler JD, Herre EA, Heath TA, Machado CA, Gómez Zúñiga A, Jandér KC, Eaton DAR, Nason JD. Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps. Ecol Evol 2023; 13:e9673. [PMID: 36699574 PMCID: PMC9848820 DOI: 10.1002/ece3.9673] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/20/2022] [Accepted: 12/02/2022] [Indexed: 01/20/2023] Open
Abstract
Obligate pollination mutualisms, in which plant and pollinator lineages depend on each other for reproduction, often exhibit high levels of species specificity. However, cases in which two or more pollinator species share a single host species (host sharing), or two or more host species share a single pollinator species (pollinator sharing), are known to occur in current ecological time. Further, evidence for host switching in evolutionary time is increasingly being recognized in these systems. The degree to which departures from strict specificity differentially affect the potential for hybridization and introgression in the associated host or pollinator is unclear. We addressed this question using genome-wide sequence data from five sympatric Panamanian free-standing fig species (Ficus subgenus Pharmacosycea, section Pharmacosycea) and their six associated fig-pollinator wasp species (Tetrapus). Two of the five fig species, F. glabrata and F. maxima, were found to regularly share pollinators. In these species, ongoing hybridization was demonstrated by the detection of several first-generation (F1) hybrid individuals, and historical introgression was indicated by phylogenetic network analysis. By contrast, although two of the pollinator species regularly share hosts, all six species were genetically distinct and deeply divergent, with no evidence for either hybridization or introgression. This pattern is consistent with results from other obligate pollination mutualisms, suggesting that, in contrast to their host plants, pollinators appear to be reproductively isolated, even when different species of pollinators mate in shared hosts.
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Affiliation(s)
- Jordan D. Satler
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | | | - Tracy A. Heath
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | | | | | - K. Charlotte Jandér
- Department of Ecology and Genetics, Plant Ecology and EvolutionUppsala UniversityUppsalaSweden
| | - Deren A. R. Eaton
- Department of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNew YorkUSA
| | - John D. Nason
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
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Zhang Z, Zhang DS, Zou L, Yao CY. Comparison of chloroplast genomes and phylogenomics in the Ficus sarmentosa complex (Moraceae). PLoS One 2022; 17:e0279849. [PMID: 36584179 PMCID: PMC9803296 DOI: 10.1371/journal.pone.0279849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/15/2022] [Indexed: 01/01/2023] Open
Abstract
Due to maternal inheritance and minimal rearrangement, the chloroplast genome is an important genetic resource for evolutionary studies. However, the evolutionary dynamics and phylogenetic performance of chloroplast genomes in closely related species are poorly characterized, particularly in taxonomically complex and species-rich groups. The taxonomically unresolved Ficus sarmentosa species complex (Moraceae) comprises approximately 20 taxa with unclear genetic background. In this study, we explored the evolutionary dynamics, hotspot loci, and phylogenetic performance of thirteen chloroplast genomes (including eleven newly obtained and two downloaded from NCBI) representing the F. sarmentosa complex. Their sequence lengths, IR boundaries, repeat sequences, and codon usage were compared. Both sequence length and IR boundaries were found to be highly conserved. All four categories of long repeat sequences were found across all 13 chloroplast genomes, with palindromic and forward sequences being the most common. The number of simple sequence repeat (SSR) loci varied from 175 (F. dinganensis and F. howii) to 190 (F. polynervis), with the dinucleotide motif appearing the most frequently. Relative synonymous codon usage (RSCU) analysis indicated that codons ending with A/T were prior to those ending with C/T. The majority of coding sequence regions were found to have undergone negative selection with the exception of ten genes (accD, clpP, ndhK, rbcL, rpl20, rpl22, rpl23, rpoC1, rps15, and rps4) which exhibited potential positive selective signatures. Five hypervariable genic regions (rps15, ycf1, rpoA, ndhF, and rpl22) and five hypervariable intergenic regions (trnH-GUG-psbA, rpl32-trnL-UAG, psbZ-trnG-GCC, trnK-UUU-rps16 and ndhF-rpl32) were identified. Overall, phylogenomic analysis based on 123 Ficus chloroplast genomes showed promise for studying the evolutionary relationships in Ficus, despite cyto-nuclear discordance. Furthermore, based on the phylogenetic performance of the F. sarmentosa complex and F. auriculata complex, the chloroplast genome also exhibited a promising phylogenetic resolution in closely related species.
