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How have orchid species diversified in the campos rupestres, Brazil? Fiorini et al. (2023) use genomic data sets and multidisciplinary approaches, including phylogenetics and population genomics, to investigate the diversity of Bulbophyllum. They demonstrate that geographic isolation alone does not explain diversification patterns in Bulbophyllum species throughout the sky forests. Some taxa show considerable evidence of gene flow, and lineages not previously identified as closely related could present a novel source of their genetic diversity.

Cophylogeny represents a framework to understand how ecological and evolutionary process influence lineage diversification. However, linking patterns to mechanisms remains a major challenge. The recently developed Random Tanglegram Partitions provides a directly interpretable statistic to quantify the strength of cophylogenetic signal, maps onto a tanglegram the contribution to phylogenetic signal of individual host-symbiont associations, and can incorporate phylogenetic uncertainty into estimation of cophylogenetic signal. We introduce Rtapas (v1.2), an R package to perform Random Tanglegram Partitions. Rtapas applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals, and nodes that maximize phylogenetic congruence. Rtapas extends the original implementation with a new algorithm that tests phylogenetic incongruence and adds ParaFit, a method designed to test for topological congruence between two phylogenies using patristic distances, to the list of global-fit methods than can be applied. Rtapas can particularly cater for the need for causal inference in cophylogeny as demonstrated herein using to two real-world systems. One involves assessing topological (in)congruence between phylogenies produced with different DNA markers and identifying the particular associations that contribute most to topological incongruence, whereas the other implies analyzing the evolutionary histories of symbiont partners in a large dataset. Rtapas facilitates and speeds up cophylogenetic analysis, as it can handle large phylogenies reducing computational time, and is directly applicable to any scenario that may show phylogenetic congruence (or incongruence).

Recent phylogenetic studies of the Araceae have confirmed the position of the duckweeds nested within the aroids, and the monophyly of a clade containing all the unisexual flowered aroids plus the bisexual-flowered Calla palustris. The main objective of this work was to better resolve the deep phylogenetic relationships among the main lineages within the family, particularly the relationships between the eight currently recognized subfamilies. We also aimed to confirm the phylogenetic position of the enigmatic genus Calla in relation to the long-debated evolutionary transition between bisexual and unisexual flowers in the family.Nuclear DNA sequence data were generated for 128 species across 111 genera (78%) of Araceae using target sequence capture and the Angiosperms353 universal probe set.The phylogenomic data confirmed the monophyly of the eight Araceae subfamilies but the phylogenetic position of subfamily Lasioideae remains uncertain. The genus Calla is included in subfamily Aroideae which has also been expanded to include Zamioculcadoideae. The tribe Aglaonemateae is newly defined to include the genera Aglaonema and Boycea.Our results strongly suggest that new research on African genera (Callopsis, Nephthytis and Anubias) and Calla will be important to understand the early evolution of the Aroideae. Also, of particular interest are the phylogenetic positions of the isolated genera Montrichardia, Zantedeschia and Anchomanes, which remain only moderately supported here. This article is protected by copyright. All rights reserved.

PREMISE: Recent phylogenetic studies of the Araceae have confirmed the position of the duckweeds nested within the aroids, and the monophyly of a clade containing all the unisexual flowered aroids plus the bisexual-flowered Calla palustris. The main objective of this work was to better resolve the deep phylogenetic relationships among the main lineages within the family, particularly the relationships between the eight currently recognized subfamilies. We also aimed to confirm the phylogenetic position of the enigmatic genus Calla in relation to the long-debated evolutionary transition between bisexual and unisexual flowers in the family. METHODS: Nuclear DNA sequence data were generated for 128 species across 111 genera (78%) of Araceae using target sequence capture and the Angiosperms353 universal probe set. RESULTS: The phylogenomic data confirmed the monophyly of the eight Araceae subfamilies but the phylogenetic position of subfamily Lasioideae remains uncertain. The genus Calla is included in subfamily Aroideae which has also been expanded to include Zamioculcadoideae. The new Boycea–Aglaonema Clade is defined. CONCLUSIONS: Our results strongly suggest that new research on African genera (Callopsis, Nephthytis and Anubias) and Calla will be important to understand the early evolution of the Aroideae. Also, of particular interest are the phylogenetic positions of the isolated genera Montrichardia, Zantedeschia and Anchomanes, which remain only moderately supported here.

Plastid sequences have long dominated phylogeny reconstruction at all time depths, predicated on a usually untested assumption that they accurately represent the evolutionary histories of phenotypically circumscribed species. We combined detailed in situ morphometrics (124 plants) and whole-plastome sequencing through genome skimming (71 plants) in order to better understand species-level diversity and speciation in arguably the most challenging monophyletic group within the taxonomically controversial, pseudo-copulatory bee orchid genus Ophrys. Using trees and ordinations, we interpreted the data at four nested demographic levels—macrospecies, mesospecies, microspecies, and local population—seeking the optimal level for bona fide species. Neither morphological nor molecular discontinuities are evident at any level below macrospecies, the observed overlap among taxa suggesting that both mesospecies and microspecies reflect arbitrary division of a continuum of variation. Plastomes represent geographic location more strongly than taxonomic assignment and correlate poorly with morphology, suggesting widespread plastid capture and possibly post-glacial expansion from multiple southern refugia. As they are rarely directly involved in the speciation process, plastomes depend on extinction of intermediate lineages to provide phylogenetic signal and so cannot adequately document evolutionary radiations. The popular ‘ethological’ evolutionary model recognizes as numerous ‘ecological species’ (microspecies) lineages perceived as actively diverging as a result of density-dependent selection on very few features that immediately dictate extreme pollinator specificity. However, it is assumed rather than demonstrated that the many microspecies are genuinely diverging. We conversely envisage a complex four-dimensional reticulate network of lineages, generated locally and transiently through a wide spectrum of mechanisms, but each unlikely to maintain an independent evolutionary trajectory long enough to genuinely speciate by escaping ongoing gene flow. The frequent but localized microevolution that characterizes the Ophrys sphegodes complex is often convergent and rarely leads to macroevolution. Choosing between the contrasting ‘discontinuity’ and ‘ethology’ models will require next-generation sequencing of nuclear genomes plus ordination of corresponding morphometric matrices, seeking the crucial distinction between retained ancestral polymorphism—consistent with lineage divergence—and polymorphisms reflecting gene flow through ‘hybridization’—more consistent with lineage convergence.

