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The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche. [ABSTRACT FROM AUTHOR]

Niche evolution refers to the process by which species undergo changes in ecological interactions, as well as their ability to disperse over time. Our study focuses on the widely distributed neotropical genus of social wasps, Synoeca (Hymenoptera, Vespidae, Epiponini). We use ecological niche modeling to investigate the niche evolution of this insects, to explore how species have evolved within and across distinct environmental boundaries, as well as to explore the overlap, equivalence, and similarity between their niches. Our analysis of Predicted Niche Occupancy reveals that species occupy heterogeneous niches in relation to temperature, precipitation, and altitude, similar to the patterns observed in the analysis of the evolutionary history of climate tolerances, which shows that species have evolved to occupy distinct niche ranges. In addition, our niche comparisons indicate that the species do not share similar niches with each other. All these results suggest that Phylogenetic Niche Conservatism may be playing a significant role as a process contributing to the allopatric pattern observed in this genus. This study represents the first investigation of niche evolution in Vespidae, providing valuable insights for future research into the evolutionary dynamics of insects. [ABSTRACT FROM AUTHOR]

Woody plant encroachment (WPE) in grassland ecosystems has been a pervasive process across the Great Plains, yet a predictive understanding of where it will occur has been elusive. As an exploration of tools of potential utility in this challenge, we mapped WPE processes over the years 2015–2021 in a set of 9 counties in central Kansas. We developed and tested two correlative models based on landscape features: one that assessed distribution of evergreen trees in 2015, and another that assessed areas of WPE in succeeding years. Both models were successful, being able to predict 2015 forest distributions and being able to predict WPE during 2015–2021, as functions of characteristics of landscapes. These simple, correlative models will certainly not be able to predict WPE processes globally, or even regionally, but provide first proof-of-concept explorations for the central Great Plains region. [ABSTRACT FROM AUTHOR]

A new stage in promoting the construction of the Silk Road Economic Belt Core Area, and Xinjiang has been transformed from a relatively closed inland area into an open border. In order to promote the high-quality development of Southern Xinjiang and solve the imbalance contradiction between the development of the Northern Xinjiang and Southern Xinjiang, taking the four districts in Southern Xinjiang as the study area, constructing a high-quality development ecological niche index system of three levels, namely economic, social and ecological, adopting the entropy method to assign weights to the evaluation indexes, and measuring the ecological niche width and the degree of ecological niche overlap of this region in the period from 2011 to 2020. The results show that: Firstly, tourism has the greatest impact on the ecological niche of economic development in state N, with a weighting of 14.18%; Secondly, the ecological status width of economic development in state N demonstrates a structural characteristic of "low level and low gap". The average value of ecological niche width is at class III, indicating a low development status and weak regional influence; Thirdly, the ecological niche overlap of state N is significantly influenced by spatial factors. Regions Z and S are closer together, resulting in higher competition for resource utilization and an average ecological niche overlap at class II. The other two regions are at class III. According to the theory of ecological niche expansion and separation, a specialization separation strategy should be adopted for areas with "low width and high overlap", and a strengthening expansion strategy should be adopted for areas with "low width and low overlap", to optimize the structure of ecological niches and promote high-quality development of the region. [ABSTRACT FROM AUTHOR]

The critical flicker fusion threshold is a psychophysical measure commonly used to quantify visual temporal resolution; the fastest rate at which a visual system can discriminate visual signals. Critical flicker fusion thresholds vary substantially among species, reflecting different ecological niches and demands. However, it is unclear how much variation exists in flicker fusion thresholds between healthy individuals of the same species, or how stable this attribute is over time within individuals. In this study, we assessed both inter- and intra-individual variation in critical flicker fusion thresholds in a cohort of healthy human participants within a specific age range, using two common psychophysical methods and three different measurements during each session. The resulting thresholds for each method were highly correlated. We found a between-participant maximum difference of roughly 30 Hz in flicker fusion thresholds and we estimated a 95% prediction interval of 21 Hz. We used random-effects models to compare between- and within-participant variance and found that approximately 80% of variance was due to between-individual differences, and about 10% of the variance originated from within-individual differences over three sessions. Within-individual thresholds did not differ significantly between the three sessions in males, but did in females (P<0.001 for two methods and P<0.05 for one method), indicating that critical flicker fusion thresholds may be more variable in females than in males. [ABSTRACT FROM AUTHOR]

Against the backdrop of a global malaria epidemic that remains severe, China has eradicated indigenous malaria but still has to be alert to the risk of external importation. Understanding the distribution of vectors can provide an adequate and reliable basis for the development and implementation of vector control strategies. However, with the decline of malaria prevalence in recent years, the capacity of vector monitoring and identification has been greatly weakened. Here we have used new sampling records, climatic data, and topographic data to establish ecological niche models of the three main malaria vectors in China. The model results accurately identified the current habitat suitability areas for the three species of Anopheles and revealed that in addition to precipitation and temperature as important variables affecting the distribution of Anopheles mosquitoes, topographic variables also influenced the distribution of Anopheles mosquitoes. Anopheles sinensis is the most widespread malaria vector in China, with a wide region from the northeast (Heilongjiang Province) to the southwest (Yunnan Province) suitable for its survival. Suitable habitat areas for Anopheles lesteri are concentrated in the central, eastern, and southern regions of China. The suitable habitat areas of Anopheles minimus are the smallest and are only distributed in the border provinces of southern China. On this basis, we further assessed the seasonal variation in habitat suitability areas for these three major malaria vectors in China. The results of this study provide new and more detailed evidence for vector monitoring. In this new era of imported malaria prevention in China, regular reassessment of the risk of vector transmission is recommended. Author summary: Malaria, as one of the most important insect-borne infectious diseases in tropical and subtropical regions, poses a serious disease burden worldwide. Malaria has been prevalent in China for more than 4,000 years, seriously endangering the health of the Chinese people and restricting socio-economic development. Nowadays, there are three major species of malaria transmission in China, Anopheles sinensis, Anopheles lesteri, and Anopheles minimus. Due to vector control and climate change in recent years, the distribution range of these Anopheles mosquitoes has changed. Here, we applied an ecological niche model to simulate the potential distribution as well as seasonal variation of three species of Anopheles and to identify the factors affecting their survival. The results revealed that precipitation, temperature, and topographic variables were important influences on the distribution of Anopheles mosquitoes. A wide region from the northeast (Heilongjiang Province) to the southwest (Yunnan Province) is suitable for An. sinensis. Suitable habitat areas for An. lesteri are concentrated in the central, eastern, and southern regions of China. The suitable habitat areas of An. minimus are the smallest, which are only distributed in the border provinces of southern China. This study provides new information for policymakers to develop vector control measures. [ABSTRACT FROM AUTHOR]

In recent years, buckwheat (Fagopyrum spp.) is being increasingly damaged by the Siberian tortoise beetle (Rhinoncus sibiricus Faust). Adults and nymphs feed on leaf tissues and caulicles, thus damaging its stems and leaves. In this study, we investigated the habits, distribution, and environmental impact of R. sibiricus using MaxEnt, an ecological niche model. Geographic information about the infestation site from previous field surveys and climatic data from 2013 to 2018 were organized and optimized using R. The impact factors were calculated using MaxEnt software. The results indicate that population fluctuations in R. sibiricus are related to changes in temperature, humidity, and their spatial distribution. Under current climatic conditions, R. sibiricus is mainly distributed in northern China, with sporadic distribution in south–western China. The values for a survival probability threshold > 0.3 were: precipitation during the wettest month (bio13), 70.31–137.56 mm; mean temperature of the coldest quarter (bio11), -15.00–0.85°C; mean temperature of the warmest quarter (bio10), 11.88–23.16°C; precipitation during the coldest quarter (biol9), 0–24.39 mm. The main factors contributing > 70% to the models were precipitation during the wettest month and coldest quarter, and mean temperature during the warmest and coldest quarters. Under both future climate models, the center of the fitness zone moves northward. Our results will be useful in guiding administrative decisions and support farmers interested in establishing control and management strategies for R. sibiricus. This study could also serve as a reference for future research on other invasive pests. [ABSTRACT FROM AUTHOR]

Contagious ecthyma is a skin disease, caused by Orf virus, creating great economic threats to livestock farming worldwide. Zoonotic potential of this disease has gained recent attention owing to the re-emergence of disease in several parts of the world. Increased public health concern emphasizes the need for a predictive understanding of the geographic distributional potential of Orf virus. Here, we mapped the current distribution using occurrence records, and estimated the ecological niche in both geographical and environmental spaces. Twenty modeling experiments, resulting from two- and three-partition models, were performed to choose the candidate models that best represent the geographic distributional potential of Orf virus. For all of our models, it was possible to reject the null hypothesis of predictive performance no better than random expectations. However, statistical significance must be accompanied by sufficiently good predictive performance if a model is to be useful. In our case, omission of known distribution of the virus was noticed in all Maxent models, indicating inferior quality of our models. This conclusion was further confirmed by the independent final evaluation, using occurrence records sourced from the Centre for Agriculture and Bioscience International. Minimum volume ellipsoid (MVE) models indicated the broad range of environmental conditions under which Orf virus infections are found. The excluded climatic conditions from MVEs could not be considered as unsuitable owing to the broad distribution of Orf virus. These results suggest two possibilities: that the niche models fail to identify niche limits that constrain the virus, or that the virus has no detectable niche, as it can be found throughout the geographic distributions of its hosts. This potential limitation of component-based pathogen-only ENMs is discussed in detail. [ABSTRACT FROM AUTHOR]

