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publicSep 2023View details →

A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

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publicJun 2022View details →

Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks

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publicNov 2024View details →

Asymmetrical hybridization and environmental factors influence the spatial genetic structure of a killifish hybrid zone

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publicDec 2024View details →

Data from: Defaunation increases clustering and fine-scale spatial genetic structure in a small-seeded palm despite remaining small-bodied frugivores

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Genetic Diversity and Spatial Structure of Spartina alterniflora in on the Eastern Shore of Virginia

Nine polymorphic microsatellite loci were used to quantify the genetic characteristics (e.g., allelic richness,diversity, polyploidy, fixation index) of the S. alterniflora populations at five salt marshes on the Eastern Shore of Virginia (Northampton Co.), as well as to measure the spatial structure (size and shape of clones) of a single population in Upper Phillips Creek marsh (UPC), a marsh that experienced dieback. Over 250 individual plant samples were collected at three spatial scales for these experiments

openCustomJun 2014View details →

opencc-zeroAug 2020View details →

Data from: Multi-scale spatial genetic structure within and between populations of wild cherry trees in nuclear genotypes and chloroplast haplotypes

Spatial genetic structure (SGS) of plants mainly depends on the effective population size and gene dispersal. Maternally inherited loci are expected to have higher genetic differentiation between populations and more intensive SGS within populations than biparentally inherited loci because of smaller effective population sizes and fewer opportunities of gene dispersal in the maternally inherited loci. We investigated biparentally inherited nuclear genotypes and maternally inherited chloroplast haplotypes of microsatellites in 17 tree populations of three wild cherry species under different conditions of tree distribution and seed dispersal. As expected, inter-population genetic differentiation was 6–9 times higher in chloroplast haplotypes than in nuclear genotypes. This difference indicated that pollen flow 4–7 times exceeded seed flow between populations. However, no difference between nuclear and chloroplast loci was detected in within-population SGS intensity due to their substantial variation among the populations. The SGS intensity tended to increase as trees became more aggregated, suggesting that tree aggregation biased pollen and seed dispersal distances toward shorter. The loss of effective seed dispersers, Asian black bears, did not affect the SGS intensity probably because of mitigation of the bear loss by other vertebrate dispersers and too few tree generations after the bear loss to alter SGS. The findings suggest that SGS is more variable in smaller spatial scales due to various ecological factors in local populations.

opencc-zeroDec 2020View details →

Host spatial structure and disperser activity determine mistletoe infection patterns

What processes and factors are responsible for species distribution are long-standing questions in ecology and a key element for conservation and management. Mistletoes provide the opportunity to study a forest species whose occurrence is expected to be constrained by multiple factors as a consequence of their life form. We studied the mistletoe Tristerix corymbosus (Loranthaceae) on its most common hosts species in northwest Patagonia. The seeds of this mistletoe are almost exclusively dispersed by the small arboreal and endemic marsupial Dromiciops gliroides (Microbiotheridae). We assessed the underlying causes of plant spatial patterns through point pattern analysis and we used different variables that characterize the neighborhood around each host to analyze the relative effect of host availability, potential for disperser movement, and canopy light conditions. We found that potential hosts were strongly aggregated and that the three most common host species were distributed independent of each other. Considering all host species together, infected and non-infected host were individually aggregated but segregated from each other. The aggregated pattern of infected hosts could be explained in part by the template of potential hosts distribution, but was subsequently modulated by the activity of the mistletoe disperser. Potential for disperser movement, the proximity to reproductive mistletoes and habitat complexity, increased mistletoe infection probability. However, neighboring host availability decreased mistletoe infection probability, and tree DBH (used as surrogate for light conditions) had no detectable effect. Our results suggested that the distribution of mistletoe infection was determined by the structure of potential host populations and by the marsupial disperser activity. Compared to bird dispersed mistletoes, the scale of the infection was smaller and the proximity to reproductive mistletoes and habitat complexity were important for seed arrival and infection. The interplay between landscape structure and disperser activity determine the spatial structure of mistletoe future generations.

opencc-zeroDec 2016View details →

Data from: Bringing multivariate support to multiscale codependence analysis: assessing the drivers of community structure across spatial scales

