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Area cladograms are widely used in historical biogeography to summarize area relationships. Constructing such cladograms is complicated by the existence of widespread taxa (terminal taxa distributed in more than one area), redundant distributions (areas harboring more than one taxon) and missing areas (areas of interest absent from some of the compared cladograms). These problems have traditionally been dealt with using Assumptions 0, 1, and 2, but the assumptions are inapplicable to event-based methods of biogeographic analysis because they do not specify the costs of alternative solutions and may result in non-overlapping solution sets. The present paper presents the argument that only widespread terminals pose a problem to event-based methods, and three possible solutions are described. Under the recent option, the widespread distribution is assumed to be the result of recent dispersal. The ancient option assumes that the widespread distribution is the result of a failure to vicariate, and explains any mismatch between the distribution and the area cladogram by extinction. The free option treats the widespread taxon as an unresolved higher taxon consisting of one lineage occurring in each area, and permits any combination of events and any resolution of the terminal polytomy in explaining the widespread distribution. Algorithms implementing these options are described and applied to Rosen (1978)’s classical data set on Heterandria and Xiphophorus.

A response by authors C. Hoorn et al. to a letter to the editor about their article "Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity” in the November 12, 2010 issue is presented.

Background and Aims: Biogeographical relationships between the Canary Islands and north-west Africa are often explained by oceanic dispersal and geographical proximity. Sister-group relationships between Canarian and eastern African/Arabian taxa, the 'Rand Flora' pattern, are rare among plants and have been attributed to the extinction of north-western African populations. Euphorbia balsamifera is the only representative species of this pattern that is distributed in the Canary Islands and north-west Africa; it is also one of few species present in all seven islands. Previous studies placed African populations of E. balsamifera as sister to the Canarian populations, but this relationship was based on herbarium samples with highly degraded DNA. Here, we test the extinction hypothesis by sampling new continental populations; we also expand the Canarian sampling to examine the dynamics of island colonization and diversification., Methods: Using target enrichment with genome skimming, we reconstructed phylogenetic relationships within E. balsamifera and between this species and its disjunct relatives. A single nucleotide polymorphism dataset obtained from the target sequences was used to infer population genetic diversity patterns. We used convolutional neural networks to discriminate among alternative Canary Islands colonization scenarios., Key Results: The results confirmed the Rand Flora sister-group relationship between western E. balsamifera and Euphorbia adenensis in the Eritreo-Arabian region and recovered an eastern-western geographical structure among E. balsamifera Canarian populations. Convolutional neural networks supported a scenario of east-to-west island colonization, followed by population extinctions in Lanzarote and Fuerteventura and recolonization from Tenerife and Gran Canaria; a signal of admixture between the eastern island and north-west African populations was recovered., Conclusions: Our findings support the Surfing Syngameon Hypothesis for the colonization of the Canary Islands by E. balsamifera, but also a recent back-colonization to the continent. Populations of E. balsamifera from northwest Africa are not the remnants of an ancestral continental stock, but originated from migration events from Lanzarote and Fuerteventura. This is further evidence that oceanic archipelagos are not a sink for biodiversity, but may be a source of new genetic variability., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company.)

The figwort family, Scrophulariaceae, comprises c. 2000 species whose evolutionary relationships at the tribal level have proven difficult to resolve, hindering our ability to understand their origin and diversification. We designed a specific probe kit for Scrophulariaceae, targeting 849 nuclear loci and obtaining plastid regions as by-products. We sampled c. 87% of the genera described in the family and use the nuclear dataset to estimate evolutionary relationships, timing of diversification, and biogeographic patterns. Ten tribes, including two new tribes, Androyeae and Camptolomeae, are supported, and the phylogenetic positions of Androya, Camptoloma, and Phygelius are unveiled. Our study reveals a major diversification at c. 60 million yr ago in some Gondwanan landmasses, where two different lineages diversified, one of which gave rise to nearly 81% of extant species. A Southern African origin is estimated for most modern-day tribes, with two exceptions, the American Leucophylleae, and the mainly Australian Myoporeae. The rapid mid-Eocene diversification is aligned with geographic expansion within southern Africa in most tribes, followed by range expansion to tropical Africa and multiple dispersals out of Africa. Our robust phylogeny provides a framework for future studies aimed at understanding the role of macroevolutionary patterns and processes that generated Scrophulariaceae diversity., (© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation.)