Bacteria like E. coli grow at vastly different rates on different substrates, however, the precise reason for this variability is poorly understood. Different growth rates have been attributed to 'nutrient quality', a key parameter in bacterial growth laws. However, it remains unclear to what extent nutrient quality is rooted in fundamental biochemical constraints like the energy content of nutrients, the protein cost required for their uptake and catabolism, or the capacity of the plasma membrane for nutrient transporters. Here, we show that while nutrient quality is indeed reflected in protein investment in substrate-specific transporters and enzymes, this is not a fundamental limitation on growth rate, at least for certain 'poor' substrates. We show that it is possible to turn mannose, one of the 'poorest' substrates of E. coli, into one of the 'best' substrates by reengineering chromosomal promoters of the mannose transporter and metabolic enzymes required for mannose degradation. This result falls in line with previous observations of more subtle growth rate improvement for many other carbon sources. However, we show that this faster growth rate comes at the cost of diverse cellular capabilities, reflected in longer lag phases, worse starvation survival and lower motility. We show that addition of cAMP to the medium can rescue these phenotypes but imposes a corresponding growth cost. Based on these data, we propose that nutrient quality is largely a self-determined, plastic property that can be modulated by the fraction of proteomic resources devoted to a specific substrate in the much larger proteome sector of catabolically activated genes. Rather than a fundamental biochemical limitation, nutrient quality reflects resource allocation decisions that are shaped by evolution in specific ecological niches and can be quickly adapted if necessary. Author summary: Bacteria grow at very different rates on different substrates. Therefore, the substrates themselves are often denoted as 'rich' substrates versus 'poor' substrates. However, it remains unclear what makes a nutrient a 'rich' or a 'poor' substrate. A host of different explanations have been suggested, such as the energy content and chemical composition of the nutrient, the amount of protein required for efficient catabolism of the substrate, or limitations of 'space' in the plasma membrane for fitting transporters of the substrate. All of these hypotheses are actively debated today. Here, we show instead that at least for certain substrates, nutrient quality can be a plastic property that can be dialed by evolution. Different nutrients enable bacteria to grow, but they also serve as a major signal that allows microbes to infer information about their environment. We propose that nutrient quality encoded in a combination regulatory architecture and enzymatic properties, serves as both as a map of the safety and reliability of the environment and as a regulatory mechanism that implements proteome allocation decisions. [ABSTRACT FROM AUTHOR]

The relationship between morphological traits and ecological performance in birds is an important area of research, as it can help us to understand how birds are able to adapt and how they are affected by changes in their environment. Many studies have investigated the relationship between morphological traits and certain aspects of the performance and ecological niche of these animals. However, the relationship between morphological traits and the primary lifestyle of birds has not previously been explored. This paper aims to evaluate the predictive potential of morphological data to determine the primary lifestyle of birds through a tree-based machine learning algorithm. By doing this, it is also possible to evaluate these artificial categories that we used to split up birds and know whether they are suitable for dividing them in function of shared morphological characteristics or need a redefinition under more discriminant criteria. Supplementary dataset 1 of the AVONET project was used, which comprises the 11 morphological predictors used in this work and the classification according to the primary lifestyle for more than 95% of the existing bird species. For all morphological traits used, statistically significant univariate differences were found between primary lifestyles. The three fitted machine learning models showed high accuracy, in all cases above 78% and superior to the ones achieved through traditional approaches used as contrasts. The results obtained provide evidence that primary lifestyle can be predicted in birds based on morphological traits, as well as more insights about the relevance of functional traits for ecological modeling. This is another step forward in our mechanistic understanding of bird ecology, while exploring how birds have adapted to their environments and how they interact with their surroundings. [ABSTRACT FROM AUTHOR]

The genus Paracoccus capable of inhabiting a variety of different ecological niches both, marine and terrestrial, is globally distributed. In addition, Paracoccus is taxonomically, metabolically and regarding lifestyle highly diverse. Until now, little is known on how Paracoccus can adapt to such a range of different ecological niches and lifestyles. In the present study, the genus Paracoccus was phylogenomically analyzed (n = 160) and revisited, allowing species level classification of 16 so far unclassified Paracoccus sp. strains and detection of five misclassifications. Moreover, we performed pan-genome analysis of Paracoccus-type strains, isolated from a variety of ecological niches, including different soils, tidal flat sediment, host association such as the bluespotted cornetfish, Bugula plumosa, and the reef-building coral Stylophora pistillata to elucidate either i) the importance of lifestyle and adaptation potential, and ii) the role of the genomic equipment and niche adaptation potential. Six complete genomes were de novo hybrid assembled using a combination of short and long-read technologies. These Paracoccus genomes increase the number of completely closed high-quality genomes of type strains from 15 to 21. Pan-genome analysis revealed an open pan-genome composed of 13,819 genes with a minimal chromosomal core (8.84%) highlighting the genomic adaptation potential and the huge impact of extra-chromosomal elements. All genomes are shaped by the acquisition of various mobile genetic elements including genomic islands, prophages, transposases, and insertion sequences emphasizing their genomic plasticity. In terms of lifestyle, each mobile genetic elements should be evaluated separately with respect to the ecological context. Free-living genomes, in contrast to host-associated, tend to comprise (1) larger genomes, or the highest number of extra-chromosomal elements, (2) higher number of genomic islands and insertion sequence elements, and (3) a lower number of intact prophage regions. Regarding lifestyle adaptations, free-living genomes share genes linked to genetic exchange via T4SS, especially relevant for Paracoccus, known for their numerous extrachromosomal elements, enabling adaptation to dynamic environments. Conversely, host-associated genomes feature diverse genes involved in molecule transport, cell wall modification, attachment, stress protection, DNA repair, carbon, and nitrogen metabolism. Due to the vast number of adaptive genes, Paracoccus can quickly adapt to changing environmental conditions. [ABSTRACT FROM AUTHOR]

Kin-recognition is observed across diverse species forming an important behavioral adaptation influencing organismal interactions. In many species, the molecular mechanisms involved are difficult to characterize, but in the nematode Pristionchus pacificus molecular components regulating its kin-recognition system have been identified. These determine its predatory behaviors towards other con-specifics which prevents the killing and cannibalization of kin. Importantly, their impact on other interactions including collective behaviors is unknown. Here, we explored a high altitude adapted clade of this species which aggregates abundantly under laboratory conditions, to investigate the influence of the kin-recognition system on their group behaviours. By utilizing pairwise aggregation assays between distinct strains of P. pacificus with differing degrees of genetic relatedness, we observe aggregation between kin but not distantly related strains. In assays between distantly related strains, the aggregation ratio is frequently reduced. Furthermore, abolishing predation behaviors through CRISPR/Cas9 induced mutations in Ppa-nhr-40 result in rival strains successfully aggregating together. Finally, as Caenorhabditis elegans are found naturally occurring with P. pacificus, we also explored aggregation events between these species. Here, aggregates were dominated by P. pacificus with the presence of only a small number of predators proving sufficient to disrupt C. elegans aggregation dynamics. Thus, aggregating strains of P. pacificus preferentially group with kin, revealing competition and nepotism as previously unknown components influencing collective behaviors in nematodes. Author summary: Many species are able to recognize their relatives from other organisms and this influences how they behave with one another. In some species, this kin-recognition ability results in cooperation while in others it can induce more competitive and aggressive behaviors. Importantly, in many species we do not know the mechanisms which regulate these interactions. In the predatory nematode (round worm) Pristionchus pacificus, we have previously observed that they attack and kill other nematode larvae but their kin-recognition abilities prevent them from harming their close relatives. Importantly, in P. pacificus we have an abundance of genetic and molecular tools and can begin to understand how they are able to carry out this recognition behavior. Here, we have shown that their kin-recognition and predatory abilities also influence other interactions including how these nematodes group together. Many nematode species form aggregates to help them find food or to avoid harmful environmental conditions. In P. pacificus, we have observed that they preferentially aggregate with their close relatives and avoid grouping with more distantly related strains. This may ensure that they give their relatives an advantage within their ecological niche. Therefore, our work will help us understand more about the significance of kin-recognition behaviors and their evolution. [ABSTRACT FROM AUTHOR]

Schistosomiasis is a vector-borne disease transmitted by freshwater snails and is prevalent in rural areas with poor sanitation and no access to tap water. Three snail species are known to transmit schistosomiasis in South Africa (SA), namely Biomphalaria pfeifferi, Bulinus globosus and Bulinus africanus. In 2003, a predicted prevalence of 70% was reported in tropical climates in SA. Temperature and rainfall variability can alter schistosomiasis-transmitting snails' development by increasing or decreasing their abundance and geographical distribution. This study aimed to map the historical distribution of schistosomiasis from 1950 to 2006 in SA. The snail sampling data were obtained from the historical National Snail Freshwater Collection (NFSC). Bioclimatic variables were extracted using ERA 5 reanalysis data provided by the Copernicus Climate Change Service. In this study, we used 19 bioclimatic and four soil variables. The temporal aggregation was the mean climatological period pre-calculated over the 40-year reference period with a spatial resolution of 0.5° x 0.5°. Multicollinearity was reduced by calculating the Variance Inflation Factor Core (VIF), and highly correlated variables (> 0.85) were excluded. To obtain an "ensemble" and avoid the integration of weak models, we averaged predictions using the True Skill Statistical (TSS) method. Results showed that the ensemble model achieved the highest Area Under the Curve (AUC) scores (0.99). For B. africanus, precipitation-related variables contributed to determining the suitability for schistosomiasis. Temperature and precipitation-related variables influenced the distribution of B. globosus in all three models. Biomphalaria pfeifferi showed that Temperature Seasonality (bio4) contributed the most (47%) in all three models. According to the models, suitable areas for transmitting schistosomiasis were in the eastern regions of South Africa. Temperature and rainfall can impact the transmission and distribution of schistosomiasis in SA. The results will enable us to develop future projections for Schistosoma in SA based on climate scenarios. [ABSTRACT FROM AUTHOR]

