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289 results for “natural variation”
Data from: Climate-related adaptive genetic variation and population structure in natural stands of Norway spruce in the South-Eastern Alps
Forest trees dominate many Alpine landscapes that are currently exposed to changing climate. Norway spruce is one of the most important conifer species of the Italian Alps, and natural populations are found across steep environmental gradients with large differences in temperature and moisture availability. This study seeks to determine and quantify patterns of genetic diversity in natural populations toward understanding adaptive responses to changing climate. Across the Italian species range, 24 natural stands were sampled with a major focus on the Eastern Italian Alps. Sampled trees were genotyped for 384 selected single nucleotide polymorphisms (SNPs) from 285 genes. A wide array of potential candidate genes was tested for correlation with climatic parameters. To minimize false-positive association between genotype and climate, population structure was investigated. Pairwise F ST estimates between sampled populations ranged between 0.000 and 0.075, with the highest values involving the two disjoint populations, Valdieri, on the western Italian Alps, and Campolino, the most southern population on the Apennines. Despite considerable genetic admixture among populations, both Bayesian and multivariate approach identified four genetic clusters. Selection scans revealed five F ST outliers, and the environmental association analysis detected ten SNPs associated to one or more climatic variables. Overall, 13 potentially adaptive loci were identified, three of which have been reported in a previous study on the same species conducted on a broader geographical scale. In our study, precipitation, more than temperature, was often associated with genotype; therefore, it appears as the most important environmental variable associated with the high sensitivity of Norway spruce to soil water supply. These findings provide relevant information for understanding and quantifying climate change effects on this species and its ability to genetically adapt.
Data from: Is biotic resistance enhanced by natural variation in diversity?
Theories linking diversity to ecosystem function have been challenged by the widespread observation of more exotic species in more diverse native communities. Few studies have addressed the underlying processes by dissecting how biotic resistance to new invaders may be shaped by the same environmental influences that determine diversity and other community properties. In grasslands with heterogeneous soils, we added invaders and removed competitors to analyze the causes of invasion resistance. Abiotic resistance was measured using invader success in the absence of the resident community. Biotic resistance was measured as the reduction in invader success in the presence of the resident community. Invaders were most successful where biotic resistance was lowest and abiotic resistance was highest, confirming the dominant role of biotic resistance. Contrary to theory, though, biotic resistance was highest where both species richness and functional diversity were lowest. In the multivariate framework of a structural equation model, biotic resistance was independent of community diversity, and was highest where fertile soils led to high community biomass. Seed predation slightly augmented biotic resistance without qualitatively changing the results. Soil-related genotypic variation in the invader also did not affect the results. We conclude that in natural systems, diversity may be correlated with invasibility and yet have little effect on biotic resistance to invasion. More generally, the environmental causes of variation in diversity should be considered when examining the potential functional consequences of diversity.
Changing environments and genetic variation: natural variation in inbreeding does not compromise short-term physiological responses
<p>Selfing plant lineages are surprisingly widespread and successful in a broad range of environments, despite showing reduced genetic diversity, which is predicted to reduce long-term evolutionary potential. However, appropriate short-term plastic responses to new environmental conditions might not require high levels of standing genetic variation. In this study, we tested whether mating system variation among populations, and associated changes in genetic variability, affected short-term responses to environmental challenges. We compared relative fitness and metabolome profiles of naturally outbreeding (genetically diverse) and inbreeding (genetically depauperate) populations of a perennial plant, Arabidopsis lyrata, under constant growth chamber conditions and an outdoor common garden environment outside its native range. We found no effect of inbreeding on survival, flowering phenology or short-term physiological responses. Specifically, naturally occurring inbreeding had no significant effects on the plasticity of metabolome profiles, using either multivariate approaches or analysis of variation in individual metabolites, with inbreeding populations showing similar physiological responses to outbreeding populations over time in both growing environments. We conclude that low genetic diversity in naturally inbred populations may not always compromise fitness or short-term physiological capacity to respond to environmental change, which could help to explain the global success of selfing mating strategies.</p>
Data from: Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii
We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ∼3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates conservation of genes associated with core cellular functions, while genes in large gene families and poorly characterized genes show a greater incidence of major effect mutations. De novo assembly of unmapped reads recovered genes in the field isolates that are absent from the CC-503 assembly. The laboratory reference strains show a genomic pattern of polymorphism consistent with their origin as the recombinant progeny of a diploid zygospore. Large duplications or amplifications are a prominent feature of laboratory strains and appear to have originated under laboratory culture. Extensive natural variation offers a new source of genetic diversity for studies of Chlamydomonas, including naturally occurring alleles that may prove useful in studies of gene function and the dissection of quantitative genetic traits.
