Biology subjects

de Jager, M.

Publications and source records attributed to de Jager, M..

9 recordsLinked to original sources

bioRxiv2026

Predicting Species-Area Relationships in Fragmented Forests

Habitat destruction leads to a severe decline in biodiversity. Ascertaining effects of habitat loss afterwards is regularly done, whereas predicting the effects of different habitat loss scenarios on biodiversity beforehand is much preferred but as of yet rarely possible. Such predictions would help inform management decisions to prevent biodiversity loss in the first place, or at least mitigate effects if necessary, by providing handles to set priorities in making trade-offs. To this end, we developed and applied an adapted version of the information-theoretical framework of Maximum Entropy Theory in Ecology (METE) to predict species-area relationships in tropical forest landscapes undergoing habitat loss and fragmentation. Species-area relationships provide information about biodiversity and can, in undisturbed systems, be predicted using METE, based on state variables such as the total number of individuals, the total number of species, and the total area size. In disturbed systems, however, it is established that METEs predictions are off. Using an individual-based model, we explore how METEs state variables should be adjusted, based on the landscape characteristics habitat cover and degree of habitat fragmentation, to restore its accuracy of species-area relationship predictions in disturbed environments. We validate our adjusted METE predictions with empirical data. Our adjusted METE predictions demonstrate the severity of fragmentations impact on biodiversity, relative to what could be expected in a pristine, continuous environment. With this new method, we can estimate the immediate effects of habitat loss on biodiversity, as well as its long-term effects.

ecology↗

bioRxiv2024

Solving the SLoSS debate: Scale-dependent effects of habitat fragmentation on biodiversity loss

Should what is left of nature be contained in a Single Large or Several Small (SLoSS) areas? This question of what would minimize the impact severity of habitat destruction on biodiversity loss is much debated, mainly because studies generally focus on different spatial and temporal scales. Using a semi-spatially explicit, (near-)neutral, individual-based model, we investigate the effects of fragmentation on biodiversity loss at two spatial (landscape-versus subcommunity level) and two temporal scales (static versus dynamic effects). Our results show that the role of spatial configuration of habitat destruction depends on when and at what scale we measure biodiversity loss. When considering the more realistic assumption that species differ in dispersal capacity, differences between spatial configurations are likely to be amplified. Our results indicate that the spatial configuration of habitat loss needs to be considered when evaluating the risks of further habitat destruction.

ecology↗

bioRxiv2024

OPTIMIZING SEGMENTATION IN OCCUPANCY MODELLING OF CAMERA-TRAP DATA

O_LIAccurate estimation of species abundances is a common challenge in conservation biology, particularly when abundances are compared in space or time. Occupancy modelling provides relative abundance estimates from camera-trapping data without the need for individual recognition. This requires segmentation of continuous records into a series of intervals with either detection or non-detection. While the segmentation method may have profound effects on the accuracy of occupancy modelling, no form of segmentation optimization is yet available. C_LIO_LIWe assessed how segmentation, defined by interval length and number, influences the accuracy of predictions by the Royle-Nichols occupancy model and how this relationship depends on species density, study duration, and the number of sampling points. We simulated capture data using an individual-based model in which we varied the species densities between study locations, and then fitted models using different segmentations. Using the simulation results, we developed a simple tool for choosing optimal segmentation and the best minimum number of intervals to use. To provide an example, we used the optimization tool on actual data from a camera-trapping study in Western Equatorial Africa and compared relative wildlife abundances between two forest management types. C_LIO_LIWe found that the optimum interval length for the Royle-Nichols occupancy model varied with species density, study duration, and the number of sampling points. By analyzing the empirical data, we found that optimal segmentation and minimum number of intervals differed substantially between species. Modelling with optimized, species-specific interval numbers and lengths yielded more conservative outcomes (i.e. fewer significant effects) than did modelling with fixed numbers and lengths. Furthermore, the choice of interval length can affect the direction of relationships. C_LIO_LIOur results indicate that the interval length is by no means a parameter to be standardized at a given value but should be carefully chosen based on the properties of the data at hand. This study shows that the arbitrary segmentation that is commonly used in occupancy modelling may not be optimal. Our tool helps to optimize segmentation, increases the accuracy of relative abundance estimations, and thus facilitates the use of camera-trapping studies to evaluate conservation measures. C_LI