The field of phylogenetics has burgeoned into a great diversity of statistical models, providing researchers with a vast amount of analytical tools for investigating the evolutionary theory. This abundance of theoretical work has the merit that many different aspects of evolution can be investigated using various types of data. However, empiricists may sometimes struggle to find the right model for their needs amid such variety. In particular, some computer programs gather the theory of many different models, published in hundreds of different papers, within the same operational framework. This makes it particularly difficult for users to obtain comprehensive information about the assumptions and structure of various models. Yet, a large part of phylogenetic models are structured in individual modules that can be linked together in the same conceptual framework, akin to some sort of phylogenetic supermodel. In this paper, we propose to browse through the network of phylogenetic models, emphasizing their modular structure, with the purpose to outline the commonalities and differences of individual models. Focusing on probabilistic models, we describe how to go from the model assumptions to the corresponding probability distributions as pedagogically as possible. To achieve this task, we resort heavily on graph theory to represent the probabilistic relationships among parameters and data, and present the models in their most elementary form (i.e. including parameters that are generally marginalized out), which simplifies the mathematics considerably. We concentrate on models designed for species trees, but evoke the link with other types of trees (e.g. gene trees)., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

Angiosperm lineages in aquatic environments are characterized by high structural and functional diversity, and wide distributions. A long-standing evolutionary riddle is what processes have caused the relatively low diversity of aquatic angiosperms compared to their terrestrial relatives. We use diversification and ancestral reconstruction models with a comprehensive > 10 000 genus angiosperm phylogeny to elucidate the macroevolutionary dynamics associated with transitions of terrestrial plants to water. Our study reveals that net diversification rates are significantly lower in aquatic than in terrestrial angiosperms due to lower speciation and higher extinction. Shifts from land to water started early in angiosperm evolution, but most events were concentrated during the last c. 25 million years. Reversals to a terrestrial habitat started only 40 million years ago, but occurred at much higher rates. Within aquatic angiosperms, the estimated pattern is one of gradual accumulation of lineages, and relatively low and constant diversification rates throughout the Cenozoic. Low diversification rates, together with infrequent water transitions, account for the low diversity of aquatic angiosperms today. The stressful conditions and small global surface of the aquatic habitat available for angiosperms are hypothesized to explain this pattern., (© 2022 The Authors New Phytologist © 2022 New Phytologist Foundation.)

New RNA-binding small-molecule scaffolds are needed to unleash the pharmacological potential of RNA targets. Here we have applied a pharmacophore-based virtual screening approach, seldom used in the RNA recognition field, to identify novel conformational inhibitors of the hepatitis C virus internal ribosome entry site. The conformational effect of the screening hits was assessed with a fluorescence resonance energy transfer assay, and the affinity, specificity, and binding site of the ligands were determined using a combination of fluorescence intensity and NMR spectroscopy experiments. The results indicate that this strategy can be successfully applied to discover RNA conformational inhibitors bearing substantially less positive charge than the reference ligands. This methodology can potentially be accommodated to other RNA motifs of pharmacological interest, facilitating the discovery of novel RNA-targeted molecules.

