Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation

Persistent Habitat Instability and Patchiness, Sexual Attraction, Founder Events, Drift and Selection: A Recipe for Rapid Diversification of Orchids

Orchidaceae is one of the most species-rich families of flowering plants, with most current diversity having evolved within the last 5 My. Patterns associated with species richness and rapid diversification have been identified but have not often been associated with evolutionary processes. We review the most frequently identified correlates of diversity and suggest that the processes and rate by which they occur vary geographically and are largely dependent on persistent pulses of habitat instabilities, especially for epiphytes. Aggressive orogenesis creates fragmented habitats while global climatic cycles exacerbate the ecological instabilities. The need for repeated cycles of dispersal results in frequent founder events, which sets the stage for allopatric diversification via bouts of genetic drift and natural selection. The allopatry requirement can be bypassed by pollination systems involving flowers attracting pollinators through the production of sex signaling semiochemicals. The drift-selection model of diversification, coupled with persistent habitat instability throughout ecological and geological time scales, and sex signaling are the likely components of a multifactorial process leading to the rapid, recent diversification in this family.

Biome conservatism prevailed in repeated long-distance colonization of Madagascar's mountains by Helichrysum (Compositae, Gnaphalieae)

Colonization and diversification processes are responsible for the distinctiveness of island biotas, with Madagascar standing out as abiodiversity hotspot exceptionally rich in species and endemism. Regardless of its significance, the evolutionary history and diversification drivers of Madagascar's flora remain understudied. Here we focus on Helichrysum (Compositae, Gnaphalieae) to investigate the evolutionary and biogeographic origins of the Malagasy flora. We inferred a highly resolved phylogeny based on target-enrichment data from 327 species (including 51 % of Malagasy endemics) and conducted ancestral range estimation analyses. Our results revealed at least six trans-oceanic dispersal events from different African regions to Madagascar during the Pliocene. In this process, biome conservatism prevailed, as evidenced by similarities between Malagasy lineages and their African relatives. The southern African grasslands, known to be the center of diversification and the main source of African Helichrysum lineages, played a key role in the colonization of Madagascar as the ancestral source area of at least three clades. The Tropical Afromontane region was revealed as the source of at least two montane Malagasy lineages that substantially radiated in-situ. Finally, a dispersal event from southwestern Africa led to a lineage represented by a single species adapted to the island's southwestern arid conditions. The main radiations of Helichrysum in Madagascar's mountains occurred within the last 2 My, coinciding with a transition towards cooler and drier conditions and the expansion of open habitats, likely driven by a combination of geographic and ecological speciation. Overall, our findings highlight the affinities between the montane floras of continental Africa and Madagascar.

Polyploidy linked with species richness but not diversification rates or niche breadth in Australian Pomaderreae (Rhamnaceae)

BACKGROUND AND AIMS

Polyploidy is an important evolutionary driver for plants and has been linked with higher species richness and increases in diversification rate. These correlations between ploidy and plant radiations could be the result of polyploid lineages exploiting broader niche space and novel niches due to their enhanced adaptability. The evolution of ploidy and its link to plant diversification across the Australian continent is not well understood. Here, we focus on the ploidy evolution of the Australasian Rhamnaceae tribe Pomaderreae.

METHODS

We generated a densely sampled phylogeny (90 %, 215/240 species) of the tribe and used it to test for the evolution of ploidy. We obtained 30 orthologous nuclear loci per sample and dated the phylogeny using treePL. Ploidy estimates for each sequenced species were obtained using nQuire, based on phased sequence data. We used MiSSE to obtain tip diversification rates and tested for significant relationships between diversification rates and ploidy. We also assessed for relationships between ploidy level and niche breadth, using distributional records, species distributional modelling and WorldClim data.

KEY RESULTS

Polyploidy is extensive across the tribe, with almost half (45 %) of species and the majority of genera exhibiting this trait. We found a significant positive relationship between polyploidy and genus size (i.e. species richness), but a non-significant positive relationship between polyploidy and diversification rates. Polyploidy did not result in significantly wider niche space occupancy for Pomaderreae; however, polyploidy did allow transitions into novel wetter niches. Spatially, eastern Australia is the diversification hotspot for Pomaderreae in contrast to the species hotspot of south-west Western Australia.

CONCLUSIONS

The relationship between polyploidy and diversification is complex. Ancient polyploidization events likely played an important role in the diversification of species-rich genera. A lag time effect may explain the uncoupling of tip diversification rates and polyploidy of extant lineages. Further studies on other groups are required to validate these hypotheses.

