Particulate-Droplet Coalescence and Self-Transport on Superhydrophobic Surfaces

Particulate transport from surfaces governs a variety of phenomena including fungal spore dispersal, bioaerosol transmission, and self-cleaning. Here, we report a previously unidentified mechanism governing passive particulate removal from superhydrophobic surfaces, where a particle coalescing with a water droplet (∼10 to ∼100 μm) spontaneously launches. Compared to previously discovered coalescence-induced binary droplet jumping, the reported mechanism represents a more general capillary-inertial dominated transport mode coupled with particle/droplet properties and is typically mediated by rotation in addition to translation. Through wetting and momentum analyses, we show that transport physics depends on particle/droplet density, size, and wettability. The observed mechanism presents a simple and passive pathway to achieve self-cleaning on both artificial as well as biological materials as confirmed here with experiments conducted on butterfly wings, cicada wings, and clover leaves. Our findings provide insights into particle-droplet interaction and spontaneous particulate transport, which may facilitate the development of functional surfaces for medical, optical, thermal, and energy applications.

Convergent Morphological Evolution in Silene Sect. Italicae (Caryophyllaceae) in the Mediterranean Basin

Recent divergence can obscure species boundaries among closely related taxa. Silene section Italicae (Caryophyllaceae) has been taxonomically controversial, with about 30 species described. We investigate species delimitation within this section using 500 specimens sequenced for one nuclear and two plastid markers. Despite the use of a small number of genes, the large number of sequenced samples allowed confident delimitation of 50% of the species. The delimitation of other species (e.g., Silene nemoralis, S. nodulosa and S. andryalifolia) was more challenging. We confirmed that seven of the ten chasmophyte species in the section are not related to each other but are, instead, genetically closer to geographically nearby species belonging to Italicae yet growing in open habitats. Adaptation to chasmophytic habitats therefore appears to have occurred independently, as a result of convergent evolution within the group. Species from the Western Mediterranean Basin showed more conflicting species boundaries than species from the Eastern Mediterranean Basin, where there are fewer but better-delimited species. Significant positive correlations were found between an estimation of the effective population size of the taxa and their extent of occurrence (EOO) or area of occupancy (AOO), and negative but non-significant correlations between the former and the posterior probability (PP) of the corresponding clades. These correlations might suggest a lower impact of incomplete lineage sorting in species with low effective population sizes and small distributional ranges compared with that in species inhabiting large areas. Finally, we confirmed that S. italica and S. nemoralis are distinct species, that S. nemoralis might furthermore include two different species and that S. velutina from Corsica and S. hicesiae from the Lipari Islands are sister species.

Using all gene families vastly expands data available for phylogenomic inference

Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most phylogenomic studies identify putative single-copy orthologs using clustering approaches and retain families with a single sequence per species. This limits the amount of data available by excluding larger families. Recent advances have suggested several ways to include data from larger families. For instance, tree-based decomposition methods facilitate the extraction of orthologs from large families. Additionally, several methods for species tree inference are robust to the inclusion of paralogs and could use all of the data from larger families. Here, we explore the effects of using all families for phylogenetic inference by examining relationships among 26 primate species in detail and by analyzing five additional data sets. We compare single-copy families, orthologs extracted using tree-based decomposition approaches, and all families with all data. We explore several species tree inference methods, finding that identical trees are returned across nearly all subsets of the data and methods for primates. The relationships among Platyrrhini remain contentious; however, the species tree inference method matters more than the subset of data used. Using data from larger gene families drastically increases the number of genes available and leads to consistent estimates of branch lengths, nodal certainty and concordance, and inferences of introgression in primates. For the other data sets, topological inferences are consistent whether single-copy families or orthologs extracted using decomposition approaches are analyzed. Using larger gene families is a promising approach to include more data in phylogenomics without sacrificing accuracy, at least when high-quality genomes are available.