Data from: Wide variation in spatial genetic structure between natural populations of the European beech (Fagus sylvatica) and its implications for SGS comparability
Identification and quantification of spatial genetic structure (SGS) within populations remains a central element of understanding population structure at the local scale. Understanding such structure can inform on aspects of the species' biology, such as establishment patterns and gene dispersal distance, in addition to sampling design for genetic resource management and conservation. However, recent work has identified that variation in factors such as sampling methodology, population characteristics, and marker system can all lead to significant variation in SGS estimates. Consequently, the extent to which estimates of SGS can be relied upon to inform on the biology of a species or differentiate between experimental treatments is open to doubt. Following on from a recent report of unusually extensive SGS when assessed using amplified fragment length polymorphisms (AFLP) in the tree Fagus sylvatica, we explored whether this marker system led to similarly high estimates of SGS extent in other apparently similar populations of this species. In the three populations assessed, SGS extent was even stronger than this previously reported maximum, extending up to 360 m, an increase of up to 800% in comparison with the generally accepted maximum of 30 - 40 m based on the literature. Within this species, wide variation in SGS estimates exists, whether quantified as SGS intensity, extent, or the Sp parameter. Consequently, we argue that greater standardisation should be applied in sample design and SGS estimation and highlight five steps that can be taken to maximize the comparability between SGS estimates.
Variation at an adhesin locus suggests sociality in natural populations of the yeast Saccharomyces cerevisiae
<p>Microbes engage in numerous social behaviors that are critical for survival and reproduction, and that require individuals to act as a collective. Various mechanisms ensure that collectives are composed of related, cooperating cells, thus allowing for the evolution and stability of these traits, and for selection to favor traits beneficial to the collective. Since microbes are difficult to observe directly, sociality in natural populations can instead be investigated using evolutionary genetic signatures, as social loci can be evolutionary hotspots. The budding yeast has been studied for over a century, yet little is known about its social behavior in nature. Flo11 is a highly regulated cell adhesin required for most lab social phenotypes; studies suggest it may function in cell recognition and its heterogenous expression may be adaptive for collectives such as biofilms. We investigated this locus and found positive selection in the areas implicated in cell-cell interaction, suggesting selection for kin discrimination. We also found balancing selection at an upstream activation site, suggesting selection on the level of variegated gene expression. Our results suggest this model yeast is surprisingly social in natural environments and is likely engaging in various forms of sociality. By utilizing genomic data, this research provides a glimpse of otherwise unobservable interactions.</p>
Data from: Natural variation, differentiation and genetic tradeoffs of ecophysiological traits in response to water limitation in Brachypodium distachyon and its descendent allotetraploid B. hybridum (Poaceae)
Differences in tolerance to water stress may underlie ecological divergence of closely-related ploidy lineages. However, the mechanistic basis of physiological variation governing eco-geographical cytotype segregation is not well understood. Here, using Brachypodium distachyon and its derived allotetraploid B. hybridum as model, we test the hypothesis that, for heteroploid annuals, ecological divergence of polyploids in drier environments is based on trait differentiation enabling drought-escape. We demonstrate that under water limitation allotetraploids maintain higher photosynthesis and stomatal conductance and show earlier flowering than diploids, concordant with a drought-escape strategy to cope with water stress. Increased heterozygosity, greater genetic variability and plasticity of polyploids could confer a superior adaptive capability. Consistent with these predictions, we document (1) greater standing within-population genetic variation in water use efficiency and flowering time in allotetraploids, and (2) the existence of (non-linear) environmental clines in physiology across allotetraploid populations. Increased gas exchange and diminished WUE occurred at the driest end of the gradient, consistent with a drought-escape strategy. Finally, we found that allotetraploids showed weaker genetic correlations than diploids congruous with the expectation of relaxed pleiotropic constraints in polyploids. Our results suggest evolutionary divergence of ecophysiological traits in each ploidy lineage.
Data from: Differential hippocampal gene expression is associated with climate-related natural variation in memory and the hippocampus in food-caching chickadees
There is significant and often heritable variation in cognition and its underlying neural mechanisms, yet specific genetic contributions to such variation are not well characterized. Black-capped chickadees present a good model to investigate the genetic basis of cognition because they exhibit tremendous climate-related variation in memory, hippocampal morphology and neurogenesis rates throughout the North American continent, and these cognitive traits appear to have a heritable basis. We examined the hippocampal transcriptome profiles of laboratory-reared chickadees from the two most divergent populations to test whether differential gene expression in the hippocampus is associated with population differences in spatial memory, hippocampal morphology and adult hippocampal neurogenesis rates. Using high-resolution mRNA sequencing coupled to a de novo transcriptome assembly, we generated 23 295 consensus sequences, which predicted 16 206 protein sequences with 13 982 showing high similarity to known protein sequences or conserved hypothetical proteins in other species. Of these, we identified differential expression in nearly 380 genes, with 47 genes specifically linked to neurogenesis, apoptosis, synaptic function, and learning and memory processes. Many of the other differentially expressed genes, however, may be associated with other functions. Our study presents the first avian hippocampal transcriptome, and it is the first study identifying differential gene expression associated with natural variation in cognition and the hippocampus. Our results provide additional support to the hypothesis that population differences in memory, hippocampal morphology and neurogenesis in chickadees have likely resulted from natural selection that appears to act on memory and its underlying neural mechanisms.