The mega-diversity of herbivorous insects is attributed to their co-evolutionary associations with plants. Despite abundant studies on insect-plant interactions, we do not know whether host-plant shifts have impacted both genomic adaptation and species diversification over geological times. We show that the antagonistic insect-plant interaction between swallowtail butterflies and the highly toxic birthworts began 55 million years ago in Beringia, followed by several major ancient host-plant shifts. This evolutionary framework provides a valuable opportunity for repeated tests of genomic signatures of macroevolutionary changes and estimation of diversification rates across their phylogeny. We find that host-plant shifts in butterflies are associated with both genome-wide adaptive molecular evolution (more genes under positive selection) and repeated bursts of speciation rates, contributing to an increase in global diversification through time. Our study links ecological changes, genome-wide adaptations and macroevolutionary consequences, lending support to the importance of ecological interactions as evolutionary drivers over long time periods., Arms races between herbivores and plants have likely affected their evolutionary histories, which could have led to their high diversity. Allio et al. find that butterflies shifting to new host plants have more adaptive molecular signatures across their genomes and show repeated bursts of speciation rates.

Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of species undergoing inter-specific gene flow. However, hybridization in Amazonia’s megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, our results uncovered several historical introgression events betweenBrownealineages and indicated that gene tree incongruence inBrowneais best explained by introgression, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ∼19,000 ddRAD loci recovered a high degree of shared variation between twoBrowneaspecies which co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and a persistence of hybridization over time. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization’s rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.

Societal Impact Statement Biodiversity is essential to food security and nutrition locally and globally. By reviewing the global state of edible plants and highlighting key neglected and underutilized species (NUS), we attempt to unlock plant food resources and explore the role of fungi, which along with the wealth of traditional knowledge about their uses and practices, could help support sustainable agriculture while ensuring better protection of the environment and the continued delivery of its ecosystem services. This work will inform a wide range of user communities, including scientists, conservation and development organizations, policymakers, and the public of the importance of biodiversity beyond mainstream crops. Summary As the world's population is increasing, humanity is facing both shortages (hunger) and excesses (obesity) of calorie and nutrient intakes. Biodiversity is fundamental to addressing this double challenge, which involves a far better understanding of the global state of food resources. Current estimates suggest that there are at least 7,039 edible plant species, in a broad taxonomic sense, which includes 7,014 vascular plants. This is in striking contrast to the small handful of food crops that provide the majority of humanity's calorie and nutrient intake. Most of these 7,039 edible species have additional uses, the most common being medicines (70%), materials (59%), and environmental uses (40%). Species of major food crops display centers of diversity, as previously proposed, while the rest of edible plants follow latitudinal distribution patterns similarly to the total plant diversity, with higher species richness at lower latitudes. The International Union for Conservation of Nature Red List includes global conservation assessments for at least 30% of edible plants, with ca. 86% of them conserved ex situ. However, at least 11% of those species recorded are threatened. We highlight multipurpose NUS of plants from different regions of the world, which could be key for a more resilient, sustainable, biodiverse, and community participation‐driven new “green revolution.” Furthermore, we explore how fungi could diversify and increase the nutritional value of our diets. NUS, along with the wealth of traditional knowledge about their uses and practices, offer a largely untapped resource to support food security and sustainable agriculture. However, for these natural resources to be unlocked, enhanced collaboration among stakeholders is vital.

Symbiosis is a key driver of evolutionary novelty and ecological diversity, but our understanding of how macroevolutionary processes originate extant symbiotic associations is still very incomplete. Cophylogenetic tools are used to assess the congruence between the phylogenies of two groups of organisms related by extant associations. If phylogenetic congruence is higher than expected by chance, we conclude that there is cophylogenetic signal in the system under study. However, how to quantify cophylogenetic signal is still an open issue. We present a novel approach, Random Tanglegram Partitions (Random TaPas) that applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals, and nodes that maximize phylogenetic congruence. By means of simulations, we show that the output value produced is inversely proportional to the number and proportion of cospeciation events employed to build simulated tanglegrams. In addition, with time-calibrated trees, Random TaPas can also distinguish cospeciation from pseudocospeciation. Random TaPas can handle large tanglegrams in affordable computational time and incorporates phylogenetic uncertainty in the analyses. We demonstrate its application with two real examples: passerine birds and their feather mites, and orchids and bee pollinators. In both systems, Random TaPas revealed low cophylogenetic signal, but mapping its variation onto the tanglegram pointed to two different coevolutionary processes. We suggest that the recursive partitioning of the tanglegram buffers the effect of phylogenetic nonindependence occurring in current global-fit methods and therefore Random TaPas is more reliable than regular global-fit methods to identify host–symbiont associations that contribute most to cophylogenetic signal. Random TaPas can be implemented in the public-domain statistical software R with scripts provided herein. A User’s Guide is also available at GitHub.[Codiversification; coevolution; cophylogenetic signal; Symbiosis.]

International audience; Premise To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. Methods We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). Results Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. Conclusions High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

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Is Amazona a 'museum' for Neotropical trees? The evolution of the Brownea clade (Detarioideae, Leguminosae). Molecular Phylogenetics and Evolution 126: 279-292.", "Schley, R. J., R. T. Pennington, O. A. Perez-Escobar, A. J. Helmstetter, M. de la Estrella, I. Larridon, I. A. B. Sabino Kikuchi, et al. 2020. Introgression across evolutionary scales suggests reticulation contribu

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.