Crimean-Congo haemorrhagic fever (CCHF) is the most widely distributed tick-borne viral disease in humans and is caused by the Crimean-Congo haemorrhagic fever virus (CCHFV). The virus has a broader distribution, expanding from western China and South Asia to the Middle East, southeast Europe, and Africa. The historical known distribution of the CCHFV vector Hyalomma marginatum in Europe includes most of the Mediterranean and the Balkan countries, Ukraine, and southern Russia. Further expansion of its potential distribution may have occurred in and out of the Mediterranean region. This study updated the distributional map of the principal vector of CCHFV, H. marginatum, in the Old World using an ecological niche modeling approach based on occurrence records from the Global Biodiversity Information Facility (GBIF) and a set of covariates. The model predicted higher suitability of H. marginatum occurrences in diverse regions of Africa and Asia. Furthermore, the model estimated the environmental suitability of H. marginatum across Europe. On a continental scale, the model anticipated a widespread potential distribution encompassing the southern, western, central, and eastern parts of Europe, reaching as far north as the southern regions of Scandinavian countries. The distribution of H. marginatum also covered countries across Central Europe where the species is not autochthonous. All models were statistically robust and performed better than random expectations (p < 0.001). Based on the model results, climatic conditions could hamper the successful overwintering of H. marginatum and their survival as adults in many regions of the Old World. Regular updates of the models are still required to continually assess the areas at risk using up-to-date occurrence and climatic data in present-day and future conditions. Author summary: Hyalomma marginatum is a vector of numerous highly important human and animal pathogens. It is the principal vector of the Crimean-Congo haemorrhagic fever virus (CCHFV) in Europe. This study updated the potential distribution of H. marginatum in the Old World. The model predicted a high suitability for H. marginatum in diverse regions of Africa, along with broader areas in Asia displaying medium to high suitability. The model predicted widespread potential distributions of H. marginatum on the continental European scale, encompassing southern, western, central, and eastern regions and even extending northward to the south of Scandinavian countries. Hyalomma marginatum populations have not yet been established in any country in Central Europe. However, previous studies have reported sporadic records of the species across all countries within the region. Given the frequent occurrence of immature stages of H. marginatum on migratory birds heading northward to temperate Europe, it is crucial to monitor the northward spread and establishment of permanent populations of this species. Our ecological niche model for Central Europe predicted its distribution across all countries within the region, emphasizing the need for ongoing monitoring and surveillance to detect any potential changes in the distribution and establishment of H. marginatum populations. The current prediction of H. marginatum can contribute to our understanding of the disease risk areas associated with this vector. [ABSTRACT FROM AUTHOR]

We aimed (i) to gain a better understanding of the demographic and socioeconomical distribution of ADHD risk in Sweden; and (ii) to contribute to the critical discussion on medicalization, i.e., the tendency to define and treat behavioural and social problems as medical entities. For this purpose, we analysed the risk of suffering from ADHD in the whole Swedish population aged between 5 and 60 years, across 96 different strata defined by combining categories of gender, age, income, and country of birth. The stratified analysis evidenced considerable risk heterogeneity, with prevalence values ranging from 0.03% in high income immigrant women aged 50–59, to 6.18% in middle income immigrant boys aged 10–14. Our study questions the established idea that behavioural difficulties conceptualized as ADHD should be primarily perceived as a neurological abnormality. Rather, our findings suggest that there is a strong sociological component behind how some individuals become impaired and subject to medicalization. [ABSTRACT FROM AUTHOR]

Societies of the later Early to Middle Bronze Age (ca. 2200–1600 BC) in the Carpathian Basin exhibited complex, hierarchical and regionally influential socio-political organisation that came to an abrupt end in the 16th century BC. Considered a collapse by some, this change was characterised by abandonment of virtually all central places / nodes in settlement networks. Until recently, the complexity that characterised the period was believed to have substantially diminished alongside depopulation. This model was reinforced by a combination of the loss of established external networks and low-resolution knowledge of where and how people lived in the first stages of the Late Bronze Age (between 1600 and 1200 BC). We contest the idea of a diminished Late Bronze Age and argue that a fully opposite trajectory can be identified–increased scale, complexity and density in settlement systems and intensification of long-distance networks. We present results of a settlement survey in the southern Pannonian Plain using remote and pedestrian prospection, augmented by small-scale excavations. New absolute dates are used to define the occupational history of sites dating primarily between 1500–1200 BC. We argue that climate change played a substantial role in in the transformation of settlement networks, creating a particular ecological niche enabling societies to thrive. New and specific forms of landscape exploitation developed that were characterised by proximity to wetlands and minor watercourses. In this context, the largest monuments of Bronze Age Europe were created and inhabited. In considering the origins and demise of these megasites and related settlements, we provide a new model for Late Bronze Age societies in the Carpathian Basin and their regional relevance. [ABSTRACT FROM AUTHOR]

Common species often play vital roles in ecosystem functions and processes. Globally, conservation strategies are mostly focused on threatened species and rarely explored the potential of using common species as indicators of critical ecosystems. The Himalayan mountains have unique riverine ecosystems harbouring high diversity of specialist river birds. Ecological niche modelling provides effective tools to predict suitable habitats of a species and identify habitats for conservation. We used two common water-dependent bird species, Blue Whistling Thrush and White-capped Water Redstart as indicators of riverine ecosystems within the Sikkim Himalayan region and predicted their suitable habitats using an ensemble modelling approach. We selected six predictor variables for the final model including three bioclimatic and three topographic variables. For both species, bioclimatic variables such as mean annual temperature and precipitation were the most important factors compared to topographic variables. At least 70 percent of the most suitable habitats are distributed below 2000 m elevation alongside major drainages. Also, most of their potential habitats are distributed outside the protected area networks in the region. This habitat suitability pattern may be applied to other sympatric species in the region. Since major water bodies in Sikkim are largely affected by developmental activities and climate change, these riverine birds might face threats of losing suitable habitats. We recommend a dynamic approach to evaluate the habitat quality of riverine birds, especially outside protected area networks in the region to plan conservation strategies. This approach will ensure habitat conservation of many water-dependent birds and other taxa associated with the riverine ecosystems of the Eastern Himalaya. [ABSTRACT FROM AUTHOR]

Quaternary climatic cycles strongly affected the genetic diversification and ranges of organisms, shaping current genetic structures and distribution patterns. Urodeles provide ideal examples for exploring these dynamics over time and across space. In this study, we integrated a phylogeographic approach and ensemble species distribution modeling (eSDM) to infer the historical demography and distribution patterns of the Vietnam warty newt, Paramesotriton deloustali. Mitochondrial data revealed two groups, West and East, which diverged approximately 1.92 million years ago (Mya). Diversification was likely driven by change in the climate during early stages of the Pleistocene, with increasing monsoon and drought intensities. Biogeographic analysis indicated that the newt's current distribution formed as a result of vicariance events. In addition, the two groups occupy distinct ecological niches. Demographic reconstruction showed signs of expansion in the effective population sizes of the two major groups beginning around 0.11 and 0.15 Mya, respectively. However, eSDM showed fluctuating predicted distributions during the last interglacial, last glacial maximum, mid-Holocene, and present. Mountain systems in northern Vietnam are likely to have served as climatic refuges and to have played a crucial role in safeguarding species from the effects of climate change. [ABSTRACT FROM AUTHOR]

Ecological Niche Modeling is widely used for animals, but rarely for understanding the parasite ecology. Trypanosoma cruzi is a heterogeneous and widely dispersed multi-host parasite. Didelphis aurita is a generalist species, both in terms of diet and environments. We modeled the D. aurita niche and T. cruzi infection in the Brazilian Atlantic Rainforest, using the models of two common vector species (Triatoma vitticeps and Panstrongylus megistus) as biotic variables, predicting their occurrence. Records of T. cruzi infected and non-infected D. aurita were analyzed through climate and landscape approaches by the Ecoland method. Models for each triatomine species and infected and noninfected D. aurita were produced considering climate and landscape: resolution of ~1km2 selected by Pearson's correlation [-0.7≤α≤0.7]. For modeling, seven algorithms available in ModleR package were used. True Skill Statistic was used to evaluate the models' performance (≥ 0.7). T. vitticeps indicates that there is a spatial dependence with warm areas in the southeastern region while P. megistus presented a distribution with high environmental suitability concentrated in the Southeast. High values of climatic suitability, landscape and potential presence of T. vitticeps and P. megistus were considered necessary, but not sufficient for the presence of D. aurita infected by T. cruzi. Climate models showed an ecological niche with suitability variations homogeneous, and landscape models showed a distribution of habitat conditions along the biome, with a fragmented profile and heterogeneous between locations. Ecoland demonstrated that D. aurita has different degrees of impact on its role in the enzootic cycle in different locations of the Atlantic Rainforest. Associating the models with the Ecoland method allowed the recognition of areas where D. aurita are important T. cruzi reservoirs. Areas of high suitability for the presence of marsupials are a necessary, but not sufficient for D. aurita to act as a reservoir for T. cruzi. [ABSTRACT FROM AUTHOR]

Mesocarnivores play a key role in ecosystem dynamics through the regulation of prey populations and are sensitive to environmental changes; thus, they are often considered good model organisms for conservation planning. However, data regarding the factors that influence the habitat use of threatened small wild felids such as the Andean tiger cat (Leopardus tigrinus pardinoides) are scarce. We conducted a two-year survey with 58 camera trap stations to evaluate the determinants of Andean tiger cat habitat use in three protected areas in the Middle Cauca, Colombia. We developed site occupancy models and found that Andean tiger cat habitat use increased with leaf litter depth at intermediate elevations and far from human settlements. Through conditional cooccurrence models, we found that Andean tiger cat habitat use was invariant to the presence of prey or potential intraguild competitors and killers/predators, but its detectability increased when they were present and detected. This suggests that Andean tiger cats may be more likely to be detected in sites with high prey availability. We found that Andean tiger cats preferred sites with deep leaf litter, which is a particular feature of cloud forests that provides suitable conditions for ambush hunting and hiding from intraguild enemies. Our results showed that Andean tiger cats avoided human settlements, which may minimize potential mortality risks in those areas. Moreover, the restricted use of middle elevations by Andean tiger cats suggested that they could be used as a sentinel species to track the effects of climate change since their suitable habitat is likely to be projected upward in elevation. Future conservation actions must be focused on identifying and mitigating human-related threats close to the Andean tiger cat habitat while preserving microhabitat conditions and the existing networks of protected areas. [ABSTRACT FROM AUTHOR]

