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39 results for “contrast adaptation”
Contrasting plant adaptation strategies to latitude in the native and invasive range of Spartina alterniflora: geographic survey (2014) and Common garden (2015-2017)
We examined trait differences and evolution across geographic clines among continents of the intertidal grass Spartina alterniflora within its invasive and native ranges. Between September and November 2014, we sampled vegetative and reproductive traits in the field at 20 sites over 20° latitude in China (invasive range) and 28 sites over 17° latitude in the US (native range). We grew both Chinese and US plants in a greenhouse common garden for three years (2015 - 2017) to determine if differences in performance of S. alterniflora between the introduced and native ranges were due to genetic differences or differences in abiotic conditions.
Adaptation to distinct habitats is maintained by contrasting selection at different life stages in sunflower ecotypes
<p><span>Conspecific populations living in adjacent but contrasting microenvironments represent excellent systems for studying natural selection. These systems are valuable because gene flow is expected to force genetic homogeneity except at loci experiencing divergent selection. A history of reciprocal transplant and common garden studies in such systems, and a growing number of genomic studies, have contributed to understanding how selection operates in natural populations. While selection can vary across different fitness components and life stages, few studies have investigated how this ultimately affects allele frequencies and the maintenance of divergence between populations. Here, we study two sunflower ecotypes in distinct, adjacent habitats by combining demographic models with genome-wide sequence data to estimate fitness and allele frequency change at multiple life stages. This framework allows us to estimate that only local ecotypes are likely to experience positive population growth</span> <span>(λ>1) and that the maintenance of divergent adaptation appears to be mediated via habitat- and life-stage-specific selection. We identify genetic variation, significantly driven by loci in chromosomal inversions, associated with different life history strategies in neighbouring ecotypes that optimize different fitness components and may contribute to the maintenance of distinct ecotypes. </span></p>
Adaptation to distinct habitats is maintained by contrasting selection at different life stages in sunflower ecotypes
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Data from: Contrasting patterns of local adaptation along climatic gradients between a sympatric parasitic and autotrophic tree species
<p>Sympatric tree species are subject to similar climatic drivers, posing a question as to whether they display comparable adaptive responses. However, no study has explicitly examined local adaptation of co-occurring parasitic and autotrophic plant species to the abiotic environment. Here we test the hypotheses that a generalist parasitic tree would display a weaker signal of selection and genomic variation would associate with fewer climatic variables (particularly precipitation) but have similar spatial patterns to a sympatric autotrophic tree species. To test these hypotheses, we collected samples from 17 sites across the range of two tree species, the hemi-parasite <i>Nuytsia floribunda</i> (<i>n</i>=264) and sympatric autotroph<i> Melaleuca rhaphiophylla </i>(<i>n</i>=272). We obtained 5,531 high-quality genome-wide single nucleotide polymorphisms (SNPs) for <i>M. rhaphiophylla</i> and 6,727 SNPs for <i>N. floribunda</i> using DArTseq™ genome scan technology. Population differentiation and environmental association approaches were used to identify signals of selection. Generalized dissimilarly modelling was used to detect climatic and spatial patterns of local adaptation across climatic gradients. Overall, 322 SNPs were identified as putatively adaptive for the autotroph, while only 57 SNPs were identified for the parasitic species. We found genomic variation to associate with different sets of bioclimatic variables for each species, with precipitation relatively less important for the parasite. Spatial patterns of predicted adaptive variability were different and indicate that co-occurring species with disparate life history traits may not respond equally to selective pressures (i.e. temperature and precipitation). Together, these findings provide insight into local adaptation of sympatric parasitic and autotrophic tree species to abiotic environments.</p>
Data from: Adaptive maternal investment in the wild? Links between maternal growth trajectory and offspring size, growth, and survival in contrasting environments
Life history theory predicts that investment per offspring should correlate negatively with the quality of environment offspring are anticipated to encounter; parents may use their own experience as juveniles to predict this environment and may modulate offspring traits such as growth capacity as well as initial size. We manipulated nutrient levels in the juvenile habitat of wild Atlantic salmon Salmo salar to investigate the hypothesis that the egg size maximizing juvenile growth and survival depends on environmental quality. We also tested whether offspring traits were related to parental growth trajectory. Mothers that grew fast when young produced more, smaller offspring than mothers that had grown slowly to reach the same size. Despite their size disadvantage, offspring of faster-growing mothers grew faster than those of slow-growing mothers in all environments, counter to the expectation that they would be competitively disadvantaged. However, they had lower relative survival in environments where the density of older predatory/competitor fish was relatively high. These links between maternal (but not paternal) growth trajectory and offspring survival rate were independent of egg size, underscoring that mothers may be adjusting egg traits other than size to suit the anticipated environment faced by their offspring.
