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Commensal bacteria maintain a Qa-1b-restricted unconventional CD8+ T population in gut epithelium

Intestinal intraepithelial lymphocytes (IELs) are characterized by an unusual phenotype and developmental pathway, yet their specific ligands and functions remain largely unknown. Here by analysis of QFL T cells, a population of CD8+ T cells critical for monitoring the MHC I antigen processing pathway, we established that unconventional Qa-1b-restricted CD8+ T cells are abundant in intestinal epithelium. We found that QFL T cells showed a Qa-1b-dependent unconventional phenotype in the spleen and small intestine of naïve wild-type mice. The splenic QFL T cells showed innate-like functionality exemplified by rapid response to cytokines or antigens, while the gut population was refractory to stimuli. Microbiota was required for the maintenance, but not the initial gut homing of QFL T cells. Interestingly, monocolonization with Pediococcus pentosaceus, which expresses a peptide that cross-activated QFL T cells, was sufficient to maintain QFL T cells in the intestine. Thus, microbiota is critical for shaping the Qa-1b-restricted IEL landscape.

Characterizing contemporary evolutionary change in a recently isolated population of Threespine Stickleback (Gasterosteus aculeatus L.)

Parallel evolution of lateral plates and body shape in threespine stickleback (Gasterosteus aculeatus) is an iconic example of adaptation. We test a case of contemporary evolutionary transition in a recently isolated population of marine G. aculeatus in British Columbia, Canada. We investigate Ectodysplasin (Eda) genotypes, plate counts, neutral genetic divergence and whole-body phenotypes to determine genetic and phenotypic distance between this population and nearby comparative populations. Our focal population is in the process of adapting both genetically and phenotypically to a freshwater environment and we provide an example of the genetic basis for parallel evolutionon a contemporary timescale. The frequency of Eda genotypes and lateral plate phenotypes in our focal population are not consistent with those of marine or fully freshwater populations. Although our focal population is genetically distinct from nearby marine populations, these fish still more closely resemble marine populations in overall body shape while demonstrating an intriguing intermediate phenotype. Eda frequency and lateral plate phenotype change faster than body shape in response to freshwater conditions, suggesting that the pace of adaptation differs across traits in response to the same environmental conditions. Our results further bolster the case for G. aculeatus as a key model of contemporary evolution.

Combining bioenergetics and movement models to improve understanding of the population consequences of disturbance

We developed dynamic bioenergetics models to investigate how behavioural responses to anthropogenic disturbance events might affect the population dynamics of three marine mammal species (harbour porpoise, grey seal and harbour seal) with contrasting life-history traits (capital vs income breeders) and movement behaviour (resident vs nomadic). We used these models to analyse how individual vital rates were affected by differences in the probability of disturbance and the duration of any behavioural response, while taking account of uncertainty in the model parameters and heterogeneity in behaviour. The outputs of individual movement models and telemetry data were then used to determine how the probability of exposure might vary among species, individuals, and geographical locations. We then demonstrate how these estimated probabilities of exposure can be translated into probabilities of disturbance. For illustrative purposes, we modelled the potential effects of a temporary decrease in energy assimilation associated with a series of disturbance events that might realistically occur during the construction of an offshore windfarm. Offspring starvation mortality was the vital rate that was most affected by these disturbance events. Monitoring of rates should be considered as standard practice so that populations' responses can be detected as early as possible. Predicted effects on individual vital rates depended on the species' movement behaviour and the likely density of animals where the modelled construction activity was assumed to take place. The magnitude of these effects also depended critically on the assumed duration of the reduction in energy assimilation. No direct estimates of this variable are currently available, but we suggest some ways in which it could be estimated. The described approach could be extended to other species and activities, given sufficient information to parameterise the component models. However, we emphasise the need to account for among-individual heterogeneities and uncertainties in the values of the many model parameters.

opencc-by-4.0Dec 2023View details →

zenodo36/100

Data for section 3.2 of Stellar Population Properties in the Stellar Streams Around SPRC047

