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Trypanosoma cruzi, the causative agent of Chagas disease (American trypanosomiasis), colonizes the intestinal tract of triatomines. Triatomine bugs act as vectors in the life cycle of the parasite and transmit infective parasite stages to animals and humans. Contact of the vector with T. cruzi alters its intestinal microbial composition, which may also affect the associated metabolic patterns of the insect. Earlier studies suggest that the complexity of the triatomine fecal metabolome may play a role in vector competence for different T. cruzi strains. Using high-resolution mass spectrometry and supervised machine learning, we aimed to detect differences in the intestinal metabolome of the triatomine Rhodnius prolixus and predict whether the insect had been exposed to T. cruzi or not based solely upon their metabolic profile. We were able to predict the exposure status of R. prolixus to T. cruzi with accuracies of 93.6%, 94.2% and 91.8% using logistic regression, a random forest classifier and a gradient boosting machine model, respectively. We extracted the most important features in producing the models and identified the major metabolites which assist in positive classification. This work highlights the complex interactions between triatomine vector and parasite including effects on the metabolic signature of the insect.
The Miocene is a key time in the evolution of African mammals and their ecosystems witnessing the origin of the African apes and the isolation of eastern coastal forests through an expanding biogeographic arid corridor. Until recently, however, Miocene sites from the southeastern regions of the continent were unknown. Here we report discovery of the first Miocene fossil teeth from the shoulders of the Urema Rift in Gorongosa National Park, Mozambique, at the southern East African Rift System. We provide the first 1) radiometric age determinations of the fossiliferous Mazamba Formation, 2) reconstructions of past vegetation in the region based on pedogenic carbonates and fossil wood, and 3) description of fossil teeth from the southern rift. Gorongosa is unique in the East African Rift System in combining marine invertebrates, marine vertebrates, terrestrial mammals, and fossil woods in coastal paleoenvironments. The Gorongosa fossil sites offer the first evidence of persistent woodlands and forests on the coastal margins of southeastern Africa during the Miocene, and an exceptional assemblage of fossil vertebrates including new species. Further work will allow the testing of hypotheses positing the formation of a northeast-southwest arid corridor isolating species on the eastern coastal forests from those elsewhere in Africa.
Brief The Miocene is a key time in the evolution of African mammals and their ecosystems encompassing hominine origins and the establishment of an arid corridor that isolated eastern Africa’s coastal forests. Until now, however, Miocene sites from southeastern Africa have been unknown. We report the discovery of the first Miocene fossil sites from Gorongosa National Park, Mozambique, and show that these sites formed in coastal settings. We provide radiometric ages for the fossiliferous sediments, reconstructions of past vegetation based on stable isotopes and fossil wood, and a description of the first fossil teeth from the region. Gorongosa is the only paleontological site in the East African Rift that combines fossil woods, marine invertebrates, marine vertebrates, and terrestrial mammals. Gorongosa offers the first evidence of persistent woodlands and forests on the coastal margins of southeastern Africa during the Miocene.
Tree water relations of mature oaks in southwest Germany under extreme drought stress in summer 2018
(2021)
Mature oak stands of different tree height at four sandy valley river sites (Quercus robur) and one south-exposed schist slope (Qu. petraea) in the middle Rhine and lower Main valley were studied from early summer 2017 (normal wet year) until the end of 2018 (extremely hot and dry year). Tree water relations (ΨPD, RWC, sap flow rates) were monitored together with soil water relations, LAI and leaf chl content. In two sandy sites with presumed continuous capillary water access from the groundwater aquifer, sap flow rates of the large trees (30 m) and estimated canopy conductance decreased to about 50% of the maximum value in the course of summer 2018, but recovered in autumn. At two other sites, with smaller trees (14–24 m) and presumed interrupted capillary water access during mid-summer 2018, sap flow rates and canopy conductance broke down completely and trees shed a large proportion of leaves in summer. In one of these sites, ΨPD decreased (reversibly) to -4 MPa, one of the lowest values reported in the literature for central Europe, and tree damage resulted not only in extreme leaf shedding, but also in susceptibility to uprooting (in 2 out of 5 measured trees) by thunderstorm gusts in autumn 2018. At the schist slope site, where oaks reached the lowest height and stand density of all sites, sap flow rates remained similar to the values found at the presumed capillary-water supplied sandy sites, indicating access to rock fissure water even at the peak of the drought period. Our findings corroborate the prediction from vegetation modelling that several Qu. robur stands in the Rhine-Main valleys will be prone to severe forest dieback in the forthcoming decades.