Regional and fine-scale local adaptation in salinity tolerance in Daphnia inhabiting contrasting clusters of inland saline waters
<p>Freshwater salinisation is an important threat to biodiversity, ecosystem functioning, and the provision of ecosystem services. Therefore, understanding the capacity of species to adapt to salinity gradients is crucial. Clusters of naturally saline habitats represent ideal test cases to study the extent and scale of local adaptation to salinisation. We studied local genetic adaptation of the water flea Daphnia magna, a key component of pond food webs, to salinity in two contrasting landscapes - a dense cluster of sodic bomb crater ponds and a larger-scale cluster of soda pans. We show regional differentiation in salinity tolerance reflecting the higher salinity levels of soda pans versus bomb crater ponds. We found local adaptation to differences in salinity levels at the scale of tens of metres among bomb crater pond populations but not among geographically more distant soda pan populations. The population-level salinity tolerance range was reduced in more saline bomb crater ponds through an upward shift of the minimum salt tolerance observed across clones and a consequent gradual loss of less tolerant clones in a nested pattern. Our results show genetic adaptation to salinity gradients at different spatial scales and fine-tuned local adaptation in neighbouring habitat patches in a natural landscape.</p>
Local climate adaptation and gene flow in the native range of two co-occurring fruit moths with contrasting invasiveness
<p><span class="fontstyle01"><span>Invasive species pose increasing threats to global biodiversity and ecosystems. While previous studies have characterized successful invaders from ecological traits, characteristics related to evolutionary processes have rarely been investigated. Here we compared gene flow and local adaptation using demographic analyses and outlier tests in two co-occurring moth pests across their common native range of China, one of which (the peach fruit moth, </span></span><span class="fontstyle01"><span><i>Carposina</i></span></span> <span class="fontstyle01"><span><i>sasakii</i></span></span><span class="fontstyle01"><span>) has maintained its native distribution, while the other (the oriental fruit moth, </span></span><span class="fontstyle01"><span><i>Grapholita molesta</i></span></span><span class="fontstyle01"><span>)</span></span><span class="fontstyle01"><span> has expanded its range globally during the past century. We found that both species showed a pattern of genetic differentiation and an evolutionary history consistent with a common southwestern origin and northward expansion in their native range. However, for the noninvasive species, genetic differentiation was closely aligned with the environment, and there was a relatively low level of gene flow, whereas in the invasive species, genetic differentiation was associated with geography. Genome scans </span></span><span class="fontstyle01"><span>indicated stronger patterns of climate-associated loci</span></span><span class="fontstyle01"><span> in the noninvasive species. While s</span></span><span class="fontstyle01"><span>trong local adaptation and reduced gene flow across its native range may have decreased the invasiveness of </span></span><span class="fontstyle01"><span><i>C. sasakii</i></span></span><span class="fontstyle01"><span>, this requires further validation with additional comparisons of invasive and non-invasive species across their native range.</span></span></p>
Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
<p class="MsoNormal"><strong><u><span>Aim:</span></u></strong><span> Discerning when, where, and how processes of isolation lead to differing biogeography is especially complex for marine species with similar ecological niches and within the same geographic location. We assessed population genetics of congeneric and ecologically similar damselfishes within their overlapping distributions and across potential barriers to geneflow.</span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Taxon:</span></u></strong><span> <em>Dascyllus marginatus </em>(endemic) and <em>Dascyllus abudafur </em>(widespread)<em>.</em></span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Location:</span></u></strong><span> Coral reefs from the Red Sea, Djibouti, Yemen, Oman, and Madagascar. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Methods:</span></u></strong><span> We used RADseq derived SNPs to investigate key differences in population genetics between both species and discuss barriers shaping genetic differentiation (neutral vs. selective) and biogeography. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Results:</span></u></strong><strong><span> </span></strong><em><span>Dascyllus marginatus </span></em><span>inhabited the Red Sea, the coasts of Yemen (including Socotra), and the Gulf of Oman. <em>Dascyllus abudafur</em> species was present from the Red Sea to Madagascar but was absent from Yemen and Oman. Populations of <em>D. marginatus </em>had an order of magnitude higher genetic differentiation compared to <em>D. abudafur</em>, as well as several outlier loci (suggesting selective pressure), which were absent in <em>D. abudafur</em> despite equal sampling locations. In both species, specimens from the Red Sea and Djibouti formed one genetic cluster separated from all other locations. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Main conclusions:</span></u></strong><span> The stronger genetic structure at smaller geographic scale of the endemic species seems associated to faster adaptation to environmental differences; whereas the widespread species only experienced reduced geneflow and neutral differentiation at much larger geographic scales. Restrictive transitions (between the Gulf of Aqaba and the Red Sea or the Red Sea and the Gulf of Aden) did not affect the genetic architecture of either species, while the environmental shift within the Red Sea (at 22°N/20°N) affected the endemic but not the widespread species. Samples from continental Yemen revealed that a genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes.</span></p>