The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding., Molecular Biology and Evolution, 38 (10), ISSN:0737-4038, ISSN:1537-1719

Wild relatives or progenitors of crops are important resources for breeding and for understanding domestication. Identifying them, however, is difficult because of extinction, hybridization, and the challenge of distinguishing them from feral forms. Here, we use collection-based systematics, iconography, and resequenced accessions of Citrullus lanatus and other species of Citrullus to search for the potential progenitor of the domesticated watermelon. A Sudanese form with nonbitter whitish pulp, known as the Kordofan melon (C. lanatus subsp. cordophanus), appears to be the closest relative of domesticated watermelons and a possible progenitor, consistent with newly interpreted Egyptian tomb paintings that suggest that the watermelon may have been consumed in the Nile Valley as a dessert by 4360 BP. To gain insights into the genetic changes that occurred from the progenitor to the domesticated watermelon, we assembled and annotated the genome of a Kordofan melon at the chromosome level, using a combination of Pacific Biosciences and Illumina sequencing as well as Hi-C mapping technologies. The genetic signature of bitterness loss is present in the Kordofan melon genome, but the red fruit flesh color only became fixed in the domesticated watermelon. We detected 15,824 genome structural variants (SVs) between the Kordofan melon and a typical modern cultivar, "97103," and mapping the SVs in over 400 Citrullus accessions revealed shifts in allelic frequencies, suggesting that fruit sweetness has gradually increased over the course of watermelon domestication. That a likely progenitor of the watermelon still exists in Sudan has implications for targeted modern breeding efforts.

The origins and evolution of the outstanding Neotropical biodiversity are still debated. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we evaluate four evolutionary scenarios assuming different diversification trajectories and drivers of Neotropical diversification, and assess their variation across Neotropical regions and taxa. Our analysis of 150 phylogenies (12,512 species) of seed plants and tetrapods reveals that Neotropical diversity has mostly expanded through time (70% of the clades), while scenarios of saturated and declining diversity also account for 21% and 9% of Neotropical diversity, respectively. We identify five biogeographic areas that represent distinctive units of long-term Neotropical evolution (Pan-Amazonia, Dry Diagonal, Bahama-Antilles, Galapagos, and an ‘elsewhere’ region) and find that diversity dynamics do not differ across these areas, suggesting no geographic structure in long-term Neotropical diversification. In contrast, diversification dynamics differ substantially across taxa: plant diversity mostly expanded through time (88%), while a substantial fraction (43%) of tetrapod diversity accumulated at a slower pace or declined toward the present. These opposite evolutionary patterns may reflect different capacities for plants and tetrapods to cope with climate change, with potential implications for future adaptation and ecosystem resilience.

Understanding the biogeographical and diversification processes explaining current diversity patterns of subcosmopolitan-distributed groups is challenging. We aimed at disentangling the historical biogeography of the subcosmopolitan liverwort genus Lejeunea with estimation of ancestral areas of origin and testing if sexual system and palaeotemperature variations can be factors of diversification. We assembled a dense taxon sampling for 120 species sampled throughout the geographical distribution of the genus. Lejeunea diverged from its sister group after the Paleocene-Eocene boundary (52.2 Ma, 95% credibility intervals 50.1–54.2 Ma), and the initial diversification of the crown group occurred in the early to middle Eocene (44.5 Ma, 95% credibility intervals 38.5–50.8 Ma). The DEC model indicated that (1) Lejeunea likely originated in an area composed of the Neotropics and the Nearctic, (2) dispersals through terrestrial land bridges in the late Oligocene and Miocene allowed Lejeunea to colonize the Old World, (3) the Boreotropical forest covering the northern regions until the late Eocene did not facilitate Lejeunea dispersals, and (4) a single long-distance dispersal event was inferred between the Neotropics and Africa. Biogeographical and diversification analyses show the Miocene was an important period when Lejeunea diversified globally. We found slight support for higher diversification rates of species with both male and female reproductive organs on the same individual (monoicy), and a moderate positive influence of palaeotemperatures on diversification. Our study shows that an ancient origin associated with a dispersal history facilitated by terrestrial land bridges and not long-distance dispersals are likely to explain the subcosmopolitan distribution of Lejeunea. By enhancing the diversification rates, monoicy likely favoured the colonisations of new areas, especially in the Miocene that was a key epoch shaping the worldwide distribution.

The date palm (Phoenix dactylifera) has been a cornerstone of Middle Eastern and North African agriculture for millennia. It is presumed that date palms were first domesticated in the Persian Gulf and subsequently introduced into North Africa, where their evolution in the latter region appears to have been influenced by gene flow from the wild relative P. theophrasti, which is restricted to Crete and Turkey. However, the timing of gene flow from P. theophrasti to P. dactylifera remains unknown due to the limited archaeobotanical evidence of P. theophrasti and their exclusion from population genomic studies.We addressed this issue by investigating the relatedness and ancestry of a ~2,100-year-old P. dactylifera leaf from Saqqara (Egypt), combining genome sequencing of this ancient specimen with a broad sample of date palm cultivars and closely related species.The ancient Saqqara date palm shares close genetic ancestry with North African date palm populations. We find clear genomic admixture between the Saqqara date palm, P. theophrasti and the closest known relative P. sylvestris.Our study highlights that gene flow from P. theophrasti and P. sylvestris to North African date palms had already occurred at least ~2,100 years ago, providing a minimum timestamp for hybridisation between species.

