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Aim: Worldwide, floras are becoming homogenized at global scales, but regional patterns vary. Here, we present the first assessment for the Malesian phytogeographical region in terms of the timing of introductions, direction, magnitude and drivers of floristic change due to alien plant naturalizations. Location: Malesian phytogeographic region, including Southeast Asia and the Pacific. Taxon: Tracheophyta (vascular plants). Methods: We compiled data on first records of naturalized plants in Malesia to investigate temporal trends in the rate and origin of introductions. We then calculated β‐diversity (including turnover and nestedness) for the native, naturalized and Anthropocene (native + naturalized) floras for each pair of island groups (36 pairs), and a homogenization index for the native and Anthropocene floras, using presence/absence data for 31,580 plant species. Mantel tests were used to investigate the geographic, climatic and anthropogenic correlates of dissimilarity and homogenization. Results: Around 75% of all naturalized species documented to date were already reported for the first time within Malesia prior to 1950. This has led to homogenization between the historic (native) and contemporary (Anthropocene) floras for all island group pairs. Turnover was the most important process for driving compositional dissimilarity between island groups in Malesia in the native and Anthropocene floras, but homogenization resulted from decreases in nestedness and turnover. Differences in average taxonomic homogenization for island groups were associated with differences in their level of anthropogenic modification. Main Conclusions: This study improves current understanding of the direction and drivers of floristic homogenization in one of the world's most diverse tropical regions. Alien plant introductions carry a long historical legacy in Malesia, and naturalizations of these plants have led to overall taxonomic homogenization of the region's flora. Expected increases in the magnitude of human modification, without appropriate policy, will likely lead to further reductions in the floristic uniqueness of island groups. [ABSTRACT FROM AUTHOR]

Intensive transformation of lowland rainforest into oil palm and rubber monocultures is the most common land-use practice in Sumatra (Indonesia), accompanied by invasion of weeds. In the Jambi province, Centotheca lappacea is one of the most abundant alien grass species in plantations and in jungle rubber (an extensively used agroforest), but largely missing in natural rainforests. Here, we investigated putative genetic differentiation and signatures for adaptation in the introduced area. We studied reproductive mode and ploidy level as putative factors for invasiveness of the species. We sampled 19 populations in oil palm and rubber monocultures and in jungle rubber in two regions (Bukit Duabelas and Harapan). Amplified fragment length polymorphisms (AFLP) revealed a high diversity of individual genotypes and only a weak differentiation among populations (FST = 0.173) and between the two regions (FST = 0.065). There was no significant genetic differentiation between the three land-use systems. The metapopulation of C. lappacea consists of five genetic partitions with high levels of admixture; all partitions appeared in both regions, but with different proportions. Within the Bukit Duabelas region we observed significant isolation-by-distance. Nine AFLP loci (5.3% of all loci) were under natural diversifying selection. All studied populations of C. lappacea were diploid, outcrossing and self-incompatible, without any hints of apomixis. The estimated residence time of c. 100 years coincides with the onset of rubber and oil palm planting in Sumatra. In the colonization process, the species is already in a phase of establishment, which may be enhanced by efficient selection acting on a highly diverse gene pool. In the land-use systems, seed dispersal might be enhanced by adhesive spikelets. At present, the abundance of established populations in intensively managed land-use systems might provide opportunities for rapid dispersal of C. lappacea across rural landscapes in Sumatra, while the invasion potential in rainforest ecosystems appears to be moderate as long as they remain undisturbed. [ABSTRACT FROM AUTHOR]

At a regional scale, the high species numbers (gamma diversity) of tropical forests have been explained by either a gradual accumulation of species through time (museum hypothesis) or, by contrast, rapid recent speciation in large genera. However, the origins of local rain forest diversity (alpha diversity) have been given little attention. Cyrtandra (Gesneriaceae), an understorey genus in the highly species-rich Indo-Malayan rain forest, has considerable capacity for producing local endemics, making it particularly suitable for studying diversity on a local scale. We sampled Cyrtandra species from one community on Mount Kerinci, Sumatra, and phylogenetic analyses of ITS sequences suggest that this community is an assembly of three distinct phyletic lineages: (1) a group of herbaceous or subshrub plants of Bornean affinity, (2) one member of a group of widespread shrubs forming Cyrtandra section Dissimiles and (3) a second group of shrubs. The evolutionary origin of this community is therefore not a result of rapid and recent speciation: it is assembled from species resulting from a gradual accumulation of diversity through time (museum hypothesis), although one lineage shows evidence of more recent, continuing speciation than the other two. The community includes two distantly related, apparently endemic species, but there is no evidence for a local adaptive radiation. The protection of representative species from each lineage would allow the conservation of genetic diversity. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81, 49–62. [ABSTRACT FROM AUTHOR]

DNA barcoding has been used as a universal tool for phylogenetic inferences and diversity assessments, especially in poorly studied species and regions. The aim of this study was to contrast morphological taxonomy and DNA barcoding, using the three frequently used markers matK, rbcL, and trnL-F, to assess the efficiency of DNA barcoding in the identification of dipterocarps in Sumatra, Indonesia. The chloroplast gene matK was the most polymorphic among these three markers with an average interspecific genetic distance of 0.020. The results of the molecular data were mostly in agreement with the morphological identification for the clades of Anthoshorea, Hopea, Richetia, Parashorea, and Anisoptera, nonetheless these markers were inefficient to resolve the relationships within the Rubroshorea group. The maximum likelihood and Bayesian inference phylogenies identified Shorea as a paraphyletic genus, Anthoshorea appeared as sister to Hopea, and Richetia was sister to Parashorea. A better discriminatory power among dipterocarp species provided by matK and observed in our study suggests that this marker has a higher evolutionary rate than the other two markers tested. However, a combination of several different barcoding markers is essential for reliable identification of the species at a lower taxonomic level. [ABSTRACT FROM AUTHOR]

Smallholder-dominated agricultural mosaic landscapes are highlighted as model production systems that deliver both economic and ecological goods in tropical agricultural landscapes, but trade-offs underlying current land-use dynamics are poorly known. Here, using the most comprehensive quantification of land-use change and associated bundles of ecosystem functions, services and economic benefits to date, we show that Indonesian smallholders predominantly choose farm portfolios with high economic productivity but low ecological value. The more profitable oil palm and rubber monocultures replace forests and agroforests critical for maintaining above- and below-ground ecological functions and the diversity of most taxa. Between the monocultures, the higher economic performance of oil palm over rubber comes with the reliance on fertilizer inputs and with increased nutrient leaching losses. Strategies to achieve an ecological-economic balance and a sustainable management of tropical smallholder landscapes must be prioritized to avoid further environmental degradation.