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.

BioOne Complete (complete.BioOne.org) is a full-text database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences published by nonprofit societies, associations, museums, institutions, and presses.

We describe and illustrate a new species, Hanguana neglecta (Commelinales, Hanguanaceae), from the Bukit Timah Nature Reserve in Singapore, one of the most heavily collected and frequently visited forests in the world. The species, growing prominently near the path at the nature reserve, was not described despite being identified as new fifteen years ago, owing to long-standing taxonomic misconceptions in Hanguana. The key to Hanguana in Peninsular Malaysia is here updated.

The genus Hoya is highly diverse and many of its species are popular ornamental plants. However, the relationships between Hoya and related genera (the Hoya group) are not fully resolved. In this study, we report 20 newly sequenced plastomes of species in the Hoya group. The complete plastomes vary in length from 175,405 to 178,525 bp while the LSCs vary from 90,248 to 92,364 bp and the complete SSCs vary from 2,285 to 2,304 bp, making the SSC in the Hoya group one of the shortest known in the angiosperms. The plastome structure in the Hoya group is characterised by a massive increase in the size of the inverted repeats as compared to the outgroups. In all ingroup species, the IR/SSC boundary moved from ycf1 to ndhF while this was not observed in outgroup taxa, making it a synapomorphy for the Hoya group. We have also assembled the mitogenome of Hoya lithophytica, which, at 718,734 bp, is the longest reported in the family. The phylogenetic analysis using exons from 42 taxa in the Hoya group and three outgoups confirms that the earliest divergent genus in the Hoya group is Papuahoya, followed by Dischidia. The relationship between Dischidia and the clade which includes all Hoya and Oreosparte taxa, is not fully supported. Oreosparte is nested in Hoya making it paraphyletic unless Clemensiella is recognised as a separate genus.

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.

No abstract

Background and Aims The abundance of apomixis in tropical plant genera is poorly understood, and this affects the understanding of speciation and evolution. Hanguanaceae is a tropical monogeneric, dioecious plant family. All but two species are solitary herbs with no capability to spread vegetatively. Viable seeds are often produced when males have not been observed. Our aim was to investigate the presence of apomixis in Hanguana. Methods We used reduced representation genomics to study phylogenetics and genetic variability in all populations of Hanguana in Singapore. We measured genome sizes and estimated ploidy levels in 10 species. Key Results Almost all taxa tested were genetically uniform (uniclonal) regardless of the extent of their distribution. The distribution of single clones over distinct localities support our hypothesis of apomictic reproduction. Only one sexually reproducing native species was detected. Triploid and pentaploid states support our hypothesis that the type of apomixis in Hanguana is gametophytic. Conclusions Population genomics tools offer a quick and cost-effective way of detecting excess clonality and thereby inferring apomixis. In the case of Hanguana, the presence of male plants is a strong indicator of sexual reproduction, whereas genome triplication is indicative of apomictic reproduction.

Last seen in 1958, the Ascension Island endemic fern, Anogramma ascensionis, was listed as extinct on the 2003 IUCN Red List. However, a 2009 survey rediscovered four plants on Green Mountain. Spores were collected and cultured in vitro at the Royal Botanic Gardens, Kew, where a living collection of thousands of gametophytes and hundreds of sporophytes has been developed. To gain further insights into the biology of this species and the potential implications of in vitro multiplication for conservation purposes, samples were characterized from the karyological point of view. Chromosome analysis of root tips has confirmed that the species is tetraploid, and flow cytometry assessments have revealed that haploid gametophytes produce diploid sporophytes, which confirms natural fertilization. In addition, an rbcL sequence from A. ascensionis has been generated and compared with those published for other Anogramma spp., suggesting a close relationship with A. chaerophylla from Brazil. Further surveys of Green Mountain have reported the presence of 40 A. ascensionis sporophytes in total. Vegetation community analyses have suggested that the present population may be confined to suboptimal habitats. We therefore propose that, prior to the dramatic transformation of the vegetation on the island as a result of the invasion of alien species (particularly Adiantum spp.), A. ascensionis may have flourished in more humid and shaded parts of the mountain. A multidisciplinary approach involving in vitro culture, invasive species clearance and controlled translocation is discussed as the future roadmap for the conservation of this critically endangered fern. Our experiences have also highlighted lessons more broadly applicable to the conservation of extremely rare species elsewhere in the world, especially on remote island systems. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 461–477.