Natural variation in the contribution of microbial density to inducible immune dynamics
Immune responses evolve to balance the benefits of microbial killing against the costs of autoimmunity and energetic resource use. Models that explore the evolution of optimal immune responses generally include a term for constitutive immunity, or the level of immunological investment prior to microbial exposure, and for inducible immunity, or investment in immune function after microbial challenge. However, studies rarely consider the functional form of inducible immune responses with respect to microbial density, despite the theoretical dependence of immune system evolution on microbe- versus immune-mediated damage to the host. In this study, we analyze antimicrobial peptide (AMP) gene expression from seven wild-caught flour beetle populations (Tribolium spp.) during acute infection with the virulent bacteria Bacillus thuringiensis (Bt) and Photorhabdus luminescens (P.lum) to demonstrate that inducible immune responses mediated by the humoral IMD pathway exhibit natural variation in both microbe density-dependent and independent temporal dynamics. Beetle populations that exhibited greater AMP expression sensitivity to Bt density were also more likely to die from infection, while populations that exhibited higher microbe density-independent AMP expression were more likely to survive P. luminescens infection. Reduction in pathway signaling efficiency through RNAi-mediated knockdown of the imd gene reduced the magnitude of both microbe-independent and dependent responses and reduced host resistance to Bt growth, but had no net effect on host survival. This study provides a framework for understanding natural variation in the flexibility of investment in inducible immune responses and should inform theory on the contribution of non-equilibrium host-microbe dynamics to immune system evolution.
Data from: Natural epigenetic variation contributes to heritable flowering divergence in a widespread asexual dandelion lineage
Epigenetic variation has been proposed to contribute to the success of asexual plants, either as a contributor to phenotypic plasticity or by enabling transient adaptation via selection on transgenerationally stable, but reversible, epialleles. While recent studies in experimental plant populations have shown the potential for epigenetic mechanisms to contribute to adaptive phenotypes, it remains unknown whether heritable variation in ecologically relevant traits is at least partially epigenetically determined in natural populations. Here, we tested the hypothesis that DNA methylation variation contributes to heritable differences in flowering time within a single widespread apomictic clonal lineage of the common dandelion (Taraxacum officinale s. lat.). Apomictic clone members of the same apomictic lineage collected from different field sites showed heritable differences in flowering time, which was correlated with inherited differences in methylation-sensitive AFLP marker profiles. Differences in flowering between apomictic clone members were significantly reduced after in vivo demethylation using the DNA methyltransferase inhibitor zebularine. This synchronization of flowering times suggests that flowering time divergence within an apomictic lineage was mediated by differences in DNA methylation. While the underlying basis of the methylation polymorphism at functional flowering time-affecting loci remains to be demonstrated, our study shows that epigenetic variation contributes to heritable phenotypic divergence in ecologically relevant traits in natural plant populations. This result also suggests that epigenetic mechanisms can facilitate adaptive divergence within genetically uniform asexual lineages.
FIGURE 20 in Taxonomic redefinition and natural history of the endemic silphid beetle Silpha longicornis (Coleoptera: Silphidae) of Japan, with an analysis of its geographic variation
FIGURE 20. Relationship between AMT and PC1. Females are indicated by open circles and the dashed line, and males are indicated by solid circles and the solid line.
FIGURE 19 in Taxonomic redefinition and natural history of the endemic silphid beetle Silpha longicornis (Coleoptera: Silphidae) of Japan, with an analysis of its geographic variation
FIGURE 19. Vertical distribution of Silpha longicornis Portevin based on the examined specimens (Appendix 1) and climatic vegetation zones. Solid line shows the maximum altitude along the transect. a—forest limit; b—border between evergreen coniferous and deciduous broad-leaved forests; c—hypothetical forest limit during the Last Glacial Maximum; d—hypothetical border between coniferous and broad-leaved forest during the Last Glacial Maximum. Modified from Nogami (2001: Fig. 4.2.1).
