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Figures 3-4 from: Guedes GHS, Salgado FLK, Uehara W, de Pavia Ferreira DL, Araújo FG (2020) The recapture of Leptopanchax opalescens (Aplocheiloidei: Rivulidae), a critically endangered seasonal killifish: habitat and aspects of population structure. Zoologia 37: 1-8. https://doi.org/10.3897/zoologia.37.e54982
Figures 3-4 (3) Map of recorded occurrences of Leptopanchax opalescens in the state of Rio de Janeiro, Brazil (red dots). The black dot indicates the new record in this study. References of occurrences (1, base of the Serra de Petropolis; 2, villages of Cava and Tinguá; 3, Horto Florestal Santa Cruz, in Seropédica, RJ; 4, Training camp of the Brazilian Army in Gericinó, Rio de Janeiro; and 5, a terrain of the BRF S.A. in Seropédica, Rio de Janeiro) available in the Table S1. (4) Photographic record of temporary pools flooded with marginal vegetation predominantly composed of grasses, in the municipality of Seropédica, RJ.
Data from: Dispersal capacity predicts both population genetic structure and species richness in reef fishes
Dispersal is a fundamental species characteristic that should directly affect both rates of gene flow among spatially distributed populations and opportunities for speciation. Yet no single trait associated with dispersal has been demonstrated to affect both micro- and macroevolutionary patterns of diversity across a diverse biological assemblage. Here, we examine patterns of genetic differentiation and species richness in reef fishes, an assemblage of over 7,000 species comprising approximately one-third of the extant bony fishes and over one-tenth of living vertebrates. In reef fishes, dispersal occurs primarily during a planktonic larval stage. There are two major reproductive and parental investment syndromes among reef fishes, and the differences between them have implications for dispersal: (1) benthic guarding fishes lay negatively buoyant eggs, typically guarded by the male parent, and from these eggs hatch large, strongly swimming larvae; in contrast, (2) pelagic spawning fishes release small floating eggs directly into the water column, which drift unprotected before small weakly swimming larvae hatch. Using phylogenetic comparative methods, we show that benthic guarders have significantly greater population structure than pelagic spawners and additionally that taxonomic families of benthic guarders are more species rich than families of pelagic spawners. Our findings provide a compelling case for the continuity between micro- and macroevolutionary processes of biological diversification and underscore the importance of dispersal-related traits in influencing the mode and tempo of evolution.
Data from: Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)
Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (FCT = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (FCT range 0.275–0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.
Data from: A structured population model suggests that long life and post-reproductive lifespan promote the evolution of cooperation
Social organization correlates with longevity across animal taxa. This correlation has been explained by selection for longevity by social evolution. The reverse causality is also conceivable but has not been sufficiently considered. We constructed a simple, spatially structured population model of asexually reproducing individuals to study the effect of temporal life history structuring on the evolution of cooperation. Individuals employed fixed strategies of cooperation or defection towards all neighbours in a basic Prisoner׳s Dilemma paradigm. Individuals aged and transitioned through different life history stages asynchronously without migration. An individual׳s death triggered a reproductive event by one immediate neighbour. The specific neighbour was chosen probabilistically according to the cumulative payoff from all local interactions. Varying the duration of pre-reproductive, reproductive, and post-reproductive life history stages, long-term simulations allowed a systematic evaluation of the influence of the duration of these specific life history stages. Our results revealed complex interactions among the effects of the three basic life history stages and the benefit to defect. Overall, a long post-reproductive stage promoted the evolution of cooperation, while a prolonged pre-reproductive stage has a negative effect. In general, the total length of life also increased the probability of the evolution of cooperation. Thus, our specific model suggests that the timing of life history transitions and total duration of life history stages may affect the evolution of cooperative behaviour. We conclude that the causation of the empirically observed association of life expectancy and sociality may be more complex than previously realized.
Data from: Low genetic diversity but strong population structure reflects multiple introductions of western flower thrips (Thysanoptera: Thripidae) into China followed by human-mediated spread
Historical invasion scenarios based on observational records are usually incomplete and biased, but these can be supplemented by population genetic data. The western flower thrips (WFT), Frankliniella occidentalis, invaded China in the last 13 years and has rapidly become one of the most serious pests in the country. To assess whether this invasion involved a single event or multiple events, we examined patterns of genetic diversity and population structure of WFT across 12 Chinese populations and a native US population based on mitochondrial DNA and/or 18 microsatellite loci. The average allelic richness and haplotype diversity in Chinese populations were significantly lower than in a population from its native range. The distribution of mitochondrial haplotypes suggested multiple independent invasions of WFT into China, including two invasions into the Beijing region. Based on microsatellite data, two distinct clusters were identified, with both of them splitting further into two clusters; in the Beijing region, the microsatellite data also provided evidence for two introductions. Both the absence of isolation by distance and the fact that distant populations were similar genetically suggest patterns of WFT movement linked to human activities. Our study therefore suggests multiple introductions of WFT into China and human-assisted spread.
