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Data from: Lineage-specific trait variations and plasticity of obligate parthenogenetic animals following the expansion of distribution range to a continental archipelago.

Two asexual lineages, JPN1 and JPN2, of panarctic Daphnia pulex expanded the distribution range to Japan from North America, independent of each other. According to the mutation rates within these lineages, JPN1 lineage colonized Japan earlier than JPN2 lineage. Moreover, the ratio of nonsynonymous to synonymous mutation rates (dN/dS) was lower in JPN1 than in JPN2 lineage. Accordingly, it is hypothesized that variations of phenotypic traits differ between these two lineages. In addition, since they are obligate parthenogenetic animals, the lineage occupying a larger distribution range should have a larger phenotypic plasticity. To test these hypotheses, we experimentally examined the phenotypic variations of fitness-related traits, including digestive, life history and morphological traits, among several genotypes of these lineages. We found that within-lineage variations of most traits were smaller in JPN1 than in JPN2. In addition, the overall phenotypic variations were also smaller within the JPN1 lineage than within the JPN2 lineage. These results support the idea that the JPN1 lineage has been more efficiently subjected to negative selection, as expected from the lower dN/dS ratio. However, the magnitude of the phenotypic plasticity to changing food levels was at the same level for both the JPN1 and JPN2 lineages, while variations found in the phenotypic plasticity were smaller in the JPN1 lineage. The difference in the variations of the phenotypic traits and plasticity between the two lineages suggests that these two lineages have evolved under somewhat different environmental conditions and that genotypes of the JPN2 lineage may have exploited niches that differed somewhat from that of the JPN1 genotypes.

Age-specific activation patterns and inter-subject similarity during verbal working-memory maintenance and Cognitive Reserve

Cognitive Reserve, according to a recent consensus definition of the NIH-funded Reserve and Resilience collaboratory (<a href="https://reserveandresilience.com/">https://reserveandresilience.com/</a>), is constituted by any mechanism contributing to cognitive performance beyond, or interacting with, brain structure in the widest sense. To identity multivariate activation patterns fulfilling this postulate, we investigated a verbal Sternberg fMRI task and imaged 181 people with age coverage in the ranges 20-30 (44 participants) and 55-70 (137 participants). Beyond task performance, participants were characterized in terms of demographics, and neuropsychological assessments of vocabulary, episodic memory, perceptual speed, and abstract fluid reasoning. Participants studied an array of either 1, 3, or 6 upper-case letters for 3 seconds (=encoding phase), then a blank fixation screen was presented for 7 seconds (=maintenance phase), to be probed with a lower-case letter to which they responded with a differential button press whether the letter was part of the studied array or not (=retrieval phase). We focused on identifying maintenance-related activation patterns showing memory-load increases in pattern score on an individual-participant level for both age groups. We found such a pattern that increased with memory load for all but one person in the young participants (p<0.001), and such a pattern for all participants in the older group (p<0.001). Both patterns showed broad topographic similarities; however, relationships to task performance and neuropsychological characteristics were markedly different and point to individual differences in Cognitive Reserve. Beyond the derivation of group-level activation patterns, we also investigated the inter-subject spatial similarity of individual working-memory rehearsal patterns in the older participants' group as a function of neuropsychological and task performance, education and mean cortical thickness. Higher task accuracy and neuropsychological function was reliably associated with higher inter-subject similarity of individual-level activation patterns in older participants.

Data from: A role for the local environment in driving species-specific parasitism in a multi-host parasite system

The extent and magnitude of parasitism often vary among closely related host species and across populations within species. Determining the ecological basis for this species and population-level variation in parasitism is critical for understanding infection dynamics in multi-host-parasite systems. To investigate such ecological underpinnings of variation in parasitism, we studied Enallagma damselflies host species and their water mite (Arrenurus spp.) ectoparasites in lakes. We first evaluated how host identity and density could shape parasitism. To test the effects of con- and heterospecific host density on parasitism, we used a field experiment with E. basidens and E. signatum. We found that parasitism did not vary with con- or heterospecific density and was determined by host identity alone, with no spillover effects. We also evaluated the potential role of local adaptation and resource availability in shaping parasitism. To do so, we used E. signatum in a reciprocal transplant experiment crossed with a prey resource level manipulation. This experiment revealed that parasitism declined sharply for one host population in its non-local lake, but not the other source population, with no effects of prey levels. This asymmetry implies that damselflies express enhanced defenses against parasitism that are not population specific nor dependent on resource abundance, or that mites developed heightened local host specificity. The results of multivariate modeling from an observational study generally supported these experimental findings: neither host density nor resource abundance strongly explained among population variation in parasitism. Instead, local abiotic conditions (pH) had the strongest relationship with parasitism, with minimal associations with predator density, temperature, and a measure of immune function. Collectively, our findings suggest a crucial role for the local environment in shaping host-parasite interactions within multi-host-parasite systems. More generally, these results show that research at the intersection of community ecology and disease ecology is critical for understanding host-parasite dynamics within natural communities.

