Summary1. Niche theory proposes that species differences underlie both coexistence within communities and the differentiation in species composition among communities via limiting similarity and environmental filtering. However, it has been difficult to extend niche theory to species-rich communities because of the empirical challenge of quantifying niches for many species. This has motivated the development of functional and phylogeny-based approaches in community ecology, which represent two different means of approximating niche attributes. 2. Here, we assess the utility of plant functional traits and phylogenetic relationships in predicting community assembly processes using the largest trait and phylogenetic data base to date for any set of species-rich communities. 3. We measured 17 functional traits for all 4672 individuals of 668 tree species co-occurring in nine tropical rain forest plots in French Guiana. Trait variation was summarized into two ordination axes that reflect species niche overlap. 4. We also generated a dated molecular phylogenetic tree based on DNA sequencing of two plastid loci (rbcL and matK) comprising 97% of the individuals and 91% of the species in the plots. 5. We found that, on average, co-occurring species had greater functional and, to a lesser extent, phylogenetic similarity than expected by chance. 6. We also found that functional traits and their ordination loadings showed significant, albeit weak, phylogenetic signal, suggesting that phylogenetic distance provides pertinent information on niche overlap in tropical tree communities. 7. Synthesis. We provide the most comprehensive examination to date of the relative importance of environmental filtering and limiting similarity in structuring tropical tree communities. Our results confirm that environmental filtering is the overriding influence on community assembly in these species-rich systems.

A fundamental tenet of multicellular eukaryotic evolution is that vertical inheritance is paramount, with natural selection acting on genetic variants transferred from parents to offspring. This lineal process means that an organism’s adaptive potential can be restricted by its evolutionary history, the amount of standing genetic variation, and its mutation rate. Lateral gene transfer (LGT) theoretically provides a mechanism to bypass many of these limitations, but the evolutionary importance and frequency of this process in multicellular eukaryotes, such as plants, remains debated. We address this issue by assembling a chromosome-level genome for the grassAlloteropsis semialata, a species surmised to exhibit two LGTs, and screen it for other grass-to-grass LGTs using genomic data from 146 other grass species. Through stringent phylogenomic analyses, we discovered 57 additional LGTs in theA. semialatanuclear genome, involving at least nine different donor species. The LGTs are clustered in 23 laterally acquired genomic fragments that are up to 170 kb long and have accumulated during the diversification ofAlloteropsis.The majority of the 59 LGTs inA. semialataare expressed, and we show that they have added functions to the recipient genome. Functional LGTs were further detected in the genomes of five other grass species, demonstrating that this process is likely widespread in this globally important group of plants. LGT therefore appears to represent a potent evolutionary force capable of spreading functional genes among distantly related grass species.

Physiological novelties are often studied at macro-evolutionary scales such that their micro-evolutionary origins remain poorly understood. Here, we test the hypothesis that key components of a complex trait can evolve in isolation and later be combined by gene flow. We use C 4 photosynthesis as a study system, a derived physiology that increases plant productivity in warm, dry conditions. The grass Alloteropsis semialata includes C 4 and non-C 4 genotypes, with some populations using laterally acquired C 4 -adaptive loci, providing an outstanding system to track the spread of novel adaptive mutations. Using genome data from C 4 and non-C 4 A. semialata individuals spanning the species' range, we infer and date past migrations of different parts of the genome. Our results show that photosynthetic types initially diverged in isolated populations, where key C 4 components were acquired. However, rare but recurrent subsequent gene flow allowed the spread of adaptive loci across genetic pools. Indeed, laterally acquired genes for key C 4 functions were rapidly passed between populations with otherwise distinct genomic backgrounds. Thus, our intraspecific study of C 4 -related genomic variation indicates that components of adaptive traits can evolve separately and later be combined through secondary gene flow, leading to the assembly and optimization of evolutionary innovations.

