Mathieu Perret

Accurate knowledge of phylogenetic relationships and divergence time among plant species composing a regional flora is crucial for understanding the origin of the biodiversity patterns we observe today. Despite advances in phylogenomics, resources available for reconstructing regional phylogenies are still largely incomplete and poorly resolved at the species level. We developed a workflow to assemble a phylogenetic dataset for a regional flora using Angiosperms353 target‐enrichment and high‐throughput genome sequencing. We sampled tissues from freshly collected plants and herbarium specimens representing the angiosperm diversity of the Geneva canton in Switzerland (1098 species). We used ORTHOSKIM to recover targeted nuclear genes and plastid loci from off‐target reads, estimated relationships and time divergence using IQTREE, weighted‐ASTRAL and treePL, and compared the results obtained from nuclear and plastid genes. We recovered a mean of 289 nuclear and 54 plastid genes for 1316 taxa, representing 92% of the species native to the Geneva canton. We demonstrate that nuclear genes provide increased resolution and phylogenetic support, but similar divergence time estimates compared to plastomes. Our workflow based on Angiosperms353 data provides a phylogenetic framework for an entire regional flora that is consistent with current systematic knowledge and more resolved and complete at the infrageneric level than trees obtained from phylogenetic resources available for angiosperms. This type of genomic data opens perspectives for fine‐scale biodiversity and conservation research that integrates evolutionary history.

Hyphaene is a coryphoid palm genus native to semi-arid and arid regions of continental Africa and Madagascar, with one disjunct species found in western India. Several species within the genus are particularly notable for their aerial dichotomous branching, a rare and distinctive feature among palms. Many Hyphaene species, commonly known as ‘doum palms’ or ‘gingerbread palms’, are of significant economic value, providing food, construction materials, and fibres. However, despite its importance, the taxonomy and evolutionary history of the genus remain poorly understood. In this study, we examine species delimitation, phylogenetic relationships, and the diversification dynamics of Hyphaene through a combination of population genetics, phylogenetics, and dating approaches, utilizing genomic data from targeted capture of nuclear genes. Our results reveal clear genetic boundaries for five of the seven species analysed, with low levels of introgression, indicating strong species integrity. Phylogenetic analysis suggests that the aerial dichotomous branching growth form evolved only once within the genus. Although Hyphaene likely originated in the Eocene, we estimated an Oligocene origin of the extant species diversity, with intra-specific diversification beginning in the Miocene. This diversification is closely linked to the fragmentation and subsequent expansion of arid habitats across Africa.

The alpine clematis (Clematis alpina L., Ranunculaceae) is a liana growing in mountain regions of northern Eurasia. In the European Alpine region, where the subspecies C. alpina subsp. alpina occurs, a few populations are isolated from the main range in the peripheral north-western Prealps, a relatively understudied but biogeographically important region. It has been shown that such edge populations could potentially contain a source of unique genetic variability that reflects past biogeographical and microevolutionary processes. We tested this hypothesis using sequence capture data and a large population sampling across the species range. We show that individuals from the north-western Prealps form a genetic cluster that is clearly distinct from the other individuals of the European subspecies C. alpina subsp. alpina. This cluster adds to two other geographically driven clusters with a larger spatial extent, that include populations from the rest of the Alps and from the Carpathians/Balkan Peninsula mountains, respectively. Genetic diversity indices such as inbreeding and nucleotide diversity are the highest and lowest, respectively, for the Prealps populations indicating a possible loss of diversity. Our results demonstrate the biogeographical importance of isolated, marginal populations as sources of distinctive lineages, and highlight the conservation value of the north-western Prealps populations of alpine clematis. They also point out the promising use of sequence capture of gene selected for studies at high phylogenetic level for studies at intraspecific level.

Tapina villosa (Gesneriaceae) was published by George Gardner in 1842, based on material he collected in Serra de Natividade (Tocantins, Brazil) in 1840. The species is now recognized as Goyazia villosa (Gardner) R.A. Howard. Since Gardner’s travels in Central Brazil, this species had not been collected again and the taxon was considered as possibly extinct. After a long time, we report the discovery of two new populations of G. villosa in the municipality of Palmas and in the Estação Ecológica Serra Geral do Tocantins, ca. 200 and 100 km north of the Serra de Natividade, respectively. The newly collected materials allow us to better characterize the morphology and infer the phylogenetic placement of this poorly-known species. Here we demonstrate that G. villosa is closely related to G. rupicola in a clade including Goyazia and Mandirola species, and provide an updated description of the species, including field images, photographic plate, information on its distribution and habitat, and a taxonomic key for the species of Goyazia.