Data from: Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters
Phylogeographic inferences about gene flow are strengthened through comparison of co-distributed taxa, but also depend on adequate genomic sampling. Amplified Fragment Length Polymorphisms (AFLP) provide a rapid and inexpensive source of multilocus allele frequency data for making genomically robust inferences. Every AFLP study initially generates markers with a range of locus-specific genotyping error rates and applies criteria to select a subset for analysis. However, there has been very little empirical evaluation of the best tradeoff between culling all but the lowest-error loci to minimize overall genotyping error versus the potential for increasing population genetic signal by retaining more loci. Here, we used AFLPs to compare population structure in co-distributed broadcast spawning (Crassostrea virginica) and brooding (Ostrea equestris) oyster species. Using existing methods for almost entirely automated marker selection and scoring, genotyping error tradeoffs were evaluated by comparing results across a nested series of datasets with mean mismatch errors of 0, 1, 2, 3, 4 and >4%. Artifactual population structure was diagnosed in high-error datasets and we assessed the low-error point at which expected population substructure signal was lost. In both species we identified substructure patterns deemed to be inaccurate at error rates {less than or equal to}2% and >4%. In the species comparison, the optimum datasets showed higher gene flow for the brooding oyster with more oceanic salinity tolerances. AFLP tradeoffs may differ among studies, but our results suggest that important signal may be lost in the pursuit of 'acceptable' error levels and our procedures provide a general method for empirically exploring these tradeoffs.
Data from: Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient.
House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients.
Data from: Contemporary population structure and post-glacial genetic demography in a migratory marine species, the blacknose shark, Carcharhinus acronotus
Patterns of population structure and historical genetic demography of blacknose sharks in the western North Atlantic Ocean were assessed using variation in nuclear-encoded microsatellites and sequences of mitochondrial (mt)DNA. Significant heterogeneity and/or inferred barriers to gene flow, based on microsatellites and/or mtDNA, revealed the occurrence of five genetic populations localized to five geographic regions: the southeastern U.S Atlantic coast, the eastern Gulf of Mexico, the western Gulf of Mexico, Campeche Bay in the southern Gulf of Mexico, and the Bahamas. Pairwise estimates of genetic divergence between sharks in the Bahamas and those in all other localities were more than an order of magnitude higher than between pairwise comparisons involving the other localities. Demographic modelling indicated that sharks in all five regions diverged after the last glacial maximum and, except for the Bahamas, experienced post-glacial, population expansion. The patterns of genetic variation also suggest that the southern Gulf of Mexico may have served as a glacial refuge and source for the expansion. Results of the study demonstrate that barriers to gene flow and historical genetic demography contributed to contemporary patterns of population structure in a coastal migratory species living in an otherwise continuous marine habitat. The results also indicate that for many marine species, failure to properly characterize barriers in terms of levels of contemporary gene flow could in part be due to inferences based solely on equilibrium assumptions. This could lead to erroneous conclusions regarding levels of connectivity in species of conservation concern.
Data from: New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus)
Background: Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species' range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge. Results: We sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated > 16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring > 140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~ 100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population. Conclusions: Our study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating population of prairie falcons across our sampling locations. Prairie falcons are highly mobile and relatively rare long-distance dispersal events may promote gene flow throughout the range. As such, California's prairie falcons might be managed as a single population, indicating that management actions undertaken to benefit the species at the local level have the potential to influence the species as a whole.
