Genetic characterization, structural analysis, and detection of positive selection in small heat shock proteins of Cypriniformes and Clupeiformes.

In the current investigation, a total of 42 full-length, non-redundant small heat shock proteins (sHsp) were detected in Cyprinus carpio, Labeo rohita, Danio rerio, Salmo salar, Oncorhynchus mykiss, and Clupea harengus. The sHsp genes were classified into three groups based on phylogenetic analysis. All the sHsps were shown to have higher aliphatic index values, which is an indication that these proteins are more thermally stable. The hydrophilic nature of sHsps was deduced from the fact that all fish species had negative GRAVY scores. In all of the representative fish species, sHsp genes were assigned to distinct chromosomes in an inconsistent and unequal manner. Segmental duplications are the main events that have contributed to the expansion of the sHsp genes in all species. We were also able to determine the selective pressure that was placed on particular codons and discovered several significant coding sites within the coding region of sHsps. Eventually, diversifying positive selection was found to be connected with evolutionary changes in sHsp proteins, which showed that gene evolution controlled the fish adaption event in response to environmental conditions. Clarification of the links between sHsps and environmental stress in fish will be achieved through rigorous genomic comparison, which will also yield substantial new insights.

Associations between glucocorticoids and habitat selection reflect daily and seasonal energy requirements.

BACKGROUND: Glucocorticoids are often associated with stressful environments, but they are also thought to drive the best strategies to improve fitness in stressful environments. Glucocorticoids improve fitness in part by regulating foraging behaviours in response to daily and seasonal energy requirements. However, many studies demonstrating relationships between foraging behaviour and glucocorticoids are experimental, and few observational studies conducted under natural conditions have tested whether changing glucocorticoid levels are related to daily and seasonal changes in energy requirements. METHODS: We integrated glucocorticoids into habitat selection models to test for relationships between foraging behaviour and glucocorticoid levels in elk (Cervus canadensis) as their daily and seasonal energy requirements changed. Using integrated step selection analysis, we tested whether elevated glucocorticoid levels were related to foraging habitat selection on a daily scale and whether that relationship became stronger during lactation, one of the greatest seasonal periods of energy requirement for female mammals. RESULTS: We found stronger selection of foraging habitat by female elk with elevated glucocorticoids (eß = 1.44 95% CI 1.01, 2.04). We found no difference in overall glucocorticoid levels after calving, nor a significant change in the relationship between glucocorticoids and foraging habitat selection at the time of calving. However, we found a gradual increase in the relationship between glucocorticoids and habitat selection by female elk as their calves grew over the next few months (eß = 1.01, 95% CI 1.00, 1.02), suggesting a potentially stronger physiological effect of glucocorticoids for elk with increasing energy requirements. CONCLUSIONS: We suggest glucocorticoid-integrated habitat selection models demonstrate the role of glucocorticoids in regulating foraging responses to daily and seasonal energy requirements. Ultimately, this integration will help elucidate the implications of elevated glucocorticoids under natural conditions.

How to account for behavioral states in step-selection analysis: a model comparison.

Step-selection models are widely used to study animals' fine-scale habitat selection based on movement data. Resource preferences and movement patterns, however, often depend on the animal's unobserved behavioral states, such as resting or foraging. As this is ignored in standard (integrated) step-selection analyses (SSA, iSSA), different approaches have emerged to account for such states in the analysis. The performance of these approaches and the consequences of ignoring the states in step-selection analysis, however, have rarely been quantified. We evaluate the recent idea of combining iSSAs with hidden Markov models (HMMs), which allows for a joint estimation of the unobserved behavioral states and the associated state-dependent habitat selection. Besides theoretical considerations, we use an extensive simulation study and a case study on fine-scale interactions of simultaneously tracked bank voles (Myodes glareolus) to compare this HMM-iSSA empirically to both the standard and a widely used classification-based iSSA (i.e., a two-step approach based on a separate prior state classification). Moreover, to facilitate its use, we implemented the basic HMM-iSSA approach in the R package HMMiSSA available on GitHub.

Microbial responses to stress cryptically alter natural selection on plants.

