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1,068 results for “demographic”
Demographic analysis of invasible habitat fraction identifies context-dependent roles of resource availability and biotic resistance in determining invasion success
<p>Theories of plant invasions predict that plant communities should be more easily invaded when resources increase and/or competition decreases. We tested this with an experimentally introduced plant population by manipulating precipitation and resident community biomass. We used a spatially-explicit demographic approach to develop a new population-level metric of invasibility that quantifies the invasible habitat fraction (IHF) across the landscape.</p> <p>The existing community was essentially uninvasible (median IHF ≈ 0%), but experimental manipulations greatly increased the range of outcomes, with maximum observed IHF values over 50%. However, changes in invasibility were often context-dependent, resulting in some outcomes that aligned with existing theory, and others that were not readily predicted. Moreover, variation in invasibility was often driven by specific sets of invader demographic vital rates.</p> <p>Removing competitors revealed the capacity for strong biotic resistance, but this interacted with precipitation such that little biotic resistance was detected under drought conditions. Adding precipitation typically had little positive effect on invasibility, and moderate drought relief led to relatively high invasibility. However, the latter was driven to a large extent by interactions with mammal herbivory that otherwise inhibited invasion in one year.</p> <p><i>Synthesis</i>. Our findings show that interactions between abiotic and biotic factors, as well as legacy effects, can strongly mediate invasibility. This study also highlights the importance of incorporating spatial heterogeneity into population-level assessments of invasion, as initial population declines do not necessarily indicate resistance to invasion.</p>
Forest inventory data from Finland and Sweden for: Demographic performance of European tree species at their hot and cold climatic edges, plus ancillary climate data
<p>1. Species range limits are thought to result from a decline in demographic performance at range edges. However, recent studies reporting contradictory patterns in species demographic performance at their edges cast doubt on our ability to predict climate change demographic impacts. To understand these inconsistent demographic responses at the edges, we need to shift the focus from geographic to climatic edges and analyse how species responses vary with climatic constraints at the edge and species' ecological strategy.</p> <p>2. Here we parameterised integral projection models with climate and competition effects for 27 tree species using forest inventory data from over 90,000 plots across Europe. Our models estimate size-dependent climatic responses and evaluate their effects on two life trajectory metrics: lifespan and passage time - the time to grow to a large size. Then we predicted growth, survival, lifespan, and passage time at the hot and dry or cold and wet edges and compared them to their values at the species climatic centre to derive indices of demographic response at the edge. Using these indices, we investigated whether differences in species demographic response between hot and cold edges could be explained by their position along the climate gradient and functional traits related to their climate stress tolerance.</p> <p>3. We found that at cold and wet edges of European tree species, growth and passage time were constrained, whereas at their hot and dry edges, survival and lifespan were constrained. Demographic constraints at the edge were stronger for species occurring in extreme conditions, i.e. in hot edges of hot-distributed species and cold edges of cold-distributed species. Species leaf nitrogen content was strongly linked to their demographic responses at the edge. In contrast, we found only weak links with wood density, leaf size, and xylem vulnerability to embolism.</p> <p>4. Synthesis. Our study presents a more complicated picture than previously thought with demographic responses that differ between hot and cold edges. Predictions of climate change impacts should be refined to include edge and species characteristics.</p>
Data from: Contrasting population structure and demographic history of cereal aphids in different environmental and agricultural landscapes