Holocene-era range expansions are relevant to understanding how a species might respond to the warming and drying climates of today. The harsh conditions of North American deserts have phylogenetically structured desert bat communities but differences in flight capabilities are expected to affect their ability to compete, locate, and use habitat in the face of modern climate change. A highly vagile but data-deficient bat species, the spotted bat (Euderma maculatum), is thought to have expanded its range from central Mexico to western Canada during the Holocene. With specimens spanning this latitudinal extent, we examined historical demography, and used ecological niche modeling (ENM) and phylogeography (mitochondrial DNA), to investigate historic biogeography from the rear to leading edges of the species' range. The ENM supported the notion that Mexico was largely the Pleistocene-era range, whereas haplotype pattern and Skyline plots indicated that populations expanded from the southwestern US throughout the Holocene. This era provided substantial gains in suitable climate space and likely facilitated access to roosting habitat throughout the US Intermountain West. Incongruent phylogenies among different methods prevented a precise understanding of colonization history. However, isolation at the southern-most margin of the range suggests a population was left behind in Mexico as climate space contracted and are currently of unknown status. The species appears historically suited to follow shifts in climate space but differences in flight behaviors between leading edge and core-range haplogroups suggest range expansions could be influenced by differences in habitat quality or climate (e.g., drought). Although its vagility could facilitate response to environmental change and thereby avoid extinction, anthropogenic pressures at the core range could still threaten the ability for beneficial alleles to expand into the leading edge. [ABSTRACT FROM AUTHOR]

Rhynchonycteris is a monotypic genus of Embalonurid bats, whose geographic distribution extends from southern Mexico to tropical regions of the South American continent, including Trinidad and Tobago. Although species that have a wide geographic distribution are frequently revealed to be polytypic, to date, no study has evaluated the taxonomic status of populations of Rhynchonycteris naso. Thus, the aim of this study is to address the patterns of phylogeographic structure and taxonomic subdivision of R. naso using molecular phylogenetics, morphometric data and ecological niche modeling. Phylogenetic results recovered using the genes COI, Cytb, Chd1, Dby, and Usp9x, supported the monophyly of the genus Rhynchonycteris, in addition, a deep phylogeographic structure was revealed by the mitochondrial gene COI for the populations of Belize and Panama in comparison to those of South America. The PCA, and the linear morphometry indicated an apparent differentiation between the cis-Andean and trans-Andean populations. Furthermore, according to the skull morphology, at least two morphotypes were identified. Ecological niche modeling projections in the present have shown that the Andean cordillera acts as a climatic barrier between these two populations, with the depression of Yaracuy (Northwest Venezuela) being the only putative climatically suitable path that could communicate these two populations. On the other hand, projections for the last glacial maximum showed a drastic decrease in climatically suitable areas for the species, suggesting that cycles of lower temperatures played an important role in the separation of these populations. [ABSTRACT FROM AUTHOR]

The choice of appropriate independent variables to create models characterizing ecological niches of species is of critical importance in distributional ecology. This set of dimensions in which a niche is defined can inform about what factors limit the distributional potential of a species. We used a multistep approach to select relevant variables for modeling the ecological niche of the aquatic Spirodela polyrhiza, taking into account variability arising from using distinct algorithms, calibration areas, and spatial resolutions of variables. We found that, even after an initial selection of meaningful variables, the final set of variables selected based on statistical inference varied considerably depending on the combination of algorithm, calibration area, and spatial resolution used. However, variables representing extreme temperatures and dry periods were more consistently selected than others, despite the treatment used, highlighting their importance in shaping the distribution of this species. Other variables related to seasonality of solar radiation, summer solar radiation, and some soil proxies of nutrients in water, were selected commonly but not as frequently as the ones mentioned above. We suggest that these later variables are also important to understanding the distributional potential of the species, but that their effects may be less pronounced at the scale at which they are represented for the needs of this type of modeling. Our results suggest that an informed definition of an initial set of variables, a series of statistical steps for filtering and exploring these predictors, and model selection exercises that consider multiple sets of predictors, can improve determination of variables that shape the niche and distribution of the species, despite differences derived from factors related to data or modeling algorithms. [ABSTRACT FROM AUTHOR]

Human-induced climate change impacts the oceans, increasing their temperature, changing their circulation and chemical properties, and affecting marine ecosystems. Like most marine species, sole has a biphasic life cycle, where one planktonic larval stage and juvenile/adult stages occur in a different ecological niche. The year-class strength, usually quantified by the end of the larvae stage, is crucial for explaining the species' recruitment. We implemented an experimental system for rearing larvae under laboratory conditions and experimentally investigated the effects of temperature and feeding frequencies on survival, development (growth), and metamorphosis success of S. solea larvae. Specific questions addressed in this work include: what are the effects of feeding regimes on larvae development? How does temperature impact larvae development? Our results highlight that survival depends on the first feeding, that the onset of metamorphosis varies according to rearing temperature and that poorly fed larvae take significantly longer to start (if they do) metamorphosing. Moreover, larvae reared at the higher temperature (a +4°C scenario) showed a higher incidence in metamorphosis defects. We discuss the implications of our results in an ecological context, notably in terms of recruitment and settlement. Understanding the processes that regulate the abundance of wild populations is of primary importance, especially if these populations are living resources exploited by humans. [ABSTRACT FROM AUTHOR]

Onchocerciasis caused by infection with Onchocerca volvulus is a disease of public health importance and is highly associated with disability. As Nigeria is aiming at eliminating onchocerciasis by 2030, there is a need to develop newer tools to map disease prevalence and identify environmental factors driving disease prevalence, even in places that have not been previously targeted for preventive chemotherapy. This study produced predictive risk-maps of onchocerciasis in Ogun State. Georeferenced onchocerciasis infection data obtained from a cross-sectional survey at 32 locations between March and July 2015 together with remotely-sensed environmental data were analyzed using Ecological Niche Models (ENM). A total of 107 field occurrence points for O. volvulus infection were recorded. A total of 43 positive occurrence points were used for modelling. ENMs were used to estimate the current geographic distribution of O. volvulus in Ogun State. Maximum Entropy distribution modeling (MaxEnt) was used for predicting the potential suitable habitats, using a portion of the occurrence records. A total of 19 environmental variables were used to model the potential geographical distribution area under current climatic conditions. Empirical prevalence of 9.3% was recorded in this study. The geospatial distribution of infection revealed that all communities in Odeda Local Government Area (a peri-urban LGA) showed remarkably high prevalence compared with other LGAs. The predicted high-risk areas (probability > 0.8) of O. volvulus infection were all parts of Odeda, Abeokuta South, and Abeokuta North, southern part of Imeko-Afon, a large part of Yewa North, some parts of Ewekoro and Obafemi-Owode LGAs. The estimated prevalence for these regions were >60% (between 61% and 100%). As predicted, O. volvulus occurrence showed a positive association with variables reflecting precipitation in Ogun State. Our predictive risk-maps has provided useful information for the elimination of onchocerciais, by identifying priority areas for delivery of intervention in Ogun State, Nigeria. [ABSTRACT FROM AUTHOR]

The habitat heterogeneity hypothesis states that increased habitat heterogeneity promotes species diversity through increased availability of ecological niches. We aimed at describing the local-scale (i.e. nest and adjacent substrate) effects of nests of the sea lamprey (Petromyzon marinus L.) as ecosystem engineer on macroinvertebrate assemblages. We hypothesized that increased streambed physical heterogeneity caused by sea lamprey spawning would modify invertebrate assemblages and specific biologic traits and promote reach-scale diversity. We sampled thirty lamprey nests of the Nive River, a river of the south western France with a length of 79.3 km and tributary of the Adour River, in three zones: the unmodified riverbed (upstream) and zones corresponding to the nest: the area excavated (pit) and the downstream accumulation of pebbles and cobbles (mound). The increased habitat heterogeneity created by lamprey was accompanied by biological heterogeneity with a reduced density of invertebrates (3777 ± 1332 individuals per m2 in upstream, 2649 ± 1386 individuals per m2 in pit and 3833 ± 1052 individuals per m2 in mound) and number of taxa (23.5 ± 3.9 taxa for upstream, 18.6 ± 3.9 taxa in pit and 21.2 ± 4.5 taxa for mound) in the pit compared to other zones. However the overall taxa diversity in nest increased with 82 ± 14 taxa compared to the 69 ± 8 taxa estimated in upstream zone. Diversity indices were consistent with the previous results indicating a loss of α diversity in pit but a higher β diversity between a pit and a mound than between two upstream zones, especially considering Morisita index accounting for taxa abundance. Trait analysis showed high functional diversity within zones with a reduced proportion of collectors, scrapers, shredders, litter/mud preference and small invertebrates in mound, while the proportion of "slabs, blocks, stones and pebbles" preference and largest invertebrates increased. Pit presented the opposite trend, while upstream had globally intermediate trait proportions. Our results highlight important effects on species and functional diversity due to habitat heterogeneity created by a nest-building species, what can ultimately influence food webs and nutrient processes in river ecosystems. [ABSTRACT FROM AUTHOR]

