Increased resolution in the face of conflict: phylogenomics of the Neotropical bellflowers (Campanulaceae: Lobelioideae), a rapid plant radiation

Background and Aims- The centropogonid clade (Lobelioideae: Campanulaceae) is an Andean-centered rapid radiation characterized by repeated convergent evolution of morphological traits, including fruit type and pollination syndromes. While previous studies have resolved relationships of lineages with fleshy fruits into subclades, relationships among capsular species remain unresolved. This lack of resolution has impeded reclassification of non-monophyletic genera, whose current taxonomy relies heavily on traits that have undergone convergent evolution. Methods- Targeted sequence capture using a probeset recently developed for the centropogonid clade was used to obtain phylogenomic data from DNA extracted from both silica-dried and herbarium leaf tissue. These data were used to infer relationships among species using concatenated and partitioned species tree methods, and to quantify gene tree discordance. Key Results- While silica-dried leaf tissue resulted in more and longer sequence data, the inclusion of herbarium samples improved phylogenetic reconstruction. Relationships among baccate lineages are similar previous studies, though differ within and among capsular lineages. We improve phylogenetic resolution of Siphocampylus, which forms ten groups of closely related species which we informally name. Two subclades of Siphocampylus and two individual species are rogue taxa whose placement differs widely across analyses. Gene tree discordance (including cytonuclear discordance) is rampant. Conclusions- The first phylogenomic study of the centropogonid clade considerably improves our understanding of relationships in this rapid radiation. Differences across analyses and the possibility of additional lineage discoveries still hamper a solid and stable reclassification. Rapid morphological innovation corresponds with a high degree of phylogenomic complexity, including cytonuclear discordance, nuclear gene tree conflict, and well-supported differences between analyses based on different nuclear loci. Taken together, these results point to a potential role of hemiplasy underlying repeated convergent evolution. This hallmark of rapid radiations is likely present in many other species-rich Andean plant radiations.

Rapid formation methods of arrays of randomly distributed Au and Ag nanoparticles, their morphologies and optical characteristics

By the method of rapid radiation heating (at a speed of 20-25 K/s) of Au and Ag films with a thickness of 4-35 nm to temperatures of 573-693 K in air and in the process of vacuum deposition of silver on heated (up to 700 K at a heating rate of 10 K/s ) glass substrates formed Au and Ag NPs arrays with nanoparticle sizes from several tens to hundreds of nanometers, the position λSPR of which is in the range of 520-597 nm for Au NPs and 424-509 nm for Ag NPs. It is established that the average size of nanoparticles depends on the thickness of gold and silver films and the annealing temperature. The results testify that glass substrates with arrays of randomly distributed gold NPs can be used as effective SERS-substrates for the investigation of Raman spectra of nanosized (50-100 nm) chalcogenide films.

Macroevolutionary pattern of Saussurea (Asteraceae) provides insights into the drivers of radiating diversification

Evolutionary radiations have intrigued biologists for more than a century, yet our understanding of the drivers of radiating diversification is still limited. We investigate the roles of environmental and species-intrinsic factors in driving the rapid radiation of Saussurea (Asteraceae) by deploying a number of palaeoenvironment-, diversity- and trait-dependent models, as well as ecological distribution data. We show that three main clades of Saussurea began to diversify in the Miocene almost simultaneously, with increasing diversification rates (DRs) negatively dependent on palaeotemperature but not dependent on species diversity. Our trait-dependent models detect some adaptive morphological innovations associated with DR shifts, while indicating additional unobserved traits are also likely driving diversification. Accounting for ecological niche data, we further reveal that accelerations in DRs are correlated with niche breadth and the size of species' range. Our results point out a macroevolutionary scenario where both adaptive morphological evolution and ecological opportunities provided by palaeoenvironmental fluctuations triggered an exceptionally radiating diversification. Our study highlights the importance of integrating phylogenomic, morphological, ecological and model-based approaches to illustrate evolutionary dynamics of lineages in biodiversity hotspots.

Bee flowers drive macroevolutionary diversification in long-horned bees

The role of plant–pollinator interactions in the rapid radiation of the angiosperms have long fascinated evolutionary biologists. Studies have brought evidence for pollinator-driven diversification of various plant lineages, particularly plants with specialized flowers and concealed rewards. By contrast, little is known about how this crucial interaction has shaped macroevolutionary patterns of floral visitors. In particular, there is currently no empirical evidence that floral host association has increased diversification in bees, the most prominent group of floral visitors that essentially rely on angiosperm pollen. In this study, we examine how floral host preference influenced diversification in eucerine bees (Apidae, Eucerini), which exhibit large variations in their floral associations. We combine quantitative pollen analyses with a recently proposed phylogenetic hypothesis, and use a state speciation and extinction probabilistic approach. Using this framework, we provide the first evidence that multiple evolutionary transitions from host plants with accessible pollen to restricted pollen from ‘bee-flowers’ have significantly increased the diversification of a bee clade. We suggest that exploiting host plants with restricted pollen has allowed the exploitation of a new ecological niche for eucerine bees and contributed both to their colonization of vast regions of the world and their rapid diversification.

Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species (Gila robusta complex) in the Colorado River

Species are indisputable units for biodiversity conservation, yet their delimitation is fraught with both conceptual and methodological difficulties. A classic example is the taxonomic controversy surrounding the Gila robusta complex in the lower Colorado River of southwestern North America. Nominal species designations were originally defined according to weakly diagnostic morphological differences, but these conflicted with subsequent genetic analyses. Given this ambiguity, the complex was re-defined as a single polytypic unit, with the proposed ‘threatened’ status under the U.S. Endangered Species Act of two elements being withdrawn. Here we re-evaluated the status of the complex by utilizing dense spatial and genomic sampling (N = 387 and >22k loci), coupled with SNP-based coalescent and polymorphism-aware phylogenetic models. In doing so, we found that all three species were indeed supported as evolutionarily independent lineages, despite widespread phylogenetic discordance. To juxtapose this discrepancy with previous studies, we first categorized those evolutionary mechanisms driving discordance, then tested (and subsequently rejected) prior hypotheses which argued phylogenetic discord in the complex was driven by the hybrid origin of Gila nigra. The inconsistent patterns of diversity we found within G. robusta were instead associated with rapid Plio-Pleistocene drainage evolution, with subsequent divergence within the ‘anomaly zone’ of tree space producing ambiguities that served to confound prior studies. Our results not only support resurrection of the three species as distinct entities, but also offer an empirical example of how phylogenetic discordance can be categorized within other recalcitrant taxa, particularly when variation is primarily partitioned at the species-level.

Comprehensive species sampling and sophisticated algorithmic approaches refute the monophyly of Arachnida

Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. While conflicting hypotheses prevail in morphological and molecular datasets alike, the monophyly of Arachnida is nearly universally accepted. Though a small number of phylotranscriptomic analyses have recovered arachnid monophyly, these did not sample all living chelicerate orders. We generated a dataset of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternatives algorithmic approaches to species tree inference. Investigation of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the effect of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.

Biogeographic Drivers of Evolutionary Radiations

Some lineages radiate spectacularly when colonizing a region, but others do not. Large radiations are often attributed to species’ adaptation into niches, or to other drivers, such as biogeography including dispersal ability and spatial structure of the landscape. Here we aim to disentangle the factors determining radiation size, by modeling simplified scenarios without the complexity of explicit niches. We build a spatially structured neutral model free from niches and incorporating a form of protracted speciation that accounts for gene flow between populations. We find that a wide range of radiation sizes are possible in this model depending on the combination of geographic isolation and species’ dispersal ability. At extremely low rates of dispersal between patches, each patch maintains its own endemic species. Intermediate dispersal rates foster larger radiations as they allow occasional movement between patches whilst sufficiently restricting gene flow to support further speciation in allopatry. As dispersal rates increase further, a critical point is reached at which demographically identical lineages may vary greatly in radiation size due to rare and stochastic dispersal events. At the critical point in dispersal frequency, some lineages remain a single species for a comparatively long time, whilst others with identical characteristics produce the largest radiations of all via a new mechanism for rapid radiation that we term a ‘radiation cascade’. Given a single species covering many patches connected with gene flow, a radiation cascade is triggered when stochastic dispersal is unusually low for a period, leading to an initial speciation event. This speciation means there are fewer individuals per species and thus further reduced gene flow between conspecifics. Reduced gene flow in turn makes it easier for further speciation to occur. During a radiation cascade, dispersal of individuals between patches continues at the same rate as before, but due to the increasing diversity it primarily introduces novel species that will later speciate, rather than adding to gene flow of existing species. Once a radiation cascade begins, it continues rapidly until it is arrested by a new equilibrium between speciation and extinction. We speculate that such radiation cascades may occur more generally and are not only present in neutral models. This process may help to explain rapid radiation, and the extreme radiation sizes of certain lineages with dispersing ancestors. Whilst niches no doubt play a role in community assembly, our findings lead us to question whether diversification and adaptation into niches is sometimes an effect of speciation and rapid radiation, rather than its cause.

Rapid radiation of the inner Indo-European languages: an advanced approach to Indo-European lexicostatistics

In this article we present a new reconstruction of Indo-European phylogeny based on 13 110-item basic wordlists for protolanguages of IE subgroups (Proto-Germanic, Proto-Slavic, etc.) or ancient languages of the corresponding subgroups (Hittite, Ancient Greek, etc.). We apply reasonably formal techniques of linguistic data collection and post-processing (onomasiological reconstruction, derivational drift elimination, homoplastic optimization) that have been recently proposed or specially developed for the present study. We use sequential phylogenetic workflow and obtain a consensus tree based on several algorithms (Bayesian inference, maximum parsimony, neighbor joining; without topological constraints applied). The resulting tree topology and datings are entirely compatible with established expert views. Our main finding is the multifurcation of the Inner IE clade into four branches ca. 3357–2162 bc: (1) Greek-Armenian, (2) Albanian, (3) Italic-Germanic-Celtic, (4) Balto-Slavic–Indo-Iranian. The proposed radiation scenario may be reconciled with diverse opinions on Inner IE branchings previously expressed by Indo-Europeanists.