Microbial communities can rapidly respond to stress, meaning plants may encounter altered soil microbial communities in stressful environments. These altered microbial communities may then affect natural selection on plants. Because stress can cause lasting changes to microbial communities, microbes may also cause legacy effects on plant selection that persist even after the stress ceases. To explore how microbial responses to stress and persistent microbial legacy effects of stress affect natural selection, we grew Chamaecrista fasciculata plants in stressful (salt, herbicide, or herbivory) or nonstressful conditions with microbes that had experienced each of these environments in the previous generation. Microbial community responses to stress generally counteracted the effects of stress itself on plant selection, thereby weakening the strength of stress as a selective agent. Microbial legacy effects of stress altered plant selection in nonstressful environments, suggesting that stress-induced changes to microbes may continue to affect selection after stress is lifted. These results suggest that soil microbes may play a cryptic role in plant adaptation to stress, potentially reducing the strength of stress as a selective agent and altering the evolutionary trajectory of plant populations.

Male song structure predicts offspring recruitment to the breeding population in a migratory bird.

Bird song is a classic example of a sexually selected trait, but much of the work relating individual song components to fitness has not accounted for song typically being composed of multiple, often-correlated components, necessitating a multivariate approach. We explored the role of sexual selection in shaping the complex male song of house wrens (Troglodytes aedon) by simultaneously relating its multiple components to fitness using multivariate selection analysis, which is widely used in insect and anuran studies but not in birds. The analysis revealed significant variation in the form and strength of selection acting on song across different selection episodes, from nest-site defense to recruitment of offspring to the breeding population. Males that sang more song typically employed in close communication sired more offspring that were subsequently recruited to the breeding population than those that sang more far-communication song. However, this relationship was not consistent across earlier selection episodes, as evidenced by non-linear selection acting on these song components in other contexts. Collectively, our results present a complex picture of multivariate selection on male song structure that would not be evident using univariate approaches and suggest possible trade-offs within and among song components at different points of the breeding season.

Estimating the relationship between fitness and metabolic rate: which rate should we use?

As physiologists seek to better understand how and why metabolism varies, they have focused on how metabolic rate covaries with fitness-that is, selection. Evolutionary biologists have developed a sophisticated framework for exploring selection, but there are particular challenges associated with estimating selection on metabolic rate owing to its allometric relationship with body mass. Most researchers estimate selection on mass and absolute metabolic rate; or selection on mass and mass-independent metabolic rate (MIMR)-the residuals generated from a nonlinear regression. These approaches are sometimes treated as synonymous: their coefficients are often interpreted in the same way. Here, we show that these approaches are not equivalent because absolute metabolic rate and MIMR are different traits. We also show that it is difficult to make sound biological inferences about selection on absolute metabolic rate because its causal relationship with mass is enigmatic. By contrast, MIMR requires less-desirable statistical practices (i.e. residuals as a predictor), but provides clearer causal pathways. Moreover, we argue that estimates of selection on MIMR have more meaningful interpretations for physiologists interested in the drivers of variation in metabolic allometry. This article is part of the theme issue 'The evolutionary significance of variation in metabolic rates'.

Resource selection by New York City deer reveals the effective interface between wildlife, zoonotic hazards and humans.

Although the role of host movement in shaping infectious disease dynamics is widely acknowledged, methodological separation between animal movement and disease ecology has prevented researchers from leveraging empirical insights from movement data to advance landscape scale understanding of infectious disease risk. To address this knowledge gap, we examine how movement behaviour and resource utilization by white-tailed deer (Odocoileus virginianus) determines blacklegged tick (Ixodes scapularis) distribution, which depend on deer for dispersal in a highly fragmented New York City borough. Multi-scale hierarchical resource selection analysis and movement modelling provide insight into how deer's movements contribute to the risk landscape for human exposure to the Lyme disease vector-I. scapularis. We find deer select highly vegetated and accessible residential properties which support blacklegged tick survival. We conclude the distribution of tick-borne disease risk results from the individual resource selection by deer across spatial scales in response to habitat fragmentation and anthropogenic disturbances.

Identification and adaptive evolution analysis of glutaredoxin genes in Populus spp.

