Jean-Baptiste Leschenault de La Tour

Abstract After many decades of effective control of stem rust caused by the Puccinia graminis f.sp. tritici, (hereafter Pgt) the reported emergence of race TTKSK/Ug99 of Pgt in Uganda reignited concerns about epidemics worldwide because ∼90% of world wheat cultivars had no resistance to the new race. Since it was initially detected in Uganda in 1998, Ug99 variants have now been identified in thirteen countries in Africa and the Middle East. Stem rust has been a major problem in the past, and concern is increasing about the risk of return to Central and East Asia. Whilst control programs in North America and Europe relied on the use of resistant cultivars in combination with eradication of barberry (Berberis spp.), the alternate host required for the stem rust pathogen to complete its full lifecycle, the focus in East Asia was principally on the use of resistant wheat cultivars. Here, we investigate potential airborne transmission pathways for stem rust outbreaks in the Middle East to reach East Asia using an integrated modelling framework combining estimates of fungal spore deposition from an atmospheric dispersion model, environmental suitability for spore germination, and crop calendar information. We consider the role of mountain ranges in restricting transmission pathways, and we incorporate a representation of a generic barberry species into the lifecycle. We find viable transmission pathways to East Asia from the Middle East to the north via Central Asia and to the south via South Asia and that an initial infection in the Middle East could persist in East Asia for up to three years due to the presence of the alternate host. Our results indicate the need for further assessment of barberry species distributions in East Asia and appropriate methods for targeted surveillance and mitigation strategies should stem rust incidence increase in the Middle East region.

Marine habitats and ecosystems are increasingly being impacted by global climate change and the global spread of captive breeding. In this study, we focused on five typical Trachinotus species (Trachinotus anak, Trachinotus blochii, Trachinotus mookalee, Trachinotus goreenisi, Trachinotus ovatus) as research subjects. We utilized species distribution models and ecological niche models to predict the present and future potential distribution of these species, as well as to assess ecological niche overlap and evaluate the early warning of invasion by Trachinotus species. T. ovatus stands out with its broad distribution range and high adaptability to different environments. It occupies 1.114% of medium-high suitable areas, spanning 100,147 km2. Our predictions also suggest that T. ovatus would undergo a significant expansion (approximately 55% of the total area) under both past and future environmental scenarios, demonstrating a higher tolerance and adaptability to changes in ambient temperatures. It can be discerned that T. ovatus exhibits strong environmental adaptability, which may potentially lead to biological invasion along the southeastern coast of China. The T. anak, on the other hand, showed a higher expansion trend under high carbon dioxide concentrations (RCP8.5), indicating a certain convergence with carbon dioxide concentration. Our models showed that under future climatic conditions, T. ovatus would become the dominant species, with increased competition with T. mookalee and decreased competition with T. goreenisi, T. mookalee, and T. anak. Based on our findings and the net-pen culture mode of T. ovatus, we identified the hotspot habitat of T. ovatus to be located in the Indo-Pacific convergence zone. However, there is a possibility of an expansion trend towards the southeast coast of China in the future. Therefore, it is crucial to provide an early warning for the potential biological invasion of T. ovatus.

Premise Cleomaceae is an important model clade for studies of evolutionary processes including genome evolution, floral form diversification, and photosynthetic pathway evolution. Diversification and divergence patterns in Cleomaceae remain tangled as research has been restricted by its worldwide distribution, limited genetic sampling and species coverage, and a lack of definitive fossil calibration points.MethodsWe used target sequence capture and the Angiosperms353 probe set to perform a phylogenetic study of Cleomaceae. We estimated divergence times and biogeographic analyses to explore the origin and diversification of the family. Seed morphology across extant taxa was documented with multifocal image‐stacking techniques and morphological characters were extracted, analyzed, and compared to fossil records.ResultsWe recovered a well‐supported and resolved phylogenetic tree of Cleomaceae generic relationships that includes 236 (~86%) species. We identified 11 principal clades and confidently placed Cleomella as sister to the rest of the family. Our analyses suggested that Cleomaceae and Brassicaceae diverged ~56 mya, and Cleomaceae began to diversify ~53 mya in the Palearctic and Africa. Multiple transatlantic disjunct distributions were identified. Seeds were imaged from 218 (~80%) species in the family and compared to all known fossil species.ConclusionsOur results represent the most comprehensive phylogenetic study of Cleomaceae to date. We identified transatlantic disjunctions and proposed explanations for these patterns, most likely either long‐distance dispersals or contractions in latitudinal distributions caused by climate change over geological timescales. We found that seed morphology varied considerably but mostly mirrored generic relationships.