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Affiliation(s)
- Zhen Zhang
- College of Architecture and Urban Planning, Tongji University, Shanghai, China
| | - De-Shun Zhang
- College of Architecture and Urban Planning, Tongji University, Shanghai, China
| | - Lu Zou
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Chi-Yuan Yao
- College of Architecture and Urban Planning, Tongji University, Shanghai, China,* E-mail:
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Deng X, Cheng Y, Peng YQ, Yu H, Proffit M, Kjellberg F. Overlaps in olfactive signalling coupled with geographic variation may result in localised pollinator sharing between closely related Ficus species. BMC Ecol Evol 2022; 22:97. [PMID: 35964015 PMCID: PMC9375327 DOI: 10.1186/s12862-022-02055-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background In brood site pollination mutualisms, pollinators are attracted by odours emitted at anthesis. In Ficus, odours of receptive figs differ among species and the specific pollinators generally only enter figs of their host species ensuring a pre-zygotic barrier to plant interspecific hybridisation. However, field observations recorded that, in Guangdong province in China, Valisia javana hilli, the local pollinator of F. hirta, entered and reproduced successfully in the figs of the closely related F. triloba on a regular basis. We propose that closely related Ficus species produce similar receptive fig odours. Under particular contexts of odours locally present, the receptive fig odours of non-host figs of a Ficus species may become attractive to pollinators of closely related Ficus species. We used the headspace technique to collect in situ receptive fig odours of F. triloba in a series of locations in China. Under controlled conditions, we tested the attraction of fig pollinating wasps from F. hirta and F. triloba to host figs and non-host figs in Y tube experiments. Results Receptive fig odours of F. triloba though different from those of F. hirta, were mainly composed of a same set of volatile organic compounds. When given the choice between receptive fig odours and air, the pollinating wasps were only attracted by their host’s odours. However, when given a choice between host and non-host figs the pollinators of F. hirta were equally attracted by the two odours while the pollinators of F. triloba tended to be more attracted by their host’s fig odours. Conclusions Receptive fig odours vary geographically within species and the differentiation of receptive fig odours between closely related Ficus species is often incomplete. This allows localised or occasional pollinator sharing following different modalities. Cross stimulation when wasps are exposed simultaneously to odours of host and non-host species may be important. While occasional pollinator sharing may play a marginal role when wasp populations are robust, it may ensure the provisioning of new pollinators from the closest relative of a Ficus species if its pollinators go extinct.
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Xie H, Yang P, Xia Y, Kjellberg F, Darwell CT, Li ZB. Maintenance of specificity in sympatric host-specific fig/wasp pollination mutualisms. PeerJ 2022; 10:e13897. [PMID: 35975234 PMCID: PMC9375967 DOI: 10.7717/peerj.13897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/22/2022] [Indexed: 01/19/2023] Open
Abstract
Background Fig/wasp pollination mutualisms are extreme examples of species-specific plant-insect symbioses, but incomplete specificity occurs, with potentially important evolutionary consequences. Why pollinators enter alternative hosts, and the fates of pollinators and the figs they enter, are unknown. Methods We studied the pollinating fig wasp, Ceratosolen emarginatus, which concurrently interacts with its typical host Ficus auriculata and the locally sympatric alternative host F. hainanensis, recording frequencies of the wasp in figs of the alternative hosts. We measured ovipositor lengths of pollinators and style lengths in female and male figs in the two host species. Volatile organic compounds (VOCs) emitted by receptive figs of each species were identified using GC-MS. We tested the attraction of wasps to floral scents in choice experiments, and detected electrophysiologically active compounds by GC-EAD. We introduced C. emarginatus foundresses into figs of both species to reveal the consequences of entry into the alternative host. Results C. emarginatus entered a low proportion of figs of the alternative host, and produced offspring in a small proportion of them. Despite differences in the VOC profiles of the two fig species, they included shared semiochemicals. Although C. emarginatus females prefer receptive figs of F. auriculata, they are also attracted to those of F. hainanensis. C. emarginatus that entered male figs of F. hainanensis produced offspring, as their ovipositors were long enough to reach the bottom of the style; however, broods were larger and offspring smaller than in the typical host. Female figs of F. hainanensis failed to produce seeds when visited by C. emarginatus. These findings advance our current understanding of how these species-specific mutualisms usually remain stable and the conditions that allow their diversification.