Supplementary (input and output) data for Section 3.2 ("Measurement Uncertainties in the Deconvolved Image") of the paper "Stellar Population Properties in the Stellar Streams Around SPRC047", accepted for publication in ApJ and available in <a href="https://arxiv.org/abs/2312.05358" target="_blank" rel="noopener">arXiv:2312.05358.</a> The source code for this project is publicly available <a href="https://gitlab.com/makhlaghi/sprc047-stream-clumps-photometry" target="_blank" rel="noopener">on Gitlab</a> and is archived on<a href="https://archive.softwareheritage.org/swh:1:dir:882514891cdcfc08261409352437bc6b8a836b8b;origin=https://gitlab.com/makhlaghi/sprc047-stream-clumps-photometry;visit=swh:1:snp:11cb02c374d7856028c57fb7312b60531f1be2e6;anchor=swh:1:rev:5d81b833931e58732627c06998c2488e6d2a8fb7" target="_blank" rel="noopener"> SoftwareHeritage</a> for longevity. A brief description of the contents in this repository are given below. Note that because the AWMLE deconvolution code is not yet publicly released, the second two files below are necessary (they are used by the reproducible Makefile of this section <a href="https://gitlab.com/makhlaghi/sprc047-stream-clumps-photometry" target="_blank" rel="noopener">on Gitlab</a>). <ul> <li><a href="../records/10397812/files/sprc047_3.6um-bck.fits?download=1">sprc047_3.6um-bck.fits</a>: Spitzer image of SPRC047.</li> <li><a href="../records/10397812/files/deconvolved-it75.fits?download=1">deconvolved-it75.fits</a>: The deconvolved Spitzer image.</li> <li><a href="../records/10397812/files/deconvolved-simulated.tar.gz?download=1">deconvolved-simulated.tar.gz</a>: 100 realizations of random noise over a point-like source used to estimate the error of the deconvolved measurements.</li> </ul>

Plant size, latitude, and phylogeny explain within-population variability in herbivory

Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth.

Data from: Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population

Impacts of immigration on micro-evolution and population dynamics fundamentally depend on net rates and forms of resulting gene flow into recipient populations. Yet, the degrees to which observed rates and sex ratios of physical immigration translate into multi-generational genetic legacies have not been explicitly quantified in natural meta-populations, precluding inference on how movements translate into effective gene flow and eco-evolutionary outcomes. Our analyses of three decades of complete song sparrow (Melospiza melodia) pedigree data show that multi-generational genetic contributions from regular natural immigrants substantially exceeded those from contemporary natives, consistent with heterosis-enhanced introgression. Further, while contributions from female immigrants exceeded those from female natives by up to three-fold, male immigrants' lineages typically went locally extinct soon after arriving. Both the overall magnitude, and the degree of female bias, of effective gene flow therefore greatly exceeded those which would be inferred from observed physical arrivals, reshaping the eco-evolutionary implications of immigration.

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

<div> Coffea arabica, an allotetraploid hybrid of C. eugenioides and C. canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ∼30.5 kya, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica. </div>

Data from: Combining the resurrection approach with transplant experiments to investigate adaptation of plant populations to environmental change

Recent climatic changes, such as more frequent droughts and heatwaves, can lead to rapid evolutionary adaptations in plant populations. Such rapid evolution can be investigated using the resurrection approach by comparing plants raised from stored ancestral and contemporary seeds from the same population. This approach has so far only been used in common garden experiments, allowing it to reveal genetic differentiation but not adaptation. In this study, we performed a novel approach by testing for evolutionary adaptation in natural plant populations using a resurrection study in combination with in situ transplantations. We cultivated seedlings from ancestors (23–26 years old) and contemporary descendants of three perennial species (Melica ciliata, Leontodon hispidus and Clinopodium vulgare) from calcareous grasslands in the greenhouse and transplanted them back to their collection sites. In addition, we sowed seeds of ancestors and descendants of two species (L. hispidus and C. vulgare) to the collection sites in order to investigate germination rates. In transplanted M. ciliata seedlings, we observed lower mortality and larger plant size in descendants compared to ancestors. This indicates that descendants are better adapted than ancestors to the current environmental conditions, which proved to be exceptionally hot and dry during the study period. Descendants of C. vulgare seedlings tended to be smaller and descendants of L. hispidus seedlings produced fewer leaves compared to their ancestors in their contemporary environmental conditions. In C. vulgare and L. hispidus, we found evolution towards faster germination, and especially descendant seeds of C. vulgare were better adapted to the unfavourable conditions during the experimental period. Concluding, we demonstrate that our novel approach to combine resurrection ecology with transplant experiments is a promising avenue to rigorously test for evolutionary adaptations in changing environments.