Tiny animals in various metazoan phyla inhabit the interstices between sand and/or gravel grains, and adaptive traits in their body plan, such as simplification and size reduction, have attracted research attention. Several possible explanations of how such animals colonized interstitial habitats have been proposed, but their adaptation to this environment has generally been regarded as irreversible. However, the actual evolutionary transitions are not well understood in almost all taxa. In the present study, we show reversible evolutionary shifts from interstitial to epibenthic habitats in the lineage of the polyclad flatworm genus Boninia. In addition, we establish two new species of this genus found from different microhabitats on a single beach in Okinawa Island, Japan: (i) the interstitial species Boninia uru sp. nov. from gravelly sediments and (ii) the epibenthic species Boninia yambarensis sp. nov. from rock undersurfaces. Our observations suggest that rigid microhabitat segregation exists between these two species. Molecular phylogenetic analyses based on the partial 18S and 28S rDNA sequences of the new Boninia species and four other congeners, for which molecular sequences were available in public databases [Boninia antillara (epibenthic), Boninia divae (epibenthic), Boninia neotethydis (interstitial), and an unidentified Boninia sp. (habitat indeterminate)], revealed that the two interstitial species (B. neotethydis and B. uru sp. nov.) were not monophyletic among the three epibenthic species. According to ancestral state reconstruction analysis, the last common ancestor of the analyzed Boninia species inhabited interstitial realms, and a shift to the epibenthic environment occurred at least once. Such an "interstitial to noninterstitial" evolutionary route seems to be rare among Animalia; to date, it has been reported only in acochlidian slugs in the clade Hedylopsacea. Our phylogenetic tree also showed that the sympatric B. uru sp. nov. and B. yambarensis sp. nov. were not in a sister relationship, indicating that they colonized the same beach independently rather than descended in situ from a common ancestor that migrated and settled at the beach. [ABSTRACT FROM AUTHOR]

The role of climate change in enhancing bio-invasions in natural environments needs to be assessed to provide baseline information for effective species management and policy formulations. In this study, potential habitat suitability maps were generated through Ecological Niche Modeling for five problematic alien and native species in current and future climate simulations for the periods 2050s and 2070s under RCP2.6, RCP4.5, and RCP8.5 emission scenarios. Projected current binary suitability maps showed that 67%, 40%, 28%, 68%, and 54% of the total study area ~ 3318 Km2 is suitable for C. decapetala, L. camara, O. stricta, S. didymobotrya and S. campylacanthum species, respectively. Assuming unlimited species dispersal, two of these species, C. decapetala and S. didymobotrya, were observed to have consistent gradual increase in potential habitats and no habitat losses under the three RCPs by the end of the 2050 and 2070 future periods. The highest recorded relative potential habitat increase was observed for O. stricta at ~205% under RCP2.6 and ~223% under RCP8.5. Although L. camara and O. stricta were observed to have habitat losses, the losses will be very low as compared to that of S. campylacanthum. L. camara and O. stricta relative habitat losses were predicted to be between ~1% under RCP2.6 to ~4.5% under RCP8.5 by 2070 while that of S. campylacanthum was between ~50% under RCP2.6 to ~68% under RCP8.5 by the year 2070. From this study we conclude that the target study species are expected to remain a big threat to inhabited areas as well as biodiversity hotspot areas especially in the Mt. Kenya and the Aberdare forest and national park reserves under climate change. The information generated through this study can be used to inform policy on prioritizing management of these species and subsequent determination of their absolute distributions within the area. [ABSTRACT FROM AUTHOR]

Identifying and predicting how species ranges will shift in response to climate change is paramount for conservation and restoration. Ecological niche models are the most common method used to estimate potential distributions of species; however, they traditionally omit knowledge of intraspecific variation that can allow populations to respond uniquely to change. Here, we aim to test how population X environment relationships influence predicted suitable geographic distributions by comparing aggregated population-level models with species-level model predictions of suitable habitat within population ranges and across the species' range. We also test the effect of two variable selection methods on these predictions–both addressing the possibility of local adaptation: Models were built with (a) a common set, and number, of predictors and, (b) a unique combination and number of predictors specific to each group's training extent. Our study addresses the overarching hypothesis that populations have unique environmental niches, and specifically that (1) species-level models predict more suitable habitat within the ranges of genetic populations than individual models built from those groups, particularly when compared models are built with the same set of environmental predictors; and (2) aggregated genetic population models predict more suitable habitat across the species' range than the species-level model, an = d this difference will increase when models are trained with individualized predictors. We found the species models predicted more habitat within population ranges for two of three genetic groups regardless of variable selection, and that aggregated population models predicted more habitat than species' models, but that individualized predictors increased this difference. Our study emphasizes the extent to which changes to model predictions depend on the inclusion of genetic information and on the type and selection of predictors. Results from these modeling decisions can have broad implications for predicting population-level ecological and evolutionary responses to climate change. [ABSTRACT FROM AUTHOR]

The development of increasingly efficient and cost-effective high throughput DNA sequencing techniques has enhanced the possibility of studying complex microbial systems. Recently, researchers have shown great interest in studying the microorganisms that characterise different ecological niches. Differential abundance analysis aims to find the differences in the abundance of each taxa between two classes of subjects or samples, assigning a significance value to each comparison. Several bioinformatic methods have been specifically developed, taking into account the challenges of microbiome data, such as sparsity, the different sequencing depth constraint between samples and compositionality. Differential abundance analysis has led to important conclusions in different fields, from health to the environment. However, the lack of a known biological truth makes it difficult to validate the results obtained. In this work we exploit metaSPARSim, a microbial sequencing count data simulator, to simulate data with differential abundance features between experimental groups. We perform a complete comparison of recently developed and established methods on a common benchmark with great effort to the reliability of both the simulated scenarios and the evaluation metrics. The performance overview includes the investigation of numerous scenarios, studying the effect on methods' results on the main covariates such as sample size, percentage of differentially abundant features, sequencing depth, feature variability, normalisation approach and ecological niches. Mainly, we find that methods show a good control of the type I error and, generally, also of the false discovery rate at high sample size, while recall seem to depend on the dataset and sample size. Author summary: The Microbiota is the set of microorganisms that characterize an ecological environment or niche. Several studies have shown that the microbiota is involved in various biological mechanisms that affect the health or balance of the host organism or the ecosystem. New discoveries and insights have been possible thanks to the increasingly efficient sequencing technologies together with the development of bioinformatic computational methods. One of the most interesting analyses in this landscape is the identification of microorganisms that show significant different abundances when two groups of subjects are analysed. Although many computational methods have been developed, it is still unclear which one has the best performance. Therefore, we exploited a simulator of microbiome data to build a simulation framework that allowed us to carry out an extensive benchmarking of the known tools of differential abundance analysis. Our work is not only a starting point to guide analysts in the choice of tools, but also a first step towards a robust, reliable and fair simulation framework. [ABSTRACT FROM AUTHOR]

The advantage of sex, and its fixation in some clades and species all over the eukaryote tree of life, is considered an evolutionary enigma, especially regarding its assumed two-fold cost. Several likely hypotheses have been proposed such as (1) a better response to the negative frequency-dependent selection imposed by the "Red Queen" hypothesis; (2) the competition between siblings induced by the Tangled Bank hypothesis; (3) the existence of genetic and of (4) ecological factors that can diminish the cost of sex to less than the standard assumed two-fold; and (5) a better maintenance of genetic diversity and its resulting phenotypic variation, providing a selective advantage in randomly fluctuating environments. While these hypotheses have mostly been studied separately, they can also act simultaneously. This was advocated by several studies which presented a pluralist point of view. Only three among the five causes cited above were considered yet in such a framework: the Red Queen hypothesis, the Tangled Bank and the genetic factors lowering the cost of sex. We thus simulated the evolution of a finite mutating population undergoing negative frequency-dependent selection on phenotypes and a two-fold (or less) cost of sexuality, experiencing randomly fluctuating selection along generations. The individuals inherited their reproductive modes, either clonal or sexual. We found that exclusive sexuality begins to fix in populations exposed to environmental variation that exceeds the width of one ecological niche (twice the standard deviation of a Gaussian response to environment). This threshold was lowered by increasing negative frequency-dependent selection and when reducing the two-fold cost of sex. It contributes advocating that the different processes involved in a short-term advantage of sex and recombination can act in combination to favor the fixation of sexual reproduction in populations. [ABSTRACT FROM AUTHOR]

Understanding the ecological niche of some fishes is complicated by their frequent use of a broad range of food resources and habitats across space and time. Little is known about Broad Whitefish (Coregonus nasus) ecological niches in Arctic landscapes even though they are an important subsistence species for Alaska's Indigenous communities. We investigated the foraging ecology and habitat use of Broad Whitefish via stable isotope analyses of muscle and liver tissue and otoliths from mature fish migrating in the Colville River within Arctic Alaska. The range of δ13C (-31.8– -21.9‰) and δ15N (6.6–13.1‰) across tissue types and among individuals overlapped with isotope values previously observed in Arctic lakes and rivers, estuaries, and nearshore marine habitat. The large range of δ18O (4.5–10.9‰) and δD (-237.6– -158.9‰) suggests fish utilized a broad spectrum of habitats across elevational and latitudinal gradients. Cluster analysis of muscle δ13Cˈ, δ15N, δ18O, and δD indicated that Broad Whitefish occupied four different foraging niches that relied on marine and land-based (i.e., freshwater and terrestrial) food sources to varying degrees. Most individuals had isotopic signatures representative of coastal freshwater habitat (Group 3; 25%) or coastal lagoon and delta habitat (Group 1; 57%), while individuals that mainly utilized inland freshwater (Group 4; 4%) and nearshore marine habitats (Group 2; 14%) represented smaller proportions. Otolith microchemistry confirmed that individuals with more enriched muscle tissue δ13Cˈ, δD, and δ18O tended to use marine habitats, while individuals that mainly used freshwater habitats had values that were less enriched. The isotopic niches identified here represent important foraging habitats utilized by Broad Whitefish. To preserve access to these diverse habitats it will be important to limit barriers along nearshore areas and reduce impacts like roads and climate change on natural flow regimes. Maintaining these diverse connected habitats will facilitate long-term population stability, buffering populations from future environmental and anthropogenic perturbations. [ABSTRACT FROM AUTHOR]