The Gesneriaceae consists of around 150 genera and c. 3750 species with a predominantly tropical and subtropical distribution across all continents. Although previous studies have proposed an American origin of Gesneriaceae, the biogeographic history of this pantropical plant family is still unclear, particularly in the Old World. To address this, we assembled the most comprehensively sampled matrix of Gesneriaceae with 143 Gesneriaceae genera and 355 species, including key samples from Sri Lanka analysed here for the first time. We generated molecular phylogenies based on four plastid gene regions (ndhF, matK, rps16 and trnL-F), obtained fossil-calibrated trees, and reconstructed ancestral areas and dispersal routes using Bayesian methods. Our results confirm the origin for the family in the Early Palaeocene (67. Ma) in the region of present day Central America & Andean South America, and that diversity in the Old World originated from a longdistance dispersal event from South America around 59 Ma, most likely to the Indian plate, which was an island at the time. This lineage then dispersed to Malesia and later East Asia, which would ultimately become a major centre of diversity and source of many dispersals to other regions. Our results thus highlight the Indian plate as a likely key player in the early diversification of Old World Gesneriaceae, even though it is now more diverse elsewhere, and hence offer novel insights into this plant family’s dispersal routes and areas of diversification in the Old World.

Plant–hummingbird interactions are considered a classic example of coevolution, a process in which mutually dependent species influence each other's evolution. Plants depend on hummingbirds for pollination, whereas hummingbirds rely on nectar for food. As a step towards understanding coevolution, this review focuses on the macroevolutionary consequences of plant–hummingbird interactions, a relatively underexplored area in the current literature. We synthesize prior studies, illustrating the origins and dynamics of hummingbird pollination across different angiosperm clades previously pollinated by insects (mostly bees), bats, and passerine birds. In some cases, the crown age of hummingbirds pre‐dates the plants they pollinate. In other cases, plant groups transitioned to hummingbird pollination early in the establishment of this bird group in the Americas, with the build‐up of both diversities coinciding temporally, and hence suggesting co‐diversification. Determining what triggers shifts to and away from hummingbird pollination remains a major open challenge. The impact of hummingbirds on plant diversification is complex, with many tropical plant lineages experiencing increased diversification after acquiring flowers that attract hummingbirds, and others experiencing no change or even a decrease in diversification rates. This mixed evidence suggests that other extrinsic or intrinsic factors, such as local climate and isolation, are important covariables driving the diversification of plants adapted to hummingbird pollination. To guide future studies, we discuss the mechanisms and contexts under which hummingbirds, as a clade and as individual species (e.g. traits, foraging behaviour, degree of specialization), could influence plant evolution. We conclude by commenting on how macroevolutionary signals of the mutualism could relate to coevolution, highlighting the unbalanced focus on the plant side of the interaction, and advocating for the use of species‐level interaction data in macroevolutionary studies.

Besleria, a genus of perennial herbs, shrubs, or small trees growing in the understorey of rainforests, is one of the largest genera of neotropical Gesneriaceae, with over 165 species. Despite the ecological importance and ubiquity of Besleria in rainforest ecosystems, taxonomic and evolutionary studies of Besleria are limited. Here, we generated a phylogenetic analysis of Besleria using four nuclear and chloroplast DNA regions (ITS, matK, rps16, and trnL-trnF) covering more than 50% of the recognized species, along with two secondary calibration points to infer divergence times. Our results support the monophyly of Besleria and allowed us to revise the infrageneric classification and biogeographical history of the genus. We identified five major clades that do not correspond to sections or subsections in previous classifications. These clades are well circumscribed geographically but remain difficult to characterize using previously hypothesized morphological characters. Biogeographical reconstructions indicate an origin in the northern Andes during the Middle Miocene (ca. 15 Mya). The current distribution patterns of this plant group have been significantly shaped by geological and climatic events, particularly Andean uplift and the formation of the Panama Isthmus.

Aim: Central America is largely covered by hyperdiverse, yet poorly understood, rain forests. Understorey palms are diverse components of these forests, but little is known about their historical assembly. It is not clear when palms in Central America reached present diversity levels and whether most species arrived from neighbouring regions or evolved locally. We addressed these questions using the most species‐rich American palm clades indicative of rain forests. We reconstructed and compared their phylogenomic and biogeographical history with the diversification of 54 other plant lineages, to gain a better understanding of the processes that shaped the assembly of Central American rain forests.Location: Central America.Time period: Cretaceous to present.Major taxa studied: Arecaceae: Arecoideae: Bactridinae, Chamaedoreeae, Geonomateae.Methods: We sampled 218 species through fieldwork and living collections. We sequenced their genomic DNA using target sequence‐capture procedures. Using 12 calibration points, we reconstructed dated phylogenies under three approaches (multispecies coalescent, maximum likelihood and Bayesian inference), conducted biogeographical analyses (dispersal–extinction–cladogenesis) and estimated phylogenetic diversity metrics.Results: Dated phylogenies revealed intense diversification in Central America from 12 Ma. Local diversification events were four times more frequent than dispersal events, and we found strong phylogenetic clustering in relationship to Central America.Main conclusions: Our results suggest that most understorey palm species that characterize the Central American rain forests today evolved locally after repeated dispersal events, mostly from South America. Understorey palms in Central American rain forests diversified primarily after closure of the Central American Seaway at c. 13 Ma, suggesting that the Great American Biotic Interchange was a major trigger for plant diversification in Central American rain forests. This recent diversification contrasts with the much earlier existence of rain forest palms in neighbouring South America since c. 58 Ma. We found similar timings of diversification in 54 other seed plant lineages, suggesting an unexpectedly recent assembly of the hyperdiverse Central American flora.