Feeding exclusively on blood, vampire bats represent the only obligate sanguivorous lineage among mammals. To uncover genomic changes associated with adaptations to this unique dietary specialization, we generated a new haplotype-resolved reference-quality genome of the common vampire bat (Desmodus rotundus) and screened 26 bat species for genes that were specifically lost in the vampire bat lineage. We discovered previously-unknown gene losses that relate to metabolic and physiological changes, such as reduced insulin secretion (FFAR1, SLC30A8), limited glycogen stores (PPP1R3E), and a distinct gastric physiology (CTSE). Other gene losses likely reflect the biased nutrient composition (ERN2, CTRL) and distinct pathogen diversity of blood (RNASE7). Interestingly, the loss of REP15 likely helped vampire bats to adapt to high dietary iron levels by enhancing iron excretion and the loss of the 24S-hydroxycholesterol metabolizing enzyme CYP39A1 could contribute to their exceptional cognitive abilities. Finally, losses of key cone phototransduction genes (PDE6H, PDE6C) suggest that these strictly-nocturnal bats completely lack cone-based vision. These findings enhance our understanding of vampire bat biology and the genomic underpinnings of adaptations to sanguivory.
Mosquito species belonging to the genus Aedes have attracted the interest of scientists and public health officers for their invasive species traits and efficient capacity of transmitting viruses affecting humans. Some of these species were brought outside their native range by human activities such as trade and tourism, and colonised new regions thanks to a unique combination of eco-physiological traits.
Considering mosquito physiological and behavioural traits to understand and predict the spatial and temporal population dynamics is thus a crucial step to develop strategies to mitigate the local densities of invasive Aedes populations.
Here, we synthesised the life cycle of four invasive Aedes species (Ae. aegypti, Ae. albopictus, Ae. japonicus and Ae. koreicus) in a single multi-scale stochastic modelling framework which we coded in the R package dynamAedes. We designed a stage-based and time-discrete stochastic model driven by temperature, photo-period and inter-specific larval competition that can be applied to three different spatial scales: punctual, local and regional. These spatial scales consider different degrees of spatial complexity and data availability, by accounting for both active and passive dispersal of mosquito species as well as for the heterogeneity of the input temperature data.
Our overarching aim was to provide a flexible, open-source and user-friendly tool rooted in the most updated knowledge on species biology which could be applied to the management of invasive Aedes populations as well as for more theoretical ecological inquiries.
Global water models (GWMs) simulate the terrestrial water cycle, on the global scale, and are used to assess the impacts of climate change on freshwater systems. GWMs are developed within different modeling frameworks and consider different underlying hydrological processes, leading to varied model structures. Furthermore, the equations used to describe various processes take different forms and are generally accessible only from within the individual model codes. These factors have hindered a holistic and detailed understanding of how different models operate, yet such an understanding is crucial for explaining the results of model evaluation studies, understanding inter-model differences in their simulations, and identifying areas for future model development. This study provides a comprehensive overview of how state-of-the-art GWMs are designed. We analyze water storage compartments, water flows, and human water use sectors included in 16 GWMs that provide simulations for the Inter-Sectoral Impact Model Intercomparison Project phase 2b (ISIMIP2b). We develop a standard writing style for the model equations to further enhance model improvement, intercomparison, and communication. In this study, WaterGAP2 used the highest number of water storage compartments, 11, and CWatM used 10 compartments. Seven models used six compartments, while three models (JULES-W1, Mac-PDM.20, and VIC) used the lowest number, three compartments. WaterGAP2 simulates five human water use sectors, while four models (CLM4.5, CLM5.0, LPJmL, and MPIHM) simulate only water used by humans for the irrigation sector. We conclude that even though hydrologic processes are often based on similar equations, in the end, these equations have been adjusted or have used different values for specific parameters or specific variables. Our results highlight that the predictive uncertainty of GWMs can be reduced through improvements of the existing hydrologic processes, implementation of new processes in the models, and high-quality input data.
