Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses.

Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants.

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.

Phylogeny, taxonomy and flower-breeding ecology of the Colocasiomyia cristata species group (Diptera: Drosophilidae), with descriptions of ten new species.

The phylogeny of the Colocasiomyia cristata species group is reconstructed as a hypothesis, based on DNA sequences of two mitochondrial and six nuclear genes and 51 morphological characters. The resulting tree splits this species group into two clades, one of which corresponds to the colocasiae subgroup. Therefore, a new species subgroup named as the cristata subgroup is established for the other clade. Within the cristata subgroup, three subclades are recognized and each of them is defined as a species complex: the cristata complex composed of five species (including three new ones: C. kinabaluana sp. nov., C. kotana sp. nov. and C. matthewsi sp. nov.), the sabahana complex of two species (C. sabahana sp. nov. and C. sarawakana sp. nov.), and the xenalocasiae complex of five species (including C. sumatrana sp. nov. and C. leucocasiae sp. nov.). There are, however, three new species (C. ecornuta sp. nov., C. grandis sp. nov. and C. vieti sp. nov.) not assigned to any species complex. In addition, breeding habits are described for four cristata-subgroup species, each of which monopolizes its specific host plant. And, data of host-plant use are compiled for all species of the cristata group from records at various localities in the Oriental and Papuan regions. The evolution of host-plant selection and sharing modes is considered by mapping host-plant genera of each species on the phylogenetic tree resulting from the present study.

Two new species of Begonia, B. moneta and B. peridoticola (Begoniaceae) from Sabah, Malaysia.

BACKGROUND: Mount Kinabalu, reknowned for its high biodiversity and endemism, is a National Park in the State of Sabah on the northern end of the island of Borneo. Every year many visit the higher part of the Kinabalu National Park, while most lowland forests in the Park are under-explored. Two unknown species of Begonia were collected from a peridotic (ultramafic) cliff in the Kinabalu National Park at ca. 400 m elevation. RESULTS: The two species are named B. moneta C.-I Peng, Rimi & C. W. Lin and B. peridoticola Rimi, C.-I Peng & C. W. Lin. Begonia moneta (sect. Baryandra) is similar to B. gueritziana Gibbs, a widespread species of the same section in Borneo, differing in the peltate (vs. basifixed) leaves and the smaller flower parts. Also, their chromosome numbers are different (B. moneta, 2n = 30; B. gueritziana, 2n = 28). The peltate and succulent foliage of B. moneta is also reminiscent of B. burttii Kiew & S. Julia and B. payung S. Julia & Kiew, both of sect. Reichenheimia, from Sarawak. Begonia moneta is distinct from the two species in having branched (vs. entire) placental lamellae. Additionally, B. moneta differs from B. burttii in having 4 (vs. 5) tepals in pistillate flowers and markedly unequal (vs. equal) fruit wings. Begonia moneta differs from B. payung in the smaller leaves and conspicuously winged (vs. wingless) capsules. Begonia peridoticola (sect. Petermannia) resembles B. punchak Kiew & S. Julia from limestone areas in Kuching Division, Sarawak, differing in the entire leaf margin (vs. distantly dentate), much larger capsular wings (8-11 mm vs. 2-3 mm wide) and yellow, spiral (vs. crimson, U-shaped) styles. CONCLUSION: A careful study of the herbarium materials and literature supports the recognition of the two new species. Detailed descriptions, line drawings, color plates, chromsome data, foliar SEM observations and comparisons with phenetically similar species are provided to aid in identification.

Phylogenetic analyses of Begonia sect. Coelocentrum and allied limestone species of China shed light on the evolution of Sino-Vietnamese karst flora.

BACKGROUND: The picturesque limestone karsts across the Sino-Vietnamese border are renowned biodiversity hotspot, distinguished for extremely high endemism of calciphilous plants restricted to caves and cave-like microhabitats that have functioned as biological refugia on the otherwise harsh habitats. To understand evolutionary mechanisms underlying the splendid limestone flora, dated phylogeny is reconstructed for Asian Begonia, a species-rich genus on limestone substrates represented by no less than 60 species in southern China, using DNA sequences of nrITS and chloroplast rpL16 intron. The sampling includes 94 Begonia species encompassing most major Asian clades with a special emphasized on Chinese species. RESULTS: Except for two tuberous deciduous species and a species with upright stems, a majority of Sino-Vietnamese limestone Begonia (SVLB), including sect. Coelocentrum (19 species sampled) and five species of sect. Diploclinium, Leprosae, and Petermannia, are rhizomatous and grouped in a strongly supported and yet internally poorly resolved clade (Clade SVLB), suggesting a single evolutionary origin of the adaptation to limestone substrates by rhizomatous species, subsequent species radiation, and a strong tendency to retain their ancestral niche. Divergence-time estimates indicate a late Miocene diversification of Clade SVLB, coinciding with the onset of the East Asian monsoon and the period of extensive karstification in the area. CONCLUSIONS: Based on our phylogenetic study, Begonia sect. Coelocentrum is recircumscribed and expanded to include other members of the Clade SVLB (sect. Diploclinium: B. cavaleriei, B. pulvinifera, and B. wangii; sect. Leprosae: B. cylindrica and B. leprosa; sect. Petermannia: B. sinofloribunda). Because species of Clade SVLB have strong niche conservatism to retain in their ancestral habitats in cave-like microhabitats and Begonia are generally poor dispersers prone to diversify allopatrically, we propose that extensive and continuous karstification of the Sino-Vietnamese limestone region facilitated by the onset of East Asian monsoon since the late Miocene has been the major driving force for species accumulation via geographic isolation in Clade SVLB. Morphologically species of Clade SVLB differ mainly in vegetative traits without apparent adaptive value, suggesting that limestone Begonia radiation is better characterized as non-adaptive, an underappreciated speciation mode crucial for rapid species accumulations in organisms of low vagility and strong niche conservatism.

Development of SSR markers for the tropical alpine tree species Leptospermum recurvum (Myrtaceae) on Mount Kinabalu in Borneo.

PREMISE OF THE STUDY: Nuclear microsatellite (simple sequence repeat [SSR]) markers were developed for the woody species Leptospermum recurvum found on Mount Kinabalu, Borneo, to facilitate investigation of the genetic structure and patterns of gene flow in relation to leaf phenotypic polymorphisms. • METHODS AND RESULTS: Eleven primer pairs were developed using the compound SSR marker technique. Ten of the 11 loci were polymorphic and their expected heterozygosity ranged from 0.04 to 0.83. Neither linkage disequilibrium nor departure from Hardy-Weinberg equilibrium were detected. All primer pairs also amplified the SSR loci of L. polygalifolium. • CONCLUSIONS: These findings suggest the utility of these primers for investigating genetic structure and gene flow in L. recurvum and indicate their applicability to another species of Leptospermum.