Clownfish (subfamily Amphiprioninae) are an iconic group of coral reef fish that evolved a mutualistic interaction with sea anemones, which triggered the adaptive radiation of the clade. Within clownfishes, the “skunk complex” is particularly interesting. Besides ecological speciation, interspecific gene flow and hybrid speciation are thought to have shaped the evolution of the group. We investigated the mechanisms characterizing the diversification of this complex. By taking advantage of their disjunct geographical distribution, we obtained whole‐genome data of sympatric and allopatric populations of the three main species of the complex (Amphiprion akallopisos, A. perideraion and A. sandaracinos). We examined population structure, genomic divergence and introgression signals and performed demographic modelling to identify the most realistic diversification scenario. We excluded scenarios of strict isolation or hybrid origin of A. sandaracinos. We discovered moderate gene flow from A. perideraion to the ancestor of A. akallopisos + A. sandaracinos and weak gene flow between the species in the Indo‐Australian Archipelago throughout the diversification of the group. We identified introgressed regions in A. sandaracinos and detected in A. perideraion two large regions of high divergence from the two other species. While we found that gene flow has occurred throughout the species' diversification, we also observed that recent admixture was less pervasive than initially thought, suggesting a role of host repartition or behavioural barriers in maintaining the genetic identity of the species in sympatry.

Aim Species occurrence data are valuable information that enables one to estimate geographical distributions, characterize niches and their evolution, and guide spatial conservation planning. Rapid increases in species occurrence data stem from increasing digitization and aggregation efforts, and citizen science initiatives. However, persistent quality issues in occurrence data can impact the accuracy of scientific findings, underscoring the importance of filtering erroneous occurrence records in biodiversity analyses.InnovationWe introduce an R package, occTest, that synthesizes a growing open‐source ecosystem of biodiversity cleaning workflows to prepare occurrence data for different modelling applications. It offers a structured set of algorithms to identify potential problems with species occurrence records by employing a hierarchical organization of multiple tests. The workflow has a hierarchical structure organized in testPhases (i.e. cleaning vs. testing) that encompass different testBlocks grouping different testTypes (e.g. environmental outlier detection), which may use different testMethods (e.g. Rosner test, jacknife,etc.). Four different testBlocks characterize potential problems in geographic, environmental, human influence and temporal dimensions. Filtering and plotting functions are incorporated to facilitate the interpretation of tests. We provide examples with different data sources, with default and user‐defined parameters. Compared to other available tools and workflows, occTest offers a comprehensive suite of integrated tests, and allows multiple methods associated with each test to explore consensus among data cleaning methods. It uniquely incorporates both coordinate accuracy analysis and environmental analysis of occurrence records. Furthermore, it provides a hierarchical structure to incorporate future tests yet to be developed.Main conclusionsoccTest will help users understand the quality and quantity of data available before the start of data analysis, while also enabling users to filter data using either predefined rules or custom‐built rules. As a result, occTest can better assess each record's appropriateness for its intended application.

Present-day geographic and phylogenetic patterns often reflect the geological and climatic history of the planet. Neontological distribution data are often sufficient to unravel a lineage’s biogeographic history, yet ancestral range inferences can be at odds with fossil evidence. Here, I use the fossilized birth–death process and the dispersal–extinction cladogenesis model to jointly infer the dated phylogeny and range evolution of the tree fern order Cyatheales. I use data for 101 fossil and 442 extant tree ferns to reconstruct the biogeographic history of the group over the last 220 million years. Fossil-aware reconstructions evince a prolonged occupancy of Laurasia over the Triassic–Cretaceous by Cyathealean tree ferns, which is evident in the fossil record but hidden from analyses relying on neontological data alone. Nonetheless, fossil-aware reconstructions are affected by uncertainty in fossils’ phylogenetic placement, taphonomic biases, and specimen sampling and are sensitive to interpretation of paleodistributions and how these are scored. The present results highlight the need and challenges of incorporating fossils into joint inferences of phylogeny and biogeography to improve the reliability of ancestral geographic range estimation.

