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.

We sequenced the Syzygium grande genome using Oxford Nanopore long reads and sampled and Illumina-sequenced 292 additional accessions (including 289 Syzygium and 3 outgroup taxa) to understand evolutionary relationships within the genus Syzygium.

We sequenced and assembled the Syzygium grande genome from a single individual and obtained RNAseq data from the same plant for gene annotation purposes. Syzygium and outgroup samples were selected for study based on special consideration to the broad range of the genus in terms of morphology, geography, habitat and phylogeny.

Syzygium and outgroup samples were selected for study based on availability of material and special consideration to the broad range of the genus in terms of morphology, geography, habitat, and phylogeny.

High-molecular weight DNA was obtained from flash-frozen mature leaves and RNA from various tissues (young twig, leaf early development and leaf late development). DNA of resequenced samples was obtained from mature leaves gathered in the field and preserved in silica gel granules.

Samples were collected in Singapore, Africa (Angola and Congo), Australia (Northern Territory and Queensland), Brunei, Fiji (Viti Levu), Indonesia (Java, Papua, Papua Barat, Sulawesi and Sumbawa), Japan (Okinawa and Tokyo), Malaysia (Peninsular Malaysia, Sabah and Sarawak), New Caledonia, Sri Lanka, Thailand (Prachin Buri Province), and Vietnam (Lam Dong Province).

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