Molecular insights into the dynamics of species invasion by hybridisation in Tasmanian eucalypts.

In plants where seed dispersal is limited compared with pollen dispersal, hybridisation may enhance gene exchange and species dispersal. We provide genetic evidence of hybridisation contributing to the expansion of the rare Eucalyptus risdonii into the range of the widespread Eucalyptus amygdalina. These closely related tree species are morphologically distinct, and observations suggest that natural hybrids occur along their distribution boundaries and as isolated trees or in small patches within the range of E. amygdalina. Hybrid phenotypes occur outside the range of normal dispersal for E. risdonii seed, yet in some hybrid patches small individuals resembling E. risdonii occur and are hypothesised to be a result of backcrossing. Using 3362 genome-wide SNPs assessed from 97 individuals of E. risdonii and E. amygdalina and 171 hybrid trees, we show that (i) isolated hybrids match the genotypes expected of F1 /F2 hybrids, (ii) there is a continuum in the genetic composition among the isolated hybrid patches from patches dominated by F1 /F2 -like genotypes to those dominated by E. risdonii-backcross genotypes, and (iii) the E. risdonii-like phenotypes in the isolated hybrid patches are most-closely related to proximal larger hybrids. These results suggest that the E. risdonii phenotype has been resurrected in isolated hybrid patches established from pollen dispersal, providing the first steps in its invasion of suitable habitat by long-distance pollen dispersal and complete introgressive displacement of E. amygdalina. Such expansion accords with the population demographics, common garden performance data, and climate modelling which favours E. risdonii and highlights a role of interspecific hybridisation in climate change adaptation and species expansion.

Urocortin-1 Is Chondroprotective in Response to Acute Cartilage Injury via Modulation of Piezo1.

Post-traumatic OA (PTOA) is often triggered by injurious, high-impact loading events which result in rapid, excessive chondrocyte cell death and a phenotypic shift in residual cells toward a more catabolic state. As such, the identification of a disease-modifying OA drug (DMOAD) that can protect chondrocytes from death following impact injury, and thereby prevent cartilage degradation and progression to PTOA, would offer a novel intervention. We have previously shown that urocortin-1 (Ucn) is an essential endogenous pro-survival factor that protects chondrocytes from OA-associated pro-apoptotic stimuli. Here, using a drop tower PTOA-induction model, we demonstrate the extent of Ucn's chondroprotective role in cartilage explants exposed to excessive impact load. Using pathway-specific agonists and antagonists, we show that Ucn acts to block load-induced intracellular calcium accumulation through blockade of the non-selective cation channel Piezo1 rather than TRPV4. This protective effect is mediated primarily through the Ucn receptor CRF-R1 rather than CRF-R2. Crucially, we demonstrate that the chondroprotective effect of Ucn is maintained whether it is applied pre-impact or post-impact, highlighting the potential of Ucn as a novel DMOAD for the prevention of injurious impact overload-induced PTOA.

Microsatellite analysis of population structure in Eucalyptus globulus.

Eucalyptus globulus subsp. globulus Labill. (Tasmanian Blue Gum), native to southeast Australia, is a benchmark species for the pulp and paper industry. We genotyped 397 trees from 16 populations of E. globulus representing the native diversity in Australia using 24 microsatellite loci. Eight genetically distinct groups were detected, consistent with genetic groupings detected in previous quantitative and molecular studies. A sample of 29 Portuguese individuals was added to help clarify the origin of the Portuguese landrace. The results suggest a southern and eastern Tasmania origin for the Portuguese landrace. This genetic framework will enable researchers to investigate the provenance of individuals of unknown pedigree and assess the levels of representation of E. globulus natural variation in the Portuguese landrace.

Patterns of Reproductive Isolation in Eucalyptus-A Phylogenetic Perspective.

We assess phylogenetic patterns of hybridization in the speciose, ecologically and economically important genus Eucalyptus, in order to better understand the evolution of reproductive isolation. Eucalyptus globulus pollen was applied to 99 eucalypt species, mainly from the large commercially important subgenus, Symphyomyrtus. In the 64 species that produce seeds, hybrid compatibility was assessed at two stages, hybrid-production (at approximately 1 month) and hybrid-survival (at 9 months), and compared with phylogenies based on 8,350 genome-wide DArT (diversity arrays technology) markers. Model fitting was used to assess the relationship between compatibility and genetic distance, and whether or not the strength of incompatibility "snowballs" with divergence. There was a decline in compatibility with increasing genetic distance between species. Hybridization was common within two closely related clades (one including E. globulus), but rare between E. globulus and species in two phylogenetically distant clades. Of three alternative models tested (linear, slowdown, and snowball), we found consistent support for a snowball model, indicating that the strength of incompatibility accelerates relative to genetic distance. Although we can only speculate about the genetic basis of this pattern, it is consistent with a Dobzhansky-Muller-model prediction that incompatibilities should snowball with divergence due to negative epistasis. Different rates of compatibility decline in the hybrid-production and hybrid-survival measures suggest that early-acting postmating barriers developed first and are stronger than later-acting barriers. We estimated that complete reproductive isolation can take up to 21-31 My in Eucalyptus. Practical implications for hybrid eucalypt breeding and genetic risk assessment in Australia are discussed.