Demographics and song repertoire sizes of cirl bunting populations

In order to improve conservation outcomes translocation or reintroduction of individuals may be necessary. When song learning birds are translocated, changes in the cultural diversity of song repertoires, or abnormal vocalisations, in the new population can be a problem. We monitored song production over 8 years in a reintroduced population of the cirl bunting (Emberiza cirlus). Chicks were removed from nests in Devon, UK, between 2006-2011, translocated at six days old to be hand-reared and released in Cornwall, UK. Recordings at the release site in 2011 showed a significantly reduced population repertoire and individuals sang abnormal song types compared to the source populations in Devon. However, recordings in 2019, showed population song repertoire had reached the level of source populations of similar size, and song types were species typical. Our study shows that species can recover from a cultural bottleneck and suggests that, for some song learning birds, if translocation of nestlings is necessary it may not lead to long-term problems for communication and thus population persistence. For future translocations of nestlings, we recommend that efforts are made to provide tutoring to enable song learning. This may be achieved by providing recordings but may also include providing adult song tutors. In addition, playback of 'normal' songs to translocated populations may aid in development of species typical song repertoires, although care must be taken that this is not disturbing the reintroduced birds.

SNP data for F2 population derived from Oryza rufipogon and O. nivara

To elucidate the genetic architecture underlying phenotypic divergence is essential to the understanding of ecological adaptation and speciation. Two wild rice species (O. rufipogon and O. nivara) are a progenitor-daughter species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolved linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the perennial O. rufipogon and annual O. nivara. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots), with each involving multiple adaptive traits, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits.

Data from: Contrasting patterns of female house mouse spatial organisation among outbreaking and stable populations

The size and distribution of home ranges reflects how individuals within a population use, defend, and share space and resources, and may thus be an important predictor of population-level dynamics. In eruptive species like the house mouse in Australian grain growing regions, contrasting space use between stable and outbreaking populations allows us to test predictions regarding social or life history strategies that may contribute to an outbreak. In this study we use spatially explicit capture-recapture models to compare home range overlap (as a proxy for territoriality) in female mice from populations showing different outbreak trajectories. We found that female space use in spring varied between outbreaking and stable populations. Our analysis indicated greater home range overlap in populations with stable trajectories compared to those that would later experience an outbreak, suggesting females in these stable populations may have had greater potential for cooperative group formation as indicated by shared space use. We discuss the results with respect to intrinsic factors, such as kin structure, with potential implications for better predicting mouse outbreaks at a microgeographic scale.

Replication data for global population profile of tropical cyclone exposure during 2002 and 2019

Tropical cyclones have far-reaching impacts on livelihoods and population health that often persist years after the event. Characterizing the demographic and socioeconomic profile and the vulnerabilities of the exposed populations is essential to assess health and other risks associated with future tropical cyclone events. Estimates of exposure to tropical cyclones are often regional rather than global and do not consider population vulnerabilities. Here, we combine spatially resolved annual demographic estimates with tropical cyclone wind fields estimates to construct a global profile of the populations exposed to tropical cyclones between 2002 and 2019. We find that approximately 560 million people are exposed yearly and that the number of people exposed has increased across all cyclone intensities over the study period. The age distribution of those exposed has shifted away from children (under-5) and towards older people (over-60) in recent years compared to the early 2000s. Populations exposed to tropical cyclones are more socioeconomically deprived than those unexposed within the same country, and this relationship is more pronounced for people exposed to higher intensity storms. By characterizing the patterns and vulnerabilities of populations exposed to tropical cyclones, our results can help identify mitigation strategies and assess the global burden and future risks of tropical cyclones.