Progress in systematics and biogeography of Orchidaceae

Orchidaceae are one of the largest families of angiosperms in terms of species richness. In the last decade, numerous studies have delved into reconstructing the phylogenetic framework of Orchidaceae, leveraging data from plastid, mitochondrial and nuclear sources. These studies have provided new insights into the systematics, diversification and biogeography of Orchidaceae, establishing a robust foundation for future research. Nevertheless, pronounced controversies persist regarding the precise placement of certain lineages within these phylogenetic frameworks. To address these discrepancies and deepen our understanding of the phylogenetic structure of Orchidaceae, we provide a comprehensive overview and analysis of phylogenetic studies focusing on contentious groups within Orchidaceae since 2015, delving into discussions on the underlying reasons for observed topological conflicts. We also provide a novel phylogenetic framework at the subtribal level. Furthermore, we examine the tempo and mode underlying orchid species diversity from the perspective of historical biogeography, highlighting factors contributing to extensive speciation. Ultimately, we delineate avenues for future research aimed at enhancing our understanding of Orchidaceae phylogeny and diversity.

Characterization of Angraecum (Angraecinae, Orchidaceae) Plastomes and Utility of Sequence Variability Hotspots

Angraecum, commonly known as Darwin's orchid, is the largest genus of Angraecinae (Orchidaceae). This genus exhibits a high morphological diversity, making it as a good candidate for macroevolutionary studies. In this study, four complete plastomes of Angraecum were firstly reported and the potential variability hotspots were explored. The plastomes possessed the typical quadripartite structure and ranged from 150,743 to 151,818 base pair (bp), with a guanine-cytosine (GC) content of 36.6-36.9%. The plastomes all contained 120 genes, consisting of 74 protein-coding genes (CDS), 38 transfer RNA (tRNA) genes and 8 ribosomal RNA (rRNA) genes; all ndh genes were pseudogenized or lost. A total of 30 to 46 long repeats and 55 to 63 SSRs were identified. Relative synonymous codon usage (RSCU) analysis indicated a high degree of conservation in codon usage bias. The Ka/Ks ratios of most genes were lower than 1, indicating that they have undergone purifying selection. Based on the ranking of Pi (nucleotide diversity) values, five regions (trnSGCU-trnGGCC, ycf1-trnNGGU, trnNGUU-rpl32, psaC-ndhE and trnSGCU-trnGGCC) and five protein-coding genes (rpl32, rps16, psbK, rps8, and ycf1) were identified. The consistent and robust phylogenetic relationships of Angraecum were established based on a total of 40 plastomes from the Epidendroideae subfamily. The genus Angraecum was strongly supported as a monophyletic group and sister to Aeridinae. Our study provides an ideal system for investigating molecular identification, plastome evolution and DNA barcoding for Angraecum.

The evolution of flower-pollinator trait matching, and why do some alpine gingers appear to be mismatched?

BACKGROUND AND AIMS

Morphological matching between flower and pollinator traits has been documented in diverse plant lineages. Indeed, the matching of corolla tube length and pollinator tongue length has been cited repeatedly as a classic case of coevolution. However, there are many possible evolutionary routes to trait matching. Our aim here is both to review the evolutionary mechanisms of plant-pollinator trait matching and to investigate a specific case of trait matching/mismatching in a genus of alpine gingers.

METHODS

Roscoea gingers with long corolla tubes in the western Himalayas have pollinators with correspondingly long tongues, but the match between corolla tube and pollinator tongue lengths is not seen in the eastern Himalayas. Six floral traits were measured, including corolla tube depth, an internal trait controlling pollinator access to nectar. We calculated coefficients of variation and phylogenetically controlled correlation patterns of these traits in six Roscoea species in order to gain possible insights into stabilizing selection and modularization of these traits.

KEY RESULTS

The distal (nectar-containing) portion of the corolla tube exhibited lower coefficients of variations than did the basal portion. This is consistent with the hypothesis that pollinators mediate stabilizing selection on the distal, but not basal, portion of the corolla tube. This result, combined with phylogenetic data, suggests that the elevated liquid level of nectar in the distal tube evolved subsequent to dispersal into the eastern Himalayan region and loss of long-tongue pollinators. After accounting for phylogeny, corolla tube length, anther length, style length and labellum width were all intercorrelated. Corolla-tube depth was not part of this covariational module, however, suggesting separate adaptation to short-tongued pollinators.