Light environment interacts with visual displays in a species-specific manner in multimodal signaling wolf spiders

Light availability is highly variable, yet predictable, over various timescales and the light environment is expected to play an important role in the evolution of visual signals. Courtship displays within the wolf spider genus Schizocosa always involve the use of substrate borne vibrations, however, there is substantial variation between species in the use of visual displays. We assessed the impact of light intensity on the courtship of four species of Schizocosa that vary in their use of visual signals during courtship. To examine the effects of the light environment on mating success and courtship effort in each species, we ran behavioral trials at three light intensities (bright, dim and dark). We also examined each species' circadian activity patterns. We found multiple effects of the light environment and these varied between species. Circadian activity patterns also differed between species and sexes. Our results suggest that dim-light might favor more conspicuous visual displays, while less conspicuous displays might be favored in bright light conditions. Additionally, we found evidence for light-dependent changes in selection on male traits, illustrating that short-term changes in light intensity have the potential for strong effects on the dynamics of sexual selection.

Drosophila melanogaster hosts coevolving with Pseudomonas entomophila pathogen show sex-specific patterns of local adaptation

Background: In spatially structured populations, local adaptation improves organisms' fitness in their native environment. Host and pathogens can rapidly adapt to their local antagonist. Since males and females can differ in their immunocompetence, the patterns of local adaptation can be different between the sexes. However, there is little information about sex differences in local adaptation in host-pathogen systems. Results: In the current study, we experimentally coevolved four different replicate populations of Drosophila melanogaster (host) and Pseudomonas entomophila (pathogen) along with appropriate controls. We used the four host-pathogen coevolution populations to investigate the occurrence of local adaptation separately in males and females of the coevolving hosts. We also assessed local adaptation in pathogens. We set up a reciprocal infection experiment where we infected each of the four coevolving hosts with their local pathogen or non-local pathogens from the other three replicate populations. We found that overall, male and female hosts had better survivorship when infected with local pathogens, indicating that they were locally adapted. Interestingly, males were more susceptible to non-local pathogens compared to females. In addition, we found no fecundity cost in females infected with either local or non-local pathogens. We found no evidence of local adaptation among the pathogens. Conclusion: Our study showed sex-specific adaptation in the coevolving hosts where female hosts had a broader response against allopatric coevolving pathogens with no cost in fecundity. Thus, our results might suggest a novel mechanism that can maintain variation in susceptibility in spatially structured populations.

No evidence of bacterial symbionts influencing host specificity in Aphis gossypii Glover (Hemiptera: Aphididae)

The cotton-melon aphid, Aphis gossypii Glover, is a polyphagous insect pest with many host-specialized biotypes, such as Cucurbitaceae- and Malvaceae-specialized (CU and MA) biotype. Bacterial symbionts were reported to determine host range in some aphids. Whether this is the case in A. gossypii remains unknown. Here, we tested host specificity of CU and MA biotype and compared host specificity between wingless and winged morph within the same biotype, and analyzed the composition of bacterial symbionts. The reproduction of CU and MA biotype reduced by 66.67% and 82.79% respectively on non-native hosts, compared with that on native hosts. The composition of bacterial symbionts was not significantly different between CU and MA biotype, with Buchnera abundance >95% in both biotypes. While, winged morph produced significantly more nymphs than wingless morph on non-native hosts, and<a name="OLE_LINK1"></a> Buchnera abundance in winged morph was only about 10% of that in wingless morph. There seemed to be a relationship between Buchnera abundance and host specificity. We regulated Buchnera abundance by temperature and antibiotics, but did not find that low Buchnera abundance resulted in high reproduction on non-native hosts. We conclude that host specificity of A. gossypii is not controlled by specific bacterial symbionts or by Buchnera abundance.