Simplified, Shear Induced Generation of Double Emulsions for Robust Compartmentalization during Single Genome Analysis

Drop microfluidics has driven innovations for high throughput, low input analysis techniques such as single-cell RNA-seq. However, the instability of single emulsion (SE) drops occasionally causes significant merging during drop processing, limiting most applications to single-step reactions in drops. Here, we show that double emulsion (DE) drops address this critical limitation and completely prevent drop contents from mixing. DEs show excellent stability during thermal cycling. More importantly, DEs undergo rupture into the continuous phase instead of merging, preventing content mixing and eliminating unstable drops from the downstream analysis. Due to the lack of drop merging, the monodispersity of drops is maintained throughout a workflow, enabling the deterministic manipulation of drops downstream. We also developed a simple, one-layer DE drop maker compatible with simple surface treatment using a plasma cleaner. The device allows for the robust production of single-core DEs at a wide range of flow rates and better control over the shell thickness, both of which have been significant limitations of conventional two-layer devices. This approach makes the fabrication of DE devices much more accessible, facilitating its broader adoption. Finally, we show that DE droplets eliminate content mixing and maintain compartmentalization of single virus genomes during PCR-based amplification and barcoding, while SEs mixed contents due to merging. With their resistance to content mixing, DE drops have key advantages for multistep reactions in drops, which is limited in SEs due to merging and content mixing.

Peptide-Induced Fractal Assembly of Silver Nanoparticles for Visual Detection of Disease Biomarkers

We report the peptide-programmed fractal assembly of silver nanoparticles (AgNPs) in a diffusion-limited aggregation (DLA) mode, and this change in morphology generates a significant color change. We show that peptides with specific repetitions of defined amino acids (i.e., arginine, histidine, or phenylalanine) can induce assembly and coalescence of the AgNPs (20 nm) into a hyperbranched structure (AgFSs) (∼2 μm). The dynamic process of this assembly was systematically investigated, and the extinction of the nanostructures can be modulated from 400 to 600 nm by varying the peptide sequences and molar ratio. According to this rationale, two strategies of SARS-CoV-2 detection were investigated. The activity of the main protease (Mpro) involved in SARS-CoV-2 was validated with a peptide substrate that can bridge the AgNPs after the proteolytic cleavage. A sub-nanomolar limit of detection (0.5 nM) and the capacity to distinguish by the naked eye in a wide concentration range (1.25-30 nM) were achieved. Next, a multichannel sensor-array based on multiplex peptides that can visually distinguish SARS-CoV-2 proteases from influenza proteases in doped human samples was investigated.

Ecological and Evolutionary Implications of Microbial Dispersal

Dispersal is simply defined as the movement of species across space and time. Despite this terse definition, dispersal is an essential process with direct ecological and evolutionary implications that modulate community assembly and turnover. Seminal ecological studies have shown that environmental context (e.g., local edaphic properties, resident community), dispersal timing and frequency, and species traits, collectively account for patterns of species distribution resulting in either their persistence or unsuccessful establishment within local communities. Despite the key importance of this process, relatively little is known about how dispersal operates in microbiomes across divergent systems and community types. Here, we discuss parallels of macro- and micro-organismal ecology with a focus on idiosyncrasies that may lead to novel mechanisms by which dispersal affects the structure and function of microbiomes. Within the context of ecological implications, we revise the importance of short- and long-distance microbial dispersal through active and passive mechanisms, species traits, and community coalescence, and how these align with recent advances in metacommunity theory. Conversely, we enumerate how microbial dispersal can affect diversification rates of species by promoting gene influxes within local communities and/or shifting genes and allele frequencies via migration or de novo changes (e.g., horizontal gene transfer). Finally, we synthesize how observed microbial assemblages are the dynamic outcome of both successful and unsuccessful dispersal events of taxa and discuss these concepts in line with the literature, thus enabling a richer appreciation of this process in microbiome research.

Numerical Modeling of Transient Two-Phase Flow and the Coalescence and Breakup of Bubbles in a Continuous Casting Mold

