1
|
Yang L, Harris AJ, Wen F, Li Z, Feng C, Kong H, Kang M. Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation. Syst Biol 2023; 72:1064-1083. [PMID: 37158589 PMCID: PMC10627561 DOI: 10.1093/sysbio/syad029] [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: 08/09/2021] [Revised: 04/15/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023] Open
Abstract
Allopolyploid plants have long been regarded as possessing genetic advantages under certain circumstances due to the combined effects of their hybrid origins and duplicated genomes. However, the evolutionary consequences of allopolyploidy in lineage diversification remain to be fully understood. Here, we investigate the evolutionary consequences of allopolyploidy using 138 transcriptomic sequences of Gesneriaceae, including 124 newly sequenced, focusing particularly on the largest subtribe Didymocarpinae. We estimated the phylogeny of Gesneriaceae using concatenated and coalescent-based methods based on five different nuclear matrices and 27 plastid genes, focusing on relationships among major clades. To better understand the evolutionary affinities in this family, we applied a range of approaches to characterize the extent and cause of phylogenetic incongruence. We found that extensive conflicts between nuclear and chloroplast genomes and among nuclear genes were caused by both incomplete lineage sorting (ILS) and reticulation, and we found evidence of widespread ancient hybridization and introgression. Using the most highly supported phylogenomic framework, we revealed multiple bursts of gene duplication throughout the evolutionary history of Gesneriaceae. By incorporating molecular dating and analyses of diversification dynamics, our study shows that an ancient allopolyploidization event occurred around the Oligocene-Miocene boundary, which may have driven the rapid radiation of core Didymocarpinae.
Collapse
Affiliation(s)
- Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Fang Wen
- Guangxi Institute of Botany, Guangxi Zhang Autonomous Region and the Chinese Academy of Sciences, 541006 Guilin, China
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., Tucson, AZ 85721, USA
| | - Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
2
|
Folk RA, Gaynor ML, Engle-Wrye NJ, O’Meara BC, Soltis PS, Soltis DE, Guralnick RP, Smith SA, Grady CJ, Okuyama Y. Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method. Syst Biol 2023; 72:856-873. [PMID: 37073863 PMCID: PMC10405357 DOI: 10.1093/sysbio/syad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 03/23/2023] [Accepted: 04/17/2023] [Indexed: 04/20/2023] Open
Abstract
Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit. [Ancestral niche reconstruction; hybridization; paleoclimate; pleistocene.].
Collapse
Affiliation(s)
- Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Michelle L Gaynor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Nicholas J Engle-Wrye
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Brian C O’Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Charles J Grady
- Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
| | - Yudai Okuyama
- Tsukuba Botanical Garden, National Museum of Nature and Science, Tsukuba, Japan
| |
Collapse
|
3
|
Staude IR, Ebersbach J. Neophytes may promote hybridization and adaptations to a changing planet. Ecol Evol 2023; 13:e10405. [PMID: 37593753 PMCID: PMC10427993 DOI: 10.1002/ece3.10405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
Human activities erode geographic barriers, facilitating hybridization among previously isolated taxa. However, limited empirical research exists on the consequences of introduced species (neophytes) for hybridization and subsequent evolutionary outcomes. To address this knowledge gap, we employed a macroecological approach. First, we examined the spatial and phylogenetic overlap between neophytes and hybrids by integrating the Plants of the World Online database with the Global Naturalized Alien Flora database. Second, leveraging the largest dated plant phylogeny available, we compared diversification rates between genera containing hybrids and neophytes versus those without. Third, focusing on the extensively studied hybrid flora of Britain, we studied the spatial distributions of hybrids in relation to neophyte and native parents, assessing potential adaptations to anthropogenic disturbances and impacts on native species. Overall, our findings highlight positive ties between contemporary biodiversity redistribution and hybridization. Spatially (across countries) and phylogenetically (across genera), neophyte incidence was positively associated with hybrid incidence. Genera comprising both hybrids and neophytes displayed significantly higher diversification rates. Neophyte hybrids primarily occupied areas with a higher human footprint, with limited evidence of hybrids threatening native species throughout their range in more natural habitats. These results challenge the notion that species naturalizations and hybridizations exclusively yield negative outcomes for biodiversity. While it is conceivable that anthropogenic hybridization may facilitate recombination of genetic variation and contribute to conserving genetic diversity in disturbed environments, further research is needed to fully understand these processes.
