Genomic insights into rapid speciation within the world’s largest tree genus Syzygium

Low, Yee Wen; Rajaraman, Sitaram; Tomlin, Crystal; 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; Crayn, Darren M.; Fleck, Steven J.; Ford, Andrew J.; Forster, Paul I.; Girmansyah, Deden; Goyder, D. J.; Gray, Bruce H.; Heatubun, Charlie D.; Ibrahim, Ali Abdulhafidh; Ibrahim, Bazilah; Jayasinghe, H.D.; Kalat, Muhammad Ariffin; Kathriarachchi, Hashendra; Kintamani, Endang; Koh, Sin Lan; Lai, Joseph Tuck Kwong; Lee, Serena M. L.; Leong, P.K.F.; Lim, Wei Hao; Lum, Shawn; Mahyuni, Ridha; McDonald, William J.; Metali, Faizah; Mustaqim, Wendy A.; Naiki, Akiyo; Ngo, Kang Min; Niissalo, Matti A.; Ranasinghe, Subhani; Repin, Rimi; Rustiami, Himmah; Simbiak, Victor I.; Sukri, Rahayu Sukmaria; Sunarti, Siti; Trethowan, Liam A.; Trias‐Blasi, Anna; Vasconcelos, Thaís; Wanma, Jimmy F.; Widodo, Pudji; Wijesundara, Siril; Worboys, Stuart; Yap, Jing Wei; Yong, Kien-Thai; Khew, Gillian; Salojärvi, Jarkko; Michael, Todd P.; Middleton, David J.; Burslem, David F. R. P.; Lindqvist, Charlotte; Lucas, Eve

doi:10.1038/s41467-022-32637-x

Cited by 27 publications

(59 citation statements)

References 111 publications

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“…Our results show that significantly negative f3 values reflected close phylogenetic relationships among samples, as anticipated based on previous studies 16 . Crosses of negative values in our f3 heat maps (wherein all source combinations showed negative f3) likely reflected strong identity by descent (IBD), as also seen in other organisms, such as Syzygium 22 and Ursus 61 . For example, the two representatives of Phyllostegia warshaueri was marked by the cross pattern of negative values when one was configured as a target and the other as a source (Supplementary Fig.…”

Section: The Majority Of Present-day Hawaiian Mints Appear Unadmixedmentioning

confidence: 58%

“…19c; also see below discussion). The clinal variation observed among the Hawaiian mints may correspond to progressive cladogenesis via geographic speciation 22 . For example, allelic variation may have become fixed along an ongoing cladogenetic process caused by serial founder events in an island-hopping model of geographic speciation 56 .…”

Section: Stenogyne Haplostachys and Phyllostegia Show Contrasting Gen...mentioning

confidence: 97%

“…19b). Such clinal variation may correspond to progressive cladogenesis via geographic speciation 22 . Among the first four PCs identified, Stachys chamissonis and S. bullata were the taxa most proximate to the 4a).…”

Section: Stenogyne Haplostachys and Phyllostegia Show Contrasting Gen...mentioning

confidence: 99%

“…It is important to note that ADMIXTURE results are often overinterpreted as indicative of crosslineage admixture 62 , and the K components from ADMIXTURE simply represent subsets of inherited SNP variation that could reflect any underlying mixtures, of which ILS may be another underlying causal factor 22 .…”

Section: The Majority Of Present-day Hawaiian Mints Appear Unadmixedmentioning

confidence: 99%

“…With such rapid divergence and little genetic differentiation it can be challenging to distinguish ILS from hybridization using either maternally inherited (even whole plastome) or single-copy nuclear loci. Plant radiations studied to-date, including the Hawaiian silverswords 12 , lobeliads 13,14 , and Hawaiian endemic mints [15][16][17][18][19] , have mostly fallen into this experimental realm, although recent research, including the o'hia tree, Metrosideros polymorpha 20,21 , and the species-rich Southeast Asian Syzygium 22 , has taken advantage of a reference genome and large-scale genome resequencing.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Genomic histories of polyploidy, diversification, and admixture in a Hawaiian plant radiation