The multiphase flow and spatial distribution of bubbles inside a continuous casting (CC) mold is a popular research issue due to its direct impact on the quality of the CC slab. The behavior of bubbles in the mold, and how they coalesce and break apart, have an important influence on the flow pattern and entrapment of bubbles. However, due to the limitations of experiments and measurement methods, it is impossible to directly observe the multiphase flow and bubble distribution during the CC process. Thus, a three-dimensional mathematical model which combined the large eddy simulation (LES) turbulent model, VOF multiphase model, and discrete phase model (DPM) was developed to study the transient two-phase flow and spatial distribution of bubbles in a continuous casting mold. The interaction between the liquid and bubbles and the coalescence, bounce, and breakup of bubbles were considered. The measured meniscus speed and bubble diameter were in good agreement with the measured results. The meniscus speed increased first and then decreased from the nozzle to the narrow face, with a maximum value of 0.07 m/s, and appeared at 1/4 the width of the mold. The current mathematical model successfully predicted the transient asymmetric two-phase flow and completely reproduced the coalescence, bounce, and breakup of bubbles in the mold. The breakup mainly occurred near the bottom of the submerged entry nozzle (SEN) due to the strong turbulent motion of the molten steel after hitting the bottom of the SEN. The average bubble diameter was about 0.6 mm near the nozzle and gradually decreased to 0.05 mm from the nozzle to the narrow face. The larger bubbles floated up near the SEN due to the effect of their greater buoyancy, while the small bubbles were distributed discretely in the entire mold with the action of the molten steel jet. Overall, the bubbles were distributed in a fan shape. The largest concentration of bubbles was in the lower part of the SEN and the upper edge of the SEN outlet.

Abscisic acid activation of oleosin gene HvOle3 expression prevents the coalescence of protein storage vacuoles in barley aleurone cells

Protein storage vacuoles (PSVs) in aleurone cells coalesce during germination, and this process is highly coupled with mobilization of PSV reserves, allowing de novo synthesis of various hydrolases in aleurone cells for endosperm degradation. Here we show that in barley (Hordeum vulgare L.) oleosins, the major integral proteins of oleosomes are encoded by four genes (HvOle1 to 4), and the expression of HvOle1 and HvOle3 is strongly up-regulated by abscisic acid (ABA), which shows antagonism to gibberellic acid. In aleurone cells, all HvOLEs were subcellularly targeted to the tonoplast of PSVs. Gain-of-function analyses revealed that HvOLE3 effectively delayed PSV coalescence, whereas HvOLE1 only had a moderate effect, with no notable effect of HvOLE2 and 4. With regard to longevity, HvOLE3 chiefly outperformed other HvOLEs, followed by HvOLE1. Experiments swapping the N- and C-terminal domain between HvOLE3 and other HvOLEs showed that the N-terminal region of HvOLE3 is mainly responsible, with some positive effect by the C-terminal region, for mediating the specific preventive effect of HvOLE3 on PSV coalescence. Three ACGT-core elements and the RY-motif were responsible for ABA induction of HvOle3 promoter activity. Transient expression assays using aleurone protoplasts demonstrated that transcriptional activation of the HvOle3 promoter was mediated by transcription factors HvABI3 and HvABI5, which acted downstream of protein kinase HvPKABA1.

Reassessment of Annamocarya sinesis (Carya sinensis) Taxonomy through Concatenation and Coalescence Phylogenetic Analysis

Due to its peculiar morphological characteristics, there is dispute as to whether the genus of Annamocarya sinensis, a species of Juglandaceae, is Annamocarya or Carya. Most morphologists believe it should be distinguished from the Carya genus while genomicists suggest that A. sinensis belongs to the Carya genus. To explore the taxonomic status of A. sinensis using chloroplast genes, we collected chloroplast genomes of 16 plant species and assembled chloroplast genomes of 10 unpublished Carya species. We analyzed all 26 species' chloroplast genomes through two analytical approaches (concatenation and coalescence), using the entire and unique chloroplast coding sequence (CDS) and entire and protein sequences. Our results indicate that the analysis of the CDS and protein sequences or unique CDS and unique protein sequence of chloroplast genomes shows that A. sinensis indeed belongs to the Carya genus. In addition, our analysis shows that, compared to single chloroplast genes, the phylogeny trees constructed using numerous genes showed higher consistency. Moreover, the phylogenetic analysis calculated with the coalescence method and unique gene sequences was more robust than that done with the concatenation method, particularly for analyzing phylogenetically controversial species. Through the analysis, our results concluded that A. sinensis should be called C. sinensis.

