Phylogenetic studies in the Hoya group (Apocynaceae, Marsdenieae): the position of Anatropanthus and Oreosparte

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Genomic insights into rapid speciation within the world’s largest 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

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

Acknowledgements Y.W.L. was supported by a postgraduate scholarship research grant from the Ministry of National Development, Singapore awarded through the National Parks Board, Singapore (NParks; NParks’ Garden City Fund). Principal research funding from NParks and the School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, is acknowledged. We thank Peter Preiser, Associate Vice President for Biomedical and Life Sciences, for facilitating NTU support, and Kenneth Er, CEO of NParks, for facilitating research funding through that organisation. V.A.A. and C.L. were funded by SBS, NTU for a one-year research leave. V.A.A. and C.L. also acknowledge support from the United States National Science Foundation (grants 2030871 and 1854550, respectively). S.R. was supported by a postdoctoral research fellowship under the NTU Strategic Plant Programme. S.R. and N.R.W.C. acknowledge funding from NTU start-up and the Academy of Finland (decisions 318288, 319947) grants to J.S. Fieldwork conducted by Y.W.L. was supported by an Indonesian Government RISTEK research permit (Application ID: 1517217008) and an Access License from the Sabah State government [JKM/MBS.1000-2/2JLD.7(84)]. T.N.C.V. is grateful to the Assemblée de la Province Nord and Assemblée de la Province Sud (New Caledonia) for facilitating relevant collection permits. A.N. was partly supported by the Research Project Promotion Grant (Strategic Research Grant No. 17SP01302) from the University of the Ryukyus, and partly by the Environment Research and Technology Development Fund (JPMEERF20204003) from the Environmental Restoration and Conservation Agency of Japan. Fieldwork in Fiji conducted by R.B. was hosted and facilitated by Elina Nabubuniyaka-Young (The Pacific Community’s Centre for Pacific Crops and Trees, Fiji). We thank the NTU-Smithsonian Partnership for tree data obtained for the Bukit Timah Nature Reserve (BTNR) long-term forest dynamics plots. Administrative support provided by Mui Hwang Khoo-Woon and Peter Ang at the molecular laboratory of the Singapore Botanic Gardens (SBG) is acknowledged. Rosie Woods and Imalka Kahandawala (DNA and Tissue Bank, Royal Botanic Gardens, Kew) facilitated additional DNA samples. Daniel Thomas (SBG) and Yan Yu (Sichuan University) commented on biogeographical analyses. NovogeneAIT in Singapore is acknowledged for personalised sequencing service.Peer reviewedPublisher PD

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, 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.Peer reviewe

CONSERVATION GENOMICS, BIODIVERSITY AND EXTINCTION OF UNDERSTOREY HERBS IN FRAGMENTED TROPICAL FORESTS OF SINGAPORE

Ph.DDOCTOR OF PHILOSOPH

Claderia_leontocampus_supplementary_files

Analyses files relating to the position of Claderia in Orchidaceae and the relationship of newly described Claderia leontocampus to Claderia viridiflora.Includes sequence files, alignments, and phylogenetic trees as well as structure input file, as well as annotated plastomes and ITS sequences.Published: http:/doi.org/10.26492/gbs75(1).2023-02</p

Hanguana deflexa (Hanguanaceae), a new forest species from Sarawak, Borneo

Hanguana deflexa sp. nov. (Hanguanaceae) from Lawas district, Sarawak, Malaysia (northern Borneo) is described and illustrated, bringing the total number of species in Borneo to eight. The new species differs from all other recognized Hanguana species by a combination of flat leaf blade, deflexed infructescences, one-seeded dull red fruits with centrally positioned stigma and globose seed with wedge-shaped ostiole. Revised key for Bornean Hanguana species is presented