<p>Single Nucleotide Polymorphisms files and phylogonetic trees of S. miscanthi samples collected in China and S. avenae from the UK used to study the population genetics analyses of these species. These are:</p> <p>China_samples_vcf.zip: dataset of SNPs from S. miscanthi sampled in 10 populations of China obtained using FreeBayes (in vcf format).</p> <p>China_samples_vcf_filtered.zip: SNPs from S. miscanthi after filtering the file China_samples_vcf.zip using vcftools (max-missing 0.75, minDP 3, mac 3, minQ 30, remove-indels, thin 2000, max-missing 0.9, thin 5000). This file was used in all population genetic analyses of the Chinese populations in the paper, transforming to the appropriate formats.</p> <p>China_samples_SNPs.fas: fasta file of phased SNPs used to estimate the phylogeny of S. miscanthi haplotypes using RAxML.</p> <p>China_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format obtained with China_samples_SNPs.fas.</p> <p>England_samples_vcf.zip: dataset of SNPs from S. avenae sampled in 12 populations of England obtained using FreeBayes (in vcf format).</p> <p>England_samples_vcf_filtered.zip: SNPs from S. avenae after filtering the file England_samples_vcf.zip using vcftools (max-missing 0.5, mac 3, minQ 30, minDP 3, max-missing 0.5, exclude individuals with 50% missing data, max-missing 0.75, remove-indels, thin 2000). This file was used in all population genetic analyses of the English populations in the paper, transforming the vcf to the corresponding formats.</p> <p>England_samples_SNPs.fas: fasta file of phased SNPs.</p> <p>England_samples_SNPs_polymorphic.fas: fasta file of phased SNPs used in the phylogenetic reconstruction of S. avenae haplotypes using RAxML. This file is the same as England_samples_SNPs.fas after removing sites which were not polymorphic (e.g. a site that contains N and T in different samples is not considered polymorphic for RAxML and has to be removed)</p> <p>England_RAxML_phylogeny_newick.tre: RAxML phylogenetic tree in newick format obtained with England_samples_SNPs_polymorphic.fas.</p>
Contrasting responses to climate change at Himalayan treelines revealed by population demographics of two dominant species
<ol> <li><span>Alpine treelines are expected to shift upward due to recent climate change. However, interpretation of changes in montane systems has been problematic because effects of climate change are frequently confounded with those of land use changes. The eastern Himalaya, particularly Langtang National Park, Central Nepal, has been relatively undisturbed for centuries and thus presents an opportunity for studying climate change impacts on alpine treeline uncontaminated by potential confounding factors.</span></li> <li><span>We studied two dominant species, <i>Abies spectabilis </i>and <i>Rhododendron campanulatum</i>, above and below the treeline on two mountains. We constructed 13 transects, each spanning up to 400m in elevation, in which we recorded height and state (dead or alive) of all trees, as well as slope, aspect, canopy density, and measures of anthropogenic and animal disturbance. In a subset of individuals, we determined the age of the plants with tree rings.</span></li> <li>All size classes of <i>R. campanulatum</i> plants had lower mortality above treeline than below it, and young <i>R. campanulatum</i> plants (<2m tall) were at higher density above treeline than below. <i>A. spectabilis</i> shows little evidence of a position change from the historic treeline, with a sudden extreme drop in density above treeline compared to below. Recruitment, as measured by size class distribution, was greater above treeline than below for both species but <i>A. spectabilis</i> is confined to ~25m above treeline whereas <i>R. campanulatum</i> is luxuriantly growing up to 200m above treeline. </li> <li> <i>Synthesis.</i> Evidence suggests that the elevational limits of <i>R. campanulatum</i> have shifted upward both because (1) young <i>R. campanulatum</i> plants above treeline benefited from facilitation of recruitment by surrounding vegetation, allowing upward expansion of recruitment, and (2) increased adult survival due to a general temperature amelioration to mature plants. We predict that the current pure stand of <i>R. campanulatum</i> growing above treeline will be colonized by <i>A. spectabilis</i> that will, in turn, outshade and eventually relegate <i>R. campanulatum </i>to be a minor component of the community, as is the current situation below the treeline. </li> </ol>
The demographic contributions of connectivity versus local dynamics to population growth of an endangered bird