Glutaredoxin (GRX) is a class of small redox proteins widely involved in cellular redox homeostasis and the regulation of various cellular processes. The role of GRX gene in the differentiation of Populus spp. is rarely reported. We compared the similarities and differences of GRX genes among four sections of poplar using bioinformatics, corrected the annotations of some GRX genes, and focused on analysing their transcript profiling and adaptive evolution in Populus spp. A total of 219 GRX genes were identified in four sections of poplar, among which annotations for 13 genes were corrected. Differences in GRX genes were found between sect. Turanga, represented by P. euphratica, and other poplar sections. Most notably, P. euphratica had the smallest number of duplication events for GRX genes (n = 9) and no tandem duplications, whereas there were >25 duplication events for all other poplars. Furthermore, we detected 18 pairs of GRX genes under positive selection pressure in various sections of poplar, and identified two groups of GRX genes in the Salicaceae that potentially underwent positive selection. Expression profiling results showed that the PtrGRX34 and its orthologous genes were upregulated under stress treatments. In summary, the GRX gene family underwent expansion during poplar differentiation, and some genes underwent rapid evolution during this process, which may be beneficial for Populus spp. to adapt to environmental changes. This study may provide more insights into the molecular mechanisms of Populus spp. adaptation to environmental changes and the adaptive evolution of GRX genes.

Dynamic balancing of risks and rewards in a large herbivore: Further extending predator-prey concepts to road ecology.

Animal behaviour is shaped by the ability to identify risks and profitably balance the levels of risks encountered with the payoffs experienced. Anthropogenic disturbances like roads generate novel risks and opportunities that wildlife must accurately perceive and respond to. Basic concepts in predator-prey ecology are often used to understand responses of animals to roads (e.g. increased vigilance, selection for cover in their vicinity). However, prey often display complex behaviours such as modulating space use given varying risks and rewards, and it is unclear if such dynamic balancing is used by animals in the context of road crossings. We tested whether animals dynamically balance risks and rewards relative to roads using extensive field-based and GPS collar data from elk in Yoho National Park (British Columbia, Canada), where a major highway completely bisects their range during most of the year. We analysed elk behaviour by combining hidden Markov movement models with a step-selection function framework. Rewards were indexed by a dynamic map of available forage biomass, and risks were indexed by road crossings and traffic volumes. We found that elk generally selected intermediate and high forage biomass, and avoided crossing the road. Most of the time, elk modulated their behaviour given varying risks and rewards. When crossing the highway compared with not crossing, elk selected for greater forage biomass and this selection was stronger as the number of highway crossings increased. However, with traffic volume, elk only balanced foraging rewards when they crossed a single time during a travel sequence. Using a road ecology system, we empirically tested an important component of predator-prey ecology-the ability to dynamically modulate behaviour in response to varying levels of risks and rewards. Such a test articulates how decision-making processes that consider the spatiotemporal variation in risks and rewards allow animals to successfully and profitably navigate busy roads. Applying well-developed concepts in predator-prey theory helps understand how animals respond to anthropogenic disturbances and anticipate the adaptive capacity for individuals and populations to adjust to rapidly changing environments.

Le comportement animal est influencé par la capacité des animaux à identifier et minimiser les risques rencontrés, tout en maximisant les gains obtenus. Les perturbations anthropiques, telles que les routes, engendrent de nouveaux risques et opportunités pour la faune. Les concepts de l'écologie prédateur-proie sont fréquemment utilisés pour comprendre les réactions des animaux aux routes (e.g. vigilance accrue, choix de couvert à proximité des routes). Cependant, même s'il est connu que les proies ajustent fréquemment leur utilisation de l'espace de façon à minimiser les risques et maximiser les récompenses, il n'est pas clair si une telle optimisation est utilisée par les animaux lorsqu'ils traversent des routes. Ici, nous avons évalué comment les animaux ajustent leur sélection d'habitat par rapport aux routes en fonction des risques et des récompenses disponibles. Nous avons examiné cette question chez les wapitis du parc national Yoho (Colombie-Britannique, Canada), où une autoroute majeure divise complètement leur domaine vital pendant une majeure partie de l'année. À l'aide d'une analyse de sélection d'habitat à fine échelle, nous avons testé si les wapitis optimisent les risques liés aux traversées d'autoroute et les récompenses alimentaires obtenues lorsqu'ils se déplacent entre des zones d'alimentation. Les récompenses ont été estimées à l'aide d'une carte dynamique de la biomasse végétale disponible pour les wapitis, et les risques ont été estimés en fonction des traversées de route et du trafic automobile rencontré. Nos résultats indiquent que les wapitis sélectionnaient généralement des zones d'alimentation avec une biomasse intermédiaire à élevée, et évitaient de traverser l'autoroute. La plupart du temps, les wapitis ajustaient leur sélection d'habitat en fonction des risques et des récompenses. Les wapitis sélectionnaient des zones d'alimentation avec une biomasse plus élevée lorsqu'ils traversaient l'autoroute, comparé à lorsqu'ils ne traversaient pas. Ils optimisaient également la biomasse végétale obtenue en fonction du nombre de traversées de l'autoroute effectuées durant une séquence de déplacement. Cependant, les wapitis optimisaient uniquement les récompenses alimentaires avec le trafic automobile durant les séquences de déplacement avec une seule traversée. Nous avons testé empiriquement un élément essentiel de l'écologie prédateur-proie, soit la capacité d'ajuster de façon dynamique un comportement en réponse à des niveaux variables de risques et de récompenses, dans le contexte de l'écologie routière. Notre étude permet d'illustrer comment les processus décisionnels considérant à la fois les risques, les récompenses et leur variation spatiotemporelle, permettent aux animaux de naviguer de façon optimale les routes très fréquentées. L'utilisation de concepts bien établis de l'écologie prédateur-proie aide à comprendre comment les animaux réagissent aux perturbations anthropiques, et contribue à anticiper la capacité d'adaptation des individus et des populations face à des environnements en transformation rapide.