Data and code from: Dynamics of cortical contrast adaptation predict perception of signals in noise
<p>Neurons throughout the sensory pathway adapt their responses depending on the statistical structure of the sensory environment. Contrast gain control is a form of adaptation in the auditory cortex, but it is unclear whether the dynamics of gain control reflect efficient adaptation, and whether they shape behavioral perception. Here, we trained mice to detect a target presented in background noise shortly after a change in the contrast of the background. The observed changes in cortical gain and behavioral detection followed the dynamics of a normative model of efficient contrast gain control; specifically, target detection and sensitivity improved slowly in low contrast, but degraded rapidly in high contrast. Auditory cortex was required for this task, and cortical responses were not only similarly affected by contrast but predicted variability in behavioral performance. Combined, our results demonstrate that dynamic gain adaptation supports efficient coding in auditory cortex and predicts the perception of sounds in noise.</p>
Data from: Contrasting patterns of local adaptation along climatic gradients between a sympatric parasitic and autotrophic tree species
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Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
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Data and code from: Dynamics of cortical contrast adaptation predict perception of signals in noise
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Data from: Contrasted patterns of local adaptation to climate change across the range of an evergreen oak, Quercus aquifolioides
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Local climate adaptation and gene flow in the native range of two co-occurring fruit moths with contrasting invasiveness
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Data from: Adaptive maternal investment in the wild? Links between maternal growth trajectory and offspring size, growth, and survival in contrasting environments
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Regional and fine-scale local adaptation in salinity tolerance in Daphnia inhabiting contrasting clusters of inland saline waters
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Contrasting biomass allocation responses across ontogeny and stress gradients reveal plant adaptations to drought and cold
How plants allocate their biomass to different organs is essential to understand plant adaptation and distribution. Overall, biomass allocation may follow fixed rules across taxa. They are also likely to exhibit substantial departure from these rules during ontogeny and in response to particular limiting factors to optimize their growth and maximize their survival. However, how plants adjust their allocation priorities depending on size and age across stress gradients remain largely unkown in wild populations. We examined ontogenetic variation in biomass allocation in Himalayan forb Potentilla pamirica across its 5250-5900 m elevation range, between populations from dry steppe, wet alpine and cold subnival zone. We tested whether biomass allocation followed optimal partitioning or fixed allometric rules using organ mass in 1019 individuals spanning 1-73 years. We found shifting biomass fractions with plant size and age, supporting the optimal partitioning theory. Young plants (<10 years) allocated similar proportions of biomass to leaves, stems, and roots, intermediate-aged plants (10-30 years) allocated more biomass to roots, while the oldest plants had 90% biomass in belowground stems. Major developmental processes including secondary thickening, branching and flowering begin 10-15 years earlier under more thermally favorable steppe conditions. Young steppe plants are larger than alpine and subnival plants, but these differences disappear in plants aged ~30, and the oldest alpine and subnival plants are larger than steppe plants. Plant age exerted significant control over biomass allocation after controlling for plant size. While in steppe plants the preference for stem biomass allocation increases with both size and age, for large alpine and subnival plants the stem prioritization decreases with age in favour of root and leaf mass fractions. We interpret the root and leaf prioritization in the oldest plants as a way to reduce carbon imbalances and the risk of frost damage to secure long life. Our analyses rejected ontogenetically fixed allometry and instead found high variation in biomass allocation depending on age, size and environment, supporting optimal partitioning theory. The uneven allocation of resources to different structures and functions during ontogenesis reflects plant adaptations to different levels of low-temperature and water stress across species elevation range.
