Biology subjects

Cram, D.

Publications and source records attributed to Cram, D..

4 recordsLinked to original sources

bioRxiv2025

The bind of the burrow: space use is dominated by selection for burrow habitat over foraging habitat in an arid-adapted carnivore

Our understanding of habitat selection in wild vertebrates has been heavily influenced by observations of preferred foraging areas. However, foraging is only one of many ways animals interact with their environment, and preferences for habitat features that support resting, breeding, and safety, along with trade-offs between these needs, remain underexplored. These trade-offs are likely to be particularly acute in complex environments where these needs are met in different locations. Using a long-term dataset of movements and life history, we examine how preferences for foraging areas and burrow sites shape space use in Kalahari meerkats (Suricata suricatta). Meerkats cannot dig new sleeping and breeding burrows and must use those abandoned by other species, potentially generating trade-offs in daily space use if overnight refuges are far from optimal foraging areas. We find that space use is strongly anchored by burrow location, with burrows in calcareous pans and dry riverbed ("white sand") habitat being preferred year-round and showing lower burrow switching rates. However, white sand areas were not preferred for foraging, and yielded lower weight gains, particularly during the dry season. As a result, meerkats faced a trade-off between optimal burrow locations and productive foraging grounds, as indicated by faster, longer, and more energetically costly travel when moving through or waking up in white sands. Our results suggest that changes in the distribution or abundance of key burrow-constructing species in desert environments may have cascading effects on the many secondary burrow-using species that depend on them for survival and reproduction. More broadly, our results highlight that limited refuge availability across the landscape can impose strong ecological constraints on animals and may restrict behavioural plasticity under environmental change, particularly if productive foraging areas shift.

ecology↗

bioRxiv2025

Contrastive modelling of transcription and transcript abundance in legumes using PlanTT

Predicting the impacts of sequence variation on gene expression remains a challenging task. Further, in plants, we have a limited understanding of the relative contributions of different gene expression regulatory mechanisms. To address these limitations we generated a comparative multiomic dataset comprising matched 3-RNA-seq and PRO-seq data from matched tissues of reference genotypes of four legumes of the invert repeat lacking clade (Pisum sativum, Vicia faba, Lathyrus sativa and Medicago truncatula). Focused on the challenging task of predicting expression differences between ortholog pairs from unseen orthogroups, we used this dataset and a novel prediction framework to build contrastive models that predict quantitative differences (effect size differences) in transcription and transcript abundance.

bioinformatics↗

bioRxiv2023

Evolution of sex differences in cooperation:the role of trade-offs with dispersal

AbstractExplaining the evolution of sex differences in cooperation remains a major challenge. Comparative studies highlight that offspring of the more philopatric sex tend to be more cooperative within their family groups than those of the more dispersive sex but we do not understand why. The leading Philopatry hypothesis proposes that the more philopatric sex cooperates more because their higher likelihood of natal breeding increases the direct fitness benefits of natal cooperation. However, the Dispersal trade-off hypothesis proposes that the more dispersive sex cooperates less because preparations for dispersal, such as extra-territorial prospecting, trade-off against natal cooperation. Here, we test both hypotheses in cooperatively breeding white-browed sparrow weavers (Plocepasser mahali), using a novel high-resolution automated radio-tracking method. First, we show that males are the more dispersive sex (a rare reversal of the typical avian sex-difference in dispersal) and that, consistent with the predictions of both hypotheses, females contribute substantially more than males to cooperative care while within the natal group. However, the Philopatry hypothesis cannot readily explain this female-biased cooperation, as females are not more likely than males to breed within their natal group. Instead, our radio-tracking findings support the Dispersal trade-off hypothesis: males conduct pre-dispersal extra-territorial prospecting forays at higher rates than females and prospecting appears to trade-off against natal cooperation. Our findings thus highlight that the evolution of sex differences in cooperation could be widely attributable to trade-offs between cooperation and dispersal; a potentially general explanation that does not demand that cooperation yields direct fitness benefits.

evolutionary biology↗

bioRxiv2020

Wheat transcriptome profiling reveals abscisic and gibberellic acid treatments regulate early-stage phytohormone defense signaling, cell wall fortification, and metabolic switches following Fusarium graminearum-challenge

BackgroundApplication of the wheat phytohormones abscisic acid (ABA) or gibberellic acid (GA) affect Fusarium head blight (FHB) disease severity; however, the molecular underpinnings of the elicited phenotypes remain unclear. Herein, the transcriptomic responses of an FHB-susceptible wheat cultivar Fielder were characterized upon treatment with ABA, an ABA receptor antagonist (AS6), or GA in the presence or absence of Fusarium graminearum (Fg) challenge. ResultsA total of 30,876 differentially expressed genes (DEGs) where identified in Fielder (26,004) and Fg (4,872). Fg challenge alone resulted in the most substantial wheat DEGs contributing to 57.2% of the total transcriptomic variation. Using a combination of topology overlap and correlation analyses, 9,689 Fg-related wheat DEGs were defined. Further enrichment analysis of the top 1% networked wheat DEGs identified critical expression changes within defense responses, cell structural metabolism, molecular transport, and membrane/lipid metabolism. Fg-challenged conditions also included the expression of a putative Fg ABA-biosynthetic cytochrome P450 and repression of wheat FUS3 for dysregulating ABA and GA crosstalk. ABA treatment alone elicited 4536 (32%) wheat DEGs common to those of the Fg-challenge, and Fg+ABA further enhanced 888 (12.5%) of them. These ABA elicited DEGs are involved in defense through both classical and non-classical phytohormone signaling and regulating cell wall structures including polyphenolic metabolism. Conversely, Fg+GA opposed 2239 (33%) Fg-elicited wheat DEGs, including modulating primary and secondary metabolism, defense responses, and flowering genes. ABA and jointly ABAFg[Fg+ABA] treatments repressed, while Fg+GA induced an over-representation of wheat DEGs mapping to chromosome 6BL. Finally, compared to Fg+ABA, co-application of Fg+AS6 did not antagonize ABA biosynthesis or signal but rather elicited antagonistic Fg (557) and wheat (11) DEGs responses directly tied to stress responses, phytohormone transport, and FHB. ConclusionsComparative transcriptomics highlight the effects of wheat phytohormones on individual pathway and global metabolism simultaneously. Application of ABA may reduce FHB severity through misregulating defense mechanisms and cell wall fortification pathways. GA application may alter primary and secondary metabolism, creating a metabolic shift to ultimately reduce FHB severity. By comparing these findings to those previously reported for four additional plant genotypes, an additive model of the wheat-Fg interaction is proposed.

genomics↗