The salinity barrier that separates marine and freshwater biomes is probably the most important division in biodiversity on Earth. Those organisms that successfully performed this transition had access to new ecosystems while undergoing changes in selective pressure, which often led to major shifts in diversification rates. While these transitions have been extensively investigated in animals, the tempo, mode, and outcome of crossing the salinity barrier have been scarcely studied in other eukaryotes. Here, we reconstructed the evolutionary history of the species complex Cyphoderia ampulla (Euglyphida: Cercozoa: Rhizaria) based on DNA sequences from the nuclear SSU rRNA gene and the mitochondrial cytochrome oxidase subunit I gene, obtained from publicly available environmental DNA data (GeneBank, EukBank) and isolated organisms. A tree calibrated with euglyphid fossils showed that four independent transitions towards freshwater systems occurred from the mid-Miocene onwards, coincident with important fluctuations in sea level. Ancestral trait reconstructions indicated that the whole family Cyphoderiidae had a marine origin and suggest that ancestors of the freshwater forms were euryhaline and lived in environments with fluctuating salinity. Diversification rates did not show any obvious increase concomitant with ecological transitions, but morphometric analyses indicated that species increased in size and homogenized their morphology after colonizing the new environments. This suggests adaptation to changes in selective pressure exerted by life in freshwater sediments., (© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Quaternary climatic oscillations had a large impact on European biogeography. Alternation of cold and warm stages caused recurrent glaciations, massive vegetation shifts, and large-scale range alterations in many species. The Eurasian steppe biome and its grasslands are a noteworthy example; they underwent climate-driven, large-scale contractions during warm stages and expansions during cold stages. Here, we evaluate the impact of these range alterations on the late Quaternary demography of several phylogenetically distant plant and insect species, typical of the Eurasian steppes. We compare three explicit demographic hypotheses by applying an approach combining convolutional neural networks with approximate Bayesian computation. We identified congruent demographic responses of cold stage expansion and warm stage contraction across all species, but also species-specific effects. The demographic history of the Eurasian steppe biota reflects major paleoecological turning points in the late Quaternary and emphasizes the role of climate as a driving force underlying patterns of genetic variance on the biome level., (© 2022. The Author(s).)

Changes in life history traits are often considered speciation triggers and can have dramatic effects on the evolutionary history of a lineage. Here, we examine the consequences of changes in two life history traits, host-type and phoresy, in the hypermetamorphic blister beetles, Meloidae. Subfamilies Nemognathinae and Meloinae exhibit a complex life cycle involving multiple metamorphoses and parasitoidism. Most genera and tribes are bee-parasitoids, and include phoretic or nonphoretic species, while two tribes feed on grasshopper eggs. These different life strategies are coupled with striking differences in species richness among clades. We generated a mitogenomic phylogeny for Nemognathinae and Meloinae, confirming the monophyly of these two clades, and used the dated phylogeny to explore the association between diversification rates and changes in host specificity and phoresy, using state-dependent speciation and extinction (SSE) models that include the effect of hidden traits. To account for the low taxon sampling, we implemented a phylogenetic-taxonomic approach based on birth-death simulations, and used a Bayesian framework to integrate parameter and phylogenetic uncertainty. Results show that the ancestral hypermetamorphic Meloidae was a nonphoretic bee-parasitoid, and that transitions towards a phoretic bee-parasitoid and grasshopper parasitoidism occurred multiple times. Nonphoretic bee-parasitoid lineages exhibit significantly higher relative extinction and lower diversification rates than phoretic bee-and grasshopper-parasitoids, but no significant differences were found between the latter two strategies. This suggests that Orthopteran host shifts and phoresy contributed jointly to the evolutionary success of the parasitoid meloidae. We also demonstrate that SSE models can be used to identify hidden traits coevolving with the focal trait in driving a lineage's diversification dynamics., (© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Lineage dispersal is a basic macroevolutionary process shaping the distribution of biodiversity. Probabilistic approaches in biogeography, epidemiology, and macroecology often model dispersal as a background process to explain extant or infer past distributions. We propose framing questions around the mode, timing, rate, and direction of lineage dispersal itself, from a lineage- or geography-centric perspective. We review available methods for modelling lineage dispersal. Likelihood- and simulation-based approaches to modelling dispersal have made progress in accounting for the variation of lineage dispersal over space, time, and branches of a phylogeny and its interaction with diversification. Methodological improvements, guided by a focus on model adequacy, will lead to more realistic models that can answer fundamental questions about the tempo and mode of lineage dispersal., Competing Interests: Declaration of interests No interests are declared., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Premise: Genera that are widespread, with geographically discontinuous distributions and represented by few species, are intriguing. Is their achieved disjunct distribution recent or ancient in origin? Why are they species-poor? The Rand Flora is a continental-scale pattern in which closely related species appear codistributed in isolated regions over the continental margins of Africa. Genus Camptoloma (Scrophulariaceae) is the most notable example, comprising three species isolated from each other on the northwest, eastern, and southwest Africa., Methods: We employed Sanger sequencing of nuclear and plastid markers, together with genomic target sequencing of 2190 low-copy nuclear genes, to infer interspecies relationships and the position of Camptoloma within Scrophulariaceae by using supermatrix and multispecies-coalescent approaches. Lineage divergence times and ancestral ranges were inferred with Bayesian Markov chain Monte Carlo (MCMC) approaches. The population history was estimated with phylogeographic coalescent methods., Results: Camptoloma rotundifolium, restricted to Southern Africa, was shown to be a sister species to the disjunct clade formed by C. canariense, endemic to the Canary Islands, and C. lyperiiflorum, distributed in the Horn of Africa-Southern Arabia. Camptoloma was inferred to be sister to the mostly South African tribes Teedieae and Buddlejeae. Stem divergence was dated in the Late Miocene, while the origin of the extant disjunction was inferred as Early Pliocene., Conclusions: The current disjunct distribution of Camptoloma across Africa was likely the result of fragmentation and extinction and/or population bottlenecking events associated with historical aridification cycles during the Neogene; the pattern of species divergence, from south to north, is consistent with the "climatic refugia" Rand Flora hypothesis., (© 2021 The Authors. American Journal of Botany published by Wiley Periodicals LLC on behalf of Botanical Society of America.)

