Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs.

Studies investigating the evolution of flowering plants have long focused on isolating mechanisms such as pollinator specificity. Some recent studies have proposed a role for introgressive hybridization between species, recognizing that isolating processes such as pollinator specialization may not be complete barriers to hybridization. Occasional hybridization may therefore lead to distinct yet reproductively connected lineages. We investigate the balance between introgression and reproductive isolation in a diverse clade using a densely sampled phylogenomic study of fig trees (Ficus, Moraceae). Codiversification with specialized pollinating wasps (Agaonidae) is recognized as a major engine of fig diversity, leading to about 850 species. Nevertheless, some studies have focused on the importance of hybridization in Ficus, highlighting the consequences of pollinator sharing. Here, we employ dense taxon sampling (520 species) throughout Moraceae and 1,751 loci to investigate phylogenetic relationships and the prevalence of introgression among species throughout the history of Ficus. We present a well-resolved phylogenomic backbone for Ficus, providing a solid foundation for an updated classification. Our results paint a picture of phylogenetically stable evolution within lineages punctuated by occasional local introgression events likely mediated by local pollinator sharing, illustrated by clear cases of cytoplasmic introgression that have been nearly drowned out of the nuclear genome through subsequent lineage fidelity. The phylogenetic history of figs thus highlights that while hybridization is an important process in plant evolution, the mere ability of species to hybridize locally does not necessarily translate into ongoing introgression between distant lineages, particularly in the presence of obligate plant-pollinator relationships.

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.

Hanguanadeflexa (Hanguanaceae), a new forest species from Sarawak, Borneo.

Hanguanadeflexa 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.

Plastome evolution and organisation in the Hoya group (Apocynaceae).

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.

Population genomics reveal apomixis in a novel system: uniclonal female populations dominate the tropical forest herb family, Hanguanaceae (Commelinales).

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. 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. Almost all taxa tested were genetically uniform (uniclonal) regardless of the extent of their distribution. The distribution of single clones over distinct localities supports 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. 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.

Very small relict populations suggest high extinction debt of gingers in primary forest fragments of a tropical city.

PREMISE OF THE STUDY: Tropical plant communities in fragmented forests are likely to experience an extinction debt, i.e., the habitat cannot support as many species as are present due to reduced habitat size and connectivity. There are few estimates of the number of species that represent extinction debt, and the number of extinctions over time has rarely been recorded. We recorded population sizes to assess threats and extinctions in gingers (sensu Zingiberales) in fragmented rainforest in Singapore, ca. 200 yr after fragmentation began. METHODS: We surveyed extant diversity and population sizes of gingers and used the results to estimate species survival. We critically assessed historic specimens to estimate initial extinctions and extinctions realized in present habitats. KEY RESULTS: We recorded 23 species, including five species previously presumed nationally extinct and four species omitted from the national checklist. The revised extinction rate is much lower than previously reported (12 vs. 37%). Most gingers have very small populations or miniscule ranges, implying that extinction debt has not been paid off. CONCLUSIONS: Ginger diversity remains high, but the number of species at immediate risk of extinction outnumber recorded extinctions. Although tropical forest fragments remain arks of plant diversity for a long time, extinction debt may be prevalent in all plant groups in Singapore. Slow relaxation of extinction debt should be explicitly identified as a conservation challenge and opportunity. For conserving plant diversity in tropical fragments, relaxation must be reversed through restoration of degraded landscapes and, where feasible, targeted ex situ conservation and planting.