Collapse
Affiliation(s)
- Ingmar R. Staude
- Institute of BiologyLeipzig UniversityLeipzigGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Jana Ebersbach
- Institute of BiologyLeipzig UniversityLeipzigGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Stull GW, Pham KK, Soltis PS, Soltis DE. Deep reticulation: the long legacy of hybridization in vascular plant evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:743-766. [PMID: 36775995 DOI: 10.1111/tpj.16142] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 05/27/2023]
Abstract
Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.
Collapse
Affiliation(s)
- Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| |
Collapse
|
6
|
Mitchell N, Luu H, Owens GL, Rieseberg LH, Whitney KD. Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus). Evolution 2022; 76:1512-1528. [PMID: 35665925 PMCID: PMC9544064 DOI: 10.1111/evo.14536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 01/22/2023]
Abstract
To what extent is evolution repeatable? Little is known about whether the evolution of hybrids is more (or less) repeatable than that of nonhybrids. We used field experimental evolution in annual sunflowers (Helianthus) in Texas to ask the extent to which hybrid evolution is repeatable across environments compared to nonhybrid controls. We created hybrids between Helianthus annuus (L.) and H. debilis (Nutt.) and grew plots of both hybrids and nonhybrid controls through eight generations at three sites in Texas. We collected seeds from each generation and grew each generation × treatment × home site combination at two final common gardens. We estimated the strength and direction of evolution in terms of fitness and 24 traits, tested for repeated versus nonrepeated evolution, and assessed overall phenotypic evolution across lineages and in relation to a locally adapted phenotype. Hybrids consistently evolved higher fitness over time, while controls did not, although trait evolution varied in strength across home sites. Repeated evolution was more evident in hybrids versus nonhybrid controls, and hybrid evolution was often in the direction of the locally adapted phenotype. Our findings have implications for both the nature of repeatability in evolution and the contribution of hybridization to evolution across environmental contexts.
Collapse
Affiliation(s)
- Nora Mitchell
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA,Department of BiologyUniversity of Wisconsin – Eau ClaireEau ClaireWisconsinUSA
| | - Hoang Luu
- Department of Environmental and Plant BiologyOhio UniversityAthensOhioUSA
| | - Gregory L. Owens
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaBritish ColumbiaCanada
| | | |
Collapse
|
7
|
Singhal S, Derryberry GE, Bravo GA, Derryberry EP, Brumfield RT, Harvey MG. The dynamics of introgression across an avian radiation. Evol Lett 2021; 5:568-581. [PMID: 34917397 PMCID: PMC8645201 DOI: 10.1002/evl3.256] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/11/2021] [Accepted: 08/31/2021] [Indexed: 01/20/2023] Open
Abstract
Hybridization and resulting introgression can play both a destructive and a creative role in the evolution of diversity. Thus, characterizing when and where introgression is most likely to occur can help us understand the causes of diversification dynamics. Here, we examine the prevalence of and variation in introgression using phylogenomic data from a large (1300+ species), geographically widespread avian group, the suboscine birds. We first examine patterns of gene tree discordance across the geographic distribution of the entire clade. We then evaluate the signal of introgression in a subset of 206 species triads using Patterson's D‐statistic and test for associations between introgression signal and evolutionary, geographic, and environmental variables. We find that gene tree discordance varies across lineages and geographic regions. The signal of introgression is highest in cases where species occur in close geographic proximity and in regions with more dynamic climates since the Pleistocene. Our results highlight the potential of phylogenomic datasets for examining broad patterns of hybridization and suggest that the degree of introgression between diverging lineages might be predictable based on the setting in which they occur.
Collapse
Affiliation(s)
- Sonal Singhal
- Department of Biology California State University, Dominguez Hills Carson California 90747
| | - Graham E Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Gustavo A Bravo
- Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts 02138.,Museum of Comparative Zoology Harvard University Cambridge Massachusetts 02138
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Robb T Brumfield
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana 70803.,Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803
| | - Michael G Harvey
- Department of Biological Sciences The University of Texas at El Paso El Paso Texas 79968.,Biodiversity Collections The University of Texas at El Paso El Paso Texas 79968
| |
Collapse
|