Global water models (GWMs) simulate the terrestrial water cycle on the global scale and are used to assess the impacts of climate change on freshwater systems. GWMs are developed within different modelling frameworks and consider different underlying hydrological processes, leading to varied model structures. Furthermore, the equations used to describe various processes take different forms and are generally accessible only from within the individual model codes. These factors have hindered a holistic and detailed understanding of how different models operate, yet such an understanding is crucial for explaining the results of model evaluation studies, understanding inter-model differences in their simulations, and identifying areas for future model development. This study provides a comprehensive overview of how 16 state-of-the-art GWMs are designed. We analyse water storage compartments, water flows, and human water use sectors included in models that provide simulations for the Inter-Sectoral Impact Model Intercomparison Project phase 2b (ISIMIP2b). We develop a standard writing style for the model equations to enhance model intercomparison, improvement, and communication. In this study, WaterGAP2 used the highest number of water storage compartments, 11, and CWatM used 10 compartments. Six models used six compartments, while four models (DBH, JULES-W1, Mac-PDM.20, and VIC) used the lowest number, three compartments. WaterGAP2 simulates five human water use sectors, while four models (CLM4.5, CLM5.0, LPJmL, and MPI-HM) simulate only water for the irrigation sector. We conclude that, even though hydrological processes are often based on similar equations for various processes, in the end these equations have been adjusted or models have used different values for specific parameters or specific variables. The similarities and differences found among the models analysed in this study are expected to enable us to reduce the uncertainty in multi-model ensembles, improve existing hydrological processes, and integrate new processes.
Combinatorial CRISPR-Cas screens have advanced the mapping of genetic interactions, but their experimental scale limits the number of targetable gene combinations. Here, we describe 3Cs multiplexing, a rapid and scalable method to generate highly diverse and uniformly distributed combinatorial CRISPR libraries. We demonstrate that the library distribution skew is the critical determinant of its required screening coverage. By circumventing iterative cloning of PCR-amplified oligonucleotides, 3Cs multiplexing facilitates the generation of combinatorial CRISPR libraries with low distribution skews. We show that combinatorial 3Cs libraries can be screened with minimal coverages, reducing associated efforts and costs at least 10-fold. We apply a 3Cs multiplexing library targeting 12,736 autophagy gene combinations with 247,032 paired gRNAs in viability and reporter-based enrichment screens. In the viability screen, we identify, among others, the synthetic lethal WDR45B-PIK3R4 and the proliferation-enhancing ATG7-KEAP1 genetic interactions. In the reporter-based screen, we identify over 1,570 essential genetic interactions for autophagy flux, including interactions among paralogous genes, namely ATG2A-ATG2B, GABARAP-MAP1LC3B and GABARAP-GABARAPL2. However, we only observe few genetic interactions within paralogous gene families of more than two members, indicating functional compensation between them. This work establishes 3Cs multiplexing as a platform for genetic interaction screens at scale.
Natural products can contribute to abiotic stress tolerance in plants and fungi. We hypothesize that biosynthetic gene clusters (BGCs), the genomic elements that underlie natural product biosynthesis, display structured differences along elevation gradients. We analysed biosynthetic gene variation in natural populations of the lichen-forming fungus Umbilicaria pustulata. We collected a total of 600 individuals from the Mediterranean and cold-temperate climates. Population genomic analyses indicate that U. pustulata contains three clusters that are highly differentiated between the Mediterranean and cold-temperate populations. One entire cluster is exclusively present in cold-temperate populations, and a second cluster is putatively dysfunctional in all cold-temperate populations. In the third cluster variation is fixed in all cold-temperate populations due to hitchhiking. In these two clusters the presence of consistent allele frequency differences among replicate populations/gradients suggests that selection rather than drift is driving the pattern. We advocate that the landscape of fungal biosynthetic genes is shaped by both positive and hitchhiking selection. We demonstrate, for the first time, the presence of climate-associated BGCs and BGC variations in lichen-forming fungi. While the associated secondary metabolites of the candidate clusters are presently unknown, our study paves the way for targeted discovery of natural products with ecological significance.
Nature benefits human health. To date, however, little is known whether biodiversity relates to human health. While some local and city level studies show that species diversity, as a measure of biodiversity, can have positive effects, there is a lack of studies about the relationship between different species diversity measures and human health, especially at larger spatial scales. Here, we conduct cross-sectional analyses of the association between species diversity and human health across Germany, while controlling for socio-economic factors and other nature characteristics. As indicators for human health, we use the mental (MCS) and physical health (PCS) component scales of the German Socio-Economic Panel (SOEP, Short Form Health Questionnaire – SF12). For species diversity, we use species richness and abundance estimates of two species groups: plants and birds. We phrase the following hypotheses: plant and bird species are positively associated with mental and physical health (H1 & H3); bird abundance is positively related to mental health (H2). Our results demonstrate a significant positive relationship between plant and bird species richness and mental health across all model variations controlling for a multitude of other factors. These results highlight the importance for species diversity for people’s mental health and well-being. Therefore, policy makers, landscape planners and greenspace managers on the local and national level should consider supporting biodiverse environments to promote mental health and wellbeing. For this purpose, we propose to use species diversity measures as indicators for salutogenic (health promoting) characteristics of nature, landscape and urban green space.