<p>1. Conservation and management increasingly focus on connectivity, because connectivity driven by variation in immigration rates across landscapes is thought to be crucial for maintaining local population and metapopulation persistence. Yet, efforts to quantify the relative role of immigration on population growth across the entire range of species and over time have been lacking.</p> <p>2. We assessed whether immigration limited local and range-wide population growth of the endangered snail kite (Rostrhamus sociabilis) in Florida, USA, over 18 years using multi-state, reverse-time modeling that accounts for imperfect detection of individuals and unobservable states. Demographic contributions of immigration varied depending on the dynamics and geographic position of the local populations, were scale-dependent, and changed over time.</p> <p>3. By comparing the relative contributions of immigration versus local demography for periods of significant change in local abundance, we found empirical evidence for a disproportionately large role of immigration in facilitating population growth of a centrally-located population—a connectivity 'hub'. The importance of connectivity changed depending of the spatial scale considered, such that immigration was more important driver of population growth at small versus large spatial scales. Furthermore, the contribution of immigration was much greater during time periods when local population size was small, emphasizing abundance-dependent rescue effects.</p> <p>4. Our findings suggest that efforts aimed at improving local breeding habitat will likely be most effective at increasing snail kite population growth. More broadly, our results provide much needed information on the role of connectivity for population growth, suggesting that connectivity conservation may have the greatest benefits when efforts focus on centrally located habitat patches and small populations. Furthermore, our results highlight that connectivity is highly dynamic over time and that interpreting the effects of connectivity at local scales may not transfer to region-wide dynamics.</p>
Demographic and growth rings data of Pentaclethra macrolona in the Amazon River estuary
<p>Little is known about the natural history of the hyperdominant Amazonian tree <em>Pentaclethra macroloba</em>. It has multiple uses and is widely explored, due to the important phytotherapy properties of the oil of its seeds. We determined the demographic and growth patterns of <em>P. macroloba</em> and analyzed the influence of the daily tide in its growth trajectory. We studied populations of <em>P. macroloba</em> in the APA and CEM, northeast of the Brazilian Amazon. In 136.59 ha of the APA, all adult trees with diameter ≥ 5 cm were quantified and two plots of 1 ha each were installed for sampling of the regeneration (diameter < 5 cm). Samples of the radial wood of 38 trees were obtained to determine age and growth rates, through dendrochronological analyzes. In CEM, exchange activity of 30 trees, at different topographic levels, was monitored by dendrometer bands. The effect of precipitation, temperature and flood on the exchange activity of <em>P. macroloba</em> was evaluated using multiple regressions. We model the growth of the species based on the widths of its growth rings. We invented 2,072 adult trees (15 individuals ha<sup>-1</sup>), distributed in 12 diametric classes (log-normal pattern), mean diameter of 23 cm, total basal area 98.13 m², height mean of 12.7 m and aggregate distribution pattern (R = 0.63, p <0.002). 240 regenerants (120 individuals ha-1) were quantified, distributed in nine diametric classes (negative exponential pattern), mean height of 0.63 m and aggregate pattern. Growth rings formed by marginal parenchyma show maximum age of 102 years and mean of 60 years for <em>P. macroloba</em>. The relationship between age and diameter was highly significant (r<sup>2</sup> = 0.98; p <0.001), as well as the relationship between height and diameter (r<sup>2</sup> = 0.79; p <0.001). The growth models show increment peaks in diameter and height at the age of 46 years (9.38 mm year<sup>-1</sup>) and 20 years (48.2 cm year<sup>-1</sup>) respectively. Greatest accumulation of biomass occurred at the age of 66 years (40.8 kg year<sup>-1</sup>). <em>P. macroloba</em> presents exchange dormancy in the rainy season (t = -2.62; p <0.01) and of river flooding (t = -3.01; p < 0.01). The existence of rings in <em>P. macroloba</em> is an important discovery, as only <em>Mora paraensis</em> had growth rings record in the Amazon estuary. The structural and growth patterns of <em>P. macroloba</em> are reflections of its life history and interactions with the environmental dynamics of estuarine floodplain.</p>
Using demographic model selection to untangle allopatric divergence and diversification mechanisms in the Rheum palmatum complex in the Eastern Asiatic Region