CONCLUSIONS

The reduction in functional corolla tube depth in the Roscoea appears to be related to the loss of long-tongued pollinators associated with dispersal to the eastern Himalayas and pollination by short-tongued pollinators. The apparent mismatch between floral tubes and pollinator tongues is a case of cryptic trait matching between flowers and pollinators, underscoring the importance of combining floral anatomy with pollination ecology in assessing plant-pollinator trait matching.

Madagascar’s extraordinary biodiversity: Evolution, distribution, and use

Madagascar’s biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar’s past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique “living laboratory” for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth’s biodiversity.

Evidence for selectively constrained 3D flower shape evolution in a Late Miocene clade of Malagasy Bulbophyllum orchids

Questions concerning the evolution of complex biological structures are central to the field of evolutionary biology. Yet, still little information is known about the modes and temporal dynamics of three-dimensional (3D) flower shape evolution across the history of clades. Here, we combined high-resolution X-ray computed tomography with 3D geometric morphometrics and phylogenetic comparative methods to test models of whole-flower shape evolution in the orchid family, using an early Late Miocene clade (c. 50 spp.) of Malagasy Bulbophyllum as model system. Based on landmark data of 38 species, our high-dimensional model fitting decisively rejects a purely neutral mode of evolution, suggesting instead that flower shapes evolved towards a primary adaptive optimum. Only a small number of recently evolved species/lineages attained alternative shape optima, resulting in an increased rate of phenotypic evolution. Our findings provide evidence of constrained 3D flower shape evolution in a small-sized clade of tropical orchids, resulting in low rates of phenotypic evolution and uncoupled trait-diversification rates. We hypothesise that this deep imprint of evolutionary constraint on highly complex floral structures might reflect long-term (directional and/or stabilizing) selection exerted by the group's main pollinators (flies).

Evolution of crassulacean acid metabolism (CAM) as an escape from ecological niche conservatism in Malagasy Bulbophyllum (Orchidaceae)

Despite growing evidence that niche shifts are more common in flowering plants than previously thought, little is known of whether such shifts are promoted by changes in photosynthetic pathways. Here we combine the most complete phylogeny for epiphytic Malagasy Bulbophyllum orchids (c. 210 spp.) with climatic niche and carbon isotope ratios to infer the group's spatial-temporal history, and the role of strongly expressed crassulacean acid metabolism (CAM) in facilitating niche shifts and diversification. We find that most extant species still retain niche (Central Highland) and photosynthesis (C₃ ) states as present in the single mid-Miocene (c. 12.70 million yr ago (Ma)) ancestor colonizing Madagascar. However, we also infer a major transition to CAM, linked to a late Miocene (c. 7.36 Ma) invasion of species from the sub-humid highland first into the island's humid eastern coastal, and then into the seasonally dry 'Northwest Sambirano' rainforests, yet without significant effect on diversification rates. These findings indicate that CAM in tropical epiphytes may be selectively advantageous even in high rainfall habitats, rather than presenting a mere adaptation to dry environments or epiphytism per se. Overall, our study qualifies CAM as an evolutionary 'gateway' trait that considerably widened the spatial-ecological amplitude of Madagascar's most species-rich orchid genus.

Rapid radiation of angraecoids (Orchidaceae, Angraecinae) in tropical Africa characterised by multiple karyotypic shifts under major environmental instability

Angraecoid orchids present a remarkable diversity of chromosome numbers, which makes them a highly suitable system for exploring the impact of karyotypic changes on cladogenesis, diversification and morphological differentiation. We compiled an annotated cytotaxonomic checklist for 126 species of Angraecinae, which was utilised to reconstruct chromosomal evolution using a newly-produced, near-comprehensive phylogenetic tree that includes 245 angraecoid taxa. In tandem with this improved phylogenetic framework, using combined Bayesian, maximum likelihood and parsimony approaches on ITS-1 and five plastid markers, we propose a new cladistic nomenclature for the angraecoids, and we estimate a new timeframe for angraecoid radiation based on a secondary calibration, and calculate diversification rates using a Bayesian approach. Coincident divergence dates between clades with identical geographical distributions in the angraecoids and the pantropical orchid genus Bulbophyllum suggest that the same events may have intervened in the dispersal of these two epiphytic groups between Asia, continental Africa, Madagascar and the Neotropics. The major angraecoid lineages probably began to differentiate in the Middle Miocene, and most genera and species emerged respectively around the Late Miocene-Pliocene boundary and the Pleistocene. Ancestral state reconstruction using maximum likelihood estimation revealed an eventful karyotypic history dominated by descending dysploidy. Karyotypic shifts seem to have paralleled cladogenesis in continental tropical Africa, where approximately 90% of the species have descended from at least one inferred transition from n = 17-18 to n = 25 during the Middle Miocene Climatic Transition, followed by some clade-specific descending and ascending dysploidy from the Late Miocene to the Pleistocene. Conversely, detected polyploidy is restricted to a few species lineages mostly originating during the Pleistocene. No increases in net diversification could be related to chromosome number changes, and the apparent net diversification was found to be highest in Madagascar, where karyotypic stasis predominates. Finally, shifts in chromosome number appear to have paralleled the evolution of rostellum structure, leaflessness, and conspicuous changes in floral colour.