The origins of novel traits are often studied using species trees and modeling phenotypes as different states of the same character, an approach that cannot always distinguish multiple origins from fewer origins followed by reversals. We address this issue by studying the origins of C4 photosynthesis, an adaptation to warm and dry conditions, in the grass Alloteropsis. We dissect the C4 trait into its components, and show two independent origins of the C4 phenotype via different anatomical modifications, and the use of distinct sets of genes. Further, inference of enzyme adaptation suggests that one of the two groups encompasses two transitions to a full C4 state from a common ancestor with an intermediate phenotype that had some C4 anatomical and biochemical components. Molecular dating of C4 genes confirms the introgression of two key C4 components between species, while the inheritance of all others matches the species tree. The number of origins consequently varies among C4 components, a scenario that could not have been inferred from analyses of the species tree alone. Our results highlight the power of studying individual components of complex traits to reconstruct trajectories toward novel adaptations.

The plastid rbcL and matK genes have recently been adopted as the DNA barcoding regions for plants by the Consortium for the Barcoding of Life. However, some researchers have reported problems in successfully amplifying the matK fragment across the plant kingdom. This study focused on designing order-specific primers for monocot and eudicots. In total, 6514 matK sequences were downloaded from GenBank/EBI. The percentage sequence match of three sets of previously published barcoding primers was recorded in 39 orders. In 22 of these, at least one primer was required to be redesigned. We propose 26 new PCR primers so that the matK barcode can easily and successfully be amplified. It should also be possible to increase the amplification success rate of the previously published barcoding primers by introducing degeneracy or a deoxyinosine base to the second position from the 3′ end of the primer. This will increase primer match for monocots and eudicots to approximately 97%. Finally, we argue that DNA barcoding using multiple primers (rather than a single pair) is adequate, especially in light of the recent developments in next-generation DNA sequencing.

Species trees have traditionally been inferred from a few selected markers, and genome‐wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historical species diversity. The genomes of an increasing number of species, including specimens extracted from natural history collections, are being sequenced at low depth. While these data sets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored. Here we evaluate different reference‐based methods to infer phylogenies of large taxonomic groups from such data sets. Using the example of the Oleeae tribe, a worldwide‐distributed group, we build phylogenies based on single nucleotide polymorphisms (SNPs) obtained using two reference genomes (the olive and ash trees). The inferred phylogenies are overall congruent, yet present differences that might reflect the effect of distance to the reference on the amount of missing data. To limit this issue, genome complexity was reduced by using pairs of orthologous coding sequences as the reference, thus allowing us to combine SNPs obtained using two distinct references. Concatenated and coalescence trees based on these combined SNPs suggest events of incomplete lineage sorting and/or hybridization during the diversification of this large phylogenetic group. Our results show that genome‐wide phylogenetic trees can be inferred from low‐depth sequence data sets for eukaryote groups with complex genomes, and histories of reticulate evolution. This opens new avenues for large‐scale phylogenomics and biogeographical analyses covering both the extant and the historical diversity stored in museum collections.

C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata . We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin.

Among birds, white-eyes (genus Zosterops) have diversified so extensively that Jared Diamond and Ernst Mayr referred to them as the “great speciator.” The Zosterops lineage exhibits some of the fastest rates of species diversification among vertebrates, and its members are the most prolific passerine island colonizers. We present a high-quality genome assembly for the silvereye (Zosterops lateralis), a white-eye species consisting of several subspecies distributed across multiple islands. We investigate the genetic basis of rapid diversification in white-eyes by conducting genomic analyses at varying taxonomic levels. First, we compare the silvereye genome with those of birds from different families and searched for genomic features that may be unique to Zosterops. Second, we compare the genomes of different species of white-eyes from Lifou island (South Pacific), using whole genome resequencing and restriction site associated DNA. Third, we contrast the genomes of two subspecies of silvereye that differ in plumage color. In accordance with theory, we show that white-eyes have high rates of substitutions, gene duplication, and positive selection relative to other birds. Below genus level, we find that genomic differentiation accumulates rapidly and reveals contrasting demographic histories between sympatric species on Lifou, indicative of past interspecific interactions. Finally, we highlight genes possibly involved in color polymorphism between the subspecies of silvereye. By providing the first whole-genome sequence resources for white-eyes and by conducting analyses at different taxonomic levels, we provide genomic evidence underpinning this extraordinary bird radiation.