High density, genome-wide markers and intra-specific replication yield an unprecedented phylogenetic reconstruction of a globally significant, speciose lineage of Eucalyptus.

We used genome-wide markers and an unprecedented scale of sampling to construct a phylogeny for a globally significant Eucalyptus lineage that has been impacted by hybridisation, recent radiation and morphological convergence. Our approach, using 3109 DArT markers distributed throughout the genome and 540 samples covering 185 terminal taxa in sections Maidenaria, Exsertaria, Latoangulatae and related smaller sections, with multiple geographically widespread samples per terminal taxon, produced a phylogeny that largely matched the morphological treatment of sections, though sections Exsertaria and Latoangulatae were polyphyletic. At lower levels there were numerous inconsistencies between the morphological treatment and the molecular phylogeny, and taxa within the three main sections were generally not monophyletic at the series (at least 62% polyphyly) or species (at least 52% polyphyly) level. Some of the discrepancies appear to be the result of morphological convergence or misclassifications, and we propose some taxonomic reassessments to address this. However, many inconsistencies appear to be the products of incomplete speciation and/or hybridisation. Our analysis represents a significant advance on previous phylogenies of these important eucalypt sections (which have mainly used single samples to represent each species), thus providing a robust phylogenetic framework for evolutionary and ecological studies.

The floral transcriptome of Eucalyptus grandis.

As a step toward functional annotation of genes required for floral initiation and development within the Eucalyptus genome, we used short read sequencing to analyze transcriptomes of floral buds from early and late developmental stages, and compared these with transcriptomes of diverse vegetative tissues, including leaves, roots, and stems. A subset of 4807 genes (13% of protein-coding genes) were differentially expressed between floral buds of either stage and vegetative tissues. A similar proportion of genes were differentially expressed among all tissues. A total of 479 genes were differentially expressed between early and late stages of floral development. Gene function enrichment identified 158 gene ontology classes that were overrepresented in floral tissues, including 'pollen development' and 'aromatic compound biosynthetic process'. At least 40 floral-dominant genes lacked functional annotations and thus may be novel floral transcripts. We analyzed several genes and gene families in depth, including 49 putative biomarkers of floral development, the MADS-box transcription factors, 'S-domain'-receptor-like kinases, and selected gene family members with phosphatidylethanolamine-binding protein domains. Expanded MADS-box gene subfamilies in Eucalyptus grandis included SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), SEPALLATA (SEP) and SHORT VEGETATIVE PHASE (SVP) Arabidopsis thaliana homologs. These data provide a rich resource for functional and evolutionary analysis of genes controlling eucalypt floral development, and new tools for breeding and biotechnology.

Novel distances for dollo data.

We investigate distances on binary (presence/absence) data in the context of a Dollo process, where a trait can only arise once on a phylogenetic tree but may be lost many times. We introduce a novel distance, the Additive Dollo Distance (ADD), that applies to data generated under a Dollo model and show that it has some useful theoretical properties including an intriguing link to the LogDet/paralinear distance. Simulations of Dollo data are used to compare a number of binary distances including ADD, LogDet, a restriction-site-based distance, and some simple, but to our knowledge previously unstudied, variations on common binary distances. The simulations suggest that ADD outperforms other distances on Dollo data. Interestingly, we found that the LogDet distance performs poorly in the context of a Dollo process; this may have implications for its use in connection with conditioned genome reconstruction. We apply the ADD to two Diversity Arrays Technology data sets, one that broadly covers Eucalyptus species and one that focuses on the Eucalyptus series Adnataria. We also reanalyze gene family presence/absence data from bacterial genomes obtained from the COG database and compare the results with previous phylogenies estimated using the conditioned genome reconstruction approach. The results for these case studies are largely congruent with previous studies, in some cases giving more phylogenetic resolution.

Cold temperature and aridity shape the evolution of drought tolerance traits in Tasmanian species of Eucalyptus.