Behavioural and morphological traits influence sex-specific floral resource use by hummingbirds

Research on resource partitioning in plant-pollinator mutualistic systems is mainly concentrated at the levels of species and communities, whereas differences between males and females are typically ignored. Nevertheless, pollinators often show large sexual differences in behaviour and morphology, which may lead to sex-specific patterns of resource use with the potential to differentially affect plant reproduction and diversification. We investigated variation in behavioural and morphological traits between sexes of hummingbird species as potential mechanisms underlying sex-specific flower resource use in ecological communities. To do so, we compiled a dataset of plant-hummingbird interactions based on pollen loads for 31 hummingbird species from 13 localities across the Americas, complemented by data on territorial behaviour (territorial or nonterritorial) and morphological traits (bill length, bill curvature, wing length and body mass). We assessed the extent of intersexual differences in niche breadth and niche overlap in floral resource use across hummingbird species. Then, we tested whether floral niche breadth and overlap between sexes are associated with sexual dimorphism in behavioural or morphological traits of hummingbird species, while accounting for evolutionary relatedness among the species. We found striking differences in patterns of floral resource use between sex. Females had a broader floral niche breadth and were more dissimilar in the plant species visited with respect to males of the same species, resulting in a high level of resource partitioning between sexes. We found that both territoriality and morphological traits were related to sex-specific resource use by hummingbird species. Notably, niche overlap between sexes was greater for territorial than nonterritorial species, and moreover, niche overlap was negatively associated with sexual dimorphism in bill curvature across hummingbird species. These results reveal the importance of behavioural and morphological traits of hummingbird species in sex-specific resource use and that resource partitioning by sex is likely to be an important mechanism to reduce intersexual competition in hummingbirds. These findings highlight the need for better understanding the putative role of intersexual variation in shaping patterns of interactions and plant reproduction in ecological communities.

opencc-by-4.0May 2022View details →

Additional data for "Tissue-specific impacts of aging and genetics on gene expression patterns in humans"

Additional files for paper "Tissue-specific impacts of aging and genetics on gene expression patterns in humans" by Yamamoto and Chung et al. 2021. Contains file of results from joint age and genetics model.

Data from: Interannual consistency of migration phenology is season- and breeding region-specific in North American Golden Eagles

Avian migrants can adjust the time they depart for migration and arrive at their destination (i.e. phenology) based on environmental conditions, the period of the annual cycle, and the distance of migration. Our study shows that interannual consistency (an indicator of the strength of adjustments) in migration schedule of Golden Eagles (Aquila chrysaetos) in North America was greatest in boreal spring migration and the breeding regions of eastern Canada, suggesting that migration schedule is partly environmentally driven. Using multi-year GPS tracks of 83 adults breeding in three spatially distant regions (Alaska, northeast Canada, and southeast Canada), we quantified the interannual consistency of migration timing with variations within individuals tracked across multiple years and among-individuals and repeatability (r) of migration schedule, duration, and wintering latitude by breeding regions and seasons. By comparing regions and seasons, we found that consistency was highest (r > 0.85) for the schedule of the boreal spring migration in eastern Canada while Alaska had the lowest value (r < 0.15). Since seasonal consistency of migration schedule was only detected in eastern Canada, we conclude that seasonal features are not the main constraint on consistency of migration schedule. While regional differences in consistency were not related to differences in migratory distances, they could be the result of genetic or habitat differences. We also found that warmer temperatures than the decadal average at the region of departure delayed the start of boreal spring migration by ~10 days and advanced boreal autumn migration by ~20 days. It suggests that warmer temperatures would reduce residence time on breeding grounds, which is contrary to expectations and trends found in other studies. Wide variations in migratory strategies across a species distribution can add to the lists of challenges for conservation yet such variations can give migrants the capacity to acclimate to environmental changes.

Data from: It's all about food: Environmental factors cause species-specific dispersal

Dispersal is a vital component of the life- history of nearly all organisms. The ability to disperse determines the distribution and abundance of a species and thus its community dynamic at different sites. The scientific challenge is to design standardized laboratory experiments that not only record the effects of single factors but also includes the multi-causal nature of dispersal. Here we tested the effect of the environmental factors density, food availability and predation and the combinations thereof on the dispersal of five free- living nematode species by performing experiments in two-patched systems. We hypothesized that emigration is generally positively correlated with the intrinsic rate of natural increase and would decrease with increasing food availability and increase both with the presence of a predator and at higher initial population densities. These predictions were tested both using single-species tests with laboratory cultures as well as using intact natural nematode communities to investigate whether environmental factors determine the composition of dispersing species. The results of our study revealed a positive correlation between dispersal and intrinsic growth ability, whereas the studied nematode species differed in their dispersal patterns, both under control conditions and in response to bottom-up, top-down, and density dependent stimuli. Despite the species- specific differences in dispersal behavior in response to the environmental factors, the availability of food appeared as the main driver. This was especially pronounced regarding a natural nematode community. Our experiments emphasize the central role of food availability in spatial structuring nematode communities.