The Effects of Copolymer Compatibilizers on the Phase Structure Evolution in Polymer Blends-A Review

This paper summarizes the results of studies describing the effect of block and graft copolymers on the phase structure formation and evolution in immiscible polymer blends. The main phenomenological rules for prediction of the copolymer compatibilization efficiency are briefly described and compared with selected experimental data. The results of the theories of equilibrium distribution of a copolymer between the blend interface and the bulk phases and its effect on the blend interfacial tension are summarized. The theories of the compatibilizer effect on the droplet breakup in flow are analyzed. The mechanisms of the copolymer effect on the coalescence of droplets in flow are compared and their effect on the droplet size is shown. The problems of reliable description of the effect of a copolymer on the coalescence in quiescent state are presented. Obstacles to derivation of a realistic theory of the copolymer effect on the competition between the droplet breakup and coalescence are discussed. Selected experimental data are compared with the theoretical results.

Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone

A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and ASTRAL_BP, are statistically consistent estimators of the unrooted species tree topology under the coalescent when RIs follow a neutral infinite-sites model of mutation and the expected number of new RIs per generation is constant across the species tree. The accuracy of these (and other) methods for inferring species trees from RIs has yet to be assessed on simulated data sets, where the true species tree topology is known. Therefore, we evaluated eight methods given RIs simulated from four model species trees, all of which have short branches and at least three of which are in the anomaly zone. In our simulation study, ASTRAL_BP and SDPquartets always recovered the correct species tree topology when given a sufficiently large number of RIs, as predicted. A distance-based method (ASTRID_BP) and Dollo parsimony also performed well in recovering the species tree topology. In contrast, unordered, polymorphism, and Camin-Sokal parsimony typically fail to recover the correct species tree topology in anomaly zone situations with more than four ingroup taxa. Of the methods studied, only ASTRAL_BP automatically estimates internal branch lengths (in coalescent units) and support values (i.e. local posterior probabilities). We examined the accuracy of branch length estimation, finding that estimated lengths were accurate for short branches but upwardly biased otherwise. This led us to derive the maximum likelihood (branch length) estimate for when RIs are given as input instead of binary gene trees; this corrected formula produced accurate estimates of branch lengths in our simulation study, provided that a sufficiently large number of RIs were given as input. Lastly, we evaluated the impact of data quantity on species tree estimation by repeating the above experiments with input sizes varying from 100 to 100 000 parsimony-informative RIs. We found that, when given just 1 000 parsimony-informative RIs as input, ASTRAL_BP successfully reconstructed major clades (i.e clades separated by branches > 0.3 CUs) with high support and identified rapid radiations (i.e. shorter connected branches), although not their precise branching order. The local posterior probability was effective for controlling false positive branches in these scenarios.

A recovery network leads to the natural recolonization of an archipelago and a potential trailing edge refuge

Rapid environmental change is reshaping ecosystems and driving species loss globally. Carnivore populations have declined and retracted rapidly and have been the target of numerous translocation projects. Success, however, is complicated when these efforts occur in novel ecosystems. Identifying refuges, locations that are resistant to environmental change, within a translocation framework should improve population recovery and persistence. American martens (Martes americana) are the most frequently translocated carnivore in North America. As elsewhere, martens were extirpated across much of the Great Lakes region by the 1930s and, despite multiple translocations beginning in the 1950s, martens remain of regional conservation concern. Surprisingly, martens were rediscovered in 2014 on the Apostle Islands of Lake Superior after a putative absence of >40 yr. To identify the source of martens to the islands and understand connectivity of the reintroduction network, we collected genetic data on martens from the archipelago and from all regional reintroduction sites. In total, we genotyped 483 individual martens, 43 of which inhabited the Apostle Islands (densities 0.42-1.46 km^-2 ). Coalescent analyses supported the contemporary recolonization of the Apostle Islands with progenitors likely originating from Michigan, which were sourced from Ontario. We also identified movements by a first-order relative between the Apostle Islands and the recovery network. We detected some regional gene flow, but in an unexpected direction: individuals moving from the islands to the mainland. Our findings suggest that the Apostle Islands were naturally recolonized by progeny of translocated individuals and now act as a source back to the reintroduction sites on the mainland. We suggest that the Apostle Islands, given its protection from disturbance, complex forest structure, and reduced carnivore competition, will act as a potential refuge for marten along their trailing range boundary and a central node for regional recovery. Our work reveals that translocations, even those occurring along southern range boundaries, can create recovery networks that function like natural metapopulations. Identifying refuges, locations that are resistant to environmental change, within these recovery networks can further improve species recovery, even within novel environments. Future translocation planning should a priori identify potential refuges and sources to improve short-term recovery and long-term persistence.