Data from: Parental environmental effects due to contrasting watering adapt competitive ability, but not drought tolerance, in offspring of a semi-arid annual Brassicaceae
1. Parental effects (PE) can be adaptive and improve offspring performance when parents and offspring experience similar environmental conditions. However, it is unknown whether adaptive PE exist also in habitats where such similarity is unlikely due to strong temporal variation. In particular, we do not know whether PE can adapt offspring to fluctuating levels of neighbour competition in such habitats. 2. Here, we tested for adaptive PE in terms of two key environmental factors in a semi-arid annual system, competition and drought. While rainfall was stochastic in the study site, the competitive environment was partly predictable: higher plant densities followed after favourable (rainy) years due to high seed production. We therefore expected PE to adapt the offspring's competitive ability to these (predictable) fluctuations in plant densities, rather than to adapt the offspring's drought tolerance to the (unpredictable) occurrence of intensified drought. 3. Parental plants of Biscutella didyma, an annual Brassicaceae, were raised under favourable watering and under drought conditions. Offspring performance was then tested under a full-factorial combination of two neighbour regimes and six watering levels in the glasshouse. 4. Offspring of parents grown under favourable conditions were stronger competitors. This was associated with a small shift in phenology but not with higher parental seed provisioning. Offspring from parents grown under drought showed no improved drought tolerance. Moreover, no PE were detectable when offspring were grown without neighbours. 5. Our results suggest a novel path of adaptive PE: higher competitive ability was induced in offspring that were more likely to experience high neighbour densities. Together with the lack of adaptive PE towards drought tolerance, this emphasizes that a correlation between parental and offspring environment is crucial for adaptive PE to evolve. Our results also call for the inclusion of competitive effects in future PE studies. 6. Synthesis. This study demonstrates the important role of adaptive PE for plant fitness (regarding competition) but also their limits (regarding drought) in temporally variable environments, based on the predictability of the respective environmental factor.
Data from: Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments
<p>Understanding how eco-evolutionary processes and environmental factors drive population differentiation and adaptation are key challenges in evolutionary biology of relevance for biodiversity protection. Differentiation requires at least partial reproductive separation, which may result from different modes of isolation such as geographic isolation (allopatry) or isolation by distance (IBD), resistance (IBR), and environment (IBE). Despite that multiple modes might jointly influence differentiation, studies that compare the relative contributions are scarce. Using RADseq, we analyse neutral and adaptive genetic diversity and structure in 11 pike (<i>Esox lucius</i>) populations along a latitudinal gradient (54.9 - 63.6°N), to investigate the relative effects of IBD, IBE and IBR, and to assess whether the effects differ between neutral and adaptive variation, or across structural levels. Patterns of neutral and adaptive variation differed, likely reflecting that they have been differently affected by stochastic and deterministic processes. The importance of the different modes of isolation differed between neutral and adaptive diversity, yet were consistent across structural levels. Neutral variation was influenced by interactions among all three modes of isolation, with IBR (seascape features) playing a central role, wheares adaptive variation was mainly influenced by IBE (environmental conditions). Taken together, this and previous studies suggest that it is common that multiple modes of isolation interactively shape patterns of genetic variation, and that their relative contributions differ among systems. To enable identification of general patterns and understand how various factors influence the relative contributions, it is important that several modes are simultaneously investigated in additional populations, species and environmental settings.</p>
Data from: Latitudinal divergence in a wide-spread amphibian: contrasting patterns of neutral and adaptive genomic variation
Stochastic effects from demographic processes and selection are expected to shape the distribution of genetic variation in spatially heterogeneous environments. As the amount of genetic variation is central for long-term persistence of populations, understanding how these processes affect variation over large-scale geographic gradients is pivotal. We investigated the distribution of neutral and putatively adaptive genetic variation, and reconstructed demographic history in the moor frog (Rana arvalis) using 136 individuals from 15 populations along a 1700 km latitudinal gradient from northern Germany to northern Sweden. Using ddRAD-seq we obtained 27590 SNPs, and identified differentiation outliers and SNPs associated with growing season length. Populations grouped into a southern and a northern cluster, representing two phylogeographical lineages from different post-glacial colonization routes. Hybrid index estimation and demographic model selection showed strong support for a southern and northern lineage and evidence of gene flow between regions located on each side of a contact zone. However, patterns of past gene flow over the contact zone differed between neutral and putatively adaptive SNPs. While neutral nucleotide diversity was higher along the southern than the northern part of the gradient, nucleotide diversity in differentiation outliers showed the opposite pattern suggesting differences in the relative strength of selection and drift along the gradient. Variation associated with growing season length decreased with latitude along the southern part of the gradient, but not along the northern part where variation was lower, suggesting stronger climate-mediated selection in the north. Outlier SNPs included loci involved in immunity and developmental processes.
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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.