Genomic insights into rapid speciation within the world's largest tree genus Syzygium
The relative importance of the mechanisms underlying species radiation remains unclear. Here, the authors combine reference genome assembly and population genetics analyses to show that neutral forces have contributed to the radiation of the most species-rich tree genus Syzygium. Species radiations,...
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2022
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QK Botany Low, Yee Wen Rajaraman, Sitaram Tomlin, Crystal M. Ahmad, Joffre Ali Ardi, Wisnu H. Armstrong, Kate Athen, Parusuraman Berhaman, Ahmad Bone, Ruth E. Cheek, Martin Cho, Nicholas R. W. Choo, Le Min Cowie, Ian D. Crayn, Darren Fleck, Steven J. Ford, Andrew J. Forster, Paul Girmansyah, Deden Goyder, David J. Gray, Bruce Heatubun, Charlie D. Ibrahim, Ali Ibrahim, Bazilah Jayasinghe, Himesh D. Kalat, Muhammad Ariffin Kathriarachchi, Hashendra S. Kintamani, Endang Koh, Sin Lan Lai, Joseph T. K. Lee, Serena M. L. Leong, Paul K. F. Lim, Wei Hao Lum, Shawn K. Y. Mahyuni, Ridha McDonald, William J. F. Metali, Faizah Mustaqim, Wendy A. Naiki, Akiyo Ngo, Kang Min Niissalo, Matti Ranasinghe, Subhani Repin, Rimi Rustiami, Himmah Simbiak, Victor Sukri, Rahayu S. Sunarti, Siti Trethowan, Liam A. Trias-Blasi, Anna Vasconcelos, Thais N. C. Wanma, Jimmy F. Widodo, Pudji Wijesundara, Douglas Siril A. Worboys, Stuart Yap, Jing Wei Yong, Kien Thai Khew, Gillian S. W. Salojarvi, Jarkko Michael, Todd P. Middleton, David J. Burslem, David F. R. P. Lindqvist, Charlotte Lucas, Eve J. Albert, Victor A. Genomic insights into rapid speciation within the world's largest tree genus Syzygium |
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The relative importance of the mechanisms underlying species radiation remains unclear. Here, the authors combine reference genome assembly and population genetics analyses to show that neutral forces have contributed to the radiation of the most species-rich tree genus Syzygium. Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification. |
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Low, Yee Wen Rajaraman, Sitaram Tomlin, Crystal M. Ahmad, Joffre Ali Ardi, Wisnu H. Armstrong, Kate Athen, Parusuraman Berhaman, Ahmad Bone, Ruth E. Cheek, Martin Cho, Nicholas R. W. Choo, Le Min Cowie, Ian D. Crayn, Darren Fleck, Steven J. Ford, Andrew J. Forster, Paul Girmansyah, Deden Goyder, David J. Gray, Bruce Heatubun, Charlie D. Ibrahim, Ali Ibrahim, Bazilah Jayasinghe, Himesh D. Kalat, Muhammad Ariffin Kathriarachchi, Hashendra S. Kintamani, Endang Koh, Sin Lan Lai, Joseph T. K. Lee, Serena M. L. Leong, Paul K. F. Lim, Wei Hao Lum, Shawn K. Y. Mahyuni, Ridha McDonald, William J. F. Metali, Faizah Mustaqim, Wendy A. Naiki, Akiyo Ngo, Kang Min Niissalo, Matti Ranasinghe, Subhani Repin, Rimi Rustiami, Himmah Simbiak, Victor Sukri, Rahayu S. Sunarti, Siti Trethowan, Liam A. Trias-Blasi, Anna Vasconcelos, Thais N. C. Wanma, Jimmy F. Widodo, Pudji Wijesundara, Douglas Siril A. Worboys, Stuart Yap, Jing Wei Yong, Kien Thai Khew, Gillian S. W. Salojarvi, Jarkko Michael, Todd P. Middleton, David J. Burslem, David F. R. P. Lindqvist, Charlotte Lucas, Eve J. Albert, Victor A. |
| author_facet |
Low, Yee Wen Rajaraman, Sitaram Tomlin, Crystal M. Ahmad, Joffre Ali Ardi, Wisnu H. Armstrong, Kate Athen, Parusuraman Berhaman, Ahmad Bone, Ruth E. Cheek, Martin Cho, Nicholas R. W. Choo, Le Min Cowie, Ian D. Crayn, Darren Fleck, Steven J. Ford, Andrew J. Forster, Paul Girmansyah, Deden Goyder, David J. Gray, Bruce Heatubun, Charlie D. Ibrahim, Ali Ibrahim, Bazilah Jayasinghe, Himesh D. Kalat, Muhammad Ariffin Kathriarachchi, Hashendra S. Kintamani, Endang Koh, Sin Lan Lai, Joseph T. K. Lee, Serena M. L. Leong, Paul K. F. Lim, Wei Hao Lum, Shawn K. Y. Mahyuni, Ridha McDonald, William J. F. Metali, Faizah Mustaqim, Wendy A. Naiki, Akiyo Ngo, Kang Min Niissalo, Matti Ranasinghe, Subhani Repin, Rimi Rustiami, Himmah Simbiak, Victor Sukri, Rahayu S. Sunarti, Siti Trethowan, Liam A. Trias-Blasi, Anna Vasconcelos, Thais N. C. Wanma, Jimmy F. Widodo, Pudji Wijesundara, Douglas Siril A. Worboys, Stuart Yap, Jing Wei Yong, Kien Thai Khew, Gillian S. W. Salojarvi, Jarkko Michael, Todd P. Middleton, David J. Burslem, David F. R. P. Lindqvist, Charlotte Lucas, Eve J. Albert, Victor A. |