Visualization of Bubble Nucleation and Growth Confined in 2D Flakes

The nucleation and growth of bubbles within a solid matrix is a ubiquitous phenomenon that affects many natural and synthetic processes. However, such a bubbling process is almost "invisible" to common characterization methods because it has an intrinsically multiphased nature and occurs on very short time/length scales. Using in situ transmission electron microscopy to explore the decomposition of a solid precursor that emits gaseous byproducts, the direct observation of a complete nanoscale bubbling process confined in ultrathin 2D flakes is presented here. This result suggests a three-step pathway for bubble formation in the confined environment: void formation via spinodal decomposition, bubble nucleation from the spherization of voids, and bubble growth by coalescence. Furthermore, the systematic kinetics analysis based on COMSOL simulations shows that bubble growth is actually achieved by developing metastable or unstable necks between neighboring bubbles before coalescing into one. This thorough understanding of the bubbling mechanism in a confined geometry has implications for refining modern nucleation theories and controlling bubble-related processes in the fabrication of advanced materials (i.e., topological porous materials).

How latex film formation and adhesion at the nanoscale correlate to performance of pressure sensitive adhesives with cellulose nanocrystals

Emulsion polymerized latex-based pressure-sensitive adhesives (PSAs) are more environmentally benign because they are synthesized in water but often underperform compared to their solution polymerized counterparts. Studies have shown a simultaneous improvement in the tack, and peel and shear strength of various acrylic PSAs upon the addition of cellulose nanocrystals (CNCs). This work uses atomic force microscopy (AFM) to examine the role of CNCs in (i) the coalescence of hydrophobic 2-ethyl hexyl acrylate/n-butyl acrylate/methyl methacrylate (EHA/BA/MMA) latex films and (ii) as adhesion modifiers over multiple length scales. Thin films with varying solids content and CNC loading were prepared by spin coating. AFM revealed that CNCs lowered the solids content threshold for latex particle coalescence during film formation. This improved the cohesive strength of the films, which was directly reflected in the increased shear strength of the EHA/BA/MMA PSAs with increasing CNC loading. Colloidal probe AFM indicated that the nano-adhesion of thicker continuous latex films increased with CNC loading when measured over small contact areas where the effect of surface roughness was negligible. Conversely, the beneficial effects of the CNCs on macroscopic PSA tack and peel strength were outweighed by the effects of increased surface roughness with increasing CNC loading over larger surface areas. This highlights that CNCs can improve both cohesive and adhesive PSA properties; however, the effects are most pronounced when the CNCs interact favourably with the latex polymer and are uniformly dispersed throughout the adhesive film. This article is part of the theme issue 'Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 1)'.

The Effect of Chemical Corrosion on Mechanics and Failure Behaviour of Limestone Containing a Single Kinked Fissure

This study concerns the influence of chemical corrosion and geometric parameters on the macroscopic damage characteristics of brittle limestone containing a kinked fissure under uniaxial compression. The specimens are prepared in chemical solutions with different NaCl concentrations and pH values. The acoustic emission (AE) technique is adopted to detect the inner distortion of the failure behaviour. The physical process of the crack coalescence of kinked fissures is synchronously captured by a high-speed camera. Seven failure patterns are identified based on the final failure mode and the failure process. Furthermore, the stress intensity factor of kinked cracks under chemical corrosion is obtained by a theoretical analysis. Chemical erosion with an acidic solution has a relatively strong effect on the compressive strength of the tested specimen, while the initial crack angle is not affected by short-term chemical corrosion.

Coalescence times, life history traits and conservation concerns: An example from four coastal shark species from the Indo-Pacific

Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographical ranges and less mobile ones organized in metapopulations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (N_e ) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed N_e trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (metapopulation) and unstructured models and then inferred the N_e variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed N_e dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.