Distinct decision-making properties underlying the species specificity of group formation of flies

Many animal species form groups. Group characteristics differ between species, suggesting that the decision-making of individuals for grouping varies across species. However, the actual decision-making properties that lead to interspecific differences in group characteristics remain unclear. Here, we compared the group formation processes of two Drosophilinae fly species, Colocasiomyia alocasiae and Drosophila melanogaster, which form dense and sparse groups, respectively. A high-throughput tracking system revealed that C. alocasiae flies formed groups faster than D. melanogaster flies, and the probability of C. alocasiae remaining in groups was far higher than that of D. melanogaster. C. alocasiae flies joined groups even when the group size was small, whereas D. melanogaster flies joined groups only when the group size was sufficiently large. C. alocasiae flies attenuated their walking speed when the inter-individual distance between flies became small, whereas such behavioural properties were not clearly observed in D. melanogaster. Furthermore, depriving C. alocasiae flies of visual input affected grouping behaviours, resulting in a severe reduction in group formation. These findings show that C. alocasiae decision-making regarding grouping, which greatly depends on vision, is significantly different from D. melanogaster, leading to species-specific group-formation properties.

opencc-by-4.0May 2022View details →

Strain specific genome scale metabolic models for 1011 Saccharomyces cerevisiae

This is generated strain-specific genome scale metabolic models for 1011 S.cerevisiae. This is linked with the paper: Lu, H. et al. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications 10, 3586 (2019). <a href="https://doi.org/10.1038/s41467-019-11581-3">doi:10.1038/s41467-019-11581-3</a>

opencc-by-4.0May 2022View details →

Computational models from: Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer

Computational models, compressed molecular dynamics (MD) simulation trajectories, and sample input files for "Allele-specific activation, enzyme kinetics, and inhibitor sensitivities of EGFR exon 19 deletion mutations in lung cancer". An early version of this manuscript is available as a preprint here: https://www.biorxiv.org/content/10.1101/2022.03.16.484661v1

Molecular data and analysis specifications for a study on Atriophallophorus parasites from New Zealand

This dataset accompanies the manuscript "Phylogeography and Cryptic Species Structure of a Locally Adapted Parasite in New Zealand". In our study we have shown that multiple species of the trematode parasite from the Atriophallophorus genus co-exist within the same lakes. When focusing on the most common of these species, Atriophallophorus winterbourni, we found that the Southern Alps and Pleistocene glaciation are a likely explanation for its phylogeographic patterns. This dataset consists of three parts: (I) An Excel file containing SNP data, all sample information and the output of phylogeographic analysis with MASCOT1, (II) all sequence alignments, including NADH5, 28S, ITS2 and COI, as they are used for the manuscript and (III) input files for the various analyses as they were prepared for the analysis. 1MASCOT: marginal approximation of the structured coalescent as implemented in BEAST2

Data from: Timbres of tolerance: Co-feeding tolerance in chimpanzees and bonobos is better explained by group-specific variation than species differences

The human species exhibits a remarkable level of social tolerance which has propelled a plethora of behavioural expressions pivotal to our biological success. To date, the evolutionary origins of humans' "ultra-sociality" remain unclear, despite a substantial research focus on our closest living evolutionary relatives, the great apes. Bonobos are typically portrayed as more socially tolerant than chimpanzees and consequentially (sometimes) presented as a better model to study the evolutionary roots of human sociality. Yet, the current evidence supporting such a species-level categorization is equivocal. Here, we used validated group-level co-feeding tasks to test 16 independent Pan groups living in zoo (n=9) and sanctuary (n=7) settings, representing 225 individuals. We found that the expressions of social tolerance substantially overlapped between species, thus precluding categorical inference at the species level. Instead, marked differences were observed among groups, with some bonobo groups exhibiting higher social tolerance than chimpanzee groups, and vice versa. Interestingly, substantial intergroup variation was found within species living in the same environment, which attests to Pan's behavioural flexibility. We conclude that the pervasive dichotomy between the tolerant bonobo and the belligerent chimpanzee requires quantitative nuance, and that accurate phylogenetic tracing of (human) social behaviour necessitates estimations of intraspecific intergroup variation.

opencc-by-4.0Jun 2022View details →

Replication package of SLR of Domain-oriented Specification Techniques

This is a MS Excel sheet containing the data from the initial search up to the classification in the framework, belonging to the manuscript Systematic Literature Review of Domain-oriented Specification techniques, to be published in Journal of Systems and Software.

opencc-by-4.0Jun 2022View details →

Replication package of SLR of Domain-oriented Specification Techniques

Data From: Advancing fence datasets: Comparing approaches to identify fence locations and specifications in southwest Montana