<p>Allopatric divergence is often initiated by geological uplift and restriction to sky-islands, climate oscillations, or river capture. However, it can be difficult to establish which mechanism was the most likely to generate the current phylogeographic structure of a species. Recently, genomic data in conjunction with a model testing framework have been applied to address this issue in animals. To test whether such an approach is also likely to be successful in plants we used population genomic data of the <i>Rheum palmatum</i> complex from the Eastern Asiatic Region, in conjunction with biogeographical reconstruction and demographic model selection to identify the potential mechanism(s) which have led to the current level of divergence. Our results indicate that the <i>R. palmatum</i> complex originated in the central Hengduan Mts. and possibly in regions further to the east, and then dispersed westward and eastward resulting in genetically distinct lineages. Populations are likely to have diverged in refugia during climate oscillations followed by subsequent expansion and secondary contact. However, model simulations within the western lineage of the <i>R. palmatum</i> complex cannot reject a restriction to sky-islands as a possible mechanism of diversification due to the genetically ambiguous position of one population. This highlights that genetically mixed populations might introduce ambiguity regarding the best diversification model in some cases. Although it might be possible to resolve this ambiguity using other data, sometimes this could prove to be difficult in complex biogeographic areas.</p>
Phylogeographic and demographic modelling analyses of the multiple origins of the rheophytic goldenrod Solidago yokusaiana
<p>Understanding adaptation mechanisms is important in evolutionary biology. Parallel adaptation provides good opportunities to investigate adaptive evolution. To confirm parallel adaptation, it is effective to examine whether the phenotypic similarity has one or multiple origins and to use demographic modelling to consider the gene flow between ecotypes. <i>Solidago yokusaiana</i> is a rheophyte endemic to the Japanese Archipelago that diverged from <i>Solidago virgaurea</i>. This study examined the parallel origins of <i>S. yokusaiana</i> by distinguishing between multiple and single origins and subsequent gene flow. The haplotypes of non-coding chloroplast DNA and genotypes at 14 nuclear simple sequence repeat (nSSR) loci and single nucleotide polymorphisms (SNPs) revealed by double-digest restriction-associated DNA sequencing (ddRADseq) were used for phylogeographic analysis; the SNPs were also used to model population demographics. Some chloroplast haplotypes were common to <i>S. yokusaiana</i> and its ancestor <i>S. virgaurea</i>. Also, the population genetic structures revealed by nSSR and SNPs did not correspond to the taxonomic species. The demographic modelling supported the multiple origins of <i>S. yokusaiana</i> in at least four districts and rejected a single origin with ongoing gene flow between the two species, implying that <i>S. yokusaiana</i> independently and repeatedly adapted to frequently flooding riversides.</p>
Data from: Where and how to restore in a changing world: a demographic-based assessment of resilience
Managers are increasingly looking to apply concepts of resilience to better anticipate and understand conservation and restoration in a changing environment. In this study, we explore how information on demography (recruitment, growth and survival) and competitive effects in different environments and with different starting species abundances can be used to better understand resilience. We use observational and experimental data to better understand dynamics between native Stipa pulchra and exotic Avena barbata and fatua, grasses characteristic of native and invaded grasslands in California, at three different levels of nitrogen (N) representative of a range of pollution via atmospheric deposition. A modelling framework that incorporates this information on demography and competition allows us to forecast dynamics over time. Our results showed that resilience of native grasslands depends on N inputs, where natural recovery should be possible at low N levels whereas native persistence would be difficult at high N levels. Hysteresis was evident at moderate N levels, where the starting conditions mattered. Synthesis and applications. The resilience of both invaded and native grasslands is influenced by nitrogen inputs. Our modelling approach gives direction about how best to allocate limited management resources as baselines shift: where natural recovery is possible, where best to allocate active restoration efforts, and where native remnants may be most vulnerable.