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Affiliation(s)
- Hua Xie
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Southwest Forestry University, Kunming, Yunnan, China
| | - Pei Yang
- Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Yan Xia
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Southwest Forestry University, Kunming, Yunnan, China
| | - Finn Kjellberg
- CEFE, CNRS, Université de Montpellier, EPHE, IRD, Montpellier, France
| | - Clive T. Darwell
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Zong-Bo Li
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Southwest Forestry University, Kunming, Yunnan, China
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Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species. Commun Biol 2022; 5:284. [PMID: 35396571 PMCID: PMC8993897 DOI: 10.1038/s42003-022-03223-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/04/2022] [Indexed: 12/11/2022] Open
Abstract
The obligate pollination mutualism between figs (Ficus, Moraceae) and pollinator wasps (Agaonidae, Hymenoptera) is a classic example of cospeciation. However, examples of phylogenetic incongruencies between figs and their pollinators suggest that pollinators may speciate by host shifting. To investigate the mechanism of speciation by host shifting, we examined the phylogenetic relationships and population genetic structures of six closely related fig species and their pollinators from southern China and Taiwan-Ryukyu islands using various molecular markers. The results revealed 1) an extraordinary case of pollinator sharing, in which five distinct fig species share a single pollinator species in southern China; 2) two types of copollination, namely, sympatric copollination by pollinator duplication or pollinator migration, and allopatric copollination by host migration and new pollinator acquisition; 3) fig species from southern China have colonized Taiwan repeatedly and one of these events has been followed by host shifting, reestablishment of host specificity, and pollinator speciation, in order. Based on our results, we propose a model for pollinator speciation by host shifting in which the reestablishment of host-specificity plays a central role in the speciation process. These findings provide important insights into understanding the mechanisms underlying pollinator speciation and host specificity in obligate pollination mutualism. Phylogenetic and population genetic analyses reveal mechanisms of pollinator sharing, copollination and speciation by host-shift in fig-wasp mutualism.
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Yu H, Liao Y, Cheng Y, Jia Y, Compton SG. More examples of breakdown the 1:1 partner specificity between figs and fig wasps. BOTANICAL STUDIES 2021; 62:15. [PMID: 34626257 PMCID: PMC8502184 DOI: 10.1186/s40529-021-00323-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/21/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND The obligate mutualism between fig trees (Ficus, Moraceae) and pollinating fig wasps (Agaonidae) is a model system for studying co-evolution due to its perceived extreme specificity, but recent studies have reported a number of examples of trees pollinated by more than one fig wasp or sharing pollinators with other trees. This will make the potential of pollen flow between species and hybridization more likely though only few fig hybrids in nature have been found. We reared pollinator fig wasps from figs of 13 Chinese fig tree species and established their identity using genetic methods in order to investigate the extent to which they were supporting more than one species of pollinator (co-pollinator). RESULTS Our results showed (1) pollinator sharing was frequent among closely-related dioecious species (where pollinator offspring and seeds develop on different trees); (2) that where two pollinator species were developing in figs of one host species there was usually one fig wasp with prominent rate than the other. An exception was F. triloba, where its two pollinators were equally abundant; (3) the extent of co-pollinator within one fig species is related to the dispersal ability of them which is stronger in dioecious figs, especially in small species. CONCLUSIONS Our results gave more examples to the breakdown of extreme specificity, which suggest that host expansion events where pollinators reproduce in figs other than those of their usual hosts are not uncommon among fig wasps associated with dioecious hosts. Because closely related trees typically have closely related pollinators that have a very similar appearance, the extent of pollinator-sharing has probably been underestimated. Any pollinators that enter female figs carrying heterospecific pollen could potentially generate hybrid seed, and the extent of hybridization and its significance may also have been underestimated.