Data from: Population size-structure dependent fitness and ecosystem consequences in Trinidadian guppies
1. Decades of theory and recent empirical results have shown that evolutionary, population, community and ecosystem properties are the result of feedbacks between ecological and evolutionary processes. The vast majority of theory and empirical research on these eco-evolutionary feedbacks has focused on interactions among population size and mean traits of populations. 2. However, numbers and mean traits represent only a fraction of the possible feedback dimensions. Populations of many organisms consist of different size classes that differ in their impact on the environment and each other. Moreover, rarely do we know the map of ecological pathways through which changes in numbers or size structure cause evolutionary change. The goal of this study was to test the role of size structure in eco-evolutionary feedbacks of Trinidadian guppies and to begin to build an eco-evolutionary map along this unexplored dimension. 3. We used a factorial experiment in mesocosms wherein we crossed high- and low-predation guppy phenotypes with population size structure. We tested the ability of changes in size structure to generate selection on the demographic rates of guppies using an integral projection model (IPM). To understand how fitness differences among high- and low-predation phenotypes may be generated, we measured the response of the biomass of lower trophic levels and nutrient cycling to the different phenotype and size structure treatments. 4. We found a significant interaction between guppy phenotype and the size structure treatments for absolute fitness. Size structure had a very large effect on invertebrate biomass in the mesocosms, but there was little or no effect of the phenotype. The effect of size structure on algal biomass depended on guppy phenotype, with no difference in algal biomass in populations with more, smaller guppies, but a large decrease in algal biomass in mesocosms with phenotypes adapted to low-predation risk. 5. These results indicate an important role for size structure partially driving eco-evolutionary feedbacks in guppies. The changes in the ecosystem suggest that the absence of a steep decline in guppy fitness of the low-predation risk populations is likely due to higher consumption of algae when invertebrates are comparatively rare. Overall, these results demonstrate size structure as a possible dimension through which eco-evolutionary feedbacks may occur in natural populations.
Data from: Combining noninvasive genetics and a new mammalian sex-linked marker provides new tools to investigate population size, structure and individual behaviour: an application to bats
Monitoring wild populations is crucial for their effective management. Noninvasive genetic methods provide robust data from individual free-ranging animals, which can be used in capture-mark-recapture (CMR) models to estimate demographic parameters without capturing or disturbing them. However, sex- and status-specific behaviour, which may lead to differences in detection probabilities, is rarely considered in monitoring. Here, we investigated population size, sex ratio, sex- and status-related behaviour in 19 Rhinolophus hipposideros maternity colonies (Northern France) with a noninvasive genetic CMR approach (using faeces) combined with parentage assignments. The use of the DDX3X/Y-Mam sexual marker designed in this study, which shows inter- and intra-chromosomal length polymorphism across placental mammals, together with 8 polymorphic microsatellite markers, produced high quality genetic data with limited genotyping errors and allowed us to reliably distinguish different categories of individuals (males, reproductive and non-reproductive females) and to estimate population sizes. We showed that visual counts represent well adult female numbers and that population composition in maternity colonies changes dynamically during the summer. Before parturition, colonies mainly harbour pregnant and non-pregnant females with a few visiting males whereas after parturition, colonies are mainly composed of mothers and their offspring with a few visiting non-mothers and males. Our approach gives deeper insight into sex- and status-specific behaviour, a prerequisite for understanding population dynamics and developing effective monitoring and management strategies. Provided sufficient samples can be obtained, this approach can be readily applied to a wide range of species.
Data from: Clonal genetic structure and diversity in populations of an aquatic plant with combined versus separate sexes
Clonality is often implicated in models of the evolution of dioecy, but few studies have explicitly compared clonal structure between plant sexual systems, or between the sexes in dioecious populations. Here, we exploit the occurrence of monoecy and dioecy in clonal Sagittaria latifola (Alismataceae) to evaluate two main hypotheses: (1) clone sizes are smaller in monoecious than dioecious populations, because of constraints imposed on clone size by costs associated with geitonogamy; (2) in dioecious populations, male clones are larger and flower more often than female clones because of sex-differential reproductive costs. Differences in clone size and flowering could result in discordance between ramet- and genet-based sex ratios. We used spatially explicit sampling to address these hypotheses in 10 monoecious and 11 dioecious populations of S. latifolia at the northern range limit in eastern N. America. In contrast to our predictions, monoecious clones were significantly larger than dioecious clones, probably due to their higher rates of vegetative growth and corm production, and in dioecious populations there was no difference in clone size between females and males; ramet- and genet-based sex ratios were therefore highly correlated. Genotypic diversity declined with latitude for both sexual systems, but monoecious populations exhibited lower genotypic richness. Differences in life history between the sexual systems of S. latifolia appear to be the most important determinants of clonal structure and diversity.