Death comes for us all: relating movement-integrated habitat selection and social behavior to human-associated and disease-related mortality among gray wolves.

Avoiding death affects biological processes, including behavior. Habitat selection, movement, and sociality are highly flexible behaviors that influence the mortality risks and subsequent fitness of individuals. In the Anthropocene, animals are experiencing increased risks from direct human causes and increased spread of infectious diseases. Using integrated step selection analysis, we tested how the habitat selection, movement, and social behaviors of gray wolves vary in the two months prior to death due to humans (being shot or trapped) or canine distemper virus (CDV). We further tested how those behaviors vary as a prelude to death. We studied populations of wolves that occurred under two different management schemes: a national park managed for conservation and a provincially managed multi-use area. Behaviors that changed prior to death were strongly related to how an animal eventually died. Wolves killed by humans moved slower than wolves that survived and selected to be nearer roads closer in time to their death. Wolves that died due to CDV moved progressively slower as they neared death and reduced their avoidance of wet habitats. All animals, regardless of dying or living, maintained selection to be near packmates across time, which seemingly contributed to disease dynamics in the packs infected with CDV. There were no noticeable differences in behavior between the two management areas. Overall, habitat selection, movement, and sociality interact to put individuals and groups at greater risks, influencing their cause-specific mortality.

Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai-Tibetan plateau.

KEY MESSAGE: Positive selection genes are related to metabolism, while differentially expressed genes are related to photosynthesis, suggesting that genetic adaptation and expression regulation may play independent roles in different gene classes. Genome-wide investigation of the molecular mechanisms for high-altitude adaptation is an intriguing topic in evolutionary biology. The Qinghai-Tibet Plateau (QTP) with its extremely variable environments is an ideal site for studying high-altitude adaptation. Here, we used transcriptome data of 100 individuals from 20 populations collected from various altitudes on the QTP to investigate the adaptive mechanisms of the aquatic plant Batrachium bungei at both the genetic and transcriptional level. To explore genes and biological pathways that may contribute to QTP adaptation, we employed a two-step approach, in which we identified positively selected genes and differentially expressed genes using the landscape genomic and differential expression approaches. The positive selection analysis showed that genes involved in metabolic regulation played a crucial role in B. bungei adaptation to the extreme environments of the QTP, especially intense ultraviolet radiation. Altitude-based differential expression analysis suggested that B. bungei could increase the rate of energy dissipation or reduce the efficiency of light energy absorption by down regulating the expression of photosynthesis-related genes to adapt to the strong ultraviolet radiation. Weighted gene co-expression network analysis identified ribosomal genes as hubs of altitude adaptation in B. bungei. Only a small part of genes (about 10%) overlapped between positively selected genes and differentially expressed genes in B. bungei, suggesting that genetic adaptation and gene expression regulation might play relatively independent roles in different categories of functional genes. Taken together, this study enriches our understanding of the high-altitude adaptation mechanism of B. bungei on the QTP.

LiDAR reveals a preference for intermediate visibility by a forest-dwelling ungulate species.