Slowly but surely: gradual diversification and phenotypic evolution in the hyper-diverse tree fern family Cyatheaceae

BACKGROUND AND AIMS

The tremendously unbalanced distribution of species richness across clades in the tree of life is often interpreted as the result of variation in the rates of diversification, which may themselves respond to trait evolution. Even though this is likely a widespread pattern, not all diverse groups of organisms exhibit heterogeneity in their dynamics of diversification. Testing and characterizing the processes driving the evolution of clades with steady rates of diversification over long periods of time are of importance in order to have a full understanding of the build-up of biodiversity through time.

METHODS

We studied the macroevolutionary history of the species-rich tree fern family Cyatheaceae and inferred a time-calibrated phylogeny of the family including extinct and extant species using the recently developed fossilized birth-death method. We tested whether the high diversity of Cyatheaceae is the result of episodes of rapid diversification associated with phenotypic and ecological differentiation or driven by stable but low rates of diversification. We compared the rates of diversification across clades, modelled the evolution of body size and climatic preferences and tested for trait-dependent diversification.

KEY RESULTS

This ancient group diversified at a low and constant rate during its long evolutionary history. Morphological and climatic niche evolution were found to be overall highly conserved, although we detected several shifts in the rates of evolution of climatic preferences, linked to changes in elevation. The diversification of the family occurred gradually, within limited phenotypic and ecological boundaries, and yet resulted in a remarkable species richness.

CONCLUSIONS

Our study indicates that Cyatheaceae is a diverse clade which slowly accumulated morphological, ecological and taxonomic diversity over a long evolutionary period and provides a compelling example of the tropics as a museum of biodiversity.

Afropectinariella (Vandeae, Orchidaceae), a new genus of the Angraecum alliance

A recent phylogenetic study showed that species assigned to the newly recognised genus Pectinariella Szlach., Mytnik & Grochocka (previously treated as Angraecum Bory sect. Pectinaria Benth.) are polyphyletic, comprising a clade with species primarily in Madagascar and the Western Indian Ocean islands (including the type) and another non-sister clade whose members occur in continental Africa and the Gulf of Guinea islands. In order to render Pectinariella monophyletic, the five continental African species must therefore be removed. A new genus, Afropectinariella M.Simo & Stévart, is described and the following combinations are made: Afropectinariella atlantica (Stévart & Droissart) M.Simo & Stévart, Afropectinariella doratophylla (Summerh.) M.Simo & Stévart, Afropectinariella gabonensis (Summerh.) M.Simo & Stévart, Afropectinariella pungens (Schltr.) M.Simo & Stévart and Afropectinariella subulata (Lindl.) M.Simo & Stévart.

Phylogenetic climatic niche conservatism and evolution of climatic suitability in Neotropical Angraecinae (Vandeae, Orchidaceae) and their closest African relatives

In the present study we investigate the concept of phylogenetic niche conservatism (PNC) within the American species of angraecoid orchids (Campylocentrum and Dendrophylax) and their closest relatives in the Old World (Angraecum) using ecological niche modelling (ENM). The predicted niche occupancy profiles were matched with the outcomes of previous phylogenetic studies to reconstruct the evolution of climatic suitability within the orchid group studied and evaluate the role of niche differentiation in the speciation of Angraecinae. No correlation between preferred niches and taxonomic relationships within the orchid group studied was revealed. The climatic suitability of the majority of the species overlapped each other, either fully or partially. This pattern is also present in the species of other orchid genera. Our research confirms a significant level of PNC in Orchidaceae, even within taxa exhibiting a transatlantic disjunction. The analysis of the evolution of climatic suitability indicated that the adaptation to various climatic conditions is not a factor that has driven speciation within orchids studied.