Premise of the studyEvolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to which the maternal evolutionary history of orchids is congruent with that of the nuclear genome has remained uninvestigated.MethodsWe inferred phylogenetic relationships from 294 low-copy nuclear genes sequenced/obtained using the Angiosperms353 universal probe set from 75 species representing 69 genera, 16 tribes and 24 subtribes. To test for topological incongruence between nuclear and plastid genomes, we constructed a tree from 78 plastid genes, representing 117 genera, 18 tribes and 28 subtribes and compared them using a co-phylogenetic approach. The phylogenetic informativeness and support of the Angiosperms353 loci were compared with those of the 78 plastid genes.Key ResultsPhylogenetic inferences of nuclear datasets produced highly congruent and robustly supported orchid relationships. Comparisons of nuclear gene trees and plastid gene trees using the latest co-phylogenetic tools revealed strongly supported phylogenetic incongruence in both shallow and deep time. Phylogenetic informativeness analyses showed that the Angiosperms353 genes were in general more informative than most plastid genes.ConclusionsOur study provides the first robust nuclear phylogenomic framework for Orchidaceae plus 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 documented: nuclear and plastid phylogenetic trees are not fully congruent and therefore should not be considered interchangeable.

Societal Impact Statement Bioenergy is a major component of the global transition to renewable energy technologies. The plant and fungal kingdoms offer great potential but remain mostly untapped. Their increased use could contribute to the renewable energy transition and addressing the United Nations Sustainable Development Goal 7 “Ensure access to affordable, reliable, sustainable and modern energy for all.” Current research focuses on species cultivated at scale in temperate regions, overlooking the wealth of potential new sources of small‐scale energy where they are most urgently needed. A shift towards diversified, accessible bioenergy technologies will help to mitigate and adapt to the threats of climate change, decrease energy poverty, improve human health by reducing indoor pollution, increase energy resilience of communities, and decrease greenhouse gas emissions from fossil fuels. Summary Bioenergy derived from plants and fungi is a major component of the global transition to renewable energy technologies. There is rich untapped diversity in the plant and fungal kingdoms that offers potential to contribute to the shift away from fossil fuels and to address the United Nations Sustainable Development Goal 7 (SDG7) “Ensure access to affordable, reliable, sustainable and modern energy for all.” Energy poverty—the lack of access to modern energy services—is most acute in the Global South where biodiversity is greatest and least investigated. Our systematic review of the literature over the last 5 years (2015–2020) indicates that research efforts have targeted a very small number of plant species cultivated at scale, mostly in temperate regions. The wealth of potential new sources of bioenergy in biodiverse regions, where the implementation of SDG7 is most urgently needed, has been largely overlooked. We recommend next steps for bioenergy stakeholders—research, industry, and government—to seize opportunities for innovation to alleviate energy poverty while protecting biodiversity. Small‐scale energy production using native plant species in bioenergy landscapes overcomes many pitfalls associated with bioenergy crop monocultures, such as biodiversity loss and conflict with food production. Targeted trait‐based screening of plant species and biological screening of fungi are required to characterize the potential of this resource. The benefits of diversified, accessible bioenergy go beyond the immediate urgency of energy poverty as more diverse agricultural landscapes are more resilient, store more carbon, and could also reduce the drivers of the climate and environmental emergencies.

Unprecedented changes in the Earth's biota are prompting urgent efforts to describe and conserve plant diversity. For centuries, botanical monographs — comprehensive systematic treatments of a family or genus — have been the gold standard for disseminating scientific information to accelerate research. The lack of a monograph compounds the risk that undiscovered species become extinct before they can be studied and conserved. Progress towards estimating the Tree of Life and digital information resources now bring even the most ambitious monographs within reach. Here, we recommend best practices to complete monographs urgently, especially for tropical plant groups under imminent threat or with expected socioeconomic benefits. We also highlight the renewed relevance and potential impact of monographies for the understanding, sustainable use, and conservation of biodiversity. Fil: Grace, Olwen M.. Royal Botanic Gardens, Kew; Reino Unido Fil: Pérez-Escobar, Oscar A.. Royal Botanic Gardens, Kew; Reino Unido Fil: Lucas, Eve J.. Royal Botanic Gardens, Kew; Reino Unido Fil: Vorontsova, Maria S.. Royal Botanic Gardens, Kew; Reino Unido Fil: Lewis, Gwilym P.. Royal Botanic Gardens, Kew; Reino Unido Fil: Walker, Barnaby E.. Royal Botanic Gardens, Kew; Reino Unido Fil: Lohmann, Lúcia G.. Universidade de Sao Paulo; Brasil Fil: Knapp, Sandra. Natural History Museum; Reino Unido Fil: Wilkie, Peter. Royal Botanic Gardens; Reino Unido Fil: Sarkinen, Tiina. Royal Botanic Gardens; Reino Unido Fil: Darbyshire, Iain. Royal Botanic Gardens; Reino Unido Fil: Lughadha, Eimear Nic. Royal Botanic Gardens; Reino Unido Fil: Monro, Alexandre. Royal Botanic Gardens; Reino Unido Fil: Woudstra, Yannick. Universidad de Copenhagen; Dinamarca. Royal Botanic Gardens; Reino Unido Fil: Demissew, Sebsebe. Addis Ababa University; Etiopía Fil: Muasya, A. Muthama. University Of Cape Town; Sudáfrica Fil: Díaz, Sandra Myrna. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina Fil: Baker, William J.. Royal Botanic Gardens, Kew; Reino Unido Fil: Antonelli, Alexandre. University of Oxford; Reino Unido. University Goteborg; Suecia

Allopolyploidy is acknowledged as an important force in plant evolution. Frequent allopolyploidy in Nicotiana across different timescales permits the evaluation of genome restructuring and repeat dynamics through time. Here we use a clustering approach on high-throughput sequence reads to identify the main classes of repetitive elements following three allotetraploid events, and how these are inherited from the closest extant relatives of the maternal and paternal subgenome donors. In all three cases, there was a lack of clear maternal, cytoplasmic bias in repeat evolution, i.e., lack of a predicted bias towards maternal subgenome-derived repeats, with roughly equal contributions from both parental subgenomes. Different overall repeat dynamics were found across timescales of &lt, 0.5 (N. rustica L.), 4 (N. repanda Willd.) and 6 (N. benthamiana Domin) Ma, with nearly additive, genome upsizing, and genome downsizing, respectively. Lower copy repeats were inherited in similar abundance to the parental subgenomes, whereas higher copy repeats contributed the most to genome size change in N. repanda and N. benthamiana. Genome downsizing post-polyploidisation may be a general long-term trend across angiosperms, but at more recent timescales there is species-specific variance as found in Nicotiana.