Ziziphus mauritiana is an economically detrimental and environmentally destructive plant in non‐native areas where it has escaped cultivation. It forms dense, impenetrable thickets that restrict the movement of livestock across the landscape and has the capacity to alter various ecological functions at the site of invasion, all of which contribute towards land degradation and the reduction of economic profitability. Although there are several management strategies implemented to control Z. mauritiana, it is clear that no single‐method approach will effectively control the species in the long‐term. Whilst chemical and mechanical methods appear to show promising results, they tend to be restricted to areas that are easily accessible and, even so, can be challenging and laborious to treat evenly across dense thicket areas. Several prospective biological control agents have been identified for Z. mauritiana, although further investigations are required to ascertain the host specificity, and to explore and identify their climatic and environmental suitability of host specific agents for release in non‐native regions. Ecological burning alone is not effective in controlling Z. mauritiana and will likely increase its emergence. As such, it could be adopted as part of an integrated management approach to assist other methods for long‐term control, but again the development of such an approach requires further investigation. To contribute towards the control of Z. mauritiana, this review explores its biology, distribution and management challenges whilst identifying areas of research that will assist in the long‐term and confident control of the species, with an emphasis on its invasion in Australia.

Extant neosuchian crocodiles are represented by only 24 taxa that are confined to the tropics and subtropics. However, at other intervals during their 200 Myr evolutionary history the clade reached considerably higher levels of species-richness, matched by more widespread distributions. Neosuchians have occupied numerous habitats and niches, ranging from dwarf riverine forms to large marine predators. Despite numerous previous studies, several unsolved questions remain with respect to their biogeographic history, including the geographical origins of major groups, e.g. Eusuchia and Neosuchia itself. We carried out the most comprehensive biogeographic analysis of Neosuchia to date, based on a multivariate K-means clustering approach followed by the application of two ancestral area estimation methods (BioGeoBEARS and Bayesian ancestral location estimation) applied to two recently published phylogenies. Our results place the origin of Neosuchia in northwestern Pangaea, with subsequent radiations into Gondwana. Eusuchia probably emerged in the European archipelago during the Late Jurassic/Early Cretaceous, followed by dispersals to the North American and Asian landmasses. We show that putative transoceanic dispersal events are statistically significantly less likely to happen in alligatoroids. This finding is consistent with the saltwater intolerant physiology of extant alligatoroids, bolstering inferences of such intolerance in their ancestral lineages.

Osyris lanceolata Hochst. & Steud. ex A. DC. is a multipurpose plant with high socioeconomic and cultural values. It is endangered in the biogeographical region of eastern Africa, but of less concern in other regions where it occurs. The few natural populations remaining in the endangered sites continue to encounter many threats, and this has raised concerns about its long-term sustainability. Yet, existing knowledge about the ecology and distribution of the plant is scarce to inform strategies for the conservation and sustainable management of the species. In this study, we conducted a scoping review of the available literature on current knowledge about the plant. We recapitulated existing knowledge about the abiotic and biotic factors influencing the contemporary distribution of the plant, the anthropogenic threats, and existing conservation efforts. Based on the limited studies we reviewed, we identified that the plant prefers specific habitats (hilly areas and rocky outcrops), frequently parasitizes Fabaceae but can parasitize plants from a wide range of countries, have inadequate ex-situ propagation protocols which present issues for the survival of the species. Overharvesting from the wild driven by demand from regional and global markets poses further threats to the existing natural populations, especially in eastern Africa. A combination of ecological, social, and trade-related conservation measures can be envisioned to help improve the plant’s persistence. These include, but are not limited to, a better understanding of the species ecology to inform conservation planning, monitoring of trade flow and improve transnational environmental laws and cooperation among countries to prevent species smuggling.

Evolutionary correlations between chemical defense and protection by mutualist bodyguards have been long predicted, but tests of these pattern remain rare. We use a phylogenetic framework to test for evolutionary correlations indicative of trade-offs or synergisms between direct defense in the form of plant secondary metabolism, and indirect defense in the form of leaf domatia, across 33 species in the wild grape genus, Vitis. We also performed a bioassay with a generalist herbivore to associate our chemical phenotypes with herbivore palatability. Finally, we tested whether defensive traits correlate with the average abiotic characteristics of each species’ contemporary range and whether these correlations were consistent with plant defense theory. We found a negative evolutionary correlation between domatia size and the diversity of secondary metabolites in Vitis leaf tissue across the genus, and also that leaves with a higher diversity and richness of secondary metabolites were less palatable to a generalist herbivore, consistent with a trade-off in chemical and mutualistic defense investment. Predictions from plant defense theory were not supported by associations between investment in defense phenotypes and abiotic variables. Our work demonstrates an evolutionary pattern indicative of a trade-off between indirect and direct defense strategies across the Vitis genus.