1. Multiscale codependence analysis (MCA) quantifies the joint spatial distribution of a pair of variables in order to provide a spatially-explicit assessment of their relationships to one another. For the sake of simplicity, the original definition of MCA only considered a single response variable (e.g. a single species). However, that definition would limit the application of MCA when many response variables are studied jointly, for example when one wants to study the effect of the environment on the spatial organisation of a multi-species community in an explicit manner. 2. In the present paper, we generalize MCA to multiple response variables. We conducted a simulation study to assess the statistical properties (i.e. type I error rate and statistical power) of multivariate MCA (mMCA) and found that it had honest type I error rate and sufficient statistical power for practical purposes, even with modest sample sizes. We also exemplified mMCA by applying it to two ecological data sets. 3. The simulation study confirmed the adequacy of mMCA from a statistical standpoint: it has honest type I error rates and sufficient power to be useful in practice. Using mMCA, we were able to detect variation in fish community structure along the Doubs River (in France), which was associated with large spatial structures in the variation of physical and chemical variables related to water quality. Also, mMCA usefully described the spatial variation of an Oribatid mite community structure associated with a gradient of water content superimposed on various smaller-scale spatial features associated with vegetation cover in the peat blanket surrounding Lac Geai (in Québec, Canada). 4. In addition to demonstrating the soundness of mMCA in theory and practice, we further discuss the strengths and assumptions of mMCA and describe other potential scenarios where it would be helpful to biologists interested in assessing influence of environmental conditions on community structure in a spatially-explicit way.

opencc-zeroDec 2017View details →

Data from: Genetic diagnosis of a rare myrmecochorous species, Plagiorhegma dubium (Berberidaceae): historical genetic bottlenecks and strong spatial structures among populations

Distribution of genetic variation over time and space is relevant to demographic histories, and tightly linked to ecological disturbances as well as evolutionary potential of an organism. Therefore, understanding the pattern of genetic diversity is a primary step in conservation and management projects for rare and threatened plant species. We used 8 microsatellite markers to examine the level of genetic diversity, spatial structure and demographic history of Plagiorhegma dubium, a rare myrmecochorous herb, populations sampled across northeast Asia and Siberia. We found low within-population genetic variation associated with historical bottlenecks. Although pairwise FST values were not much higher than the ones found in similar life form species, STRUCTURE and PCoA revealed a clear broad-scale spatial pattern of genetic structure. Bayesian clustering (best K=6) and PCoA identified three populations that are distinctive from neighboring populations in the Korean peninsula, which suggests potential units for conservation and management plans in Korea. MIGRATE-N and BAYESASS showed that both contemporary (0.003-0.045) and historical migration rates (2e-5-4.6e-4) were low. Our findings provide a good example, where genetic considerations should be integrated for conservation and management plans of rare and threatened species.

opencc-zeroDec 2016View details →

Data from: Ultra-fine scale spatially-integrated mapping of habitat and occupancy using structure-from-motion

Organisms respond to and often simultaneously modify their environment. While these interactions are apparent at the landscape extent, the driving mechanisms often occur at very fine spatial scales. Structure-from-Motion (SfM), a computer vision technique, allows the simultaneous mapping of organisms and fine scale habitat, and will greatly improve our understanding of habitat suitability, ecophysiology, and the bi-directional relationship between geomorphology and habitat use. SfM can be used to create high-resolution (centimeter-scale) three-dimensional (3D) habitat models at low cost. These models can capture the abiotic conditions formed by terrain and simultaneously record the position of individual organisms within that terrain. While coloniality is common in seabird species, we have a poor understanding of the extent to which dense breeding aggregations are driven by fine-scale active aggregation or limited suitable habitat. We demonstrate the use of SfM for fine-scale habitat suitability by reconstructing the locations of nests in a gentoo penguin colony and fitting models that explicitly account for conspecific attraction. The resulting digital elevation models (DEMs) are used as covariates in an inhomogeneous hybrid point process model. We find that gentoo penguin nest site selection is a function of the topography of the landscape, but that nests are far more aggregated than would be expected based on terrain alone, suggesting a strong role of behavioral aggregation in driving coloniality in this species. This integrated mapping of organisms and fine scale habitat will greatly improve our understanding of fine-scale habitat suitability, ecophysiology, and the complex bi-directional relationship between geomorphology and habitat use.

opencc-zeroNov 2023View details →

Data from: Investigating the spatial, demographic, and genetic structures of Cylicodiscus gabunensis Harms, a light-demanding African timber species

Most Central African rainforest canopies consist of light-demanding tree species that hold high commercial value but also suffer locally from regeneration deficits, raising concerns about the sustainability of logging. Regeneration is influenced by factors such as past perturbations (including human activity), mating systems, and seed/pollen dispersal processes that impact demographic, spatial, and genetic structures within populations. To gain a better understanding of these interactions, we studied the spatial distribution and trunk diameter structure of Cylicodiscus gabunensis (Fabaceae) - a wind-dispersed, insect-pollinated, timber species - in three plots ranging from 400 to 839 ha situated in various environmental contexts (e.g. forest types and elephant densities) across Central Africa. We also genotyped adults and juveniles using microsatellite markers to analyze the spatial genetic structure of each population and infer the selfing rate, seed and pollen dispersal capacities and selection gradients using the 'neighborhood model'. The selfing rate was low (3 – 4 %), and seed dispersal distances (ds = 184 m) were much shorter than pollen dispersal distances (dp > 2 km). The three populations displayed contrasted spatial, demographic and genetic structures. One population showed no spatial aggregation or genetic structure, and a multimodal diameter structure indicating pulses of regeneration events. Two populations showed strong spatial aggregation and genetic structures. One exhibited a unimodal diameter structure indicating one ancient pulse of regeneration, while the other displayed a 'reverse J-shaped' diameter structure, typical of ongoing regeneration. In the latter, reproductive success appeared leptokurtic, three mother trees accounting for over 90 % of the regeneration and no tree below the minimum cutting diameter implemented by logging companies had offspring. The idiosyncratic nature of population characteristics observed in C. gabunensis suggests that, for sustainable management, a nuanced approach is needed. This involves protecting productive seed trees in areas where natural regeneration is occurring and actively supporting regeneration in areas exhibiting deficits, especially in contexts with low elephant densities.

Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data: intermediate results

This directory contains all intermediate results generated in the "Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data" for reproducibility purpose. Associated scripts are available at https://github.com/JiayuSuPKU/Smoother_paper. Raw and processed data can be downloaded at https://zenodo.org/records/10223862.Note that some intermediate results and figures in the notebooks may not be exactly the same as those in the paper due to the randomness in some analysis steps, but should be very close.

Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data: raw and processed data files

This directory contains all spatial and single-cell omics datasets analyzed in the "Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data". Associated scripts are available at https://github.com/JiayuSuPKU/Smoother_paper. See https://github.com/JiayuSuPKU/Smoother_paper/blob/main/data/README.md for details on folder structure and data sources.

Dataset from Reese et al.: "Local Mixing Determines Spatial Structure of Diahaline Exchange Flow in a Mesotidal Estuary: A Study of Extreme Runoff Conditions" - PART 1

Model data from the numerical setup of the tidal Elbe presented in Reese et al. (2023): "Local Mixing Determines Spatial Structure of Diahaline Exchange Flow in a Mesotidal Estuary: A Study of Extreme Runoff Conditions" [1]PART 1Each file contains data for a full month, as given through the file naming convention: description.YYYYMMDD.nc4The numerical model uses terrain-following sigma coordniates, with sigma level 0 being the bottommost layer.Certain variables are also given in salinity class bins of dimension salt_s instead of vertical coordinates.Explanation of each data type:<ul><li> 2D_elv_all: Spatially resolved simulated surface elevation from 08/2012 to 12/2013: Tidal analysis Fig. 4, Table 1 (simulated surface elevation vs. time)<ul><li>5 min snapshots</li></ul></li><li>Elbe_dia_getm_all: Diahaline analysis Fig. 8, 11: on-line GETM computation of u_dia,z^S in September 2012 and June 2013<ul><li>44700s temporal resolution (M2 tidal period); averaged over each period</li></ul></li><li>Elbe_TEF_mean_all: Total Exchange Flow analysis in  September 2012 and June 2013, Fig.s 7, 8<ul><li>1-hourly averages</li></ul></li><li>Mixing_mean_all: Physical and numerical Mixing from 08/2012 to 12/2013. Fig. 7, 8, 9, 10, 11<ul><li>44700s temporal resolution (M2 tidal period); averaged over each period</li></ul></li><li>ST_stations: Surface elevation at given location for comparison with observational data at named station from 08/2012 to 12/2013<ul><li>5 min snapshots</li></ul></li><li>SST_stations: Salinity and temperature at given location for comparison with observational data at named station from 08/2012 to 12/2013; Fig. 3, Fig. 5, Table 2<ul><li>30-min snapshots</li></ul></li></ul> [1] L. Reese, U. Graewe, K. Klingbeil, X. Li, M. Lorenz, H. Burchard, 2023:   Local mixing determines spatial structure of diahaline exchange flow in a   mesotidal estuary – a study of extreme runoff conditions.   J. Phys. Oceanogr., in press.

Dataset from Reese et al.: "Local Mixing Determines Spatial Structure of Diahaline Exchange Flow in a Mesotidal Estuary: A Study of Extreme Runoff Conditions" - PART 2

opencc-by-4.0Jan 2022View details →

FIG. 1 in Demographic and spatial structure at the stage of expansion in the populations of some alien land snails in Belgorod city (Central Russian Upland)

FIG. 1. Map of study sites. РИС. 1. Карта раЗмеЩения исследуемых участков.