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Affiliation(s)
- Hui Yu
- Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Centre for Plant Ecology, CAS Core Botanical Gardens, Guangzhou, China.
| | - Yaolin Liao
- Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yufen Cheng
- Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yongxia Jia
- Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China
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Chen L, Segar ST, Chantarasuwan B, Wong DM, Wang R, Chen X, Yu H. Adaptation of Fig Wasps (Agaodinae) to Their Host Revealed by Large-Scale Transcriptomic Data. INSECTS 2021; 12:insects12090815. [PMID: 34564255 PMCID: PMC8471397 DOI: 10.3390/insects12090815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/11/2021] [Accepted: 09/08/2021] [Indexed: 01/22/2023]
Abstract
Simple Summary Research on fig wasps has made a considerable contribution to the understanding of insect–plant interactions. However, the molecular mechanisms underlying fig wasp host specificity are poorly understood. This study reports on a relatively large-scale transcriptomic dataset of 25 fig wasp species. We outline potential genetic mechanisms underlying the specific host adaptation by investigating changes in a gene family, in evolutionary rates, and in genes under positive selection. The transcriptome datasets reported here (1) provide new insights into the evolutionary diversification and host specificity of fig wasps and (2) contribute to a growing dataset on fig wasp genomics. Abstract Figs and fig wasps are highly species-specific and comprise a model system for studying co-evolution and co-speciation. The evolutionary relationships and molecular adaptations of fig wasps to their fig hosts are poorly understood, and this is in part due to limited sequence data. Here, we present large-scale transcriptomic datasets of 25 fig wasp species with the aim of uncovering the genetic basis for host specificity. Our phylogenetic results support the monophyly of all genera associated with dioecious figs, and two genera associated with monoecious figs, Eupristina and Platyscapa, were revealed to be close relatives. We identified gene loss and gain, potentially rapidly evolving genes, and genes under positive selection. Potentially functional changes were documented and we hypothesize as to how these may determine host specificity. Overall, our study provides new insights into the evolutionary diversification of fig wasps and contributes to our understanding of adaptation in this group.
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Affiliation(s)
- Lianfu Chen
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou 510650, China; (L.C.); (D.-M.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Simon T. Segar
- Department of Crop and Environment Sciences, Harper Adams University, Newport, Shropshire TF10 8NB, UK;
| | - Bhanumas Chantarasuwan
- Thailand Natural History Museum, National Science Museum, PtthumThani 12120, Thailand; (B.C.); (R.W.)
| | - Da-Mien Wong
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou 510650, China; (L.C.); (D.-M.W.)
| | - Rong Wang
- Thailand Natural History Museum, National Science Museum, PtthumThani 12120, Thailand; (B.C.); (R.W.)
| | - Xiaoyong Chen
- School of Ecological and Environmental Sciences, Tiantong National Station for Forest Ecosystem Research, East China Normal University, Shanghai 200241, China
- Correspondence: (X.C.); (H.Y.); Tel.: +886-021-54345469 (X.C.); +886-020-37252759 (H.Y.)
| | - Hui Yu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou 510650, China; (L.C.); (D.-M.W.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Correspondence: (X.C.); (H.Y.); Tel.: +886-021-54345469 (X.C.); +886-020-37252759 (H.Y.)
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Borges RM. Interactions Between Figs and Gall-Inducing Fig Wasps: Adaptations, Constraints, and Unanswered Questions. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.685542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The ancient interaction between figs (Ficus, Moraceae) and their pollinating fig wasps is an unusual example of a mutualism between plants and gall-inducing insects. This review intends to offer fresh perspectives into the relationship between figs and the diversity of gall-inducing sycophiles which inhabit their enclosed globular inflorescences that function as microcosms. Besides gall-inducing pollinators, fig inflorescences are also inhabited by other gall-inducing wasps. This review evaluates the state of current knowledge on gall-induction by fig wasps and exposes the many lacunae in this area. This review makes connections between fig and gall-inducing wasp traits, and suggests relatively unexplored research avenues. This manuscript calls for an integrated approach that incorporates such diverse fields as life-history theory, plant mate choice, wasp sexual selection and local mate competition, plant embryology as well as seed and fruit dispersal. It calls for collaboration between researchers such as plant developmental biologists, insect physiologists, chemical ecologists and sensory biologists to jointly solve the many valuable questions that can be addressed in community ecology, co-evolution and species interaction biology using the fig inflorescence microcosm, that is inhabited by gall-inducing mutualistic and parasitic wasps, as a model system.