Consistent Thermo-Capillarity and Thermal Boundary Conditions for Single-Phase Smoothed Particle Hydrodynamics

A model for capillary phenomena including temperature-dependency and thermal boundary conditions is presented in the numerical framework of smoothed particle hydrodynamics (SPH). The model requires only a single fluid phase and is therefore computationally more efficient than surface tension schemes which need an explicit fluid-fluid or fluid-gas interface. The model makes use of a surface identification mechanism based on the SPH renormalization tensor. All relevant properties of the continuum surface force (CSF) based approach, i.e., the delta function, normal vector and curvature, are calculated in a consistent manner. The model is parametrized by physical material properties and is successfully validated by means of a large set of analytical test cases. The applicability of the proposed model to more complex scenarios is demonstrated.

Comprehending Cornales: phylogenetic reconstruction of the order using the Angiosperms353 probe set

PREMISE

Cornales is an order of flowering plants containing ecologically and horticulturally important families, including Cornaceae (dogwoods) and Hydrangeaceae (hydrangeas), among others. While many relationships in Cornales are strongly supported by previous studies, some uncertainty remains with regards to the placement of Hydrostachyaceae and to relationships among families in Cornales and within Cornaceae. Here we analyzed hundreds of nuclear loci to test published phylogenetic hypotheses and estimated a robust species tree for Cornales.

METHODS

Using the Angiosperms353 probe set and existing data sets, we generated phylogenomic data for 158 samples, representing all families in the Cornales, with intensive sampling in the Cornaceae.

RESULTS

We curated an average of 312 genes per sample, constructed maximum likelihood gene trees, and inferred a species tree using the summary approach implemented in ASTRAL-III, a method statistically consistent with the multispecies coalescent model.

CONCLUSIONS

The species tree we constructed generally shows high support values and a high degree of concordance among individual nuclear gene trees. Relationships among families are largely congruent with previous molecular studies, except for the placement of the nyssoids and the Grubbiaceae-Curtisiaceae clades. Furthermore, we were able to place Hydrostachyaceae within Cornales, and within Cornaceae, the monophyly of known morphogroups was well supported. However, patterns of gene tree discordance suggest potential ancient reticulation, gene flow, and/or ILS in the Hydrostachyaceae lineage and the early diversification of Cornus. Our findings reveal new insights into the diversification process across Cornales and demonstrate the utility of the Angiosperms353 probe set.

Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex

PREMISE

Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here.

METHODS

The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent-based species tree analysis that takes incomplete lineage sorting into account; ASTRAL-III, another coalescent-based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups.

RESULTS

The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades.

CONCLUSIONS

The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent-based processes.

Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits

PREMISE

Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships.

METHODS

We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support.

RESULTS

For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree.

CONCLUSIONS

The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.

Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming

The duplication-loss-coalescence (DLC) parsimony model is invaluable for analyzing the complex scenarios of concurrent duplication loss and deep coalescence events in the evolution of gene families. However, inferring such scenarios for already moderately sized families is prohibitive owing to the computational complexity involved. To overcome this stringent limitation, we make the first step by describing a flexible integer linear programming (ILP) formulation for inferring DLC evolutionary scenarios. Then, to make the DLC model more scalable, we introduce four sensibly constrained versions of the model and describe modified versions of our ILP formulation reflecting these constraints. Our simulation studies showcase that our constrained ILP formulations compute evolutionary scenarios that are substantially larger than scenarios computable under our original ILP formulation and the original dynamic programming algorithm by Wu et al. Furthermore, scenarios computed under our constrained DLC models are remarkably accurate compared with corresponding scenarios under the original DLC model, which we also confirm in an empirical study with thousands of gene families.

Clarifying Recent Adaptive Diversification of the Chrysanthemum-Group on the Basis of an Updated Multilocus Phylogeny of Subtribe Artemisiinae (Asteraceae: Anthemideae)