FIGURE 18 in Taxonomic redefinition and natural history of the endemic silphid beetle Silpha longicornis (Coleoptera: Silphidae) of Japan, with an analysis of its geographic variation
FIGURE 18. Geographic distribution of S. longicornis Portevin based on the examined specimens (Appendix 1) and mountain ranges. Contour interval 1,000 feet. 1—Ôu Mountains; 2—Shirakami Mountains; 3—Kitakami Hills; 4— Dewa Mountains; 5—Echigo Mountains; 6—Ôsado Mountains; 7—Chikuma Mountains; 8—Kantô Mountains; 9— Misaka Mountains; 10—Tanzawa Mountains; 11—Fuji Volcanoes; 12—Hida Mountains; 13—Kiso Mountains; 14— Akaishi Mountains; 15—Hida Hills; 16—Ryohaku Mountains; 17—Kii Mountains. Fossil sites (▲) are also shown.
FIGURE 17 in Taxonomic redefinition and natural history of the endemic silphid beetle Silpha longicornis (Coleoptera: Silphidae) of Japan, with an analysis of its geographic variation
FIGURE 17. SAMOVA grouping of population of Silpha longicornis Portevin (1–21) and S. imitator Shibata (22–23). Numbers are the sampling site numbers as described in Ikeda et al. (2009). Six symbols (●Ο□․♢♦) indicate the groups discriminated by SAMOVA.
FIGURES 1–16 in Taxonomic redefinition and natural history of the endemic silphid beetle Silpha longicornis (Coleoptera: Silphidae) of Japan, with an analysis of its geographic variation
FIGURES 1–16. Habitus of type specimens and labels (1–7): 1—Silpha longicornis Portevin, lectotype, Ψ, dorsal view; 2—same, labels; 3—Silpha yamatona Kôno, holotype, ♂, dorsal view (photo by S. Shimano); 4—same, labels (photo by S. Shimano); 5—Silpha imitator Shibata, holotype, ♂, dorsal view; 6—same, labels; 7—same, aedeagus in ventral view. Details of Silpha longicornis Portevin, showing variation of elytron color (8–9), and sculpture (10–13): 8—black specimen from Mt. Kurikoma, Iwate Pref.; 9—reddish-brown specimen from Mt. Kasa-ga-take, Nagano Pref. (with aberration of elytral costae); 10—rugose intervals; 11—flat intervals; 12—punctate microsculpture; 13—smooth microsculpture. Apex of male metatibia, showing terminal projection (14). Prothorax of larvae of Silpha perforata Gebler (15, from Moheji near Hakodate, S.W. Hokkaido) and Silpha longicornis Portevin (16, from Jikkoku-tôge, Nagano Pref.).
FIGURE 16 in Natural history and distribution of the enigmatic southern Appalachian opilionid, Fumontana deprehendor Shear (Laniatores: Triaenonychidae), with an assessment of morphological variation
FIGURE 16. Boxplot demonstrating the range of eye tubercle width for the different geographic regions of "predicted endemism".
FIGURE 17 in Natural history and distribution of the enigmatic southern Appalachian opilionid, Fumontana deprehendor Shear (Laniatores: Triaenonychidae), with an assessment of morphological variation
FIGURE 17. Results of the PCA of morphometric data taken from 25 characters (see appendix), with the two principal components explaining the greatest percentage of variation plotted against one another.
FIGURES 6–9 in Natural history and distribution of the enigmatic southern Appalachian opilionid, Fumontana deprehendor Shear (Laniatores: Triaenonychidae), with an assessment of morphological variation
FIGURES 6–9. Illustrations of the first legs of representative males from the four regions of "predicted endemism" (prolateral view). Corresponding localities indicated on Figure 1 by the following abbreviations: 6, BUMPUS; 7, FLATBR; 8, SHULER; 9, COLDMTN.
FIGURES 10–15 in Natural history and distribution of the enigmatic southern Appalachian opilionid, Fumontana deprehendor Shear (Laniatores: Triaenonychidae), with an assessment of morphological variation
FIGURES 10–15. SEM of F. deprehendor penes in ventral view (10–11, 13–15) and in ventrolateral view (12). Figures 10–11 shown to demonstrate typical morphology under optimal imaging conditions: 10, glans (FLATBR population); 11, setose lobes (FLATBR population). Figures 12–15 shown for the purpose of comparison across geographic regions: 12, NWPNF (BUMPUS population); 13, GSMR (FLATBR population); 14, JKFR (JOYCE population); 15, SWPNF (COWEEMTN population). Scale bars: 70 m (10), 100 m (11, 13–15), 200 m (12).
FIGURES 2–5 in Natural history and distribution of the enigmatic southern Appalachian opilionid, Fumontana deprehendor Shear (Laniatores: Triaenonychidae), with an assessment of morphological variation
FIGURES 2–5. Illustrations of pedipalps of representative males from the four regions of "predicted endemism" (prolateral view). Corresponding localities indicated on Figure 1 by the following abbreviations: 2, BUMPUS; 3, FLATBR; 4, SHULER; 5, COLDMTN.
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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.