Bacterial zoonoses impacts to conservation of wildlife populations: A global synthesis

Emerging infectious diseases have significantly increased in recent years; approximately 60% of these emerging diseases are of zoonotic origin, and of those, around 70% were identified to start with wild animals. To better understand the impacts of zoonotic diseases on wildlife, there is a need to identify the distribution and impact of zoonotic pathogens in wildlife, particular those species with threatened populations. To investigate this question, we constructed a zoonotic disease database identifying wildlife hosts for each bacterial zoonotic disease and recorded clinical signs of disease for each host-pathogen relationship if found. Species of least concern were found to have a significantly higher prevalence and richness of zoonotic bacterial diseases (n= 0.0608, x2= 5.898, p=0.01516). The taxonomic level Order was found to be the best predictor for pathogen richness, and the Artiodactyla and Carnivora contain a significantly higher pathogen richness than other vertebrate Orders. Species with the greatest pathogen richness include the wild boar (Sus scrofa, n=66), Northern raccoon (Procyon lotor, n=16) and the red fox (Vulpes vulpes, n=41). Our results indicate bacterial zoonoses are not likely to be a driving factor of species population declines, and future zoonotic disease surveillance efforts should target species in the Artiodactyla and Carnivora families. The wild boar (Sus scrofa) in particular may be a good candidate for zoonotic disease monitoring due to its high pathogen richness, wide range, and large population. Understanding the impacts and distribution of bacterial zoonoses in wildlife populations can help in planning for future wildlife management efforts, particularly in species of conservation concern and wildlife disease monitoring.

opencc-by-4.0Dec 2023View details →

zenodo36/100

Dataset of paper "Predicting the size of silver nanoparticles synthesised in flow reactors: Coupling population balance models with fluid dynamic simulations"

Dataset of paper "Predicting the size of silver nanoparticles synthesised in flow reactors: Coupling population balance models with fluid dynamic simulations"

Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations

Genetic diversity is fundamental to the adaptive potential and survival of species. Although its importance has long been recognized in science, it has a history of neglect within policy – until now. The new Global Biodiversity Framework recently adopted by the Convention on Biological Diversity, states that genetic diversity must be maintained at levels assuring adaptive potential of populations, and includes metrics for systematic monitoring of genetic diversity in so called indicators. Similarly, indicators for genetic diversity are being developed at national levels. Here, we apply new indicators for Swedish national use to one of the northernmost salmonid fishes, the Arctic charr (Salvelinus alpinus). We sequence whole genomes to monitor genetic diversity over four decades in three landlocked populations inhabiting protected alpine lakes in central Sweden. We find levels of genetic diversity, inbreeding and load to differ among lakes but remain stable over time. Effective population sizes are generally small (<500), suggesting a limited ability to maintain adaptive variability if genetic exchange with nearby populations became eliminated. We identify genomic regions potentially shaped by selection; SNPs exhibiting population divergence exceeding expectations under drift and a putative selective sweep acting within one lake to which the competitive brown trout was introduced during the sampling period. Identified genes appear involved in immunity and salinity tolerance. Present results suggest that genetically vulnerable populations of Arctic charr have maintained neutral and putatively adaptive genetic diversity despite small effective sizes, attesting the importance of continued protection and assurance of gene flow among populations.

Identification of non-native populations and reconstruction of invasion routes in the Redbreast Sunfish Lepomis auritus

Human-mediated introductions of non-native species are expected to increase globally and threaten native biodiversity. Lepomis auritus (Redbreast Sunfish), a carnivorous freshwater fish native to rivers in eastern North America, has been introduced far outside of its native range due to its popularity in recreational fisheries. However, poor documentation of introductions and lack of thorough ichthyofaunal surveys before the mid-20th century have complicated our understanding of the establishment and spread of non-native L. auritus over the past 90 years, precluding effective management. We conducted phylogenomic analyses using ddRAD data from 197 specimens of L. auritus collected throughout the known geographic range of the species to reconstruct the introduction history of the species. Our protocols allow for the reconstruction of complicated introduction routes and reveal that L. auritus in Texas is the result of a single-source introduction from the Suwannee River; the population in the upper Tennessee River has two sources of introduction from the Savannah River and the northeastern rivers that drain into the Atlantic Ocean; and the populations in the middle Tennessee River and the Mobile River Basin have sources from the upper Tennessee River system and the Apalachicola River Basin. Ecological and evolutionary investigations of the non-native populations of L. auritus will broaden the understanding of invasion dynamics in species of Lepomis and other non-native freshwater fishes in North America. Our study provides critical information for the conservation of native populations and invasive management of non-native populations of L. auritus.