Lindqvist

Tomlin

Rajaraman

et al. 2023

Preprint

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Island systems provide important contexts for studying processes underlying lineage migration, species diversification, and organismal extinction. The Hawaiian endemic mints (Lamiaceae family) are the second largest plant radiation on the isolated Hawaiian Islands. We generated a chromosome-scale reference genome for one Hawaiian species, Stenogyne calaminthoides, and resequenced 45 relatives, representing 34 species, to uncover the continental origins of this group and their subsequent diversification. We further resequenced 109 individuals of two Stenogyne species, and their purported hybrids, found high on the Mauna Kea volcano on the island of Hawai’i. The three distinct Hawaiian genera, Haplostachys, Phyllostegia, and Stenogyne, are nested inside a fourth genus, Stachys. We uncovered four independent polyploidy events within Stachys, including one allopolyploid hybridization event underlying the Hawaiian mints and their direct western North American ancestors. While the Hawaiian taxa may have principally diversified by parapatry, localized admixture may have played an important role early in lineage diversification. Our genomic analyses provide a view into how organisms have radiated on isolated island chains, a topic that provided one of the principal natural laboratories for Darwin’s thinking about the evolutionary process.

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Section: The Majority Of Present-day Hawaiian Mints Appear Unadmixedmentioning

confidence: 58%

Section: Stenogyne Haplostachys and Phyllostegia Show Contrasting Gen...mentioning

confidence: 97%

Section: Stenogyne Haplostachys and Phyllostegia Show Contrasting Gen...mentioning

confidence: 99%

Section: The Majority Of Present-day Hawaiian Mints Appear Unadmixedmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Genomic histories of polyploidy, diversification, and admixture in a Hawaiian plant radiation

Lindqvist

Tomlin

Rajaraman

et al. 2023

Preprint

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Evolutionary relationship of the NBS-LRR gene family in Melaleuca and Eucalyptus (Myrtaceae)

Chakrabarty

Hsieh

Chakraborty

et al. 2023

Tree Genetics & Genomes

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De-novo assembly of a reference genome for a critically threatened Aotearoa New Zealand tree species, Syzygium maire (Myrtaceae)

Balkwill,

Deslippe,

Horton

et al. 2024

Tree Genetics & Genomes

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Aotearoa New Zealand’s swamp forests have experienced significant habitat loss in fewer than two hundred years. Many of the country’s tree species are endemic with sparse to no genetic information available to underpin conservation strategies. Syzygium maire, Aotearoa’s only endemic Syzygium species, is a culturally and ecologically important component of swamp forest habitats. Unfortunately, populations of S. maire have been greatly reduced, heavily fragmented and are susceptible to the emergent pathogen Austropuccinia psidii (myrtle rust), posing eminent danger of a further decline of the species. We sought to develop genomic resources to inform conservation management of S. maire. To this end, we used long read, high accuracy sequencing technology to produce a highly complete reference quality genome for S. maire. The genome sequence was named ‘Ngā Hua o te Ia Whenua’ by the local Māori tribe where the tree used for genome sequencing grows. We assess whether genome-level divergence with other Myrtaceae may have followed geographic isolation of the species. We detect conservation of large scale synteny between three Syzygium species and Eucalyptus grandis, providing support for the stability of Syzygium genomes across evolutionary time. We annotate genes implicated in fungal pathogen defence, identifying several hundred putative NLR genes, including putative homologs of previously identified Austropuccinia psidii resistance genes. Finally, we evaluate the genetic relationships of individuals of a small, isolated population of trees. We find evidence of high levels of kinship and inbreeding within small and isolated S. maire populations, informing local-scale conservation strategies for the species. Our findings enable practical conservation actions and provide resources for larger scale studies of S. maire and other Syzygium species in the future.

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Genomic insights into rapid speciation within the world’s largest tree genus Syzygium

Cited by 27 publications

References 111 publications

Genomic histories of polyploidy, diversification, and admixture in a Hawaiian plant radiation

Genomic histories of polyploidy, diversification, and admixture in a Hawaiian plant radiation

Evolutionary relationship of the NBS-LRR gene family in Melaleuca and Eucalyptus (Myrtaceae)

De-novo assembly of a reference genome for a critically threatened Aotearoa New Zealand tree species, Syzygium maire (Myrtaceae)

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