Background: Studies of parasite communities and patterns in the Antarctic are an important knowledge base with the potential to track shifts in ecological relations and study the effects of climate change on host–parasite systems. Endemic Nototheniinae is the dominant fish group found in Antarctic marine habitats. Through their intermediate position within the food web, Nototheniinae link lower to higher trophic levels and thereby also form an important component of parasite life cycles. The study was set out to gain insight into the parasite fauna of Nototheniops larseni, N. nudifrons and Lepidonotothen squamifrons (Nototheniinae) from Elephant Island (Antarctica).
Methods: Sampling was conducted at three locations around Elephant Island during the ANT-XXVIII/4 expedition of the research vessel Polarstern. The parasite fauna of three Nototheniine species was analysed, and findings were compared to previous parasitological and ecological research collated from a literature review.
Results: All host species shared the parasites Neolebouria antarctica (Digenea), Corynosoma bullosum (Acanthocephala) and Pseudoterranova decipiens E (Nematoda). Other parasite taxa were exclusive to one host species in this study. Nototheniops nudifrons was infected by Ascarophis nototheniae (Nematoda), occasional infections of N. larseni with Echinorhynchus petrotschenkoi (Acanthocephala) and L. squamifrons with Elytrophalloides oatesi (Digenea) and larval tetraphyllidean Cestoda were detected.
Conclusion: All examined fish species’ parasites were predominantly euryxenous regarding their fish hosts. The infection of Lepidonotothen squamifrons with Lepidapedon garrardi (Digenea) and Nototheniops larseni with Echinorhynchus petrotschenkoi represent new host records. Despite the challenges and limited opportunities for fishing in remote areas, future studies should continue sampling on a more regular basis and include a larger number of fish species and sampling sites within different habitats.
Marine oomycetes are highly diverse, globally distributed, and play key roles in marine food webs as decomposers, food source, and parasites. Despite their potential importance in global ocean ecosystems, marine oomycetes are comparatively little studied. Here, we tested if the primer pair cox2F_Hud and cox2-RC4, which is already well-established for phylogenetic investigations of terrestrial oomycetes, can also be used for high-throughput community barcoding. Community barcoding of a plankton sample from Brudenell River (Prince Edward Island, Canada), revealed six distinct oomycete OTU clusters. Two of these clusters corresponded to members of the Peronosporaceae—one could be assigned to Peronospora verna, an obligate biotrophic pathogen of the terrestrial plant Veronica serpyllifolia and related species, the other was closely related to Globisporangium rostratum. While the detection of the former in the sample is likely due to long-distance dispersal from the island, the latter might be a bona fide marine species, as several cultivable species of the Peronosporaceae are known to withstand high salt concentrations. Two OTU lineages could be assigned to the Saprolegniaceae. While these might represent marine species of the otherwise terrestrial genus, it is also conceivable that they were introduced on detritus from the island. Two additional OTU clusters were grouped with the early-diverging oomycete lineages but could not be assigned to a specific family. This reflects the current underrepresentation of cox2 sequence data which will hopefully improve with the increasing interest in marine oomycetes.
Community trait assembly in highly diverse tropical rainforests is still poorly understood. Based on more than a decade of field measurements in a biodiversity hotspot of southern Ecuador, we implemented plant trait variation and improved soil organic matter dynamics in a widely used dynamic vegetation model (the Lund-Potsdam-Jena General Ecosystem Simulator, LPJ-GUESS) to explore the main drivers of community assembly along an elevational gradient. In the model used here (LPJ-GUESS-NTD, where NTD stands for nutrient-trait dynamics), each plant individual can possess different trait combinations, and the community trait composition emerges via ecological sorting. Further model developments include plant growth limitation by phosphorous (P) and mycorrhizal nutrient uptake. The new model version reproduced the main observed community trait shift and related vegetation processes along the elevational gradient, but only if nutrient limitations to plant growth were activated. In turn, when traits were fixed, low productivity communities emerged due to reduced nutrient-use efficiency. Mycorrhizal nutrient uptake, when deactivated, reduced net primary production (NPP) by 61–72% along the gradient. Our results strongly suggest that the elevational temperature gradient drives community assembly and ecosystem functioning indirectly through its effect on soil nutrient dynamics and vegetation traits. This illustrates the importance of considering these processes to yield realistic model predictions.
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology—evolutionary relatedness—is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) Consortium. The sixth QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here, we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardization and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit—from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses.