| author_sort |
Low, Yee Wen |
| title |
Genomic insights into rapid speciation within the world's largest tree genus Syzygium |
| title_short |
Genomic insights into rapid speciation within the world's largest tree genus Syzygium |
| title_full |
Genomic insights into rapid speciation within the world's largest tree genus Syzygium |
| title_fullStr |
Genomic insights into rapid speciation within the world's largest tree genus Syzygium |
| title_full_unstemmed |
Genomic insights into rapid speciation within the world's largest tree genus Syzygium |
| title_sort |
genomic insights into rapid speciation within the world's largest tree genus syzygium |
| publisher |
Nature Portfolio |
| publishDate |
2022 |
| url |
http://eprints.um.edu.my/41299/ |
| _version_ |
1783876715458592768 |
| spelling |
my.um.eprints.412992023-11-24T01:46:30Z http://eprints.um.edu.my/41299/ Genomic insights into rapid speciation within the world's largest tree genus Syzygium Low, Yee Wen Rajaraman, Sitaram Tomlin, Crystal M. Ahmad, Joffre Ali Ardi, Wisnu H. Armstrong, Kate Athen, Parusuraman Berhaman, Ahmad Bone, Ruth E. Cheek, Martin Cho, Nicholas R. W. Choo, Le Min Cowie, Ian D. Crayn, Darren Fleck, Steven J. Ford, Andrew J. Forster, Paul Girmansyah, Deden Goyder, David J. Gray, Bruce Heatubun, Charlie D. Ibrahim, Ali Ibrahim, Bazilah Jayasinghe, Himesh D. Kalat, Muhammad Ariffin Kathriarachchi, Hashendra S. Kintamani, Endang Koh, Sin Lan Lai, Joseph T. K. Lee, Serena M. L. Leong, Paul K. F. Lim, Wei Hao Lum, Shawn K. Y. Mahyuni, Ridha McDonald, William J. F. Metali, Faizah Mustaqim, Wendy A. Naiki, Akiyo Ngo, Kang Min Niissalo, Matti Ranasinghe, Subhani Repin, Rimi Rustiami, Himmah Simbiak, Victor Sukri, Rahayu S. Sunarti, Siti Trethowan, Liam A. Trias-Blasi, Anna Vasconcelos, Thais N. C. Wanma, Jimmy F. Widodo, Pudji Wijesundara, Douglas Siril A. Worboys, Stuart Yap, Jing Wei Yong, Kien Thai Khew, Gillian S. W. Salojarvi, Jarkko Michael, Todd P. Middleton, David J. Burslem, David F. R. P. Lindqvist, Charlotte Lucas, Eve J. Albert, Victor A. QK Botany The relative importance of the mechanisms underlying species radiation remains unclear. Here, the authors combine reference genome assembly and population genetics analyses to show that neutral forces have contributed to the radiation of the most species-rich tree genus Syzygium. Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification. Nature Portfolio 2022-09 Article PeerReviewed Low, Yee Wen and Rajaraman, Sitaram and Tomlin, Crystal M. and Ahmad, Joffre Ali and Ardi, Wisnu H. and Armstrong, Kate and Athen, Parusuraman and Berhaman, Ahmad and Bone, Ruth E. and Cheek, Martin and Cho, Nicholas R. W. and Choo, Le Min and Cowie, Ian D. and Crayn, Darren and Fleck, Steven J. and Ford, Andrew J. and Forster, Paul and Girmansyah, Deden and Goyder, David J. and Gray, Bruce and Heatubun, Charlie D. and Ibrahim, Ali and Ibrahim, Bazilah and Jayasinghe, Himesh D. and Kalat, Muhammad Ariffin and Kathriarachchi, Hashendra S. and Kintamani, Endang and Koh, Sin Lan and Lai, Joseph T. K. and Lee, Serena M. L. and Leong, Paul K. F. and Lim, Wei Hao and Lum, Shawn K. Y. and Mahyuni, Ridha and McDonald, William J. F. and Metali, Faizah and Mustaqim, Wendy A. and Naiki, Akiyo and Ngo, Kang Min and Niissalo, Matti and Ranasinghe, Subhani and Repin, Rimi and Rustiami, Himmah and Simbiak, Victor and Sukri, Rahayu S. and Sunarti, Siti and Trethowan, Liam A. and Trias-Blasi, Anna and Vasconcelos, Thais N. C. and Wanma, Jimmy F. and Widodo, Pudji and Wijesundara, Douglas Siril A. and Worboys, Stuart and Yap, Jing Wei and Yong, Kien Thai and Khew, Gillian S. W. and Salojarvi, Jarkko and Michael, Todd P. and Middleton, David J. and Burslem, David F. R. P. and Lindqvist, Charlotte and Lucas, Eve J. and Albert, Victor A. (2022) Genomic insights into rapid speciation within the world's largest tree genus Syzygium. Nature Communications, 13 (1). ISSN 2041-1723, DOI https://doi.org/10.1038/s41467-022-32637-x <https://doi.org/10.1038/s41467-022-32637-x>. 10.1038/s41467-022-32637-x |
| score |
13.211869 |