Food webs map feeding interactions among species, providing a valuable tool for understanding and predicting community dynamics. Using species' body sizes is a promising avenue for parameterizing food-web models, but such approaches have not yet been able to fully recover observed community dynamics. Such discrepancies suggest that traits other than body size also play important roles. For example, differences in species' use of microhabitat or non-consumptive effects of intraguild predators may affect dynamics in ways not captured by body size. In Laubmeier et al. (2018), we developed a dynamic food-web model incorporating microhabitat and non-consumptive predator effects in addition to body size, and used simulations to suggest an optimal sampling design of a mesocosm experiment to test the model. Here, we perform the mesocosm experiment to generate empirical time-series of insect herbivore and predator abundance dynamics. We minimize least squares error between the model and time-series to determine parameter values of four alternative models, which differ in terms of including vs excluding microhabitat use and non-consumptive predator-predator effects. We use both statistical and expert-knowledge criteria to compare the models and find including both microhabitat use and non-consumptive predator-predator effects best explains observed aphid and predator population dynamics, followed by the model including microhabitat alone. This ranking suggests that microhabitat plays a larger role in driving population dynamics than non-consumptive predator-predator effects, although both are clearly important. Our results illustrate the importance of additional traits alongside body size in driving trophic interactions. They also point to the need to consider trophic interactions and population dynamics in a wider community context, where non-trophic impacts can dramatically modify the interplay between multiple predators and prey. Overall, we demonstrate the potential for utilizing traits beyond body size to improve trait-based models and the value of iterative cycling between theory, data and experiment to hone current insights into how traits affect food-web dynamics. [ABSTRACT FROM AUTHOR]

Yellow fever virus (YFV) has a long history of impacting human health in South America. Mayaro virus (MAYV) is an emerging arbovirus of public health concern in the Neotropics and its full impact is yet unknown. Both YFV and MAYV are primarily maintained via a sylvatic transmission cycle but can be opportunistically transmitted to humans by the bites of infected forest dwelling Haemagogus janthinomys Dyar, 1921. To better understand the potential risk of YFV and MAYV transmission to humans, a more detailed understanding of this vector species' distribution is critical. This study compiled a comprehensive database of 177 unique Hg. janthinomys collection sites retrieved from the published literature, digitized museum specimens and publicly accessible mosquito surveillance data. Covariate analysis was performed to optimize a selection of environmental (topographic and bioclimatic) variables associated with predicting habitat suitability, and species distributions modelled across South America using a maximum entropy (MaxEnt) approach. Our results indicate that suitable habitat for Hg. janthinomys can be found across forested regions of South America including the Atlantic forests and interior Amazon. Author summary: Mayaro virus is a neglected tropical disease and there is insufficient evidence to define its geographic range. The mosquito Haemagogus janthinomys is a primary vector of Mayaro and its distribution is largely unknown at a sub-country scale. Building compendiums of collection data and creating ecological niche models provides a more precise estimation of vector species potential habitat. Our dataset stands as one of the most expansive existing for collection data of this species combining data published in literature, publicly available data repositories and digitized museum specimen records. Comparing results of niche models with near real time environmental data can give even better predictions of areas where Mayaro virus exposure could occur. The methods and results of this study can be replicated for any disease/vector of interest so long as there is data discoverable through the scientific literature, public repositories, or other civilian and governmental agencies willing to share. [ABSTRACT FROM AUTHOR]

Competence for DNA transformation is a major strategy for bacterial adaptation and survival. Yet, this successful tactic is energy-consuming, shifts dramatically the metabolism, and transitory impairs the regular cell-cycle. In streptococci, complex regulatory pathways control competence deactivation to narrow its development to a sharp window of time, a process known as competence shut-off. Although characterized in streptococci whose competence is activated by the ComCDE signaling pathway, it remains unclear for those controlled by the ComRS system. In this work, we investigate competence shut-off in the major human gut commensal Streptococcus salivarius. Using a deterministic mathematical model of the ComRS system, we predicted a negative player under the control of the central regulator ComX as involved in ComS/XIP pheromone degradation through a negative feedback loop. The individual inactivation of peptidase genes belonging to the ComX regulon allowed the identification of PepF as an essential oligoendopeptidase in S. salivarius. By combining conditional mutants, transcriptional analyses, and biochemical characterization of pheromone degradation, we validated the reciprocal role of PepF and XIP in ComRS shut-off. Notably, engineering cleavage site residues generated ultra-resistant peptides producing high and long-lasting competence activation. Altogether, this study reveals a proteolytic shut-off mechanism of competence in the salivarius group and suggests that this mechanism could be shared by other ComRS-containing streptococci. Author summary: The human oral cavity is one of the most challenging ecological niches for bacteria. In this ecosystem, hundreds of species compete for food and survival in a physicochemical fluctuating environment. To outcompete, Streptococcus salivarius has developed a particular physiological state called competence during which antibacterial compounds are produced together with the uptake of external DNA that can be integrated in its own genome. Although this strategy is of main importance for evolution and adaptation, its short-term cost in terms of energy and metabolism reprogramming are important. To restrain competence activation to a sharp window of time, bacteria use a process known as shut-off. Although described in some species, this process is still mostly unknown in streptococci. In this work, we used predictive mathematical simulations to infer the role of a pheromone-degradation machinery involved in the exit from competence. We confirmed experimentally this mechanism by identifying PepF as a competence-induced oligoendopeptidase with a specific activity towards the XIP pheromone. Importantly, we show that this peptidase is not only shutting down competence but also preventing its development under inappropriate conditions. [ABSTRACT FROM AUTHOR]

This document is a correction notice for an article titled "Ecological niche modelling of two water-dependent birds informs the conservation needs of riverine ecosystems outside protected area network in the Eastern Himalaya, India." The correction addresses an error in Table 1, specifically the incorrect percentage value for the Blue Whistling Thrush in the 0-1000 elevation zone. The correct percentage value is 25.50%. The table provides information on the suitable habitat areas for both bird species in different elevation zones in the Sikkim Himalaya. The correction was reported by multiple authors. [Extracted from the article]

Rabies transmitted by wildlife is now the main source of human rabies in the Americas. The common marmoset, Callithrix jacchus, is considered a reservoir of rabies causing sporadic and unpredictable human deaths in Brazil, but the extent of the spillover risk to humans remains unknown. In this study, we described the spatiotemporal dynamics of rabies affecting C. jacchus reported to Brazil's Ministry of Health passive surveillance system between 2008 and 2020, and combined ecological niche modelling with C. jacchus occurrence data to predict its suitable habitat. Our results show that 67 outbreaks (91 cases) of rabies affecting C. jacchus were reported by 41 municipalities between January 2008 and October 2020, with a mean of 5 outbreaks/year [range: 1–14]. The maximum number of outbreaks and municipalities reporting cases occurred in 2018, coinciding with higher surveillance of primate deaths due to Yellow Fever. A mean of 3 [1–9] new municipalities reported outbreaks yearly, suggesting potential spatial expansions of the C. jacchus variant in northeastern Brazil and emerging rabies spillover from vampire bat Desmodus rotundus to C. jacchus in the north and south. Outbreaks were concentrated in the states of Ceará (72%) and Pernambuco (16%) up to 2012, but are now reported in Piauí since 2013, in Bahia since 2017 (D. rotundus' antigenic variant, AgV3) and in Rio de Janeiro since 2019 (AgV3). Besides confirming suitable habitat for this primate in the northeast and the east coast of Brazil, our Maximum Entropy model also predicted suitable habitat on the north and the west states of the country but predicted low habitat suitability among inland municipalities of the Caatinga biome reporting rabies. Our findings revealed new areas reporting rabies infecting C. jacchus, highlighting the need to implement strategies limiting spillover to humans and to better understand the drivers of C. jacchus rabies dynamics. Author summary: Rabies virus is the deadliest virus affecting mammals. In Brazil, rabies transmitted by the common marmoset primate is emerging and causing unpredictable human deaths. This primate once endemic to the northeast of the country has now invaded regions in the south throughout human-mediated introductions. However, the dynamics of rabies in this primate and the extend of spillover risk to humans remain unknown. We found that outbreaks of rabies in this marmoset reported to the Ministry of Health are continuously reported in new areas, including three new states since 2012 and three states reporting rabies originated from the common vampire bat. We also showed that this primate has suitable habitat to invade other states in the north and west of Brazil. Preventive strategies should be implemented to limit further rabies spillover to humans in new areas. [ABSTRACT FROM AUTHOR]

Early stone tools, and in particular sharp stone tools, arguably represent one of the most important technological milestones in human evolution. The production and use of sharp stone tools significantly widened the ecological niche of our ancestors, allowing them to exploit novel food resources. However, despite their importance, it is still unclear how these early lithic technologies emerged and which behaviours served as stepping-stones for the development of systematic lithic production in our lineage. One approach to answer this question is to collect comparative data on the stone tool making and using abilities of our closest living relatives, the great apes, to reconstruct the potential stone-related behaviours of early hominins. To this end, we tested both the individual and the social learning abilities of five orangutans to make and use stone tools. Although the orangutans did not make sharp stone tools initially, three individuals spontaneously engaged in lithic percussion, and sharp stone pieces were produced under later experimental conditions. Furthermore, when provided with a human-made sharp stone, one orangutan spontaneously used it as a cutting tool. Contrary to previous experiments, social demonstrations did not considerably improve the stone tool making and using abilities of orangutans. Our study is the first to systematically investigate the stone tool making and using abilities of untrained, unenculturated orangutans showing that two proposed pre-requisites for the emergence of early lithic technologies–lithic percussion and the recognition of sharp-edged stones as cutting tools–are present in this species. We discuss the implications that ours and previous great ape stone tool experiments have for understanding the initial stages of lithic technologies in our lineage. [ABSTRACT FROM AUTHOR]