opencc-zeroNov 2021View details →

Life on a leaf: the development of spatial structure in epiphyll communities

1. The spatial structure of biotic communities can be shaped by niche-based or stochastic processes, and the importance of both can change through time. Niche-based processes include neighbour interactions, which can change in intensity and quality as communities develop in dependence of environmental conditions. Epiphylls, miniature communities of liverworts, lichens, algae and fungi on leaves, develop only in relatively moist forests, but their leaf-surface habitat is still characterised by moisture stress, especially in more exposed parts of the forest. As neighbours may alleviate moisture stress, we expected that in forest gaps (dryer, brighter) epiphyll communities would show more positive neighbour interactions, resulting in more clustered spatial patterns, than in closed forest, in accordance with the stress-gradient hypothesis. 2. To understand how the processes shaping epiphyll communities change through time and differ between gaps and closed forest, we examined the fine-scale spatial structure within and between epiphyll functional groups (algae, fungi, lichens, liverworts) during 12 months on 60 leaves across twelve sites in a tropical rainforest in Panama. We analysed changes in spatial positions and spatial associations within and between functional groups using spatial point pattern analysis based on repeated photography. 3. Epiphyll densities increased through time for most epiphyll functional groups. However, although epiphyll groups changed their positions through time, the general types of spatial patterns remained similar for most groups: only lichen patterns shifted from mostly random to mostly aggregated through time. We found only random and aggregated spatial patterns within groups, while among groups we additionally found segregated spatial associations, but no consistent temporal trend. Patterns did not differ between gaps and closed forest, thus not supporting the stress-gradient hypothesis. 4. Synthesis. Our results only weakly support the assumption that community-shaping processes change from neutral to niche-based as communities develop. We do provide empirical evidence that epiphyll communities are dynamic and exhibit different spatial association patterns within than among groups. This suggests different interactions and processes within than between groups. Experimental studies and monitoring of individual epiphyll patches are recommended to shed further light on what processes shape life on leaves.

opencc-zeroMar 2022View details →

Data from: Trait hierarchies are stronger than trait dissimilarities in structuring spatial co-occurrence patterns of common tree species in a subtropical forest

1. The dissimilarity and hierarchy of trait values that characterize niche and fitness differences, respectively, have been increasingly applied to infer mechanisms driving community assembly and to explain species co-occurrence patterns. Here, we predict that limiting similarity should result in the spatial segregation of functionally similar species, while functionally similar species will be more likely to co-occur either due to environmental filtering or competitive exclusion of inferior competitors (hereafter hierarchical competition). 2. We used a fully mapped 50-ha subtropical forest plot in southern China to explore how pairwise spatial associations between saplings and between adult trees were influenced by trait dissimilarity and hierarchy in order to gain insight into assembly mechanisms. We assessed pairwise spatial associations using two summary statistics of spatial point patterns at different spatial scales and compared the effects of trait dissimilarity and trait hierarchy of different functional traits on the interspecific spatial associations. These comparisons allow us to disentangle the effects of limiting similarity, environmental filtering and hierarchical competition on species co-occurrence. 3. We found that trait dissimilarity was generally negatively related with interspecific spatial associations for both saplings and adult trees across spatial scales, meaning that species with similar trait values were more likely to co-occur and thus supporting environmental filtering or hierarchical competition. We further found that trait hierarchy outweighed trait dissimilarity in structuring pairwise spatial associations, suggesting that hierarchical competition played a more important role in structuring our forest community than environmental filtering across life stages. 4. This study employed a novel method, by offering the integration of pairwise spatial association and trait dissimilarity as well as trait hierarchy, to disentangle the relative importance of multiple assembly mechanisms in structuring co-occurrence patterns, especially the mechanisms of environmental filtering and hierarchical competition, which lead to indistinguishable co-occurrence patterns. This study also reinforced the importance of trait hierarchy rather than trait dissimilarity in driving neighborhood competition.

opencc-zeroApr 2022View details →

Spatial variation in human disturbances and their effects on forest structure and biodiversity across an Afromontane forest

Context Human disturbances can have large impacts on forest structure and biodiversity, and thereby result in forest degradation, a property difficult to detect by remote sensing. Objectives To investigate spatial variation in anthropogenicdisturbances and their effects on forest structure and biodiversity. Methods In 144 plots of 20 x 20 m distributed across a forest area of 750 km2 in Southwest Ethiopia, we recorded: landscape variables (e.g., distance to forest edge), different human disturbances, forest structure variables, and species composition of trees and epiphyllous bryophytes. We then first assessed if landscape variables could explain the spatial distribution of disturbances. Second, we analysed how forest structure and biodiversity were influenced by disturbances. Results Human disturbances, such as coffee management and grazing declined with distance to forest edges and penetrated at least a kilometer into the forest. The slope was not related to disturbance levels, but several types of disturbances were less common at higher elevations. Among human disturbance types, coffee management reduced liana cover and was associated with altered species composition of trees. The presence of large trees and basal areas was not related to any of the disturbance gradients. Conclusions Although most anthropogenic disturbances displayed clear edge effects, surprisingly the variation in the chosen forest degradation indices was only weakly related to these disturbances. We suggest that the intersection between edge effects and forest degradation is very context-specific and relies much on how particular societies use the forests. For example, in this landscape coffee management seems to be a key driver.