Poor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci. Furthermore, biological phenomena responsible for topological incongruence such as Incomplete Lineage Sorting (ILS) and hybridisation complicate the resolution of phylogenetic relationships among closely related taxa. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. This complex includes seven taxa distributed through Central America and the Colombian Chocó, and is nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from few loci failed to provide support for internal relationships within the complex. Our Neighbour-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches taxa provided a robust phylogeny for this group. The genus Cycnoches includes three main clades that are further supported by morphological traits and geographic distributions. Similarly, a topology reconstructed through maximum likelihood (ML) inference of concatenated GBS loci produced results that are comparable with those reconstructed through coalescence and network-based methods. Our comparative phylogenetic informativeness analyses suggest that the low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species or subspecies might actually represent only three distinct segregates. We further discuss the limited phylogenetic informativeness found in our GBS approach and its utility to disentangle relationships within recent and rapidly evolving species complexes. Our study is the first to demonstrate the utility of GBS data to reconstruct relationships within young (~2 Ma) Neotropical plant clades, opening new avenues for studies of species complexes that populate the species-rich orchid family UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL)

Providing science and society with an integrated, up-to-date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience are often not straightforward due to numerous informatics barriers. While big synthetic plant phylogenies are being built, they remain static and become quickly outdated as new data are published and tree-building methods improve. Moreover, the body of existing phylogenetic evidence is hard to navigate and access for non-experts. We propose that our community of botanists, tree builders, and informaticians should converge on a modular framework for data integration and phylogenetic analysis, allowing easy collaboration, updating, data sourcing and flexible analyses. With support from major institutions, this pipeline should be re-run at regular intervals, storing trees and their metadata long-term. Providing the trees to a diverse global audience through user-friendly front ends and application development interfaces should also be a priority. Interactive interfaces could be used to solicit user feedback and thus improve data quality and to coordinate the generation of new data. We conclude by outlining a number of steps that we suggest the scientific community should take to achieve global phylogenetic synthesis.

Taxonomic delimitations are challenging because of the convergent and variable nature of phenotypic traits. This is evident in species-rich lineages, where the ancestral and derived states and their gains and losses are difficult to assess. Phylogenetic comparative methods help to evaluate the convergent evolution of a given morphological character, thus enabling the discovery of traits useful for classifications. In this study, we investigate the evolution of selected traits to test for their suitability for generic delimitations in the clade Lepanthes, one of the Neotropical species-richest groups. We evaluated every generic name proposed in the Lepanthes clade producing densely sampled phylogenies with Maximum Parsimony, Maximum Likelihood, and Bayesian approaches. Using Ancestral State Reconstructions, we then assessed 18 phenotypic characters that have been traditionally employed to diagnose genera. We propose the recognition of 14 genera based on solid morphological delimitations. Among the characters assessed, we identified 16 plesiomorphies, 12 homoplastic characters, and seven synapomorphies, the latter of which are reproductive features mostly related to the pollination by pseudocopulation and possibly correlated with rapid diversifications in Lepanthes. Furthermore, the ancestral states of some reproductive characters suggest that these traits are associated with pollination mechanisms alike promoting homoplasy. Our methodological approach enables the discovery of useful traits for generic delimitations in the Lepanthes clade and offers various other testable hypotheses on trait evolution for future research on Pleurothallidinae orchids because the phenotypic variation of some characters evaluated here also occurs in other diverse genera. Ministerio de Ambiente y Energía/[]/MINAE/Costa Rica Sistema Nacional de Áreas de Conservación/[]/SINAC/Costa Rica Universidad de Costa Rica/[814-B6-140]/UCR/Costa Rica Leiden University/[]//Países Bajos Royal Botanic Gardens, Kew/[]//Inglaterra UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL)

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 Rica Universidad de Costa Rica/[814-B6-140]/UCR/Costa Rica IDEA WILD/[]//Estados Unidos Sociedad Colombiana de Orquideología/[]/SCO/Colombia Fundação de Amparo à Pesquisa do Estado de São Paulo/[11/08308-9]/FAPESP/Brasil Fundação de Amparo à Pesquisa do Estado de São Paulo/[13/19124-1]/FAPESP/Brasil Swiss Orchid Foundation/[]//Suiza Royal Botanic Gardens, Kew/[]//Inglaterra Swedish Research Council/[2019-05191]//Suecia Swedish Foundation for Strategic Research/[FFL15-0196]/SSF/Suecia UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL)

Domestication of the watermelon (Citrullus lanatus) has alternatively been placed in South Africa, the Nile valley, or more recently West Africa, with the oldest archeological evidence coming from Libya and Egypt. The geographic origin and domestication of watermelons has therefore remained unclear. Using extensive nuclear and plastid genomic data from a 3,560-year-oldCitrullusleaf from a mummy’s sarcophagus and skimmed genomes for representatives of the seven extant species ofCitrullus, we show that modern cultivars and the ancient plant uniquely share mutations in a lycopene metabolism gene (LYCB) affecting pulp color and a stop codon in a transcription factor regulating bitter cucurbitacin compounds. This implies that the plant we sequenced had red-fleshed and sweet fruits and that New Kingdom Egyptians were cultivating domesticated watermelons. The genomic data also identify extant Sudanese watermelons with white, sweet pulp as the closest relatives of domesticated watermelons.Significance statementWith some 197.8 million tons in 2017, watermelon,Citrullus lanatus, is among the World’s most important crops, yet its area of origin and domestication have remained unclear, with competing hypotheses favoring South Africa, West Africa, Central Africa, or the Nile valley. We generated extensive nuclear and plastid genomic data from a 3500-year-old leaf from a Pharaonic sarcophagus and performed genome skimming for representatives of all otherCitrullusspecies to compare key genes involved in fruit bitterness and color. White-fleshed, non-bitter melons from southern Sudan are the closest relatives of domesticated watermelon, and the ancient genome shares unique alleles with a red-fleshed, non-bitter domesticated form (but no wild forms), implying that 18thDynasty Egyptians were cultivating domesticated watermelon by 3500 years ago.