Data from: Seed germination schedule and environmental context shaped the population genetic structure of subtropical evergreen oaks on the Yun-Gui Plateau, Southwest China
<p>The evergreen broadleaved forests (EBLFs) of Southwest China have a long-term stable environment and support a diverse flora, thus forming a global biodiversity hotspot. However, the key drivers that have shaped the genetic diversity patterns of species in these EBLFs are not well understood. <i>Quercus delavayi</i>, <i>Q. schottkyana</i>,<i> </i>and<i> Q. kerrii </i>are sympatric oak species with different seed biological traits that are typical for these EBLFs. This study combined multilocus phylogeography and ecological niche modeling to screen 33 <i>Q. delavayi</i> populations. Their population genetic structure was inferred in comparison with previous studies on <i>Q. schottkyana</i> and <i>Q. kerrii</i>. The seed germination traits of all three species were also investigated. cpDNAs showed a significant phylogeographic structure in <i>Q. delavayi</i>, which was not detected in <i>Q. schottkyana</i> or <i>Q. kerrii</i>. <i>Quercus delavayi</i>, <i>Q. kerrii</i>, and <i>Q. schottkyana </i>exhibited different pollen-to-seed migration ratios (r = 219, 117, and 22, respectively), which are linked to the germination schedules of acorns. The distributions of <i>Q. delavayi</i> and <i>Q. schottkyana</i> remained long-term stable since the last glacial maximum (LGM) with a similar nSSR genetic gradient change along latitude. Instead, <i>Q. kerrii</i> experienced a prominent range expansion since the LGM with genetic diversification between the East and the West of the Tanaka line due to environmental heterogeneity. These results identify seed traits and environmental heterogeneity as two key drivers that shape the population genetic structure of EBLF trees in Southwest China. These should be considered in regional forestry conservation and management.</p>
Data from: Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator, the common dolphin (genus Delphinus)
Climatic oscillations during the Pleistocene have greatly influenced the distribution and connectivity of many organisms, leading to extinctions but also generating biodiversity. While the effects of such changes have been extensively studied in the terrestrial environment, studies focusing on the marine realm are still scarce. Here we used sequence data from one mitochondrial and five nuclear loci to assess the potential influence of Pleistocene climatic changes on the phylogeography and demographic history of a cosmopolitan marine predator, the common dolphin (genus Delphinus). Population samples representing the three major morphotypes of Delphinus were obtained from ten oceanic regions. Our results suggest that short-beaked common dolphins are likely to have originated in the eastern Indo-Pacific Ocean during the Pleistocene and expanded into the Atlantic Ocean through the Indian Ocean. On the other hand, long-beaked common dolphins appear to have evolved more recently and independently in several oceans. Our results also suggest that short-beaked common dolphins had recurrent demographic expansions concomitant with changes in sea surface temperature during the Pleistocene and its associated increases in resource availability, which differed between the North Atlantic and Pacific Ocean basins. By proposing how past environmental changes had an effect on the demography and speciation of a widely distributed marine mammal, we highlight the impacts that climate change may have on the distribution and abundance of marine predators and its ecological consequences for marine ecosystems.
Data from: Microsatellite analysis of genetic diversity and population structure of Arabian horse populations
The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here we explore seven different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya-Arabian and Polish-Arabian) and America (American-Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, AMOVA, factorial correspondence analysis and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source of among populations variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American-Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses, and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.
Data from: Minor allele frequency thresholds strongly affect population structure inference with genomic datasets
One common method of minimizing errors in large DNA sequence datasets is to drop variable sites with a minor allele frequency below some specified threshold. Though widespread, this procedure has the potential to alter downstream population genetic inferences and has received relatively little rigorous analysis. Here we use simulations and an empirical SNP dataset to demonstrate the impacts of minor allele frequency (MAF) thresholds on inference of population structure. We find that model-based inference of population structure is confounded when singletons are included in the alignment, and that both model-based and multivariate analyses infer less distinct clusters when more stringent MAF cutoffs are applied. We propose that this behavior is caused by the combination of a drop in the total size of the data matrix and by correlations between allele frequencies and mutational age. We recommend a set of best practices for applying MAF filters in studies seeking to describe population structure with genomic data.