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Bernard J, Brock KC, Tonnell V, Walsh SK, Wenger JP, Wolkis D, Weiblen GD. New Species Assemblages Disrupt Obligatory Mutualisms Between Figs and Their Pollinators. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.564653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Cooper L, Bunnefeld L, Hearn J, Cook JM, Lohse K, Stone GN. Low-coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp. Mol Ecol 2020; 29:3649-3666. [PMID: 32567765 DOI: 10.1111/mec.15523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 12/16/2022]
Abstract
Population divergence and gene flow are key processes in evolution and ecology. Model-based analysis of genome-wide data sets allows discrimination between alternative scenarios for these processes even in nonmodel taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum [bSFS], the second on the pairwise sequentially Markovian coalescent [PSMC]) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia and are separated into The Northern population is to the north of the Southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of postdivergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196 kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57 kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome-level data for small population samples of tiny, nonmodel organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.
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Affiliation(s)
- Lisa Cooper
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Lynsey Bunnefeld
- Biological and Environmental Sciences, University of Stirling, Stirling, UK
| | - Jack Hearn
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK
| | - James M Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Graham N Stone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Shirasawa K, Yakushiji H, Nishimura R, Morita T, Jikumaru S, Ikegami H, Toyoda A, Hirakawa H, Isobe S. The Ficus erecta genome aids Ceratocystis canker resistance breeding in common fig (F. carica). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:1313-1322. [PMID: 31978270 PMCID: PMC7317799 DOI: 10.1111/tpj.14703] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/27/2019] [Accepted: 01/16/2020] [Indexed: 05/31/2023]
Abstract
Ficus erecta, a wild relative of the common fig (F. carica), is a donor of Ceratocystis canker resistance in fig breeding programmes. Interspecific hybridization followed by recurrent backcrossing is an effective method to transfer the resistance trait from wild to cultivated fig. However, this process is time consuming and labour intensive for trees, especially for gynodioecious plants such as fig. In this study, genome resources were developed for F. erecta to facilitate fig breeding programmes. The genome sequence of F. erecta was determined using single-molecule real-time sequencing technology. The resultant assembly spanned 331.6 Mb with 538 contigs and an N50 length of 1.9 Mb, from which 51 806 high-confidence genes were predicted. Pseudomolecule sequences corresponding to the chromosomes of F. erecta were established with a genetic map based on single nucleotide polymorphisms from double-digest restriction-site-associated DNA sequencing. Subsequent linkage analysis and whole-genome resequencing identified a candidate gene for the Ceratocystis canker resistance trait. Genome-wide genotyping analysis enabled the selection of female lines that possessed resistance and effective elimination of the donor genome from the progeny. The genome resources provided in this study will accelerate and enhance disease-resistance breeding programmes in fig.
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Affiliation(s)
| | | | | | - Takeshige Morita
- Agricultural Technology Research CenterHiroshima Prefectural Technology Research InstituteHigashihiroshimaJapan
| | - Shota Jikumaru
- Agricultural Technology Research CenterHiroshima Prefectural Technology Research InstituteHigashihiroshimaJapan
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Deng JY, Fu RH, Compton SG, Liu M, Wang Q, Yuan C, Zhang LS, Chen Y. Sky islands as foci for divergence of fig trees and their pollinators in southwest China. Mol Ecol 2020; 29:762-782. [PMID: 31943487 DOI: 10.1111/mec.15353] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 11/26/2019] [Accepted: 01/03/2020] [Indexed: 12/11/2022]
Abstract
The dynamics of populations and their divergence over time have shaped current levels of biodiversity and in the case of the "sky islands" of mountainous southwest (SW) China have resulted in an area of exceptional botanical diversity. Ficus tikoua is a prostrate fig tree subendemic to the area that displays unique intraspecific diversity, producing figs typical of different pollination modes in different parts of its range. By combining climate models, genetic variation in populations of the tree's obligate fig wasp pollinators and distributions of the different plant phenotypes, we examined how this unusual situation may have developed. We identified three genetically distinct groups of a single Ceratosolen pollinator species that have largely parapatric distributions. The complex topography of the region contributed to genetic divergence among the pollinators by facilitating geographical isolation and providing refugia. Migration along elevations in response to climate oscillations further enhanced genetic differentiation of the three pollinator groups. Their distributions loosely correspond to the distributions of the functionally significant morphological differences in the male figs of their host plants, but postglacial expansion of one group has not been matched by spread of its associated plant phenotype, possibly due to a major river barrier. The results highlight how interplay between the complex topography of the "sky island" complex and climate change has shaped intraspecies differentiation and relationships between the plant and its pollinator. Similar processes may explain the exceptional botanical diversity of SW China.
