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16 results for “assembly history”
Data for "Ecosystem size filters life-history strategies to shape community assembly in lakes"
<p>Dataset 1. List of 71 fish species collected from north temperate lakes in Wisconsin USA. Data include critical life-history data used for strategy classifications according to Winemiller and Rose (1992), principal component scores, and strategy classification according to the cluster analysis.</p> <p>Dataset 2. Species occurrence data in all study lakes along with results from the 'soft classification" according to Euclidean distance.</p> <p>Dataset 3. Limnological and fish community characteristics of study lakes including species richness, lake area, estimated lake volume, and convex hull statistics for the overall fish community and each life-history strategy type.</p>
Operating diagram of the incubator, two tiered modules contain six independent incubators. Three shallow hatching are (220 × 60 × 17 cm) stacked on top of each other to create a compact assembly in which each tier functions independently. Eighteen trays covered with eggs can be placed in each tier, allowing the simultaneous incubation of seven to nine lays. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of the incubator, two tiered modules contain six independent incubators. Three shallow hatching are (220 × 60 × 17 cm) stacked on top of each other to create a compact assembly in which each tier functions independently. Eighteen trays covered with eggs can be placed in each tier, allowing the simultaneous incubation of seven to nine lays.
Data and Codes used in Alonso-Crespo et al (2021) Assembly history modulates vertical root distribution in a grassland experiment.
<p>This repository contains the raw data, the RootPainter model and the annotated R and Python codes supporting the results reported in the following paper: Alonso-Crespo et al (2021) Assembly history modulates vertical root distribution in a grassland experiment.</p>
Data from: Land use history and seed dispersal drive divergent plant community assembly patterns in urban vacant lots
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Data from: Life-history dimensions indicate non-random assembly processes in tropical island tree communities
<p>Community assembly processes on islands are often non-random. The mechanisms behind non-random assembly, however, are generally difficult to disentangle. Functional diversity in combination with a null model approach that accounts for differences in species richness among islands can be used to test for non-random assembly processes, but has been applied rarely to island communities. By linking functional diversity of trees on islands with a null model approach, we bridge this gap and test for the role of stochastic vs. non-random trait-mediated assembly processes in shaping communities by studying functional diversity-area relationships. We measured 11 plant functional traits linked to species dispersal and resource acquisition strategies of 57 tree species on 40 tropical islands. We grouped traits into four life-history dimensions representing (i) dispersal ability, (ii) growth strategy, (iii) light acquisition, and (iv) nutrient acquisition. To test for non-random assembly processes, we used null models that account for differences in species richness among the islands. Our results reveal contrasting responses of the four life-history dimensions to island area. The dispersal and the growth strategy dimensions were underdispersed on smaller islands, whereas the light acquisition dimension was overdispersed. The nutrient acquisition dimension did not deviate from null expectations. With increasing island area, shifts in the strength of non-random assembly processes increased the diversity of dispersal and acquisition strategies in island communities. Our results suggest that smaller islands may be more difficult to colonize and provide more limited niche space compared to larger islands, whose tree communities are likely determined by stochastic processes and higher niche diversity. Our null model approach highlights that analysing the functional diversity of different life-history dimensions provides a powerful framework to unravel community assembly processes on islands. These complex, non-random assembly processes are masked by measures of functional diversity that do not account for differences in species richness between islands.</p>
Data from: Where did all the trees come from? A novel multispecies approach reveals the impacts of biogeographical history and functional diversity on rain forest assembly
Aim: We take advantage of next generation sequencing-based technology to assess how landscape-level dynamics, biogeographical history and functional factors shape the distribution of genetic diversity in rain forest trees. To achieve this, we explore chloroplast genomic diversity and divergence patterns across multiple, co-distributed species from three major centres of rain forest diversity. Location: Subtropical rain forests in south-eastern Australia: Nightcap–Border Ranges, Dorrigo and Washpool. Methods: We assembled chloroplast genomic data from whole-genome shotgun libraries for 71 species collected across three major centres of rain forest diversity. Chloroplast single nucleotide polymorphisms were used to measure genetic variation within and between multiple populations, species and locations, and we used this information to identify patterns related to landscape-level processes, biogeographical origins and functional characteristics. Results: We identified Nightcap–Border Ranges and Dorrigo as containing multiple refugia and Washpool as primarily a recolonized area. We found that rapidly expanding lineages of Indo-Malesian origin exhibit significantly lower levels of genetic diversity than Gondwanan lineages with longer local histories. Functional traits related to persistence and dispersal were the most important in regulating the distribution of genetic diversity. Main conclusions: The distribution and assembly of species reflect interactions and competition between different floristic elements at different stages of continental occupation. Additionally, given the multiple evolutionary origins and histories of the Australian rain forest flora, it is important to avoid treating rain forest communities as single management units.
Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies
Short-read sequencing technologies have in principle made it feasible to draw detailed inferences about the recent history of any organism. In practice, however, this remains challenging due to the difficulty of genome assembly in most organisms and the lack of statistical methods powerful enough to discriminate among recent, non-equilibrium histories. We address both the assembly and inference challenges. We develop a bioinformatic pipeline for generating outgroup-rooted alignments of orthologous sequence blocks from de novo low-coverage short-read data for a small number of genomes, and show how such sequence blocks can be used to fit explicit models of population divergence and admixture in a likelihood framework. To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa, was restricted during Pleistocene ice ages to a longitudinal series of southern refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled from a single genome from each of three major glacial refugia reveals support for an unexpected history dominated by recent admixture. Despite the fact that 80% of the genome is affected by admixture during the last glacial cycle, we are able to infer the deeper divergence history of these populations. These inferences are robust to variation in block length, mutation model, and the sampling location of individual genomes within refugia. This combination of de novo assembly and numerical likelihood calculation provides a powerful framework for estimating recent population history that can be applied to any organism without the need for prior genetic resources.
Data from: Ecomorphology of the African felid ensemble: the role of the skull and postcranium in determining species segregation and assembling history
Morphology of extant felids is regarded as highly conservative. Most previous studies have focussed on skull morphology, so a vacuum exists about morphofunctional variation in postcranium and its role in structuring ensembles of felids in different continents. The African felid ensemble is particularly rich in ecologically specialized felids. We studied the ecomorphology of this ensemble using 31 cranial and 93 postcranial morphometric variables measured in 49 specimens of all 10 African species. We took a multivariate approach controlling for phylogeny, with and without body size correction. Postcranial and skull + postcranial analyses (but not skull-only analyses) allowed for a complete segregation of species in morphospace. Morphofunctional factors segregating species included body size, bite force, zeugopodial lengths and osteological features related to parasagittal leg movement. A general gradient of bodily proportions was recovered: lightly built, long-legged felids with small heads and weak bite forces vs. the opposite. Three loose groups were recognized: small terrestrial felids, mid-to-large sized scansorial felids and specialized Acinonyx jubatus and Leptailurus serval. As predicted from a previous study, the assembling of the African felid ensemble during the Plio-Pleistocene occurred by the arrival of distinct felid lineages that occupied then vacant areas of morphospace, later diversifying in the continent.
Ecomorphological relationships and invasion history of non-native terrestrial bird species on O'ahu, Hawai'i suggests ecological fitting during community assembly
The widespread introduction of species has created novel communities in many areas of the world. Since introduced species tend to have generalized ecologies and often lack shared evolutionary history with other species in their communities, it would be expected that the relationship between form and function (i.e. ecomorphology) may change in novel communities. We tested this expectation in a subset of the novel bird community on O'ahu, Hawai'i. By relating foraging behavior observations to morphology obtained from live birds at four sites across the island, we found many relationships between species' morphology and foraging ecology that mirrored relationships found in the literature for native dominated bird communities. Both movement and certain foraging behaviors were related to a species' tarsus to wing ratio. Further, bill morphology was related to gleaning, frugivory, and flycatching behaviors. The commonness of significant ecomorphological relationships suggests that, within O'ahu's novel bird community, form is strongly related to function. We hypothesize that ecological fitting likely played a major role in the assembly of this novel community conserving the relationships between form and function found in many other bird communities. To further support this hypothesis, we used niche data from EltonTraits 1.0 to determine if the establishment of bird species introduced to O'ahu was related to the distinctiveness of their ecological niche from the incumbent community. Introduced species were more likely to establish on O'ahu if their diets were less similar to the bird species already present on the island. Our results support the idea that ecological fitting is an important mechanism in shaping ecological communities, especially in the Anthropocene, thereby influencing novel community assembly and functioning.
Ecomorphological relationships and invasion history of non-native terrestrial bird species on O‘ahu, Hawai‘i suggests ecological fitting during community assembly
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Data from: Life-history dimensions indicate non-random assembly processes in tropical island tree communities
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Data from: Ecomorphology of the African felid ensemble: the role of the skull and postcranium in determining species segregation and assembling history
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Data from: Where did all the trees come from? A novel multispecies approach reveals the impacts of biogeographical history and functional diversity on rain forest assembly
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Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies
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Data from: Assembling the forest herb community after abandonment from agriculture: long-term successional dynamics differ with land-use history
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Data from: Evolutionary history inferred from the de novo assembly of a non-model organism, the blue-eyed black lemur
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.