Data from: Population assignment reveals low migratory connectivity in a weakly structured songbird
Understanding migratory connectivity is essential for determining the drivers behind population dynamics and for implementing effective conservation strategies for migratory species. Genetic markers provide a means to describe migratory connectivity, however they can be uninformative for species with weak population genetic structure, which has limited their application. Here, we demonstrated a genomic approach to describing migratory connectivity in the prothonotary warbler, Protonotaria citrea, a Neotropical songbird of conservation concern. Using 26,189 SNPs, we revealed regional genetic structure between the Mississippi River Valley and the Atlantic Seaboard with overall weak genetic differentiation among populations (FST = 0.0055; 95% CI: 0.0051 - 0.0059). Genetic variation had a stronger association with geographic rather than environmental factors, with each explaining 14.5% and 8.2% of genetic variation, respectively. By varying the numbers of genomic markers used in population assignment models with individuals of known provenance, we identified a maximum assignment accuracy (89.7% to site, 94.3% to region) using a subset of 600 highly differentiated SNPs. We then assigned samples from nonbreeding sites to breeding region, and found low migratory connectivity. Our results highlight the importance of filtering markers for informative loci in models of population assignment. Quantifying migratory connectivity for weakly structured species will be useful for expanding studies to a wider-range of migratory species across taxonomic groups and may contribute to a deeper understanding of the evolution of migratory strategies.
Data from: Genetic diversity and population structure of wild sunflower (Helianthus annuus L.) in Argentina: reconstructing its invasion history
Studying the levels and patterns of genetic diversity of invasive populations is important to understand the evolutionary and ecological factors promoting invasions and for better designing preventive and control strategies. Wild sunflower (Helianthus annuus L.) is native to North America and was introduced, and has become invasive, in several countries, including Argentina (ARG). Here, using classical population genetic analyses and Approximate Bayesian Computation (ABC) modelling, we studied the invasion history of wild sunflower in ARG. We analyzed 115 individuals belonging to 15 populations from ARG (invasive range) and United States (US, native range) at 14 nuclear and three chloroplast simple sequence repeat markers along with 23 phenotypic variables. Populations from ARG showed similar levels of nuclear genetic diversity to US populations and higher genetic diversity in the chloroplast genome, indicating no severe genetic bottlenecks during the invasion process. Bayesian clustering analysis, based on nuclear markers, suggests the presence of three genetic clusters, all present in both US and ARG. Discriminant analysis of principal components (DAPC) detected an overall low population structure between central US and ARG populations but separated two invasive populations from the rest. ABC modelling supports multiple introductions but also a southward dispersal within ARG. Genetic and phenotypic data support the central US as a source of introduction while the source of secondary introductions could not be resolved. Finally, using genetic markers from the chloroplast genome, we found lower population structure in ARG when compared to US populations, suggesting a role for seed-mediated gene flow in Argentina.
Data from: Optimal lineage principle for age-structured populations
We present a formulation of branching and aging processes that allows distributions along lineages to be studied within populations, and provides a new interpretation of classical results in the theory of aging. We establish a variational principle for the stable age distribution along lineages. Using this optimal lineage principle, we show that the response of a population's growth rate to age-specific changes in mortality and fecundity – a key quantity which was first calculated by Hamilton – is given directly by the age distribution along lineages. We apply our method also to the Bellman-Harris process, in which both mother and progeny are rejuvenated at each reproduction event, and show that this process can be mapped to the classic aging process such that age statistics in the population and along lineages are identical. Our approach provides both a theoretical framework for understanding the statistics of aging in a population, and a new method of analytical calculations for populations with age structure. We discuss generalizations for populations with multiple phenotypes, and more complex aging processes. We also provide a first experimental test of our theory applied to bacterial populations growing in a microfluidics device.
Data from: Geographic structure and adaptive population differentiation in herbivore defense genes in European aspen (Populus tremula L., Salicaceae)
When a phenotypic trait is subjected to spatially variable selection and local adaptation, the underlying genes controlling the trait are also expected to show strong patterns of genetic differentiation because alternative alleles are favoured in different geographical locations. Here, we study 71 single nucleotide polymorphisms (SNPs) from seven genes associated with inducible defence responses in a sample of Populus tremula collected from across Sweden. Four of these genes (PPO2, TI2, TI4 and TI5) show substantial population differentiation, and a principal component analyses conducted on the defence SNPs divides the Swedish population into three distinct clusters. Several defence SNPs show latitudinal clines, although these were not robust to multiple testing. However, five SNPs (located within TI4 and TI5) show strong longitudinal clines that remain significant after multiple test correction. Genetic geographical variation, supporting local adaptation, has earlier been confirmed in genes involved in the photoperiod pathway in P. tremula, but this is, to our knowledge, one of the first times that geographical variation has been found in genes involved in plant defence against antagonists.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.