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Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

A recent floristic survey in the Pacific slope of the Talamanca Mountain (Costa Rica), has revealed a new species of Rhodospatha , characterised by a bracteolate inflorescence. We describe and fully illustrate Rhodospatha rubrinervis from the Cloudbridge Nature Reserve. A detailed taxonomic description, as well as its distribution, ecology, phenology and conservation assessment are provided, along with a comparative discussion of its morphological affinities with R. forgetii and R. wendlandii . In addition, we present a brief discussion on the presence of a bracteole in Rhodospatha , a morphological character that, although illustrated by H.W. Schott 160 years ago, has not previously been described in detail.

Wild relatives of the commercially grown Vanilla planifolia , such as Vanilla odorata and V. pompona , are understudied despite their ecological and agricultural importance. Both species are listed as endangered by the IUCN, but limited research on their genetic diversity hinders effective management. While Vanilla species reproduce extensively by cloning, wild populations may retain significant genetic diversity valuable for crop improvement and conservation. To evaluate genetic diversity and structure, we analyzed 146 individuals from 10 V. pompona populations and 75 individuals from six V. odorata populations in Costa Rica, using 11 and 10 microsatellites, respectively. Vanilla odorata showed higher clonality than V. pompona (63% vs. 35%). Both species exhibited low to moderate genetic diversity ( V. odorata : H O = 0.47, H E = 0.29; V. pompona : H O = 0.43, H E = 0.41). Vanilla odorata populations revealed greater genetic differentiation than V. pompona populations (Nei’s G ST = 0.51 vs. 0.091), with V. odorata also exhibiting isolation by distance (R² = 0.704, p  < 0.05). Both species showed fine-scale genetic structure, with higher levels linked to clonality. Gene flow in V. pompona benefits from broad distribution and sexual reproduction, while V. odorata experiences limited gene flow due to its high clonality and restricted range. Protecting habitats and promoting outcrossing may aid V. odorata viability while V. pompona serves as an important resource for increasing genetic diversity in cultivated vanilla.

ABSTRACT Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth-death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree nodes). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://doi.org/10.6084/m9.figshare.13185008.v1.