Fencing is a major anthropogenic feature affecting human relationships, ecological processes, and wildlife distributions and movements, but its impacts are difficult to quantify due to a widespread lack of spatial data. We created a fence model and compared outputs to a fence mapping approach using satellite imagery in two counties in southwest Montana, USA to advance fence data development for use in research and management. The model incorporated road, land cover, ownership, and grazing boundary spatial layers to predict fence locations. We validated the model using data collected on randomized road transects (n = 330). The model predicted 34,706.4 km of fences with a mean fence density of 0.93 km/km2 and a maximum density of 14.9 km/km2. We also digitized fences using Google Earth Pro in a random subset of our study area in survey townships (n = 50). The Google Earth approach showed greater agreement (K = 0.76) with known samples than the fence model (K = 0.56) yet was unable to map fences in forests and was significantly more time intensive. We also compared fence attributes by land ownership and land cover variables to assess factors that may influence fence specifications (e.g., wire heights) and types (e.g., number of barbed wires). Private lands were more likely to have fences with lower bottom wires and higher top wires than those on public lands with sample means at 22 cm and 26.4 cm, and 115.2 cm and 110.97, respectively. Both bottom wire means were well below recommended heights for ungulates navigating underneath fencing (≥ 46 cm), while top wire means were closer to the 107 cm maximum fence height recommendation. We found that both fence type and land ownership were correlated (χ2 = 45.52, df = 5, p = 0.001) as well as fence type and land cover type (χ2 = 140.73, df = 15, p = 0.001). We provide tools for estimating fence locations, and our novel fence type assessment demonstrates an opportunity for updated policy to encourage the adoption of "wildlife-friendlier" fencing standards to facilitate wildlife movement in the western U.S. while supporting rural livelihoods.

Phenotypic plasticity and the leaf economics spectrum: plasticity is positively associated with specific leaf area

Phenotypic plasticity is a key mechanism by which plants respond to changing or heterogeneous conditions. Efforts to predict phenotypic plasticity across plant species have mainly focused on environmental variability or abiotic conditions, i.e., site characteristics. However, the considerable variation in phenotypic plasticity within sites calls for alternative approaches. Different functional groups are thought to differ in their plasticity levels. Further, traits such as leaf specific area (SLA), leaf area (LA) and maximum photosynthetic rate (Amax) reflect central aspects of plant strategies. Lower values of SLA, LA and Amax are indicative of a resource-conservative strategy, which is thought to be associated with lower phenotypic plasticity. We used meta-analytical data to test whether plant functional group (herbs, woody deciduous and woody evergreens) and SLA, LA and Amax are associated with phenotypic plasticity in four trait types: biomass allocation, plant size, leaf morphology and physiology. We obtained data from 168 plant species and accounted for phylogenetic relationships in all analyses. We found a positive relationship between SLA and phenotypic plasticity in biomass allocation, leaf morphology and physiology, with differences across functional groups. In contrast, there was no evidence of greater plasticity in plant size in species with higher SLA; rather the opposite was true for woody evergreens. Amax and LA showed similar, but less consistent associations with phenotypic plasticity. Our results show the potential of building predictive frameworks for phenotypic plasticity based on easily measured plant functional characteristics. Results also provide insights into plant strategies and suggest the existence of potential compromises: resource-conservative, low-SLA species tend to be more stress-tolerant but may be less able to cope with variable conditions due to their generally lower phenotypic plasticity. Further studies are needed to explore the mechanisms and the potential implications of this association.

Parkinson's disease-associated, sex-specific changes in DNA methylation at PARK7 (DJ-1), ATXN1, SLC17A6, NR4A2, and PTPRN2 in cortical neurons

Evidence for epigenetic regulation playing a role in Parkinson's disease (PD) is growing, particularly for DNA methylation. Approximately 90% of PD cases are due to a complex interaction between age, genes, and environmental factors, and epigenetic marks are thought to mediate the relationship between aging, genetics, the environment, and disease risk. To date, there are a small number of published genome-wide studies of DNA methylation in PD, but none accounted for cell-type or sex in their analyses. Given the heterogeneity of bulk brain tissue samples and known sex differences in PD risk, progression, and severity, these are critical variables to account for. In this first genome-wide analysis of DNA methylation in an enriched neuronal population from PD post-mortem parietal cortex, we report sex-specific PD-associated methylation changes in PARK7 (DJ-1), SLC17A6 (VGLUT2), PTPRN2 (IA-2β), NR4A2 (NURR1), and other genes involved in developmental pathways, neurotransmitter packaging and release, and axon and neuron projection guidance.