Visibility (viewshed) plays a significant and diverse role in animals' behaviour and fitness. Understanding how visibility influences animal behaviour requires the measurement of habitat visibility at spatial scales commensurate to individual animal choices. However, measuring habitat visibility at a fine spatial scale over a landscape is a challenge, particularly in highly heterogeneous landscapes (e.g. forests). As a result, our ability to model the influence of fine-scale visibility on animal behaviour has been impeded or limited. In this study, we demonstrate the application of the concept of three-dimensional (3D) cumulative viewshed in the study of animal spatial behaviour at a landscape level. Specifically, we employed a newly described approach that combines terrestrial and airborne light detection and ranging (LiDAR) to measure fine-scale habitat visibility (3D cumulative viewshed) on a continuous scale in forested landscapes. We applied the LiDAR-derived visibility to investigate how visibility in forests affects the summer habitat selection and the movement of 20 GPS-collared female red deer Cervus elaphus in a temperate forest in Germany. We used integrated step selection analysis to determine whether red deer show any preference for fine-scale habitat visibility and whether visibility is related to the rate of movement of red deer. We found that red deer selected intermediate habitat visibility. Their preferred level of visibility during the day was substantially lower than that of night and twilight, whereas the preference was not significantly different between night and twilight. In addition, red deer moved faster in high-visibility areas, possibly mainly to avoid predation and anthropogenic risk. Furthermore, red deer moved most rapidly between locations in the twilight. For the first time, the preference for intermediate habitat visibility and the adaption of movement rate to fine-scale visibility by a forest-dwelling ungulate species at a landscape scale was revealed. The LiDAR technique used in this study offers fine-scale habitat visibility at the landscape level in forest ecosystems, which would be of broader interest in the fields of animal ecology and behaviour.

Whole-genome sequencing and evolutionary analysis of the wild edible mushroom, Morchella eohespera.

Morels (Morchella, Ascomycota) are an extremely desired group of edible mushrooms with worldwide distribution. Morchella eohespera is a typical black morel species, belonging to the Elata clade of Morchella species. The biological and genetic studies of this mushroom are rare, largely hindering the studies of molecular breeding and evolutionary aspects. In this study, we performed de novo sequencing and assembly of the M. eohespera strain m200 genome using the third-generation nanopore sequencing platform. The whole-genome size of M. eohespera was 53.81 Mb with a contig N50 of 1.93 Mb, and the GC content was 47.70%. A total of 9,189 protein-coding genes were annotated. Molecular dating showed that M. eohespera differentiated from its relative M. conica at ~19.03 Mya (million years ago) in Burdigalian. Evolutionary analysis showed that 657 gene families were contracted and 244 gene families expanded in M. eohespera versus the related morel species. The non-coding RNA prediction results showed that there were 336 tRNAs, 76 rRNAs, and 45 snRNAs in the M. eohespera genome. Interestingly, there was a high degree of repetition (20.93%) in the M. eohespera genome, and the sizes of long interspersed nuclear elements, short interspersed nuclear elements, and long terminal repeats were 0.83 Mb, 0.009 Mb, and 4.56 Mb, respectively. Additionally, selection pressure analysis identified that a total of 492 genes in the M. eohespera genome have undergone signatures of positive selection. The results of this study provide new insights into the genome evolution of M. eohespera and lay the foundation for in-depth research into the molecular biology of the genus Morchella in the future.

Chromosome-Level Genome Assembly and Multi-Omics Dataset Provide Insights into Isoflavone and Puerarin Biosynthesis in Pueraria lobata (Wild.) Ohwi.

Pueraria lobata (wild.) Ohwi is a leguminous plant and one of the traditional Chinese herbal medicines. Its puerarin extract is widely used in the pharmaceutical industry. This study reported a chromosome-level genome assembly for P. lobata and its characteristics. The genome size was ~939.2 Mb, with a contig N50 of 29.51 Mbp. Approximately 97.82% of the assembled sequences were represented by 11 pseudochromosomes. We identified that the repetitive sequences accounted for 63.50% of the P. lobata genome. A total of 33,171 coding genes were predicted, of which 97.34% could predict the function. Compared with other species, P. lobata had 757 species-specific gene families, including 1874 genes. The genome evolution analysis revealed that P. lobata was most closely related to Glycine max and underwent two whole-genome duplication (WGD) events. One was in a gamma event shared by the core dicotyledons at around 65 million years ago, and another was in the common ancestor shared by legume species at around 25 million years ago. The collinearity analysis showed that 61.45% of the genes (54,579 gene pairs) in G. max and P. lobata had collinearity. In this study, six unique PlUGT43 homologous genes were retrieved from the genome of P. lobata, and no 2-hydroxyisoflavanone 8-C-glucoside was found in the metabolites. This also revealed that the puerarin synthesis was mainly from the glycation of daidzein. The combined transcriptome and metabolome analysis suggested that two bHLHs, six MYBs and four WRKYs were involved in the expression regulation of puerarin synthesis structural genes. The genetic information obtained in this study provided novel insights into the biological evolution of P. lobata and leguminous species, and it laid the foundation for further exploring the regulatory mechanism of puerarin synthesis.