Phylogenetic relationships in species complexes and lineages derived from rapid diversifications are often challenging to resolve using morphology or standard DNA barcoding markers. The hyper-diverse genus Lepanthes from Neotropical cloud forest includes over 1200 species and many recent, explosive diversifications that have resulted in poorly supported nodes and morphological convergence across clades. Here, we assess the performance of 446 nuclear-plastid-mitochondrial markers derived from an anchored hybrid enrichment approach (AHE) coupled with coalescence- and species network-based inferences to resolve phylogenetic relationships and improve species recognition in the Lepanthes horrida species group. In addition to using orchid-specific probes to increase enrichment efficiency, we improved gene tree resolution by extending standard angiosperm targets into adjacent exons. We found high topological discordance among individual gene trees, suggesting that hybridization/polyploidy may have promoted speciation in the lineage via formation of new hybrid taxa. In addition, we identified ten loci with the highest phylogenetic informativeness values from these genomes. Most previous phylogenetic sampling in the Pleurothallidinae relies on two regions (ITS and matK), therefore, the evaluation of other markers such as those shown here may be useful in future phylogenetic studies in the orchid family. Coalescent-based species tree estimation methods resolved the phylogenetic relationships of the L. horrida species group. The resolution of the phylogenetic estimations was improved with the inclusion of extended anchor targets. This approach produced longer loci with higher discriminative power. These analyses also disclosed two undescribed species, L. amicitiae and L. genetoapophantica, formally described here, which are also supported by morphology. Our study demonstrates the utility of combined genomic evidence to disentangle phylogenetic relationships at very shallow levels of the tree of life, and in clades showing convergent trait evolution. With a fully resolved phylogeny, is it possible to disentangle traits evolving in parallel or convergently across these orchid lineages such as flower color and size from diagnostic traits such as the shape and orientation of the lobes of the petals and lip. ispartof: MOLECULAR PHYLOGENETICS AND EVOLUTION vol:129 pages:27-47 ispartof: location:United States status: published

Cephaloziaceae represent a subcosmopolitan lineage of largely terrestrial leafy liverworts with three-keeled perianths, a reduced seta, capsules with bistratose walls, filamentous sporelings, large, thin-walled cells, and vegetative distribution by gemmae. Here we present the most comprehensively sampled phylogeny available to date based on the nuclear ribosomal internal transcribed spacer region and the chloroplast markers trnL-trnF and rbcL of 184 accessions representing 41 of the 89 currently accepted species and four of the five currently accepted subfamilies. Alobielloideae are placed sister to the remainder of Cephaloziaceae. Odontoschismatoideae form a sister relationship with a clade consisting of Schiffnerioideae and Cephalozioideae. Cephalozioideae are subdivided in three genera, Fuscocephaloziopsis, Cephalozia, and Nowellia, the last two in a robust sister relationship. Most morphological species circumscriptions are supported by the molecular topologies but the Cephalozia bicuspidata complex and the Cephalozia hamatiloba complex require further study. A Neotropical clade of Odontoschisma originates from temperate ancestors. Odontoschisma yunnanense is described as new to science.

More than 31,000 useful plant species have been documented to fulfil needs and services for humans or the animals and environment we depend on. Despite this diversity, humans currently satisfy most requirements with surprisingly few plant species; for example, just three crops – rice, wheat and maize – comprise more than 50% of plant derived calories. Here, we synthesize the projected impact of global climatic change on useful plants across the spectrum of plant domestication. We illustrate the demographic, spatial, ecophysiological, chemical, functional, evolutionary and cultural traits that are likely to characterise useful plants and their resilience in the next century. Using this framework, we consider a range of possible pathways for future human use of plants. These are centred on two trade-offs: i) diversification versus specialization in the range of species we utilize, and ii) substitution of the species towards those better suited to future climate versus facilitating adaptation in our existing suite of dominant useful plants. In the coming century, major challenges to agriculture and biodiversity will be dominated by increased climatic variation, shifting species ranges, disruption to biotic interactions, nutrient limitation and emerging pests and pathogens. These challenges must be mitigated, whilst enhancing sustainable production to meet the needs of a growing population and a more resource intensive standard of living. With the continued erosion of biodiversity, our future ability to choose among these pathways and trade-offs is likely to be diminished.

Poor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci, as well as various other biological phenomena responsible for topological incongruence such as ILS and hybridization. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. The complex includes seven taxa distributed in Central America and the adjacent Chocó biogeographic region, nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from a handful of loci failed to provide support for internal relationships within the complex. Our Neighbor-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches species provided a robustly supported network. The resulting three main clades are corroborated by morphological traits and geographical distributions. Similarly, Maximum Likelihood (ML) inferences of concatenated GBS-loci produced results comparable with those derived from coalescence and network-based methods, albeit always with poor statistical support. The low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species might actually represent only three distinct segregates. Our study is the first to demonstrate the utility of GBS data in phylogenomic research of a very young Neotropical plant clade (~2 Ma), and it paves the way for the study of the many other species complexes that populate the species-rich orchid family.

