24 research outputs found
Biogeographical analyses to facilitate targeted conservation of orchid diversity hotspots in Costa Rica
Aim: We conduct a biogeographical assessment of orchids in a global biodiversity
hotspot to explore their distribution and occurrences of local hotspots while identifying geographic attributes underpinning diversity patterns. We evaluate habitat
characteristics associated with orchid diversity hotspots and make comparisons to
other centres of orchid diversity to test for global trends. The ultimate goal was to
identify an overall set of parameters that effectively characterize critical habitats to
target in local and global orchid conservation efforts.
Location: Costa Rica; Mesoamerica.
Taxon: Orchidaceae.
Methods: Data from an extensive set of herbarium records were used to map orchid
distributions and to identify diversity hotspots. Hotspot data were combined with
geographic attribute data, including environmental and geopolitical variables, and a
random forest regression model was utilized to assess the importance of each variable for explaining the distribution of orchid hotspots. A likelihood model was created based on variable importance to identify locations where suitable habitats and
unidentified orchid hotspots might occur.
Results: Orchids were widely distributed and hotspots occurred primarily in mountainous regions, but occasionally at lower elevations. Precipitation and vegetation
cover were the most important predictive variables associated with orchid hotspots.
Variable values underpinning Costa Rican orchid hotspots were similar to those reported at other sites worldwide. Models also identified suitable habitats for sustaining orchid diversity that occurred outside of known hotspots and protected areas.
Main conclusions: Several orchid diversity hotspots and potentially suitable habitats
occur outside of known distributions and/or protected areas. Recognition of these
sites and their associated geographic attributes provides clear targets for optimizing
orchid conservation efforts in Costa Rica, although certain caveats warrant consideration. Habitats linked with orchid hotspots in Costa Rica were similar to those documented elsewhere, suggesting the existence of a common biogeographical trend
regarding critical habitats for orchid conservation in disparate tropical regions.Universidad de Puerto Rico/[]/UPR/Puerto RicoUniversidad de Costa Rica/[]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL
Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution
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.Universidad de Costa Rica/[814-B8-257]/UCR/Costa RicaUniversidad de Costa Rica/[814-B6-140]/UCR/Costa RicaIDEA WILD/[]//Estados UnidosSociedad Colombiana de Orquideología/[]/SCO/ColombiaFundação de Amparo à Pesquisa do Estado de São Paulo/[11/08308-9]/FAPESP/BrasilFundação de Amparo à Pesquisa do Estado de São Paulo/[13/19124-1]/FAPESP/BrasilSwiss Orchid Foundation/[]//SuizaRoyal Botanic Gardens, Kew/[]//InglaterraSwedish Research Council/[2019-05191]//SueciaSwedish Foundation for Strategic Research/[FFL15-0196]/SSF/SueciaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL
Cross-recognition of a pit viper (Crotalinae) polyspecific antivenom explored through high-density peptide microarray epitope mapping
Snakebite antivenom is a 120 years old invention based on polyclonal mixtures of antibodies
purified from the blood of hyper-immunized animals. Knowledge on antibody recognition
sites (epitopes) on snake venom proteins is limited, but may be used to provide molecular
level explanations for antivenom cross-reactivity. In turn, this may help guide antivenom
development by elucidating immunological biases in existing antivenoms. In this study, we
have identified and characterized linear elements of B-cell epitopes from 870 pit viper venom
protein sequences by employing a high-throughput methodology based on custom designed
high-density peptide microarrays. By combining data on antibody-peptide interactions with
multiple sequence alignments of homologous toxin sequences and protein modelling, we
have determined linear elements of antibody binding sites for snake venom metalloproteases
(SVMPs), phospholipases A2s (PLA2s), and snake venom serine proteases (SVSPs). The
studied antivenom antibodies were found to recognize linear elements in each of the three
enzymatic toxin families. In contrast to a similar study of elapid (non-enzymatic) neurotoxins,
these enzymatic toxins were generally not recognized at the catalytic active site responsible
for toxicity, but instead at other sites, of which some are known for allosteric inhibition or for
interaction with the tissue target. Antibody recognition was found to be preserved for several
minor variations in the protein sequences, although the antibody-toxin interactions could
often be eliminated completely by substitution of a single residue. This finding is likely to have
large implications for the cross-reactivity of the antivenom and indicate that multiple different
antibodies are likely to be needed for targeting an entire group of toxins in these recognized
sites.Novo Nordisk Foundation/[NNF13OC0005613]/NNF/DinamarcaNovo Nordisk Foundation/[NNF16OC0019248]/NNF/DinamarcaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Instituto Clodomiro Picado (ICP
Vanilla Dispersal Data
Vanilla Dispersal Data "Karremans-et al-First evidence for multimodal animal seed dispersal in orchids. Current Biology"THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV
Loci alignments of 446 anchored hybrid enrichment generated markers of Lepanthes horrida group
Loci alignments of 446 anchored hybrid enrichment generated markers evaluated in the paper Bogarín et al
A new Maxillariella (Orchidaceae: Maxillariinae) from Costa Rica and Panama
Maxillariella prostrata, a new species from Costa Rica and Panama is described and illustrated. This species is similar to M. acervata but differs in having a prostrate habit, elliptic leaves up to 2 cm long, pseudobulbs with two unequal apical leaves, one larger and the other smaller, a red-spotted lip, the column apex entire, and the pollinarium made up of two small globose pollinia on an oblong stipe. Maxillariella prostrata also resembles M. dichaeoides from Ecuador and Peru but differs in having yellow to white flowers spotted with red, and the lip with a well-defined callusUniversidad de Costa Rica/[814-B2-161]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL
Beyond the various contrivances by which orchids are pollinated: global patterns in orchid pollination biology
Orchidaceae show remarkable diversity in pollination strategies, but how these strategies vary globally is not entirely clear. To identify regions and taxa that are data-rich and lend themselves to rigorous analyses or are data-poor and need attention, we introduce a global database of orchid reproductive biology. Our database contains > 2900 species representing all orchid subfamilies and 23 of 24 tribes. We tabulated information on habit, breeding systems, means of pollinator attraction and the identity of pollinators. Patterns of reproductive biology by habit, geography and taxonomy are presented graphically and analysed statistically. On the basis of our database, most orchid species sampled are pollinator dependent (76%) and self-compatible (88%). Pollinator attraction based on rewards occurs in 54% of the species, whereas 46% use some means of deceit. Orchids generally have highly specific pollinator interactions (median number of pollinator species = 1). Nonetheless, on average, specificity is lower for species offering rewards, occurring in multiple continental regions or Northern America (as defined by the Taxonomic Database Working Group Level 1 regions). Although our database reveals impressive knowledge gains, extensive gaps in basic observations of orchid reproductive biology exist, particularly in tropical regions and diverse lineages of fly-pollinated species. The database is expected to facilitate targeted studies, further elucidating the ecological and evolutionary drivers of orchid diversity.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL
Hundreds of nuclear and plastid loci yield novel insights into orchid relationships
PREMISE
The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed.
METHODS
We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses.
RESULTS
Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes.
CONCLUSIONS
Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution