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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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Mandagi IF, K A Sumarto B, Nuryadi H, Mokodongan DF, Lawelle SA, W A Masengi K, Nagano AJ, Kakioka R, Kitano J, Ansai S, Kusumi J, Yamahira K. Multiple colonizations and hybridization of a freshwater fish group on a satellite island of Sulawesi. Mol Phylogenet Evol 2023; 184:107804. [PMID: 37120113 DOI: 10.1016/j.ympev.2023.107804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/27/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
Repeated colonizations and resultant hybridization may increase lineage diversity on an island if introgression occurs only in a portion of the indigenous island lineage. Therefore, to precisely understand how island biodiversity was shaped, it is essential to reconstruct the history of secondary colonization and resultant hybridization both in time and space. In this study, we reconstructed the history of multiple colonizations of the Oryzias woworae species group, a freshwater fish group of the family Adrianichthyidae, from Sulawesi Island to its southeast satellite island, Muna Island. Phylogenetic and species tree analyses using genome-wide single-nucleotide polymorphisms revealed that all local populations on Muna Island were monophyletic, but that there were several genetically distinct lineages within the island. Population structure and phylogenetic network analyses demonstrated that colonization of this island occurred more than once, and that secondary colonization and resultant introgressive hybridization occurred only in one local population on the island. The spatially heterogeneous introgression induced by the multiple colonizations were also supported by differential admixture analyses. In addition, the differential admixture analyses detected reverse colonization from Muna Island to the Sulawesi mainland. Coalescence-based demographic inference estimated that these mutual colonizations occurred during the middle to late Quaternary period, during which sea level repeatedly declined; this indicates that the colonizations occurred via land bridges. We conclude that these mutual colonizations between Muna Island and the Sulawesi mainland, and the resultant spatially heterogeneous introgression shaped the current biodiversity of this species group in this area.
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Affiliation(s)
- Ixchel F Mandagi
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado 95115, Indonesia.
| | - Bayu K A Sumarto
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan.
| | - Handung Nuryadi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan.
| | - Daniel F Mokodongan
- Museum Zoologicum Bogoriense, Research Center for Biology, National Research and Innovation Agency, Cibinong 16911, Indonesia.
| | - Sjamsu A Lawelle
- Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari 93232, Indonesia.
| | - Kawilarang W A Masengi
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado 95115, Indonesia.
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan.
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan.
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan.
| | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka 819-0395, Japan.
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan.
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