The flora of the Neotropics is unmatched in its diversity, however the mechanisms by which diversity has accumulated are debated and largely unclear. The Brownea clade (Leguminosae) is a characteristic component of the Neotropical flora, and the species within it are diverse in their floral morphology, attracting a wide variety of pollinators. This investigation aimed to estimate species divergence times and infer relationships within the group, in order to test whether the Brownea clade followed the 'cradle' or 'museum' model of diversification, i.e. whether species evolved rapidly over a short time period, or gradually over many millions of years. We also aimed to trace the spatio-temporal evolution of the clade by estimating ancestral biogeographical patterns in the group. We used BEAST to build a dated phylogeny of 73 Brownea clade species using three molecular markers (ITS, trnK and psbA-trnH), resulting in well-resolved phylogenetic relationships within the clade, as well as robust divergence time estimates from which we inferred diversification rates and ancestral biogeography. Our analyses revealed an Eocene origin for the group, after which the majority of diversification happened in Amazonia during the Miocene, most likely concurrent with climatic and geological changes caused by the rise of the Andes. We found no shifts in diversification rate over time, suggesting a gradual accumulation of lineages with low extinction rates. These results may help to understand why Amazonia is host to the highest diversity of tree species on Earth.

Local adaptation in plants often requires coordinated shifts among resources. Lowry et al. provide evidence for physiological and genomic mechanisms underpinning adaptive shifts in yellow monkeyflower (Mimulus guttatus), such as the transition between annual and perennial life histories. In M. guttatus, differential activity of gibberellins, governed partially by a chromosomal inversion, is responsible for shifts between growth, reproduction, and herbivore defense (secondary compound production).

The colonization of the epiphytic niche of tropical forest canopies played an important role in orchid’s extraordinary diversification in the Neotropics. However, reversals to the terrestrial habit occurred sparsely in species of Epidendroideae. To better understand which factors might have been involved in reversals to terrestrial habits in the predominantly epiphytic Epidendroideae, we investigateGaleandradiversification in time and space. We hypothesized that the reversal to the terrestrial habitat is linked to the origin of open vegetation habitats in South America. We generated a time-calibrated phylogeny based on a matrix of 17 out of 20 species ofGaleandraplus outgroups and seven DNA markers. We found thatGaleandraoriginated towards end of the Miocene, about 10 Ma in Amazonia (including the Guiana Shield). The terrestrial clade originated synchronously with the rise of dry vegetation biomes, suggesting that aridification during the last 5 million years dramatically impacted the diversification of epiphytic lineages in the Neotropics. Habit is correlated with floral spur lengths and geographic range size. The longer spurs and narrower ranges are found in epiphytic species: probably adapted to a specialized pollination mode, associated to the long-tongued Euglossini bees, which also prefer forested habits. The terrestrial species presents variable floral spurs and wide distribution ranges, with evidence of self-pollination, suggesting the loss of specialized pollination system and concomitant range expansion.

Dioecious and thorny Rochefortia Sw. is a poorly known though distinct element of the Ehretiaceae comprising woody plants restricted to the Caribbean and the adjacent American mainland. The approximately ten species display a great morphological variability and overlapping taxonomic boundaries, which makes it difficult to differentiate them (particularly in the Caribbean region). We investigated the phylogenetic relationships of Rochefortia using DNA sequence data from one nuclear locus (Internal Transcribed Spacer) and three chloroplast DNA loci (rps16, trnL–trnF, trnS–trnG). The monophyly of Rochefortia was confirmed, with a sister group relationship between an American mainland clade and a Caribbean clade. The latter segregates into three, morphologically rather variable lineages, distributed either in the Lesser Antilles or in the eastern Greater Antilles or in the western Greater Antilles. Thus, geographic occurrence rather than morphology is indicative of taxonomic delimitation in Rochefortia.

Environmental sex determination (ESD) − a change in sexual function during an individual life span driven by environmental cues − is an exceedingly rare sexual system among angiosperms. Because ESD can directly affect reproduction success, it could influence diversification rate as compared with lineages that have alternative reproductive systems. Here we test this hypothesis using a solid phylogenetic framework of Neotropical Catasetinae, the angiosperm lineage richest in taxa with ESD. We assess whether gains of ESD are associated with higher diversification rates compared to lineages with alternative systems while considering additional traits known to positively affect diversification rates in orchids. We found that ESD has evolved asynchronously three times during the last ~5 Myr. Lineages with ESD have consistently higher diversification rates than related lineages with other sexual systems. Habitat fragmentation due to mega-wetlands extinction, and climate instability are suggested as the driving forces for ESD evolution.

The Andean uplift is one of the major orographic events in the New World and has impacted considerably the diversification of numerous Neotropical organisms. Despite its importance for biogeography, the specific role of mountain ranges as a dispersal barrier between South and Central American lowland plant lineages is still poorly understood. The swan orchids (Cycnoches) comprise ca 34 epiphytic species distributed in lowland and pre-montane forests of Central and South America. Here, we study the historical biogeography of Cycnoches to better understand the impact of the Andean uplift on the diversification of Neotropical lowland plant lineages. Using novel molecular sequences (five nuclear and plastid regions) and twelve biogeographic models with and without founder-event speciation, we infer that the most recent common ancestor of Cycnoches may have originated in Amazonia ca 5 Mya. The first colonization of Central America occurred from a direct migration event from Amazonia, and multiple bidirectional trans-Andean migrations between Amazonia and Central America took place subsequently. Notably, such biological exchange occurred well after major mountain building periods. The Andes have not acted as an impassable barrier for epiphytic lowland lineages such as orchids having a great potential for effortless dispersal because of the very light, anemochorous seeds.