Data from: The roots of the drought: hydrology and water uptake strategies mediate forest-wide demographic response to precipitation
Drought-induced tree mortality is expected to increase globally due to climate change, with profound implications for forest composition, function and global climate feedbacks. How drought is experienced by different species is thought to depend fundamentally on where they access water vertically below ground, but this remains untracked so far due to the difficulty of measuring water availability at depths at which plants access water (few to several tens of meters), the broad temporal scales at which droughts at those depths unfold (seasonal to decadal), and the difficulty in linking these patterns to forest-wide species-specific demographic responses. We address this problem through a new eco-hydrological framework: we used a hydrological model to estimate belowground water availability by depth over a period of two decades that included a multi-year drought. Given this water availability scenario and 20yr long-records of species-specific growth patterns, we inversely estimated the relative depths at which 12 common species in the forest accessed water via a model of water-stress. Finally, we tested whether our estimates of species relative uptake depths predicted mortality in multi-year drought. The hydrological model revealed clear belowground niches as precipitation was decoupled from water availability by depth at multi-annual scale. Species partitioned the hydrological niche by diverging in their uptake depths and so in the same forest stand, different species experienced very different drought patterns, resulting in clear differences in species-specific growth. Finally, species relative water uptake depths predicted species mortality patterns after the multi-year drought. Species that our method ranked as relying on deeper water were the ones that had suffered from greater mortality, as the zone from which they access water took longer to recharge after depletion. This research changes our understanding of how hydrological niches operate for trees with a trade-off between realized growth potential and survival under drought with decadal scale return time. The eco-hydrological framework highlights the importance of species-specific below ground strategies in predicting forest response to drought. Applying this framework more broadly may help us better understand species-coexistence in diverse forest communities and improve mechanistic predictions of forests productivity and compositional change under future climate.
Data from: Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil
Many studies propose that Quaternary climatic cycles contracted and /or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single-locus data we can now perform large-scale analyses, both in terms of number of species and geographic scope. Here we first compared the power of four alternative hABC models for a collection of single-locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Secondly, we applied the hABC models to a dataset of 7 squamate and 4 amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in Northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric-adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the expansion of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest.
Data from: Population genomics and demographic sampling of the ant-plant Vachellia drepanolobium and its symbiotic ants from sites across its range in East Africa.
The association between the African ant plant, Vachellia drepanolobium, and the ants that inhabit it has provided insight into the boundaries between mutualism and parasitism, the response of symbioses to environmental perturbations, and the ecology of species coexistence. We use a landscape genomics approach at sites sampled throughout the range of this system in Kenya to investigate the demographics and genetic structure of the different partners in the association. We find that different species of ant associates of V. drepanolobium show striking differences in their spatial distribution throughout Kenya, and these differences are only partly correlated with abiotic factors. A comparison of the population structure of the host plant and its three obligately arboreal ant symbionts, Crematogaster mimosae, Crematogaster nigriceps, and Tetraponera penzigi, shows that the ants exhibit somewhat similar patterns of structure throughout each of their respective ranges, but that this does not correlate in any clear way with the respective genetic structure of the populations of their host plants. A lack of evidence for local coadaptation in this system suggests that all partners have evolved to cope with a wide variety of biotic and abiotic conditions.
Data from: The demographic effects of functional traits: an integral projection model approach reveals population-level consequences of reproduction-defense tradeoffs
Quantitatively linking individual variation in functional traits to demography is a necessary step to advance our understanding of trait-based ecological processes. We constructed a population model for Asclepias syriaca to identify how functional traits affect vital rates and population growth and whether tradeoffs in chemical defense and demography alter population growth. Plants with higher foliar cardenolides had lower fiber, cellulose, and lignin levels, as well as decreased sexual and clonal reproduction. Average cardenolide concentrations had the strongest effect on population growth. In both the sexual and clonal pathway, the tradeoff between reproduction and defense affected population growth. We found that both increasing the mean of the distribution of individual plant values for cardenolides and herbivory decreased population growth. However, increasing the variance in both defense and herbivory increased population growth. Functional traits can impact population growth and quantifying individual-level variation in traits should be included in assessments of population-level processes.