Agricultural land use shapes dispersal in white-tailed deer (Odocoileus virginianus).

BACKGROUND: Dispersal is a fundamental process to animal population dynamics and gene flow. In white-tailed deer (WTD; Odocoileus virginianus), dispersal also presents an increasingly relevant risk for the spread of infectious diseases. Across their wide range, WTD dispersal is believed to be driven by a suite of landscape and host behavioral factors, but these can vary by region, season, and sex. Our objectives were to (1) identify dispersal events in Wisconsin WTD and determine drivers of dispersal rates and distances, and (2) determine how landscape features (e.g., rivers, roads) structure deer dispersal paths. METHODS: We developed an algorithmic approach to detect dispersal events from GPS collar data for 590 juvenile, yearling, and adult WTD. We used statistical models to identify host and landscape drivers of dispersal rates and distances, including the role of agricultural land use, the traversability of the landscape, and potential interactions between deer. We then performed a step selection analysis to determine how landscape features such as agricultural land use, elevation, rivers, and roads affected deer dispersal paths. RESULTS: Dispersal predominantly occurred in juvenile males, of which 64.2% dispersed, with dispersal events uncommon in other sex and age classes. Juvenile male dispersal probability was positively associated with the proportion of the natal range that was classified as agricultural land use, but only during the spring. Dispersal distances were typically short (median 5.77 km, range: 1.3-68.3 km), especially in the fall. Further, dispersal distances were positively associated with agricultural land use in potential dispersal paths but negatively associated with the number of proximate deer in the natal range. Lastly, we found that, during dispersal, juvenile males typically avoided agricultural land use but selected for areas near rivers and streams. CONCLUSION: Land use-particularly agricultural-was a key driver of dispersal rates, distances, and paths in Wisconsin WTD. In addition, our results support the importance of deer social environments in shaping dispersal behavior. Our findings reinforce knowledge of dispersal ecology in WTD and how landscape factors-including major rivers, roads, and land-use patterns-structure host gene flow and potential pathogen transmission.

Quantitation of DNA-Encoded Libraries by qPCR.

DNA-encoded library (DEL) yields can be easily measured throughout the selection process using the quantitative polymerase chain reaction (qPCR) (Sannino A, Gabriele E, Bigatti M, Mulatto S, Piazzi J, Scheuermann J, Neri D, Donckele EJ, Samain F, Chembiochem Eur J Chem Biol 20:955-962, 2019). Samples taken throughout the selection process are diluted prior to amplification and compared to standards of known DNA concentration. Here, I describe a general protocol using a double-stranded DNA binding dye for reaction monitoring. This allows the selection process to be assessed at each step prior to preparation for sequencing. The same method has additional applications in the practice of DEL technology.

Transcriptomic Insights into the Diversity and Evolution of Myxozoa (Cnidaria, Endocnidozoa) Toxin-like Proteins.

Myxozoa is a speciose group of endoparasitic cnidarians that can cause severe ecological and economic effects. Their cnidarian affinity is affirmed by genetic relatedness and the presence of nematocysts, historically called "polar capsules". Previous studies have revealed the presence of toxin-like proteins in myxozoans; however, the diversity and evolution of venom in Myxozoa are not fully understood. Here, we performed a comparative analysis using the newly sequenced transcriptomes of five Myxobolidae species as well as some public datasets. Toxin mining revealed that myxozoans have lost most of their toxin families, while most species retained Kunitz, M12B, and CRISP, which may play a role in endoparasitism. The venom composition of Endocnidozoa (Myxozoa + Polypodium) differs from that of free-living cnidarians and may be influenced by ecological and environmental factors. Phylogenetic analyses showed that toxin families of myxozoans and free-living cnidarians were clustered into different clades. Selection analyses showed that purifying selection was the dominant evolutionary pressure in toxins, while they were still influenced by episodic adaptive selection. This suggests that the potency or specificity of a particular toxin or species might increase. Overall, our findings provide a more comprehensive framework for understanding the diversity and evolution of Myxozoa venoms.