• The Andean mountains of South America are the most species-rich biodiversity hotspot worldwide with about 15% of the world’s plant species, in only 1% of the world’s land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin and diversification.• We address this knowledge gap by inferring the biogeographical history and evolutionary dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely-sampled orchid phylogenies (including 400+ newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets.• We find that the majority of Andean orchid lineages only originated in the last 15 million years. Most Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species diversification is correlated with Andean orogeny, and multiple migrations and re-colonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales.• Our study sheds new light on the timing and geography of a major Neotropical radiation, and suggests that mountain uplift promotes species diversification across all elevational zones.

DNA-based divergence time estimates suggested major changes in the composition of epiphyte lineages of liverworts during the Cretaceous; however, evidence from the fossil record is scarce. We present the first Cretaceous fossil of the predominantly epiphytic leafy liverwort genus Radula in ca. 100 Myr old Burmese amber. The fossil's exquisite preservation allows first insights into the morphology of early crown group representatives of Radula occurring in gymnosperm-dominated forests. Ancestral character state reconstruction aligns the fossil with the crown group of Radula subg. Odontoradula; however, corresponding divergence time estimates using the software BEAST lead to unrealistically old age estimates. Alternatively, assignment of the fossil to the stem of subg. Odontoradula results in a stem age estimate of Radula of 227.8 Ma (95 % highest posterior density (HPD): 165.7–306.7) and a crown group estimate of 176.3 Ma (135.1–227.4), in agreement with analyses employing standard substitution rates (stem age 235.6 Ma (142.9–368.5), crown group age 183.8 Ma (109.9–289.1)). The fossil likely belongs to the stem lineage of Radula subg. Odontoradula. The fossil's modern morphology suggests that switches from gymnosperm to angiosperm phorophytes occurred without changes in plant body plans in epiphytic liverworts. The fossil provides evidence for striking morphological homoplasy in time. Even conservative node assignments of the fossil support older rather than younger age estimates of the Radula crown group, involving origins for most extant subgenera by the end of the Cretaceous and diversification of their crown groups in the Cenozoic.

Lepanthes queremalensis, a new species of Lepanthes from Valle del Cauca, Colombia, is described and illustrated. It shows a set of mixed characters of two other species: L. sinuosa (the cymbiform shape of the lip appendix) and L. ankistra (the shape of the leaf and the lip blades). A key to the Colombian species of Lepanthes section Lepanthes subsection Lepanthes series Mucronatae is presented. Information about its habitat, ecology and distribution is provided.

The American tropics are home to about 10% of Earth's species and several biodiversity hotspots of global importance for conservation ([ 1 ][1], [ 2 ][2]), including high-elevation tropical alpine ecosystems (paramos) and Andean forests. These ecosystems deliver numerous services, such as providing

En la Reserva Bosque de Yotoco (76° 20' O, 3° 50' N, 1200 - 1700 m.s.n.m.) relicto de selva subandina de aproximadamente 500 ha, durante 3 años (marzo de 2006 y mayo de 2009) se realizaron búsquedas intensivas aleatorias de especies de la familia Orchidaceae. Hasta junio de 2009 se habían reportado 80 especies pertenecientes a 46 géneros, siendo los de mayor riqueza específica Epidendrum L. con 13 y Maxillaria Ruiz y Pav. con seis. Como exclusivas de algunas zonas fueron identificadas Macroclinium oberonia (Schltr.) Dodson y Porroglossum muscosum (Rchb. f.) Schltr.; como abundantes y ampliamente distribuidas Epidendrum porpax Rchb.f., Campylocentrum micranthum (Lindl.) Rolfe y Oncidium adelaidae Königer; y como poco abundantes Cryptocentrum latifolium Schltr. y Specklinia picta (Lindl.) Pridgeon & M.W. Chase.In the Yotoco Forest Reserve, in the Municipality of Yotoco, Department of Valle del Cauca, Colombia (3°50'N, 76° 20'W, 1200 - 1700 m.a.s.n.), a remnant sub-Andean forest of approximately 500 ha, orchids were collected during three years. Eighty species distributed in 46 genera were found. The most species-rich genera are Epidendrum L. (tirthteen species) and Maxillaria Ruiz & Pav. (six species). Macroclinium oberonia (Schltr.) Dodson and Porroglossum muscosum (Rchb. f.) Schltr. were restricted to certain zones, Epidendrum porpax Rchb. f., Campylocentrum micranthum (Lindl.) Rolfe, and Oncidium adelaidae Königer were abundant and widely distributed, and Cryptocentrum latifolium Schltr. and Specklinia picta (Lindl.) Pridgeon & M.W. Chase. were scarce.

Two sexual systems are predominant in Catasetinae (Orchidaceae), namely protandry (which has evolved in other orchid lineages as well) and environmental sex determination (ESD) being a unique trait among Orchidaceae. Yet, the lack of a robust phylogenetic framework for Catasetinae has hampered deeper insights in origin and evolution of sexual systems. To investigate the origins of protandry and ESD in Catasetinae, we sequenced nuclear and chloroplast loci from 77 species, providing the most extensive data matrix of Catasetinae available so far with all major lineages represented. We used Maximum Parsimony, Maximum Likelihood and Bayesian methods to infer phylogenetic relationships and evolution of sexual systems. Irrespectively of the methods used, Catasetinae were monophyletic in molecular phylogenies, with all established generic lineages and their relationships resolved and highly supported. According to comparative reconstruction approaches, the last common ancestor of Catasetinae was inferred as having bisexual flowers (i.e., lacking protandry and ESD as well), and protandry originated once in core Catasetinae (comprising Catasetum, Clowesia, Cycnoches, Dressleria and Mormodes). In addition, three independent gains of ESD are reliably inferred, linked to corresponding loss of protandry within core Catasetinae. Thus, prior gain of protandry appears as the necessary prerequisite for gain of ESD in orchids. Our results contribute to a comprehensive evolutionary scenario for sexual systems in Catasetinae and more generally in orchids as well.