Data from: Asynchronous demographic responses to Pleistocene climate change in Eastern Nearctic vertebrates
Pleistocene climatic cycles altered species distributions in the Eastern Nearctic of North America, yet the degree of congruent demographic response to the Pleistocene among codistributed taxa remains unknown. We use a hierarchical approximate Bayesian computational approach to test if population sizes across lineages of snakes, lizards, turtles, mammals, birds, salamanders and frogs in this region expanded synchronously to Late Pleistocene climate changes. Expansion occurred in 75% of 74 lineages, and of these, population size trajectories across the community were partially synchronous, with coexpansion found in at least 50% of lineages in each taxonomic group. For those taxa expanding outside of these synchronous pulses, factors related to when they entered the community, ecological thresholds or biotic interactions likely condition their timing of response to Pleistocene climate change. Unified timing of population size change across communities in response to Pleistocene climate cycles is likely rare in North America.
Data from: Plant demographic and functional responses to management intensification: a long-term study in a Mediterranean rangeland
1. Understanding how functional traits, which are key for plant functioning, relate to demographic parameters of populations is central to tackle pending issues in plant ecology such as the forecast of the fate of populations and communities in a changing world, the quantification of community assembly processes or the improvement of species distribution models. We addressed this question in the case of species from a Mediterranean rangeland of southern France. 2. Changes in species abundance in response to management intensification (fertilization and increased grazing pressure) were followed over a 28-year period. Probabilities of presence, and elasticities of the changes in the probability of space occupancy to colonization and survival, which are analogues of demographic parameters, were calculated for 53 species from the time series of abundance data using a space occupancy model. Nine quantitative traits pertaining to resource use, plant morphology, regeneration and phenology were measured on these species and related to demographic parameters. 3. The long-term dynamics of species in response to management intensification was associated with major changes in functional traits and strategies. Changes in the probability of occurrence – analogous to population growth rate - were correlated with traits describing the fast-slow continuum of leaf functioning. The elasticity of population growth rate to colonization was significantly related to reproductive plant height and seed mass, and to a lower extent, to leaf carbon isotopic ratio. 4. Synthesis. The functional response of species to management intensification corresponds to a shift along the second axis of a recently identified global spectrum of plant form and function, which maps, to some extent, onto the fast-slow continuum of life-history strategies. By contrast, the elasticity of colonization relates to the global spectrum axis capturing the size of organs. Seed mass contributes to this axis and is assumed to relate to one of the important traits structuring the reproductive strategy axis of life histories as well, namely net reproductive rate. While this mapping between functional and life-history traits is appealing, further tests in contrasting types of communities are required to assess its degree of generality.
Data from: Declining demographic performance and dispersal limitation influence the geographic distribution of the perennial forb, Astragalus utahensis (fabaceae)
1. A central goal of ecology is understanding the determinants of species' distributions. 'Metapopulation' models for the existence of distributional boundaries predict that species' geographic ranges arise from the landscape-scale deterioration of habitat suitability towards the range edge (i.e. niche mechanisms), which simultaneously hinders demographic performance and limits dispersal to suitable habitat beyond the edge (i.e. dispersal limitation). However, few studies have examined both of these mechanisms for the same species by examining abundance and comprehensive measures of demographic performance across the distribution and beyond its boundary. 2. We tested the predictions of metapopulation models for range limits by contrasting abundance, demographic performance, and population growth (λ) of the perennial forb Astragalus utahensis in central and northern range edge populations. We tested for dispersal limitation by transplanting individuals at and beyond the northern range boundary and monitoring their demographic performance. 3. Astragalus abundance and stochastic λ decreased from the range center to the northern range edge, with stochastic λ falling to or below replacement in range edge populations. However, transplants at some sites beyond the northern range edge survived and reproduced at levels similar to transplants within the range. Thus, in addition to deteriorating conditions at the range edge, dispersal limitation appears to contribute to limiting A. utahensis' northern distribution. 4. Synthesis: Our results support metapopulation models for range limits by suggesting that decreased demographic performance constrains the viability of range edge populations while contributing to dispersal limitation of A. utahensis' distribution. Thus, the tandem action of niche and dispersal processes appears to play an important role in constraining this species' northern latitudinal range.