ecology↗

bioRxiv2024

Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning

Protein-DNA interactions and protein-mediated DNA compaction play key roles in a range of biological processes. The length scales typically involved in DNA bending, bridging, looping, and compaction ([≥]1 kbp) are challenging to address experimentally or by all-atom molecular dynamics simulations, making coarse-grained simulations a natural approach. Here we present a simple and generic coarse-grained model for the DNA-protein and protein-protein interactions, and investigate the role of the latter in the protein-induced compaction of DNA. Our approach models the DNA as a discrete worm-like chain. The proteins are treated in the grand-canonical ensemble and the protein-DNA binding strength is taken from experimental measurements. Protein-DNA interactions are modeled as an isotropic binding potential with an imposed binding valency, without specific assumptions about the binding geometry. To systematically and quantitatively classify DNA-protein complexes, we present an unsupervised machine learning pipeline that receives a large set of structural order parameters as input, reduces the dimensionality via principal component analysis, and groups the results using a Gaussian mixture model. We apply our method to recent data on the compaction of viral genome-length DNA by HIV integrase and we find that protein-protein interactions are critical to the formation of looped intermediate structures seen experimentally. Our methodology is broadly applicable to DNA-binding proteins and to protein-induced DNA compaction and provides a systematic and quantitative approach for analyzing their mesoscale complexes. SIGNIFICANCEDNA is central to the storage and transmission of genetic information and is frequently compacted and condensed by interactions with proteins. Their size and dynamic nature make the resulting complexes difficult to probe experimentally and by all-atom simulations. We present a simple coarse-grained model to explore [~]kbp DNA interacting with proteins of defined valency and concentration. Our analysis uses unsupervised learning to define conformational states of the DNA-protein complexes and pathways between them. We apply our simulations and analysis to the compaction of viral genome-length DNA by HIV integrase. We find that protein-protein interactions are critical to account for the experimentally observed intermediates and our simulated complexes are in good agreement with experimental observations.

biophysics↗

bioRxiv2024

HIV integrase compacts viral DNA into biphasic condensates

The human immunodeficiency virus (HIV) infects non-dividing cells and its genome must be compacted to enter the cell nucleus. Here, we show that the viral enzyme integrase (IN) compacts HIV DNA mimetics in vitro. Under physiological conditions, IN-compacted genomes are consistent in size with those found for pre-integration complexes in infected cells. Compaction occurs in two stages: first IN tetramers bridge DNA strands and assemble into "rosette" structures that consist of a nucleo-protein core and extruding bare DNA. In a second stage, the extruding DNA loops condense onto the rosette core to form a disordered and viscoelastic outer layer. Notably, the core complex is susceptible towards IN inhibitors, whereas the diffuse outer layer is not. Together, our data suggest that IN has a structural role in viral DNA compaction and raise the possibility to develop inhibitors that target IN-DNA interactions in disordered condensates. TeaserSingle-molecule studies demonstrate the mechanism, dynamics, and drug-susceptibility of viral genome compaction by HIV integrase.

biophysics↗

bioRxiv2022

Critical transitions and evolutionary hysteresis in movement: Habitat fragmentation can cause abrupt shifts in dispersal that are difficult to revert

Under habitat fragmentation, plant species survival hinges on the ability of individuals to disperse from one habitat patch to another. While there is evidence that severe habitat fragmentation leads to evolution of reduced dispersal ability and that such decreased mobility is generally detrimental for species survival, it is unknown whether species adapt via a gradual loss in dispersal ability or via a sudden shift from frequent to infrequent dispersal between patches (i.e., a critical transition). Using a spatially explicit, individual-based modelling approach, we show that a small increase in inter-patch distance can generate an abrupt shift in plant seed dispersal strategy from long to short distances. Most importantly, we found that a substantial increase in connectivity between habitat fragments is required to reverse this loss of long-distance dispersal, due to an evolutionary hysteresis effect. Our theory prompts for re-consideration of the eco-evolutionary consequences of habitat fragmentation as restoring habitat connectivity may require restoration of much higher connectivity levels than currently assumed.

ecology↗

bioRxiv2021

Assessing the effectiveness of honey bee pollinators for cultivated blueberries in South Africa