MERRA/Max provides a feature selection approach to dimensionality reduction that enables direct use of global climate model outputs in ecological niche modeling. The system accomplishes this reduction through a Monte Carlo optimization in which many independent MaxEnt runs, operating on a species occurrence file and a small set of randomly selected variables in a large collection of variables, converge on an estimate of the top contributing predictors in the larger collection. These top predictors can be viewed as potential candidates in the variable selection step of the ecological niche modeling process. MERRA/Max's Monte Carlo algorithm operates on files stored in the underlying filesystem, making it scalable to large data sets. Its software components can run as parallel processes in a high-performance cloud computing environment to yield near real-time performance. In tests using Cassin's Sparrow (Peucaea cassinii) as the target species, MERRA/Max selected a set of predictors from Worldclim's Bioclim collection of 19 environmental variables that have been shown to be important determinants of the species' bioclimatic niche. It also selected biologically and ecologically plausible predictors from a more diverse set of 86 environmental variables derived from NASA's Modern-Era Retrospective Analysis for Research and Applications Version 2 (MERRA-2) reanalysis, an output product of the Goddard Earth Observing System Version 5 (GEOS-5) modeling system. We believe these results point to a technological approach that could expand the use global climate model outputs in ecological niche modeling, foster exploratory experimentation with otherwise difficult-to-use climate data sets, streamline the modeling process, and, eventually, enable automated bioclimatic modeling as a practical, readily accessible, low-cost, commercial cloud service. [ABSTRACT FROM AUTHOR]

The genus Bursera, includes ~100 shrub and trees species in tropical dry forests with its center of diversification and endemism in Mexico. Morphologically intermediate individuals have commonly been observed in Mexican Bursera in areas where closely related species coexist. These individuals are assumed to result from interspecific hybridization, but no molecular evidence has supported their hybrid origins. This study aimed to investigate the existence of interspecific hybridization among three Mexican Bursera species (Bullockia section: B. cuneata, B. palmeri and B. bipinnata) from nine populations based on DNA sequences (three nuclear and four chloroplast regions) and ecological niche modeling for three past and two future scenario projections. Results from the only two polymorphic nuclear regions (PEPC, ETS) supported the hybrid origin of morphologically intermediate individuals and revealed that B. cuneata and B. bipinnata are the parental species that are genetically closer to the putative hybrids. Ecological niche modeling accurately predicted the occurrence of putative hybrid populations and showed a potential hybrid zone extending in a larger area (74,000 km2) than previously thought. Paleo-reconstructions showed a potential hybrid zone existing from the Last Glacial Maximum (~ 21 kya) that has increased since the late Holocene to the present. Future ecological niche projections show an increment of suitability of the potential hybrid zone for 2050 and 2070 relative to the present. Hybrid zone changes responded mostly to an increase in elevational ranges. Our study provides the first insight of an extensive hybrid zone among three Mexican Bursera species based on molecular data and ecological niche modeling. [ABSTRACT FROM AUTHOR]

In an era of anthropocene, threatened and endemic species with small population sizes and habitat specialists experience a greater global conservation concern in view of being at higher risk of extinction. Predicting and plotting appropriate potential habitats for such species is a rational method for monitoring and restoring their dwindling populations in expected territories. Ecological niche modelling (ENM) coalesces species existence sites with environmental raster layers to construct models that describe possible distributions of plant species. The present study is aimed to study the potential distribution and cultivation hotspots for reintroducing the high value, vulnerable medicinal herb (Rheum webbianum) in the Union territories of Jammu and Kashmir and Ladakh using population attributes and ecological niche modelling approach. Sixty-three populations inventoried from twenty-eight areas display a significant change in the phytosociological attributes on account of various anthropogenic threats. The current potential habitats coincide with actual distribution records and the mean value of Area Under Curve (AUC) was 0.98 and the line of predicted omission was almost adjacent to omission in training samples, thus validating a robustness of the model. The potential habitat suitability map based on the current climatic conditions predicted a total of 103760 km2 as suitable area for the growth of Rheum webbianum. Under the future climatic conditions, there is a significant reduction in the habitat suitability ranging from -78531.34 Km2 (RCP 4.5 for 2050) to -77325.81 (RCP 8.5 for 2070). Furthermore, there is a slight increase in the suitable habitats under future climatic conditions, ranging from +21.99 Km2 under RCP 8.5 (2050) to +3.14 Km2 under RCP 4.5 (2070). The Jackknife tests indicated Precipitation of Driest Month (BIO14) as the most contributing climatic variable in governing the distribution of R. webbianum. Therefore, scientifically sound management strategies are urgently needed to save whatever populations are left in-situ to protect this species from getting extinct. Present results can be used by conservationists for mitigating the biodiversity decline and exploring undocumented populations of R. webbianum on one hand and by policymakers in implementing the policy of conservation of species with specific habitat requirements by launching species recovery programmes in future on the other. [ABSTRACT FROM AUTHOR]

Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of the molecular mechanisms underlying phage–host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage–host interactions by composing a well-assorted library of 68 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL (BActeriophage SElection for your Laboratory) collection. This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside 10 well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to 11 defense systems across different layers of bacterial immunity, and matched these results to the phages' host range across a panel of pathogenic enterobacterial strains. Clear patterns in the distribution of phage phenotypes and genomic features highlighted systematic differences in the potency of different immunity systems and suggested the molecular basis of receptor specificity in several phage groups. Our results also indicate strong trade-offs between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific ecological niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications. This study presents the BASEL collection of phages that infect the model bacterium Escherichia coli; this resource for the community is representative of natural E. coli phage diversity and has been extensively characterized phenotypically and genomically. [ABSTRACT FROM AUTHOR]

Background: Snakebite envenoming is listed as category 'A' Neglected Tropical Disease. To achieve the target of WHO (World Health Organization) 2019, it becomes necessary to understand various attributes associated with snakebite including community awareness, improvisation of medical facilities and to map the potential distribution of venomous snakes responsible for the bite. Hence this study is conducted in Sikkim, India to understand the epidemiology of snakebite in Sikkim. The potential distribution and risk mapping of fivecommon venomous snakes are done for effective management of snakebite cases. Methods and findings: The snakebite cases registered in six district hospitals and four PHCs (Primary Health Centers) of Sikkim were collected from the year 2011 to 2018. Community survey was also conducted to supplement the data. Ecological Niche Modeling (ENM) was performed to predict the potential habitat of five common venomous snakes of Sikkim. Therisk modeling of snakebite cases was done at the level of Gram Panchayat Unit (GPU) using Geographically Weighted Regression (GWR) and Ordinary Linear Square (OLS) model. We found higher number of male victims inflicted with snakebite envenomation. The potential distribution of the five venomous snakes showed satisfactory mean AUC (Area under Curve) value. Both the models showed significant positive association of snakebite cases with habitat suitability of the venomous snakes.Hospital data revealed no death cases whereas community data reported 24 deaths. Conclusions: Death from snakebite reflected in community data but not in hospital data strongly indicates the people's belief in traditional medicine. Though people of Sikkim have rich traditional knowledge, in case of snakebite traditional practices may be ineffective leading to loss of life. Sensitizing people and improving medical facilities along with proper transport facilities in rural areas might significantly reduce the snakebite casualties in the state. Author summary: Snakebite is a global burden especially inflicting despair and torment among agronomist rural population of the society. This study has been conducted in small state of Sikkim in India which has not been actually considered so far in any of the national statistical condensation of snakebite cases. There are around 19 venomous snakes found in Sikkim of which five common ones co-exist with humans. Such co-existence may lead to unintentional encounter posing life threatening snakebite. People of Sikkim have strong belief on traditional healers for treatment of snakebite which results in mortality and morbidity. The present epidemiological study provides the baseline information compiling both hospital and community data and predict the areas having higher risk of snakebite envenomation in Sikkim. This study will help the authorities for better preparedness to deal with snakebite emergency to achieveminimum or no mortality. Potential risk mapping will help the health department for stocking the anti-venom in nearby health centers. Most importantly, the study will create awareness among the people and the authority about the snakebite which is considered as neglected tropical disease. [ABSTRACT FROM AUTHOR]

While often deleterious, hybridization can also be a key source of genetic variation and pre-adapted haplotypes, enabling rapid evolution and niche expansion. Here we evaluate these opposing selection forces on introgressed ancestry between maize (Zea mays ssp. mays) and its wild teosinte relative, mexicana (Zea mays ssp. mexicana). Introgression from ecologically diverse teosinte may have facilitated maize's global range expansion, in particular to challenging high elevation regions (> 1500 m). We generated low-coverage genome sequencing data for 348 maize and mexicana individuals to evaluate patterns of introgression in 14 sympatric population pairs, spanning the elevational range of mexicana, a teosinte endemic to the mountains of Mexico. While recent hybrids are commonly observed in sympatric populations and mexicana demonstrates fine-scale local adaptation, we find that the majority of mexicana ancestry tracts introgressed into maize over 1000 generations ago. This mexicana ancestry seems to have maintained much of its diversity and likely came from a common ancestral source, rather than contemporary sympatric populations, resulting in relatively low FST between mexicana ancestry tracts sampled from geographically distant maize populations. Introgressed mexicana ancestry in maize is reduced in lower-recombination rate quintiles of the genome and around domestication genes, consistent with pervasive selection against introgression. However, we also find mexicana ancestry increases across the sampled elevational gradient and that high introgression peaks are most commonly shared among high-elevation maize populations, consistent with introgression from mexicana facilitating adaptation to the highland environment. In the other direction, we find patterns consistent with adaptive and clinal introgression of maize ancestry into sympatric mexicana at many loci across the genome, suggesting that maize also contributes to adaptation in mexicana, especially at the lower end of its elevational range. In sympatric maize, in addition to high introgression regions we find many genomic regions where selection for local adaptation maintains steep gradients in introgressed mexicana ancestry across elevation, including at least two inversions: the well-characterized 14 Mb Inv4m on chromosome 4 and a novel 3 Mb inversion Inv9f surrounding the macrohairless1 locus on chromosome 9. Most outlier loci with high mexicana introgression show no signals of sweeps or local sourcing from sympatric populations and so likely represent ancestral introgression sorted by selection, resulting in correlated but distinct outcomes of introgression in different contemporary maize populations. Author summary: When species expand their ranges, new encounters with diverse wild relatives can introduce deleterious genetic variation, but may also accelerate the colonization of novel environments by providing 'ready-made' genetic adaptations. Maize today is a global staple, far exceeding the original ecological niche of its wild progenitor. We show that gene flow from highland-endemic wild mexicana facilitated maize's range expansion from the valleys where it was domesticated to sites over 1500m in the mountains of Mexico. We find loci where mexicana ancestry has been repeatedly favored in highland maize populations. We also find loci (including a newly identified inversion) where mexicana ancestry increases steeply with elevation, providing evidence for adaptive trade-offs. We additionally demonstrate selection against mexicana ancestry, especially near domestication genes. We sampled mexicana growing alongside maize fields, yet find little evidence that introgression is recent or locally-sourced genomewide or at adaptive loci. Rather, the majority of mexicana ancestry was introduced into maize over 1000 generations ago, and subsequently diverged and was sorted by selection in individual populations. These results add to our understanding of the effects of introgression on range expansions and adaptation. [ABSTRACT FROM AUTHOR]