The European steppes and their biota have been hypothesized to be either young remnants of the Pleistocene steppe belt or, alternatively, to represent relicts of long-term persisting populations; both scenarios directly bear on nature conservation priorities. Here, we evaluate the conservation value of threatened disjunct steppic grassland habitats in Europe in the context of the Eurasian steppe biome. We use genomic data and ecological niche modelling to assess pre-defined, biome-specific criteria for three plant and three arthropod species. We show that the evolutionary history of Eurasian steppe biota is strikingly congruent across species. The biota of European steppe outposts were long-term isolated from the Asian steppes, and European steppes emerged as disproportionally conservation relevant, harbouring regionally endemic genetic lineages, large genetic diversity, and a mosaic of stable refugia. We emphasize that conserving what is left of Europe's steppes is crucial for conserving the biological diversity of the entire Eurasian steppe biome.

The 3'X domain of hepatitis C virus has been reported to control viral replication and translation by modulating the exposure of a nucleotide segment involved in a distal base-pairing interaction with an upstream 5BSL3.2 domain. To study the mechanism of this molecular switch, we have analyzed the structure of 3'X mutants that favor one of the two previously proposed conformations comprising either two or three stem-loops. Only the two-stem conformation was found to be stable and to allow the establishment of the distal contact with 5BSL3.2, and also the formation of 3'X domain homodimers by means of a universally conserved palindromic sequence. Nucleotide changes disturbing the two-stem conformation resulted in poorer replication and translation levels, explaining the high degree of conservation detected for this sequence. The switch function attributed to the 3'X domain does not occur as a result of a transition between two- and three-stem conformations, but likely through the sequestration of the 5BSL3.2-binding sequence by formation of 3'X homodimers., (© 2020 Castillo-Martínez et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)

Mass extinction events (MEEs), defined as significant losses of species diversity in significantly short time periods, have attracted the attention of biologists because of their link to major environmental change. MEEs have traditionally been studied through the fossil record, but the development of birth-death models has made it possible to detect their signature based on extant-taxa phylogenies. Most birth-death models consider MEEs as instantaneous events where a high proportion of species are simultaneously removed from the tree ("single pulse" approach), in contrast to the paleontological record, where MEEs have a time duration. Here, we explore the power of a Bayesian Birth-Death Skyline (BDSKY) model to detect the signature of MEEs through changes in extinction rates under a "time-slice" approach. In this approach, MEEs are time intervals where the extinction rate is greater than the speciation rate. Results showed BDSKY can detect and locate MEEs but that precision and accuracy depend on the phylogeny's size and MEE intensity. Comparisons of BDSKY with the single-pulse Bayesian model, CoMET, showed a similar frequency of Type II error and neither model exhibited Type I error. However, while CoMET performed better in detecting and locating MEEs for smaller phylogenies, BDSKY showed higher accuracy in estimating extinction and speciation rates., (© 2019 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.)