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

Abstract

Species radiations have long fascinated biologists, but the contribution of adaptation to observed diversity and speciation is still an open question. Here, we explore this question using the clove genus, Syzygium, the world’s largest genus of tree species comprising approximately 1200 species. We dissect Syzygium diversity through shotgun sequencing of 182 distinct species and 58 additional as-yet unidentified taxa, and assess their genetic diversity against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that Syzygium grande shares a whole genome duplication (WGD) event with other Myrtales. Genomic analyses confirm that Syzygium originated in Sahul (Australia-New Guinea), and later diversified eastward to the Hawaiian Islands and westward in multiple independent migration events. The migrations were associated with bursts of speciation events, visible by poorly resolved branches on phylogenies and networks, some of which were likely confounded by incomplete lineage sorting. Clinal genomic variation in some sublineages follows phylogenetic progression, which coupled with sympatric occurrences of distantly related species suggests that both geographic and ecological speciation have been important in the diversification of Syzygium. Together, these results point to a mixture of both neutral and adaptive drivers having contributed to the radiation of the genus.

Phylogenomics and the flowering plant tree of life

“…Their work on Vitaceae suggested that 10× coverage genome sequencing data was optimum to assemble a sufficient number of high-quality nuclear genes for phylogenetic inference (Liu et al, 2021a). Low et al (2022) illustrated how DGS data can provide evidence both for investigating phylogeny and speciation processes in recently radiated groups. Using 30 Gb of WGS data for each of 289 Syzygium individuals, they generated parallel genome-wide SNPs, single-copy nuclear genes, as well as plastomic data sets to reconstruct well-supported phylogenies.…”

Syzygium nusatenggaraense (Myrtaceae), a new rainforest tree species with a calyptrate calyx from the Lesser Sunda Islands, Indonesia

“…This species is known only from two collections made between 1961-1971 and more efforts are needed to document this species carefully in its habitat and to reassess its range, population size and threats considering almost all tropical rainforest regions have been identified as biodiversity hotspots (Myers et al 2000;Nic Lughadha et al 2020). Notes: Phylogenetic studies (see Harrington and Gadek, 2004;Biffin et al 2006;Low et al 2021) have shown Syzygium species with calycine calyptra derive from multiple lineages and anatomical analysis (Vasconcelos et al 2020) indicates that closed Syzygium calyces have multiple developmental origins. As a result, locating the species most closely related to Syzygium nusatenggaraense will be a challenge, further compounded by the lack of a complete inventory of Syzygium species occurring in the Lesser Sunda Islands and surrounding regions.…”

“…However, the genus was not recognised by subsequent workers (such as Henderson, 1949;Kochummen, 1978;Hyland, 1983) due to lack of corroborative evidence acquired from anatomical studies (Dadswell and Ingle, 1947;Ingle and Dadswell, 1953;Pike, 1956;Schmid, 1972). Results obtained from molecular phylogenetic analyses showed Cleistocalyx to be polyphyletic; members of the genus were found to have derived from multiple lineages across the Syzygium phylogeny (Harrington and Gadek, 2004;Biffin et al 2006;Craven and Biffin, 2010;Vasconcelos et al 2020;Low et al 2021). In addition, molecular results supported uniting of the various segregate syzygioid genera such as Acmena DC., Jambosa Adans., Piliocalyx Brongn.…”