Hanguana Blume 1827

Key to Hanguana in Peninsular Malaysia and Singapore 1. Stoloniferous colonial helophytes................................................................................................................................................… 2 – Clumping mesophytes lacking stolons.........................................................................................................................................… 3 2. Leaves stiffly erect, acute; fruits ellipsoid, ripening glossy purple-red; stigma lobes flat, connate at base, the whole 3–4 mm diam. and almost obscuring the end of the fruit. Plants of open situations along muddy banks of large rivers, margins of freshwater bodies, and of freshwater swamp forest........................................................................................................................... H. malayana – Leaves arching, long-attenuate; fruits globose, ripening semiglossy black; stigma lobes small, separate, erect, pointed. Plants of shaded peatswamp mires..................................................................................................................................................... H. nitens 3. Stigma inserted obliquely................................................................................................................................................................. 4 – Stigma terminal................................................................................................................................................................................ 5 4. Fertile portion of infructescence not exceeding leaves, panicle dense, branches of the partial inflorescences ascending in fruit; plants sessile even in old age....................................................................................................................................… H. pantiensis – Fertile portion of infructescence far exceeding leaves, panicle very open, branches of the partial inflorescences spreading and forming regular tiers; plants developing an erect, leafless stem up to 1.5 m tall …................................................... H. podzolicola 5. Fruits ripening black....................................................................................................................................................… H. neglecta – Fruits ripening glossy white to pale yellow...................................................................................................................................… 6 6. Infructescence with caducous foliaceous bracts; partial inflorescences each with 2 or rarely 3 branches, spreading in fruit; fruits globose with a briefly stipitate stigma, lobes connate basally, deep chocolate brown; fruit ripening white with conspicuous black speckles; old plants developing a short (to ca. 25 cm) slender, leafless stem. Plants of well-drained slopes and low ridges in lowland humid, moist mixed dipterocarp forest on yellow clay soils....................................................................................… H. stenopoda – Infructescence with persistent foliaceous bracts; partial inflorescences each with 4–5 branches, these rather sharply ascending in fruit; fruits ventrally gibbose-ellipsoid, stigma sessile, comprising 3 free orange brown lobes; fruit ripening pale yellow without conspicuous black speckles. Plants of low-lying wet podzols in peatforest................................................................. H. exultansPublished as part of Niissalo, Matti A., Wijedasa, Lahiru S., Boyce, Peter C. & Leong-Škorničková, Jana, 2014, Hanguana neglecta (Hanguanaceae): a new plant species from a heavily collected and visited reserve in Singapore, pp. 14-20 in Phytotaxa 188 (1) on page 18, DOI: 10.11646/phytotaxa.188.1.2, http://zenodo.org/record/514710

Data from: Persistence of long-distance, insect-mediated pollen movement for a tropical canopy tree species in remnant forest patches in an urban landscape

As deforestation and urbanization continue at rapid rates in tropical regions, urban forest patches are essential repositories of biodiversity. However, almost nothing is known about gene flow of forest-dependent tree species in urban landscapes. In this study, we investigated gene flow in the insect-pollinated, wind-dispersed tropical tree Koompassia malaccensis in and among three remnant forest patches in the urbanized landscape of Singapore. We genotyped the vast majority of adults (N=179) and a large number of recruits (N=2103) with 8 highly polymorphic microsatellite markers. Spatial genetic structure of the recruit and adult cohorts was significant, showing routine gene dispersal distances of ~100–400 m. Parentage analysis showed that 97% of recruits were within 100 m of their mother tree, and a high frequency of relatively short-distance pollen dispersal (median ~143–187 m). Despite routine seed and pollen dispersal distances of within a few hundred meters, interpatch gene flow occurred between all patches and was dominated by pollen movement: parentage analysis showed 76 pollen versus 2 seed interpatch dispersal events, and the seedling neighborhood model estimated ~1–6% seed immigration and ~21–46% pollen immigration rates, depending on patch. In addition, the smallest patch (containing five adult K. malaccensis trees) was entirely surrounded by >2.5 km of ‘impervious’ substrate, yet had the highest proportional pollen and seed immigration estimates of any patch. Hence, contrary to our hypothesis, insect-mediated gene flow persisted across an urban landscape, and several of our results also parallel key findings from insect-pollinated canopy trees sampled in mixed agricultural–forest landscapes

Hanguana thailandica (Hanguanaceae): a new peat swamp forest species from Thailand

A new species of Hanguana (Hanguanaceae), H. thailandica, is described and illustrated from Trang province, Peninsular Thailand. This is the second Hanguana species recorded in Thailand, along with the widespread helophytic H. malayana. The species is morphologically similar to Hanguana exultans and H. nitens found in swamp forests habitats in southern Peninsular Malaysia and Singapore. The conservation status of this species is accessed as Endangered according to the IUCN Red List Category and Criteria