Globally, agricultural crops are often dependent on insect pollination. Blueberries are an example of such a crop and owing to their proposed health benefits they are grown around the world, including locations where their native bumble bee pollinators do not occur. In the absence of bumble bees, blueberry pollination in South Africa and many other parts of the non-native, commercial range is performed primarily by honey bees. Despite this, the effectiveness of honey bee pollination on blueberries remains understudied. This study determined the effect of honey bee pollination on components of fruit yield (fruit set and mass) of five blueberry varieties that are extensively planted in South Africa. For each variety, two metrics were calculated: 1) the benefit of bees -- a comparison of fruit yields after exposure to honey bees and fruit yields after honey bee exclusion, 2) the pollination deficit -- the difference in yield between hand pollination (maximum yield potential) and yields after exposure to honey bee pollinators. Honey bee pollination consistently resulted in improved yields, although the magnitude of this improvement (i.e., the benefit of bees) was dependent on the variety considered. Similarly, the pollination deficit also varied considerably across varieties and while some varieties appeared to perform close to maximum potential (small pollination deficit), others yielded well below their maximum potential under honey bee pollination. This study demonstrates that honey bees are functional pollinators of blueberries in areas where native blueberry pollinators are absent. However, in such areas, it is important that special focus be given to selecting blueberry varieties that perform well with honey bees as their sole pollinator. Further research is necessary to determine how the pollination deficit of blueberry varieties can be decreased as well as how to increase the effectiveness of honey bee pollination.

plant biology↗

bioRxiv2019

Cross-compatibility of five highbush blueberry varieties and ideal crossing combinations

Blueberry plants require large quantities of pollen deposited on stigmas to produce commercial-quality fruit. Like many agricultural crops, the interaction between pollen-source variety and pollen-recipient variety can be a major determinant of fruit quality in blueberries. However, little information exists to guide growers in optimising fruit set and quality. Using five commonly grown blueberry varieties, I determined whether crossing between varieties (inter-varietal) increased fruit mass and decreased developmental time relative to crossing within a variety (intra-varietal), and if so, what the best crossing combinations are. While intra-varietal pollination often produced fruit, for certain varieties the fruit set and fruit mass were highly reduced compared to inter-varietal pollination. Furthermore, intra-varietal pollination resulted in longer fruit developmental time in comparison to pollination between varieties. For the same pollen-recipient variety, inter-varietal crosses typically outperformed intra-varietal crosses in fruit mass and developmental time; however, the extent to which inter-varietal crosses outperformed intra-varietal crosses differed between pollen-donor varieties. This result suggests that combinations of varieties are not trivial as some inter-varietal combinations may outperform others. Furthermore, some varieties appear to be more susceptible to the negative effects of intra-varietal crosses than others and that less susceptible varieties may be better suited to conditions where pollinator movement is poor. While our study can guide growers in determining optimal co-planting schemes for the varieties tested, for example in South Africa where these varieties are frequently grown. It also serves as a blueprint for similar compatibility studies that can easily be performed prior to planting to determine the best inter-varietal combinations.

plant biology↗

bioRxiv2019

Honey bees, Apis mellifera, are important pollinators of the highbush blueberry variety Ventura despite the inability to sonicate

Animal-mediated pollination is an essential ecosystem service which over a third of the worlds agricultural crops depend on. Blueberry fruit production is highly dependent on pollinators and in their native range they are pollinated mostly by bumble bees (Bombus spp.). Demand for blueberries has increased in recent years due to their perceived health benefits. Consequently, blueberry cultivation has expanded well beyond their native range, including several regions where bumble bees are not present. In many areas, honey bees may be the only commercially available pollinators of blueberries because many countries ban the importation of bumble bees. This study aimed to determine the benefits of honey bee pollination on blueberry fruit quality and quantity for the variety Ventura by comparing yields of honey-bee-pollinated flowers to flowers where pollinators had been excluded. Honey bees significantly increased berry mass and diameter. Our results suggest that the presence of honey bee pollinators potentially increases revenue by approximately $864 501/ha in areas without bumble bees. We conclude that Ventura is reliably pollinated by honey bees, and that honey bee pollination may be a useful substitute for bumble bees in areas where bumble bees are absent. We also determined the extent to which blueberry yields could still be improved by comparing fruit quality and quantity under honey bee pollination to fruit quality and quantity achieved through ideal hand pollination. We found that blueberry yields may be still be significantly increased relative to ideal hand pollination and we discuss potential ways to improve the efficiency of honeybee pollination in the future. Additional research is required to study how beneficial honey bees are to fruit yield on varieties as the benefits of honey bees are likely to vary across different varieties.

plant biology↗