Mangroves invade some very marginal habitats for woody plants—at the interface between land and sea. Since mangroves anchor tropical coastal communities globally, their origin, diversification and adaptation are of scientific significance, particularly at a time of global climate change. In this study, a combination of single-molecule long reads and the more conventional short reads are generated from Rhizophora apiculata for the de novo assembly of its genome to a near chromosome level. The longest scaffold, N50 and N90 for the R. apiculata genome, are 13.3 Mb, 5.4 Mb and 1.0 Mb, respectively. Short reads for the genomes and transcriptomes of eight related species are also generated. We find that the ancestor of Rhizophoreae experienced a whole-genome duplication ~70 Myrs ago, which is followed rather quickly by colonization and species diversification. Mangroves exhibit pan-exome modifications of amino acid (AA) usage as well as unusual AA substitutions among closely related species. The usage and substitution of AAs, unique among plants surveyed, is correlated with the rapid evolution of proteins in mangroves. A small subset of these substitutions is associated with mangroves’ highly specialized traits (vivipary and red bark) thought to be adaptive in the intertidal habitats. Despite the many adaptive features, mangroves are among the least genetically diverse plants, likely the result of continual habitat turnovers caused by repeated rises and falls of sea level in the geologically recent past. Mangrove genomes thus inform about their past evolutionary success as well as portend a possibly difficult future.

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Sequencing multiple species that share the same ecological niche may be a new frontier for genomic studies. While such studies should shed light on molecular convergence, genomic-level analyses have been unsuccessful, due mainly to the absence of empirical controls. Woody plant species that colonized the global tropical coasts, collectively referred to as mangroves, are ideal for convergence studies. Here, we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades. To detect convergence in a large phylogeny, a CCS+ model is implemented, extending the more limited CCS method (convergence at conservative sites). Using the empirical control for reference, the CCS+ model reduces the noises drastically, thus permitting the identification of 73 convergent genes with Ptrue (probability of true convergence) > 0.9. Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance. Importantly, convergence is more often manifested at a higher level than at amino-acid (AA) sites. Relative to >50 plant species, mangroves strongly prefer 4 AAs and avoid 5 others across the genome. AA substitutions between mangrove species strongly reflect these tendencies. In conclusion, the selection of taxa, the number of species and, in particular, the empirical control are all crucial for detecting genome-wide convergence. We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence.

We describe the elevational patterns of species richness and endemism of some important taxa in the Hengduan Mountains, southwest China. Species richness data came from publications, an online database, herbaria and Weld work. Species richness was estimated by rarefaction and interpolation. The Hengduan Mountains region was divided into a southern and northern subregion, and all species were assigned to four groups based on their distributional range within this region. The conditional autoregressive model (CAR) was used to relate species richness and explanatory variables. The elevational patterns of total, endemic and non-endemic species richness, at subregion and entire region scales, presented to be unimodal and peaked at similar elevations. Area size was strongly related with species richness, and was more powerful in explaining variation in species richness in the northern subregion than in the southern subregion. A single climatic variable (mean annual rainfall, potential evapotranspiration or moisture index) showed a weak relationship with the elevational pattern of species richness. Area and climatic variables together explained more than 67% of the variation in non-endemic richness, 53% in total richness, and 50% in endemic richness. There were three patterns of endemism at the generic level with increasing elevation: namely endemism increased, decreased, or peaked at middle elevations. All selected taxa have experienced rapid speciation and evolution within this region, which Electronic supplementary material The online version of this article (700 Biodivers Conserv (2009) 18:699-7161 C plays an important role in the uniform elevational patterns of total, endemic and nonendemic richness, and in the multiform elevational patterns of endemism.