Ecological Niche Modeling is a process by which spatiotemporal, climatic, and environmental data are analyzed to predict the distribution of an organism. Using this process, an ensemble ecological niche model for West Nile virus habitat prediction in the state of Florida was developed. This model was created through the weighted averaging of three separate machine learning models—boosted regression tree, random forest, and maximum entropy—developed for this study using sentinel chicken surveillance and remote sensing data. Variable importance differed among the models. The highest variable permutation value included mean dewpoint temperature for the boosted regression tree model, mean temperature for the random forest model, and wetlands focal statistics for the maximum entropy mode. Model validation resulted in area under the receiver curve predictive values ranging from good [0.8728 (95% CI 0.8422–0.8986)] for the maximum entropy model to excellent [0.9996 (95% CI 0.9988–1.0000)] for random forest model, with the ensemble model predictive value also in the excellent range [0.9939 (95% CI 0.9800–0.9979]. This model should allow mosquito control districts to optimize West Nile virus surveillance, improving detection and allowing for a faster, targeted response to reduce West Nile virus transmission potential. [ABSTRACT FROM AUTHOR]

The jaguar (Panthera onca) is one of the most threatened carnivores in the Americas. Despite a long history of research on this charismatic species, to date there have been few systematic efforts to assess its population size and status in most countries across its distribution range. We present here the results of the two National Jaguar Surveys for Mexico, the first national censuses in any country within the species distribution. We estimated jaguar densities from field data collected at 13 localities in 2008–2010 (2010 hereafter) and 11 localities in 2016–2018 (2018 hereafter). We used the 2010 census results as the basis to develop a National Jaguar Conservation Strategy that identified critical issues for jaguar conservation in Mexico. We worked with the Mexican government to implement the conservation strategy and then evaluated its effectivity. To compare the 2010 and 2018 results, we estimated the amount of jaguar-suitable habitat in the entire country based on an ecological niche model for both periods. Suitable jaguar habitat covered ~267,063 km2 (13.9% of the country's territory) in 2010 and ~ 288,890 km2 (~14.8% of the country's territory) in 2018. Using the most conservative density values for each priority region, we estimated jaguar densities for both the high and low suitable habitats. The total jaguar population was estimated in ~4,000 individuals for 2010 census and ~4,800 for the 2018 census. The Yucatan Peninsula was the region with the largest population, around 2000 jaguars, in both censuses. Our promising results indicate that the actions we proposed in the National Jaguar Conservation Strategy, some of which have been implemented working together with the Federal Government, other NGO's, and land owners, are improving jaguar conservation in Mexico. The continuation of surveys and monitoring programs of the jaguar populations in Mexico will provide accurate information to design and implement effective, science-based conservation measures to try to ensure that robust jaguar populations remain a permanent fixture of Mexico's natural heritage. [ABSTRACT FROM AUTHOR]

Quantitative traits are measurable phenotypes that show continuous variation over a wide phenotypic range. Enormous effort has recently been put into determining the genetic influences on a variety of quantitative traits with mixed success. We identified a quantitative trait in a tractable model system, the GAL pathway in yeast, which controls the uptake and metabolism of the sugar galactose. GAL pathway activation depends both on galactose concentration and on the concentrations of competing, preferred sugars such as glucose. Natural yeast isolates show substantial variation in the behavior of the pathway. All studied yeast strains exhibit bimodal responses relative to external galactose concentration, i.e. a set of galactose concentrations existed at which both GAL-induced and GAL-repressed subpopulations were observed. However, these concentrations differed in different strains. We built a mechanistic model of the GAL pathway and identified parameters that are plausible candidates for capturing the phenotypic features of a set of strains including standard lab strains, natural variants, and mutants. In silico perturbation of these parameters identified variation in the intracellular galactose sensor, Gal3p, the negative feedback node within the GAL regulatory network, Gal80p, and the hexose transporters, HXT, as the main sources of the bimodal range variation. We were able to switch the phenotype of individual yeast strains in silico by tuning parameters related to these three elements. Determining the basis for these behavioral differences may give insight into how the GAL pathway processes information, and into the evolution of nutrient metabolism preferences in different strains. More generally, our method of identifying the key parameters that explain phenotypic variation in this system should be generally applicable to other quantitative traits. Author summary: Microbes adopt elaborate strategies for the preferred uptake and use of nutrients to cope with complex and fluctuating environments. As a result, yeast strains originating from different ecological niches show significant variation in the way they induce genes in the galactose metabolism (GAL) pathway in response to nutrient signals. To identify the mechanistic sources of this variation, we built a mathematical model to simulate the dynamics of the galactose metabolic regulation network, and studied how parameters with different biological implications contributed to the natural variation. We found that variations in the behavior of the galactose sensor Gal3p, the negative feedback node Gal80p, and the hexose transporters HXT were critical elements in the GAL pathway response. Tuning single parameters in silico was sufficient to achieve phenotype switching between different yeast strains. Our computational approach should be generally useful to help pinpoint the genetic and molecular bases of natural variation in other systems. [ABSTRACT FROM AUTHOR]

Climate change represents an unprecedented threat to global biodiversity and, for many species, gaps in our knowledge of their biology remain acute. Gaps in baseline knowledge, such as confirmed identifications (Linnean shortfalls) and adequate collections (Wallacean shortfalls), need to be minimized with new studies, since this is often critical for effective conservation. Despite the increase in scientific research on primates in the southwest of the Brazilian Amazon, little is known about the species Mico nigriceps (Ferrari & Lopes, 1992) Primates, Platirryni. In the current study, we sought to reduce the extent of the Wallacean shortfall for M. nigriceps, understand whether climate change represents a threat to the distribution of the species, and identify priority areas for its conservation. Accordingly, we provide 121 new records in 14 locations, obtained directly from the field, and five from the literature. Using this, we carried out ecological niche modeling, to better understand how environmental suitability might limit the area occupied by the species. We then projected a distribution for 2070 with the SSP2-4.5 (more optimistic) and SSP5-8.5 (more pessimistic) scenarios. Our data confirmed the geographic distribution of the species as being restricted to headwaters of the Ji-Paraná/Machado river, but with a 400 km extension to the south. Under the modeled climate change scenarios, the area suitable for the species declines by 21% under the most optimistic, and by 27% in the pessimistic, scenario across the projected 50-year period. Although we have expanded the area of known occurrence for this species, we point out that climate change threatens the stability of this newly-discovered population strongly, and that this danger is intensified by deforestation, fire and hunting. We recommend that further studies be carried out to confirm the presence of the species in adjacent areas, those indicated by generated models as being potential environmentally suitable. In addition, we recommend intensifying forest restoration in currently pastured areas, and protection of the areas forming the current and future habitat of this species through such measures as protected area creation. [ABSTRACT FROM AUTHOR]

Great gerbil (Rhombomys opimus Lichtenstein, 1823) is distributed in Central Asia and some parts of the Middle East. It is widely found in central and northeast parts of Iran with two distinct genetic lineages: R. o. sodalis in the northern slopes of the Elburz Mountains and R. o. sargadensis in the southern slopes. This large rodent acts as the main host of natural focal diseases. No study has surveyed the ecological niche of the lineages and how their distribution might be influenced by different climatic variables. To examine the distribution patterns of this murid rodent, we aimed to determine the habitat preferences and effects of environmental variables on the ecological niche. Using a species distribution approach for modeling of regional niche specialization, suitable habitats predicted for R. o. sodalis were mainly located in Golestan province in northern Iran, along the northern slope of Elburz, while R. o. sargadensis, showed great potential distribution along the southern slope of Elburz and around the Kavir Desert and the Lut Desert. Despite the widest potential distribution of R. o. sargadensis from northeast to northwest and through Central Iran, the geographic range of R. o. sodalis was smaller and mostly confined to Golestan province. The results support the presence of the two genetic lineages of Rhombomys in Iran and confirm that there is no significant niche overlap between the two subspecies. Furthermore, it provided several perspectives for future taxonomic studies and prevention hygiene programs for public health. [ABSTRACT FROM AUTHOR]

Identifying the historical processes that drive microhabitat transitions across deep time is of great interest to evolutionary biologists. Morphological variation can often reveal such mechanisms, but in clades with high microhabitat diversity and no concomitant morphological specialization, the factors influencing animal transitions across microhabitats are more difficult to identify. Lungless salamanders (family: Plethodontidae) have transitioned into and out of the arboreal microhabitat many times throughout their evolutionary history without substantial morphological specialization. In this study, we explore the relationship between microhabitat use and broad-scale climatic patterns across species' ranges to test the role of climate in determining the availability of the arboreal microhabitat. Using phylogenetic comparative methods, we reveal that arboreal species live in warmer, lower elevation regions than terrestrial species. We also employ ecological niche modeling as a complementary approach, quantifying species-level pairwise comparisons of niche overlap. The results of this approach demonstrate that arboreal species on average display more niche overlap with other arboreal species than with terrestrial species after accounting for non-independence of niche model pairs caused by geographic and phylogenetic distances. Our results suggest that occupation of the arboreal microhabitat by salamanders may only be possible in sufficiently warm, low elevation conditions. More broadly, this study indicates that the impact of micro-environmental conditions on temporary microhabitat use, as demonstrated by small-scale ecological studies, may scale up dramatically to shape macroevolutionary patterns. [ABSTRACT FROM AUTHOR]