We investigate patterns of historical assembly of tree communities across Amazonia using a newly developed phylogeny for the speciesrich neotropical tree genus Inga. We compare our results with those for three other ecologically important, diverse, and abundant Amazonian tree lineages, Swartzia, Protieae, and Guatteria. Our analyses using phylogenetic diversity metrics demonstrate a clear lack of geographic phylogenetic structure, and show that local communities of Inga and regional communities of all four lineages are assembled by dispersal across Amazonia. The importance of dispersal in the biogeography of Inga and other tree genera in Amazonian and Guianan rain forests suggests that speciation is not driven by vicariance, and that allopatric isolation following dispersal may be involved in the speciation process. A clear implication of these results is that over evolutionary timescales, the metacommunity for any local or regional tree community in the Amazon is the entire Amazon basin.Amazonia | biogeography | community assembly | phylogenetic structure | tropical trees

The goals of the Earth Biogenome Project—to sequence the genomes of all eukaryotic life on earth—are as daunting as they are ambitious. The Darwin Tree of Life Project was founded to demonstrate the credibility of these goals and to deliver at-scale genome sequences of unprecedented quality for a biogeographic region: the archipelago of islands that constitute Britain and Ireland. The Darwin Tree of Life Project is a collaboration between biodiversity organizations (museums, botanical gardens, and biodiversity institutes) and genomics institutes. Together, we have built a workflow that collects specimens from the field, robustly identifies them, performs sequencing, generates high-quality, curated assemblies, and releases these openly for the global community to use to build future science and conservation efforts.

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Seven plastid microsatellite markers derived from plastome sequence data were used to study the population genetic structure in two widespread Begonia spp. from Central America. In B. nelumbiifolia, no variation was found at any locus. In contrast, significant haplotype diversity was found in B. heracleifolia (hT = 0.937, hS = 0.444, 39 haplotypes, mean of 3.3 haplotypes per population), and populations showed high absolute levels of genetic differentiation (G'ST = 0.829, D = 0.407). The distribution of haplotypes showed strong phylogeographical structure (GST = 0.526, RST = 0.737, GST < RST, P < 0.05), but this pattern was poorly accounted for by commonly studied historical scenarios, such as Pleistocene refugia or Pliocene differentiation at the Isthmus of Tehuantepec. Instead, subdivision into a large number of regions, each containing local populations (e.g. when k = 9, FCT = 0.749, P < 0.05), best explained the haplotype distribution. The lack of haplotype diversity in B. nelumbiifolia, a moist adapted species, suggests that it may have been severely restricted in range during dry spells in the Pleistocene, and has subsequently expanded from this recent population bottleneck. The high haplotype diversity in B. heracleifolia may indicate that its adaptation to drought enabled it to survive in small, but ecologically suitable, pockets of isolated habitat throughout the Pleistocene. Limited seed exchange between B. heracleifolia populations is likely to be responsible for its high population substructure, and provided the opportunity for divergence through genetic drift. This interpretation is consistent with previous population genetic studies in Begonia, and suggests a common pattern of extremely low genetic exchange among a series of small, but long‐lived, populations that may predispose the genus to rapid speciation. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 00, 000–000.

The increasing availability of plastid genomes represents a new opportunity to explore molecular evolution in plants (Tonti-Filippini et al., 2017;Twyford & Ness, 2017). For example, plastid phylogenomics has resolved some persistent taxonomic uncertainties in challenging plant groups (e.g., in Rosaceae; Zhang et al., 2017), and more generally led to a better understanding of major events in plant

Imperfect historical records and complex demographic histories present challenges for reconstructing the history of biological invasions. Here, we combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. By sampling 521 plants from 158 native and introduced populations genotyped at >44,000 loci, we determined that invasive M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range. We hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide. Our results emphasise the highly admixed nature of introduced M. guttatus and demonstrate the potential of introduced populations to serve as sources of secondary admixture, producing novel hybrids. Unravelling the history of biological invasions provides a starting point to understand how invasive populations adapt to novel environments.

In this quick guide, Twyford introduces the reader to parasitic plants, explaining how they steal nutrients from host plants and how this lifestyle has evolved multiple times in plants.

Background  PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes. In eukaryotes the mitochondrial genome is sequenced alongside the nuclear genome often at very high coverage. A dedicated tool for mitochondrial genome assembly using HiFi reads is still missing. Results  MitoHiFi was developed within the Darwin Tree of Life Project to assemble mitochondrial genomes from the HiFi reads generated for target species. The input for MitoHiFi is either the raw reads or the assembled contigs, and the tool outputs a mitochondrial genome sequence fasta file along with annotation of protein and RNA genes. Variants arising from heteroplasmy are assembled independently, and nuclear insertions of mitochondrial sequences are identified and not used in organellar genome assembly. MitoHiFi has been used to assemble 374 mitochondrial genomes (368 Metazoa and 6 Fungi species) for the Darwin Tree of Life Project, the Vertebrate Genomes Project and the Aquatic Symbiosis Genome Project. Inspection of 60 mitochondrial genomes assembled with MitoHiFi for species that already have reference sequences in public databases showed the widespread presence of previously unreported repeats. Conclusions  MitoHiFi is able to assemble mitochondrial genomes from a wide phylogenetic range of taxa from Pacbio HiFi data. MitoHiFi is written in python and is freely available on GitHub (https://github.com/marcelauliano/MitoHiFi). MitoHiFi is available with its dependencies as a Docker container on GitHub (ghcr.io/marcelauliano/mitohifi:master).