Perennial plant species from water-limiting environments (including climates of extreme drought, heat and freezing temperatures) have evolved traits that allow them to tolerate these conditions. As such, traits that are associated with water stress may show evidence of adaptation to climate when compared among closely related species inhabiting contrasting climatic conditions. In this study, we tested whether key hydraulic traits linked to drought stress, including the vulnerability of leaves to embolism (P50 leaf) and the minimum diffusive conductance of shoots (gmin), were associated with climatic characteristics of 14 Tasmanian eucalypt species from sites that vary in precipitation and temperature. Across species, greater cavitation resistance (more negative P50 leaf) was associated with increasing aridity and decreasing minimum temperature. By contrast, gmin showed strong associations with aridity only. Among these Tasmanian eucalypts, evidence suggests that trait variation is influenced by both cold and dry conditions, highlighting the need to consider both aspects when exploring adaptive trait-climate relationships.

Evaluating Trends in COVID-19 Research Activity in Early 2020: The Creation and Utilization of a Novel Open-Access Database.

Introduction The coronavirus disease 2019 (COVID-19) pandemic has been unprecedented in recent history. The rapid global spread has demonstrated how the emergence of a novel pathogen necessitates new information to advise both healthcare systems and policy-makers. The directives for the management of COVID-19 have been limited to infection control measures and treatment of patients, which has left physicians and researchers alone to navigate the massive amount of research being published while searching for evidence-based strategies to care for patients. To tackle this barrier, we launched CovidReview.ca, an open-access, continually updated, online platform that screens available COVID-19 research to determine higher quality publications. This paper uses data from this review process to explore the activity and trends of COVID-19 research worldwide over time, while specifically looking at the types of studies being published. Materials and Methods The literature search was conducted on PubMed. Search terms included "COVID-19", "severe acute respiratory syndrome coronavirus 2", "coronavirus 19", "SARS-COV-2", and "2019-nCoV". All articles captured by this strategy were reviewed by a minimum of two reviewers and categorized by type of research, relevant medical specialties, and type of publication. Criteria were developed to allow for inclusion or exclusion to the website. Due to the volume of research, only a level 1 (title and abstract) screen was performed. Results The time period for the analysis was January 17, 2020, to May 10, 2020. The total number of papers captured by the search criteria was 10,685, of which 2,742 were included on the website and 7,943 were excluded. The greatest increase in the types of studies over the 16 weeks was narrative review/expert opinion papers followed by case series/reports. Meta-analyses, systematic reviews, and randomized controlled trials remained the least published types of studies. Conclusions The surge of research that accompanied the COVID-19 pandemic is unparalleled in recent years. From our analysis, it is clear that case reports and narrative reviews were the most widely published, particularly in the earlier days of this pandemic. Continued research that falls higher on the evidence pyramid and is more applicable to clinical settings is warranted.

Genetic control of heterochrony in Eucalyptus globulus.

A change in the timing or rate of developmental events throughout ontogeny is referred to as heterochrony, and it is a major evolutionary process in plants and animals. We investigated the genetic basis for natural variation in the timing of vegetative phase change in the tree Eucalyptus globulus, which undergoes a dramatic change in vegetative morphology during the juvenile-to-adult transition. Quantitative trait loci analysis in an outcross F2 family derived from crosses between individuals from a coastal population of E. globulus with precocious vegetative phase change and individuals from populations in which vegetative phase change occurs several years later implicated the microRNA EglMIR156.5 as a potential contributor to this heterochronic difference. Additional evidence for the involvement of EglMIR156.5 was provided by its differential expression in trees with early and late phase change. Our findings suggest that changes in the expression of miR156 underlie natural variation in vegetative phase change in E. globulus, and may also explain interspecific differences in the timing of this developmental transition.

Multiple evolutionary processes drive the patterns of genetic differentiation in a forest tree species complex.

Forest trees frequently form species complexes, complicating taxonomic classification and gene pool management. This is certainly the case in Eucalyptus, and well exemplified by the Eucalyptus globulus complex. This ecologically and economically significant complex comprises four taxa (sspp. bicostata, globulus, maidenii, pseudoglobulus) that are geographically and morphologically distinct, but linked by extensive "intergrade" populations. To resolve their genetic affinities, nine microsatellites were used to genotype 1200 trees from throughout the natural range of the complex in Australia, representing 33 morphological core and intergrade populations. There was significant spatial genetic structure (F(ST) = 0.10), but variation was continuous. High genetic diversity in southern ssp. maidenii indicates that this region is the center of origin. Genetic diversity decreases and population differentiation increases with distance from this area, suggesting that drift is a major evolutionary process. Many of the intergrade populations, along with other populations morphologically classified as ssp. pseudoglobulus or ssp. globulus, belong to a "cryptic genetic entity" that is genetically and geographically intermediate between core ssp. bicostata, ssp. maidenii, and ssp. globulus. Geography, rather than morphology, therefore, is the best predictor of overall genetic affinities within the complex and should be used to classify germplasm into management units for conservation and breeding purposes.