Data from: Evaluating mechanisms of diversification in a Guineo-Congolian tropical forest frog using demographic model selection
The accumulation of biodiversity in tropical forests can occur through multiple allopatric and parapatric models of diversification, including forest refugia, riverine barriers and ecological gradients. Considerable debate surrounds the major diversification process, particularly in the West African Lower Guinea forests, which contain a complex geographic arrangement of topographic features and historical refugia. We used genomic data to investigate alternative mechanisms of diversification in the Gaboon forest frog, Scotobleps gabonicus, by first identifying population structure and then performing demographic model selection and spatially explicit analyses. We found that a majority of population divergences are best explained by allopatric models consistent with the forest refugia hypothesis and involve divergence in isolation with subsequent expansion and gene flow. These population divergences occurred simultaneously and conform to predictions based on climatically stable regions inferred through ecological niche modelling. Although forest refugia played a prominent role in the intraspecific diversification of S. gabonicus, we also find evidence for potential interactions between landscape features and historical refugia, including major rivers and elevational barriers such as the Cameroonian Volcanic Line. We outline the advantages of using genomewide variation in a model-testing framework to distinguish between alternative allopatric hypotheses, and the pitfalls of limited geographic and molecular sampling. Although phylogeographic patterns are often species-specific and related to life-history traits, additional comparative studies incorporating genomic data are necessary for separating shared historical processes from idiosyncratic responses to environmental, climatic and geological influences on diversification.
Data from: Demographic model selection using random forests and the site frequency spectrum
Phylogeographic data sets have grown from tens to thousands of loci in recent years, but extant statistical methods do not take full advantage of these large data sets. For example, approximate Bayesian computation (ABC) is a commonly used method for the explicit comparison of alternate demographic histories, but it is limited by the "curse of dimensionality" and issues related to the simulation and summarization of data when applied to next-generation sequencing (NGS) data sets. We implement here several improvements to overcome these difficulties. We use a Random Forest (RF) classifier for model selection to circumvent the curse of dimensionality and apply a binned representation of the multidimensional site frequency spectrum (mSFS) to address issues related to the simulation and summarization of large SNP data sets. We evaluate the performance of these improvements using simulation and find low overall error rates (~7%). We then apply the approach to data from Haplotrema vancouverense, a land snail endemic to the Pacific Northwest of North America. Fifteen demographic models were compared, and our results support a model of recent dispersal from coastal to inland rainforests. Our results demonstrate that binning is an effective strategy for the construction of a mSFS and imply that the statistical power of RF when applied to demographic model selection is at least comparable to traditional ABC algorithms. Importantly, by combining these strategies, large sets of models with differing numbers of populations can be evaluated.
Data from: Demographic costs and benefits of natural regeneration during tropical forest restoration
For tropical forest restoration to result in long‐term biodiversity gains, native trees must establish self‐sustaining populations in degraded sites. While many have asked how seedling recruitment varies between restoration treatments, the long‐term fate of these recruits remains unknown. We address this research gap by tracking natural recruits of 27 species during the first 7 years of a tropical forest restoration experiment that included both planted and naturally regenerating plots. We used an individual‐based model to estimate the probability that a seedling achieves reproductive maturity after several years of growth and survival. We found an advantage for recruits in naturally regenerating plots, with up to 40% increased probability of reproduction in this treatment, relative to planted plots. The demographic advantage of natural regeneration was highest for mid‐successional species, with relatively minor differences between treatments for early‐successional species. Our research demonstrates the consequences of restoration decision making across the life cycle of tropical tree species.
Data from: Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)
Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed latitudinally, effective population size was highest in the north, followed by south and centre, and LD was highest in the south followed by the north and centre, suggesting a possible northern glacial refuge. FST outlier analysis revealed that promoter, 5′-UTR and intronic sites were enriched for outliers compared with coding regions, while no outliers were found among intergenic sites. Codon usage bias was evident, and genes with synonymous outliers had 30% higher average expression compared with genes containing replacement outliers. These results suggest divergent selection related to regulation of gene expression is important to local adaptation in P. trichocarpa. Finally, within-population selective sweeps were much more pronounced in the central population than in putative northern and southern refugia, which may reflect the different demographic histories of the populations and concomitant effects on signatures of genetic hitchhiking from standing variation.
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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
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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
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