Data from: Plant-soil microbe feedbacks depend on distance and ploidy in a mixed cytotype population of Larrea tridentata

Premise of the study Theory predicts that mixed ploidy populations should be short-lived due to strong fitness disadvantages for the rare ploidy. However, mixed ploidy populations are common, suggesting that the fitness costs for rare ploidies are counterbalanced by ecological benefits that emerge when rare. We investigated whether differences in ecological interactions with soil microbes help to maintain a tetraploid-hexaploid population of Larrea tridentata (creosote bush) in the Sonoran Desert, California, USA, where prior work documented ploidy-specific root-associated microbes. Methods We used a plant-soil feedback (PSF) experiment to test whether host-specific soil microbes can alter the outcomes of intra-ploidy vs. inter-ploidy competition. Host-specific soil microbes can build up over time; thus, distance from a host plant can affect the fitness of nearby plants. Key results Seedlings grown in soils from near plants of a different ploidy produced greater biomass relative to seedlings grown in soils from near plants of the same ploidy. Moreover, seedlings grown in soils from near plants of a different ploidy produced greater biomass than those grown in soils from further away from plants of a different ploidy. This suggests the ecological consequences of PSF may facilitate the persistence of mixed ploidy populations. Conclusions This is the first evidence, to our knowledge, consistent with plant-soil microbe feedback as a viable mechanism to maintain the coexistence of multiple ploidy levels in a single population.

Microgeographic population structuring in a genus of California trapdoor spiders and discovery of an enigmatic new species (Euctenizidae: Promyrmekiaphila korematsui sp. nov.)

The recognition and delineation of cryptic species remains a perplexing problem in systematics, evolution, and species delimitation. Once recognized as such, cryptic species complexes provide fertile ground for studying genetic divergence within the context of phenotypic and ecological divergence (or lack thereof). Herein we document the discovery of a new cryptic species of trapdoor spider, Promyrmekiaphila korematsui sp. nov. Using subgenomic data obtained via target enrichment, we document the phylogeography of the California endemic genus Promyrmekiaphila and its constituent species, which also includes P. clathrata and P. winnemem. Based on these data we show a pattern of strong geographic structuring among populations but cannot entirely discount recent gene flow among populations that are parapatric, particularly for deeply diverged lineages within P. clathrata. The genetic data, in addition to revealing a new undescribed species, also allude to a pattern of potential phenotypic differentiation where species likely come into contact. Alternatively, phenotypic cohesion among genetically divergent P. clathrata lineages suggests that some level of gene flow is ongoing or occurred in the recent past. Despite considerable field collection efforts over many years, additional sampling in potential zones of contact for both species and lineages is needed to completely resolve the dynamics of divergence in Promyrmekiaphila at the population-species interface.

Data from: Cross ocean-basin population genetic dynamics in a pelagic top predator of high conservation concern, the oceanic whitetip shark, Carcharhinus longimanus

The oceanic whitetip shark, Carcharhinus longimanus, is a Critically Endangered, circumtropical, and highly migratory, pelagic shark. Yet, little information exists on its population genetic dynamics to guide conservation management practice. We present a first worldwide, mitochondrial and nuclear DNA assessment of the population genetic status of this imperiled species based on sequences of the complete mitochondrial control region (n = 173) and partial ND4 gene (n = 172), and genotypes from 12 nuclear microsatellites (n = 164). Statistically significant mitochondrial and nuclear DNA population genetic differentiation was detected across all marker datasets between Western Atlantic and Indo-Pacific oceanic whitetip sharks. Additionally, our data, combined with previously published, partial (701-base pairs) mitochondrial control region sequences from additional locations in the Atlantic and Indian Oceans, confirmed significant matrilineal population structure between the Western and Eastern Atlantic. The combined data also provisionally (i.e., with FST but not ΦST) indicated differentiation between Western North and Central-South Atlantic sharks, pointing to the need for further assessment in this region. Matrilineal differentiation was also detected between Indian and Pacific Ocean sharks via pairwise analyses, albeit with the ND4 gene sequence only (ΦST = 0.051; FST = 0.092). Limited sampling in the Pacific leaves open questions about the connectivity dynamics in this large region. Despite the presence of geographic population genetic structure, the mitochondrial data showed no evidence of across ocean basin phylogeographic lineages. A provisional assessment of mitochondrial and nuclear genetic diversity indicated the oceanic whitetip shark's status falls in the middle to upper ranges compared to other shark species, potentially lending some optimism for the present adaptability and resiliency of this species if strong conservation measures are effectively implemented.