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Affiliation(s)
- Jun-Yin Deng
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China.,Division of Genetics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Rong-Hua Fu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | | | - Mei Liu
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Qin Wang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Chuan Yuan
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Lu-Shui Zhang
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
| | - Yan Chen
- Ecological Security and Protection Key Laboratory of Sichuan Province, Mianyang Normal University, Mianyang, China
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Souto‐Vilarós D, Machac A, Michalek J, Darwell CT, Sisol M, Kuyaiva T, Isua B, Weiblen GD, Novotny V, Segar ST. Faster speciation of fig‐wasps than their host figs leads to decoupled speciation dynamics: Snapshots across the speciation continuum. Mol Ecol 2019; 28:3958-3976. [DOI: 10.1111/mec.15190] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/19/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Daniel Souto‐Vilarós
- Faculty of Science University of South Bohemia České Budějovice Czech Republic
- Biology Centre of the Czech Academy of Sciences Institute of Entomology České Budějovice Czech Republic
| | - Antonin Machac
- Center for Theoretical Study Charles University and Czech Academy of Sciences Prague Czech Republic
- Department of Ecology Charles University Prague Czech Republic
- Center for Macroecology, Evolution and Climate Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- Biodiversity Research Centre University of British Columbia Vancouver BC Canada
| | - Jan Michalek
- Biology Centre of the Czech Academy of Sciences Institute of Entomology České Budějovice Czech Republic
| | | | - Mentap Sisol
- New Guinea Binatang Research Centre Madang Papua New Guinea
| | - Thomas Kuyaiva
- New Guinea Binatang Research Centre Madang Papua New Guinea
| | - Brus Isua
- New Guinea Binatang Research Centre Madang Papua New Guinea
| | - George D. Weiblen
- Institute on the Environment University of Minnesota Saint Paul MN USA
| | - Vojtech Novotny
- Biology Centre of the Czech Academy of Sciences Institute of Entomology České Budějovice Czech Republic
- New Guinea Binatang Research Centre Madang Papua New Guinea
| | - Simon T. Segar
- Biology Centre of the Czech Academy of Sciences Institute of Entomology České Budějovice Czech Republic
- Department of Crop and Environment Sciences Harper Adams University Newport UK
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Yu H, Tian E, Zheng L, Deng X, Cheng Y, Chen L, Wu W, Tanming W, Zhang D, Compton SG, Kjellberg F. Multiple parapatric pollinators have radiated across a continental fig tree displaying clinal genetic variation. Mol Ecol 2019; 28:2391-2405. [DOI: 10.1111/mec.15046] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Hui Yu
- Guangdong Provincial Key Laboratory of Digital Botanical Garden and Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden The Chinese Academy of Sciences Guangzhou China
- Centre for Plant Ecology, CAS Core Botanical Gardens Guangzhou China
| | - Enwei Tian
- Guangdong Provincial Key Laboratory of Digital Botanical Garden and Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden The Chinese Academy of Sciences Guangzhou China
| | - Linna Zheng
- Guangdong Provincial Key Laboratory of Digital Botanical Garden and Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden The Chinese Academy of Sciences Guangzhou China
| | - Xiaoxia Deng
- Guangdong Provincial Key Laboratory of Digital Botanical Garden and Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden The Chinese Academy of Sciences Guangzhou China
| | - Yufen Cheng
- Guangdong Provincial Key Laboratory of Digital Botanical Garden and Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden The Chinese Academy of Sciences Guangzhou China
| | - Lianfu Chen
- Guangdong Provincial Key Laboratory of Digital Botanical Garden and Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden The Chinese Academy of Sciences Guangzhou China
| | - Wei Wu
- Guangdong Provincial Key Laboratory of Digital Botanical Garden and Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden The Chinese Academy of Sciences Guangzhou China
| | | | - Dayong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences Beijing Normal University Beijing China
| | | | - Finn Kjellberg
- CEFE, CNR, EPHE, IRD Université de Montpellier, Université Paul‐Valéry Montpellier Montpellier France
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