Botanical Monography in the Anthropocene

South America holds the greatest diversity of native daisies (Asteraceae) in the world: an updated catalogue supporting continental-scale conservation

Asteraceae is the world's richest plant family and is found on all continents, in environments ranging from the coast to the highest mountains. The family shows all growth forms and, as in other angiosperm families, species richness is concentrated in tropical regions. South America has the highest diversity of Asteraceae in the world, yet taxonomic and distributional knowledge gaps remain. This study compiles an updated catalog of Asteraceae native to South America, based on national and regional checklists and ongoing large-scale flora projects. The resulting checklist includes a total of 6,940 species and 564 genera native to South America to date, which represent about a quarter of the family's global diversity. Countries already considered to be megadiverse show the greatest diversity, such as Brazil with 2,095 species, followed by Peru (1,588), Argentina (1,377), and Colombia (1,244), with this diversity mainly focused on the Brazilian Highlands and the Andes. Species endemism also peaks in Brazil, but Sørensen distances reveal the Chilean flora to be eminently different from the rest of the continent. Tribes better represented in the continent are Eupatorieae, Senecioneae and Astereae, also with a remarkably presence of entirely South American subfamilies representing earliest diverging lineages of the Asteraceae, such as Barnadesioideae, Wunderlichioideae, Famatinanthoideae, and Stifftioideae. It is estimated that the discovery and description curves have not yet stabilized, and the number of species is likely to increase by 5 to 10% in the coming years, posing major challenges to continental-scale conservation.

The origin and speciation of orchids

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.

Climbing mechanisms and the diversification of neotropical climbing plants across time and space

Climbers germinate on the ground but need external support to sustain their stems, which are maintained attached to supports through modified organs, that is, climbing mechanisms. Specialized climbing mechanisms have been linked to higher diversification rates. Also, different mechanisms may have different support diameter restrictions, which might influence climbers' spatial distribution. We test these assumptions by linking climbing mechanisms to the spatiotemporal diversification of neotropical climbers. A dataset of climbing mechanisms is presented for 9071 species. WCVP was used to standardize species names, map geographical distributions, and estimate diversification rates of lineages with different mechanisms. Twiners appear concentrated in the Dry Diagonal of South America and climbers with adhesive roots in the Chocó region and Central America. However, climbing mechanisms do not significantly influence the distribution of neotropical climbers. Also, we found no strong support for correlations between specialized climbing mechanisms and higher diversification rates. Climbing mechanisms do not strongly impact the spatiotemporal diversification of neotropical climbers on a macroevolutionary scale. We argue that the climbing habit is a synnovation, meaning the spatiotemporal diversification it promotes is due to the sum effect of all the habit's traits rather than isolated traits, such as climbing mechanisms.

Ancient DNA genomics and the renaissance of herbaria

Herbaria are undergoing a renaissance as valuable sources of genomic data for exploring plant evolution, ecology, and diversity. Ancient DNA retrieved from herbarium specimens can provide unprecedented glimpses into past plant communities, their interactions with biotic and abiotic factors, and the genetic changes that have occurred over time. Here, we highlight recent advances in the field of herbarium genomics and discuss the challenges and opportunities of combining data from modern and time-stamped historical specimens. We also describe how integrating herbarium genomics data with other data types can yield substantial insights into the evolutionary and ecological processes that shape plant communities. Herbarium genomic analysis is a tool for understanding plant life and informing conservation efforts in the face of dire environmental challenges.

The herbarium of the future

The ~400 million specimens deposited across ~3000 herbaria are essential for: (i) understanding where plants have lived in the past, (ii) forecasting where they may live in the future, and (iii) delineating their conservation status. An open access 'global metaherbarium' is emerging as these specimens are digitized, mobilized, and interlinked online. This virtual biodiversity resource is attracting new users who are accelerating traditional applications of herbaria and generating basic and applied scientific innovations, including e-monographs and floras produced by diverse, interdisciplinary, and inclusive teams; robust machine-learning algorithms for species identification and phenotyping; collection and synthesis of ecological trait data at large spatiotemporal and phylogenetic scales; and exhibitions and installations that convey the beauty of plants and the value of herbaria in addressing broader societal issues.

New directions in tropical phenology

Earth's most speciose biomes are in the tropics, yet tropical plant phenology remains poorly understood. Tropical phenological data are comparatively scarce and viewed through the lens of a 'temperate phenological paradigm' expecting phenological traits to respond to strong, predictably annual shifts in climate (e.g., between subfreezing and frost-free periods). Digitized herbarium data greatly expand existing phenological data for tropical plants; and circular data, statistics, and models are more appropriate for analyzing tropical (and temperate) phenological datasets. Phylogenetic information, which remains seldom applied in phenological investigations, provides new insights into phenological responses of large groups of related species to climate. Consistent combined use of herbarium data, circular statistical distributions, and robust phylogenies will rapidly advance our understanding of tropical - and temperate - phenology.

Taxonomy of the weed species of the genus Echinochloa (Poaceae, Paniceae) in Southwestern Europe: Exploring the confused current state of affairs

The taxonomy of Echinochloa, a predominantly tropical to warm-temperate genus of 40-50 species, including some of the world's worst weeds, is still poorly understood. This is because some species, including the extremely widespread E.crus-galli, show a wide range of morphological, physiological and ecological variation, in part the result of a complex recent evolutionary history. Furthermore, there is often a dearth of clear distinguishing features among species. The same applies to the species established in Southwestern Europe, where unintentionally introduced populations have now established themselves as important weeds of crops, especially maize and rice. Taxonomic and nomenclatural confusion hampers progress in weed science. In this study, we give an identification key that covers the weedy taxa encountered in Southwestern Europe, followed by notes on taxonomy and nomenclature. Moreover, a lectotype is designated for Echinochloafrumentacea. It is argued that current confusion cannot be overcome without including populations of Eastern Asian origin in taxonomic studies and without the joint efforts of experts in the fields of weed science, morphology-based taxonomy, genomics and phylogenetics.

speciesLink: rich data and novel tools for digital assessments of biodiversity

Abstract speciesLink is a large-scale biodiversity information portal that exists thanks to a broad collaborative network of people and institutions. CRIA’s involvement with the scientific community of Brazil and other countries is responsible for the significant results achieved, currently reaching more than 15 million primary biodiversity data records, 95% of which are associated with preserved specimens and about 25% with high-quality digital images. The network provides data on over 200,000 species, of which over 110,000 occur in Brazil. This article describes thematic networks within speciesLink, as well as some of the most useful tools developed. The importance and contributions of speciesLink are outlined, as are concerns about securing stable budgetary support for such biodiversity data e-infrastructures. Here we review the value of speciesLink as a major source of biodiversity information for research, education, informed decision-making, policy development, and bioeconomy.

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.

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.