The early SARS-CoV-2 epidemic in Senegal was driven by the local emergence of B.1.416 and the introduction of B.1.1.420 from Europe.

Molecular surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is growing in west Africa, especially in the Republic of Senegal. Here, we present a molecular epidemiology study of the early waves of SARS-CoV-2 infections in this country based on Bayesian phylogeographic approaches. Whereas the first wave in mid-2020 was characterized by a significant diversification of lineages and predominance of B.1.416, the second wave in late 2020 was composed primarily of B.1.1.420. Our results indicate that B.1.416 originated in Senegal and was exported mainly to Europe. In contrast, B.1.1.420 was introduced from Italy, gained fitness in Senegal, and then spread worldwide. Since both B.1.416 and B.1.1.420 lineages carry several positive selected mutations in the spike and nucleocapsid genes, each of which may explain their local dominance, their mutation profiles should be carefully monitored. As the pandemic continues to evolve, molecular surveillance in all regions of Africa will play a key role in stemming its spread.

Accounting for animal movement improves vaccination strategies against wildlife disease in heterogeneous landscapes.

Oral baiting is used to deliver vaccines to wildlife to prevent, control, and eliminate infectious diseases. A central challenge is how to spatially distribute baits to maximize encounters by target animal populations, particularly in urban and suburban areas where wildlife such as raccoons (Procyon lotor) are abundant and baits are delivered along roads. Methods from movement ecology that quantify movement and habitat selection could help to optimize baiting strategies by more effectively targeting wildlife populations across space. We developed a spatially explicit, individual-based model of raccoon movement and oral rabies vaccine seroconversion to examine whether and when baiting strategies that match raccoon movement patterns perform better than currently used baiting strategies in an oral rabies vaccination zone in greater Burlington, Vermont, USA. Habitat selection patterns estimated from locally radio-collared raccoons were used to parameterize movement simulations. We then used our simulations to estimate raccoon population rabies seroprevalence under currently used baiting strategies (actual baiting) relative to habitat selection-based baiting strategies (habitat baiting). We conducted simulations on the Burlington landscape and artificial landscapes that varied in heterogeneity relative to Burlington in the proportion and patch size of preferred habitats. We found that the benefits of habitat baiting strongly depended on the magnitude and variability of raccoon habitat selection and the degree of landscape heterogeneity within the baiting area. Habitat baiting improved seroprevalence over actual baiting for raccoons characterized as habitat specialists but not for raccoons that displayed weak habitat selection similar to radiocollared individuals, except when baits were delivered off roads where preferred habitat coverage and complexity was more pronounced. In contrast, in artificial landscapes with either more strongly juxtaposed favored habitats and/or higher proportions of favored habitats, habitat baiting performed better than actual baiting, even when raccoons displayed weak habitat preferences and where baiting was constrained to roads. Our results suggest that habitat selection-based baiting could increase raccoon population seroprevalence in urban-suburban areas, where practical, given the heterogeneity and availability of preferred habitat types in those areas. Our novel simulation approach provides a flexible framework to test alternative baiting strategies in multiclass landscapes to optimize bait-distribution strategies.

Evidence for evolution and selection of drought-resistant genes based on high-throughput resequencing in weedy rice.

Weedy rice (Oryza sativa f. spontanea) is a relative of cultivated rice that propagates in paddy fields and has strong drought resistance. In this study, we used 501 rice accessions to reveal the selection mechanism of drought resistance in weedy rice through a combination of selection analysis, genome-wide association studies, gene knockout and overexpression analysis, and Ca2+ and K+ ion flux assays. The results showed that the weedy rice species investigated have gene introgression with cultivated rice, which is consistent with the hypothesis that weedy rice originated from de-domestication of cultivated rice. Regions related to tolerance have particularly diversified during de-domestication and three drought-tolerance genes were identified. Of these, Os01g0800500 was also identified using an assay of the degree of leaf withering under drought, and it was named as PAPH1, encoding a PAP family protein. The drought-resistance capacity of PAPH1-knockout lines was much lower than that of the wild type, while that of overexpression lines was much higher. Concentrations of Ca2+ and K+ were lower in the knockout lines and higher in the overexpression lines compared with those of the wild type, suggesting that PAPH1 plays important roles in coping with drought stress. Our study therefore provides new insights into the genetic mechanisms underlying adaptive tolerance to drought in wild rice and highlights potential new resistance genes for future breeding programs in cultivated rice.