The complete genome sequences of 56 Erythroxylum species.

We present the whole genome sequences of 56 wild Erythroxylum species from Africa, China, and the American tropics. Deep Illumina sequencing was performed on a single leaf of each voucher. We de novo assembled sequence reads and then identified and used conserved regions across all preassemblies join contigs in a finishing step. The raw and assembled data is publicly available via Genbank.

The complete genome sequences of three species of Mountain Avens (Dryas, Rosaceae).

We present the whole genome sequences of Dryas alaskensis, D. ajanensis, and D. integrifolia from plants collected from interior Alaska. We performed deep Illumina sequencing of a single leaf of each voucher. The sequence reads were then de novo assembled and conserved regions across all preassemblies were used to join contigs in a finishing step. The raw and assembled data is publicly available via Genbank.

The complete genome sequences of Erythroxylum coca and Erythroxylum novogranatense.

The flowering plant genus Erythroxylum contains approximately 300 species, including the economically and socially consequential crops called coca. We present the genome sequences of Erythroxylum coca and E. novogranatense, two cultigens produced for medicinal and quotidian use in the Andes and Amazon regions of South America, as well as the international cocaine industry. Sequencing was performed on an Illumina X-Ten platform, and reads were assembled by a de novo method followed by finishing via comparison with several species from the same genus. The BioProject, raw and assembled data can be accessed in GenBank for E. coca (PRJNA676123; JAJMLV000000000) and E. novogranatense (PRJNA675212; JAJKBF000000000).

Rediscovery of Gasteranthusextinctus L.E.Skog & L.P.Kvist (Gesneriaceae) at multiple sites in western Ecuador.

We report the rediscovery of the Critically Endangered cloud forest herb Gasteranthusextinctus, not seen since 1985. In 2019 and 2021, G.extinctus was recorded at five sites in the western foothills of the Ecuadorian Andes, 4-25 km from the type locality at the celebrated Centinela ridge. We describe the species' distribution, abundance, habitat and conservation status and offer recommendations for further research and conservation efforts focused on G.extinctus and the small, disjunct forest remnants it occupies.

Reading light: leaf spectra capture fine-scale diversity of closely related, hybridizing arctic shrubs.

Leaf reflectance spectroscopy is emerging as an effective tool for assessing plant diversity and function. However, the ability of leaf spectra to detect fine-scale plant evolutionary diversity in complicated biological scenarios is not well understood. We test if reflectance spectra (400-2400 nm) can distinguish species and detect fine-scale population structure and phylogenetic divergence - estimated from genomic data - in two co-occurring, hybridizing, ecotypically differentiated species of Dryas. We also analyze the correlation among taxonomically diagnostic leaf traits to understand the challenges hybrids pose to classification models based on leaf spectra. Classification models based on leaf spectra identified two species of Dryas with 99.7% overall accuracy and genetic populations with 98.9% overall accuracy. All regions of the spectrum carried significant phylogenetic signal. Hybrids were classified with an average overall accuracy of 80%, and our morphological analysis revealed weak trait correlations within hybrids compared to parent species. Reflectance spectra captured genetic variation and accurately distinguished fine-scale population structure and hybrids of morphologically similar, closely related species growing in their home environment. Our findings suggest that fine-scale evolutionary diversity is captured by reflectance spectra and should be considered as spectrally-based biodiversity assessments become more prevalent.

The Origins of Coca: Museum Genomics Reveals Multiple Independent Domestications from Progenitor Erythroxylum gracilipes.

Coca is the natural source of cocaine as well as a sacred and medicinal plant farmed by South American Amerindians and mestizos. The coca crop comprises four closely related varieties classified into two species (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and Colombian and Trujillo varieties within Erythroxylum novogranatense (D. Morris) Hieron.) but our understanding of the domestication and evolutionary history of these taxa is nominal. In this study, we use genomic data from natural history collections to estimate the geographic origins and genetic diversity of this economically and culturally important crop in the context of its wild relatives. Our phylogeographic analyses clearly demonstrate the four varieties of coca comprise two or three exclusive groups nested within the diverse lineages of the widespread, wild species Erythroxylum gracilipes; establishing a new and robust hypothesis of domestication wherein coca originated two or three times from this wild progenitor. The Colombian and Trujillo coca varieties are descended from a single, ancient domestication event in northwestern South America. Huánuco coca was domesticated more recently, possibly in southeastern Peru. Amazonian coca either shares a common domesticated ancestor with Huánuco coca, or it was the product of a third and most recent independent domestication event in the western Amazon basin. This chronology of coca domestication reveals different Holocene peoples in South America were able to independently transform the same natural resource to serve their needs; in this case, a workaday stimulant. [Erythroxylum; Erythroxylaceae; Holocene; Museomics; Neotropics; phylogeography; plant domestication; target-sequence capture.].

Phylogenetic inference in section Archerythroxylum informs taxonomy, biogeography, and the domestication of coca (Erythroxylum species).

PREMISE OF THE STUDY: This investigation establishes the first DNA-sequence-based phylogenetic hypothesis of species relationships in the coca family (Erythroxylaceae) and presents its implications for the intrageneric taxonomy and neotropical biogeography of Erythroxylum. We also identify the closest wild relatives and evolutionary relationships of the cultivated coca taxa. METHODS: We focused our phylogenomic inference on the largest taxonomic section in the genus Erythroxylum (Archerythroxylum O.E.Schulz) using concatenation and gene tree reconciliation methods from hybridization-based target capture of 427 genes. KEY RESULTS: We show that neotropical Erythroxylum are monophyletic within the paleotropical lineages, yet Archerythroxylum and all of the other taxonomic sections from which we sampled multiple species lack monophyly. We mapped phytogeographic states onto the tree and found some concordance between these regions and clades. The wild species E. gracilipes and E. cataractarum are most closely related to the cultivated E. coca and E. novogranatense, but relationships within this "coca" clade remain equivocal. CONCLUSIONS: Our results point to the difficulty of morphology-based intrageneric classification in this clade and highlight the importance of integrative taxonomy in future systematic revisions. We can confidently identify E. gracilipes and E. cataractarum as the closest wild relatives of the coca taxa, but understanding the domestication history of this crop will require more thorough phylogeographic analysis.