Refuting the hypothesis of Centinelan extinction at its place of origin.

Scientists' limited understanding of tropical plant communities obscures the true extent of species loss caused by habitat destruction1. The Centinelan extinction hypothesis2,3 posits an extreme but widely referenced scenario wherein forest clearing causes the immediate extinction of species known only from a single geographic location. It remains unclear, however, whether the disappearance of such microendemics reflects their global extinction or insufficient collection effort at larger scales. Here we test these hypotheses by synthesizing decades of floristic data from the heavily deforested tropical cloud forest (TCF) at Centinela, Ecuador. We find that 99% of its putative microendemics have been collected elsewhere and are not extinct. Our field work also revealed new species, highlighting the enduring conservation value of TCFs and the intense efforts required to illuminate such plant diversity 'darkspots'4. Field and herbarium research remain essential to the conservation action needed to forestall large-scale plant extinctions in Earth's beleaguered cloud forests.

The phylogeny of the Triticeae: Resolution and phylogenetic conflict based on genomewide nuclear loci.

PREMISE: The wheat tribe, Triticeae, has been the subject of molecular phylogenetic analyses for nearly three decades, and extensive phylogenetic conflict has been apparent from the earliest comparisons among DNA-based data sets. While most previous analyses focused primarily on nuclear vs. chloroplast DNA conflict, the present analysis provides a broader picture of conflict among nuclear loci throughout the tribe. METHODS: Exon data were generated from over 1000 nuclear loci using targeted sequence capture with custom baits, and nearly complete chloroplast genome sequences were recovered. Phylogenetic conflict was assessed among the trees from the chloroplast genomes, the concatenated nuclear loci, and a series of nuclear-locus subsets guided by Hordeum chromosome gene maps. RESULTS: At the intergeneric level, the analyses collectively revealed a few broadly consistent relationships. However, the prevailing pattern was one of extensive phylogenetic conflict throughout the tribe, among both deep and shallow branches, and with the extent of the conflict varying among data subsets. CONCLUSIONS: The results suggest continual introgression or lineage sorting within and among the named lineages of the Triticeae, shaping both deep and shallow relationships in the tribe.

Amalophyllonmiraculum (Gesneriaceae), an exceptionally small lithophilous new species from the western Andean slopes of Ecuador.

Recent exploratory field expeditions to the western slopes of the Ecuadorian Andes resulted in the discovery of a new species of Amalophyllon (Gesneriaceae). Amalophyllonmiraculum J.L.Clark, sp. nov. is described from two localities in the Centinela region in the Santo Domingo de los Tsáchilas province. The new species is differentiated from congeners by the pendent habit, basal rosette of leaves, leaf blades with deeply serrate margins, and miniature size. Based on IUCN guidelines, a preliminary conservation status is assigned as Critically Endangered (CR).

ResumenRecientes expediciones exploratorias de campo a las laderas occidentales de los Andes ecuatorianos dieron como resultado el descubrimiento de una nueva especie de Amalophyllon (Gesneriaceae). Amalophyllonmiraculum J.L.Clark, sp. nov. se describe de dos localidades de la región de Centinela en la provincia de Santo Domingo de los Tsáchilas. La nueva especie se diferencia de otros congéneres por el hábito colgante, la roseta basal de las hojas, las láminas foliares con márgenes profundamente aserrados y su tamaño en miniatura. Según las directrices de la UICN, se le asigna el estado de conservación preliminar de En Peligro Crítico (CR).

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.

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.