Understanding the roles played by geography and ecology in driving species diversification and in the maintenance of species cohesion is the central objective of evolutionary and ecological studies. The multi-phased orogenesis of Qinghai-Tibetan Plateau (QTP) and global climate changes over late-Miocene has profoundly influenced the environments and evolution of organisms in this region and the vast areas of Asia. In this study, we investigate the lineage diversification of Chrysanthemum-group in subtribe Artemisiinae (tribe Anthemideae, Asteraceae) likely under the effects of climate changes during this period. Using DNA sequences of seven low-copy nuclear loci and nrITS and the coalescent analytical methods, a time-calibrated phylogeny of subtribe Artemisiinae was reconstructed with emphasis on Chrysanthemum-group. The monophyletic Chrysanthemum-group was well resolved into two major clades corresponding to Chrysanthemum and Ajania, two genera which can be well identified by capitulum morphology but have been intermingled in previous plastid and ITS trees. Within Chrysanthemum, a later divergence between Ch. indicum-complex and Ch. zawadskii-complex can be recognized. The time frames of these sequential divergences coincide with the late Cenozoic uplift of the Northern QTP and the concomitant climatic heterogeneity between eastern and inland Asia. Reconstruction of historical biogeography suggested the origin of Chrysanthemum-group in Central Asia, followed by eastward migration of Chrysanthemum and in situ diversification of Ajania. Within Chrysanthemum, Ch. indicum-complex and Ch. zawadskii-complex exhibited contemporary distributional division, the former in more southern and the latter in more northern regions. The geographic structure of the three lineages in Chrysanthemum-group have been associated with the niche differentiation, and environmental heterogenization in Asia interior.

Pond chironomid communities revealed by molecular species delimitation reflect eutrophication

Farm ponds, a valued habitat for freshwater organisms, are being negatively affected by the recent changes in the environment as well as anthropological activities. In these ponds, biodiversity researchers have tended to focus on species that prefer natural habitats and/or can be identified based on morphological characters. In contrast, this study focused on the insect family Chironomidae, which is widely distributed from clear to polluted waters of ponds, but is hard to identify morphologically as an aquatic larva. We adopted DNA barcoding and molecular species delimitation to identify every single specimen of quantitative collections. From bottom sediments of 17 ponds in summer in the Banshu Plain of Japan, a total of 62 species were delimited based on the DNA sequences of the mitochondrial COI region. Chironomid communities from these ponds were classified into four groups in a two-dimensional ordination of multivariate analysis (NMDS). One of the dimensions was well correlated with the gradient of eutrophication, while another dimension was not clearly assigned to any general feature of the environmental gradient, but rice cultivation could possibly be involved.

A genome-scale phylogeny of the kingdom Fungi

Phylogenomic studies using genome-scale amounts of data have greatly improved understanding of the tree of life. Despite the diversity, ecological significance, and biomedical and industrial importance of fungi, evolutionary relationships among several major lineages remain poorly resolved, especially those near the base of the fungal phylogeny. To examine poorly resolved relationships and assess progress toward a genome-scale phylogeny of the fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 species that includes representatives from most major fungal lineages. We also compiled 11 data matrices by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. Analyses of these 12 data matrices using concatenation- and coalescent-based approaches yielded a robust phylogeny of the fungal kingdom, in which ∼85% of internal branches were congruent across data matrices and approaches used. We found support for several historically poorly resolved relationships as well as evidence for polytomies likely stemming from episodes of ancient diversification. By examining the relative evolutionary divergence of taxonomic groups of equivalent rank, we found that fungal taxonomy is broadly aligned with both genome sequence divergence and divergence time but also identified lineages where current taxonomic circumscription does not reflect their levels of evolutionary divergence. Our results provide a robust phylogenomic framework to explore the tempo and mode of fungal evolution and offer directions for future fungal phylogenetic and taxonomic studies.

Growth of Colloidal Nanocrystals by Liquid-Like Coalescence*

We here describe, model, and predict the growth kinetics of amine-capped PbS colloidal nanoparticles in the absence of supersaturation. The particles grow by coalescence rather than by Ostwald ripening. A comparison of different models indicates that the effective activation energy of coalescence (67.65 kJ mol^-1 ) is associated with two terms: a term proportional to the contact area between the ligand shells of two colliding particles, and a constant term. Our Brownian dynamics simulations show (i) how the remarkably low activation energy (or large rate constants) are most likely due to the large difference in size between the particles and their mean free path of diffusion, and (ii) how the low polydispersity is the likely result of the suppression of collision rates between rare populations due to crowding. The model successfully predicts the growth kinetics of nanoparticles, therefore enabling the precise control of the average particle size without the need of supersaturation.