Plastid DNA sequence data have been traditionally widely used in plant phylogenetics because of the high copy number of plastids, their uniparental inheritance, and the blend of coding and non-coding regions with divergent substitution rates that allow the reconstruction of phylogenetic relationships at different taxonomic ranks. In the present study, we evaluate the utility of the plastome for the reconstruction of phylogenetic relationships in the pantropical plant family Ochnaceae (Malpighiales). We used the off-target sequence read fraction of a targeted sequencing study (targeting nuclear loci only) to recover more than 100 kb of the plastid genome from the majority of the more than 200 species of Ochnaceae and all but two genera using de novo and reference-based assembly strategies. Most of the recalcitrant nodes in the family’s backbone were resolved by our plastome-based phylogenetic inference, corroborating the most recent classification system of Ochnaceae and findings from a phylogenomic study based on nuclear loci. Nonetheless, the phylogenetic relationships within the major clades of tribe Ochnineae, which comprise about two thirds of the family’s species diversity, received mostly low support. Generally, the phylogenetic resolution was lowest at the infrageneric level. Overall there was little phylogenetic conflict compared to a recent analysis of nuclear loci. Effects of taxon sampling were invoked as the most likely reason for some of the few well-supported discords. Our study demonstrates the utility of the off-target fraction of a target enrichment study for assembling near-complete plastid genomes for a large proportion of samples.
The Global South is facing severe challenges in ensuring livelihood security due to climate change impacts, environmental degradation and population growth as well as changing lifestyles. These complex problems cannot be solely solved by single scientific disciplines – they require transdisciplinary research (TDR). Stakeholders from civil society, the corporate sector, government and science need to pool their knowledge to find solutions for sustainable transformations. In Namibia, we have been involved in TDR projects on water supply, and sanitation services as well as livestock management in rangeland systems. In this paper, we review two TDR projects that differ in multiple ways and hence allow us to carve out structural differences and critically discuss research outcomes, lessons learned and the challenge of North–South collaborations. Our review builds upon published and unpublished project documents as well as expert interviews with Namibian and German researchers who were involved in the projects. Our results show that TDR can be put into practice in different ways, depending on the research focus and the period available. The TDR phases of problem framing, inter- and transdisciplinary integration were implemented with different tools and foci points. We discuss the role of project length and funding conditions for project success and outcome generation. In addition, we critically consider the role of Namibian and German researchers in these international collaborations. The conclusions we draw touch upon the points of preparatory research funding, the equal acknowledgement of Global South contributions to joint research projects and the explicit handling of TDR components in project work. Significance: • The current social-ecological challenges are complex and require TDR as a mode of knowledge coproduction, particularly in a development context. • Inter- and transdisciplinary integration are critical processes for a project to be successful and require the allocation of adequate time and monetary resources. • Longer-term projects with a funded preparatory research phase constitute a structural model for TDR as project outcomes can evolve over time. • Global South researchers carry a hidden burden in international collaborations that has to be adequately acknowledged upfront in project planning and final products.
The Mediterranean realm, comprising the Mediterranean and Macaronesian regions, has long been recognized as one of the world’s biodiversity hotspots, owing to its remarkable species richness and endemism. Several hypotheses on biotic and abiotic drivers of species diversification in the region have been often proposed but rarely tested in an explicit phylogenetic framework. Here, we investigate the impact of both species-intrinsic and -extrinsic factors on diversification in the species-rich, cosmopolitan Limonium, an angiosperm genus with center of diversity in the Mediterranean. First, we infer and time-calibrate the largest Limonium phylogeny to date. We then estimate ancestral ranges and diversification dynamics at both global and regional scales. At the global scale, we test whether the identified shifts in diversification rates are linked to specific geological and/or climatic events in the Mediterranean area and/or asexual reproduction (apomixis). Our results support a late Paleogene origin in the proto-Mediterranean area for Limonium, followed by extensive in situ diversification in the Mediterranean region during the late Miocene, Pliocene, and Pleistocene. We found significant increases of diversification rates in the “Mediterranean lineage” associated with the Messinian Salinity Crisis, onset of Mediterranean climate, Plio-Pleistocene sea-level fluctuations, and apomixis. Additionally, the Euro-Mediterranean area acted as the major source of species dispersals to the surrounding areas. At the regional scale, we infer the biogeographic origins of insular endemics in the oceanic archipelagos of Macaronesia, and test whether woodiness in the Canarian Nobiles clade is a derived trait linked to insular life and a biotic driver of diversification. We find that Limonium species diversity on the Canary Islands and Cape Verde archipelagos is the product of multiple colonization events followed by in situ diversification, and that woodiness of the Canarian endemics is indeed a derived trait but is not associated with a significant shift to higher diversification rates. Our study expands knowledge on how the interaction between abiotic and biotic drivers shape the uneven distribution of species diversity across taxonomic and geographical scales.