Search bioRxiv⌕ Search

Biology subjects

Kalirad, A.

Publications and source records attributed to Kalirad, A..

11 recordsLinked to original sources

The topology of ecological drift

Ecological drift, the random fluctuation of abundance in communities, can drastically affect the possibility of coexistence. However, ecological drift has mostly been considered at the macro-ecological scale, whereas its potential contribution to short-term ecological dynamics remains underexplored. Here, we propose a stage-structured ecological graph theory (ssEcoGT) to include complex life cycles and multiple ecological interactions to study the topology of ecological drift. ssEcoGT enables rigorous exploration of how topology of a community can affect the possibility of coexistence between two species. Using ssEcoGT, it is possible to compare the behavior of a range of models - e.g., random graphs, random graphs with intraguild predation, and random graphs with rewiring - against a complete graph of the same size. Thus, ssEcoGT provides a new tool to explore the interplay between ecological drift, competition, and stage-specific interactions.

ecology↗

Diet-derived vitamin B12 induces transgenerational inheritance of nematode predation through elevated vitellogenin provisioning

Dietary and nutritional effects can alter organismal phenotypes and influence trait inheritance over generations, so-called transgenerational epigenetic inheritance. However, the chemical nature of the stimuli and the downstream events inducing such memory remain largely elusive. The nematode Pristionchus pacificus exhibits mouth-form plasticity including predation and was recently shown to respond to a multigenerational Novosphingobium diet with the induction and subsequent transgenerational inheritance of the predatory morph. Here, we show that bacteria-derived vitamin B12 is both necessary and sufficient for transgenerational memory. Different vitamin B12 concentrations are required for the original induction and the subsequent transgenerational inheritance of the predatory morph. Mutant analysis revealed that vitamin B12 functions through methionine-synthase and involves methionine but not vitamin B9. The inherited effect acts through increased multigenerational vitellogenin transcription indicating elevated nutrient provisioning. Consistently, mutants in the vitellogenin receptor Ppa-rme-2 are memory-defective. Thus, vitamin B12 induces vitellogenin provisioning to control organismal physiology and behavior.

genetics↗

The dynamics of coexistence and succession in a decaying ecosystem

Elucidating the rules that govern community assembly and enable the coexistence of species is central to ecology. Much of the current understanding revolves around the composition of communities at equilibrium. In contrast, transient ecological dynamics, in particular the succession of species following an environmental disturbance, remain largely unexplored. We present Gymnogaster buphthalma beetle carcasses as a model to study species coexistence in disequilibrium. In this community, nematodes appear in succession - with multiple feeding and reproductive strategies, transience, and associated dispersal - creating a perfect model for metacommunity ecology. We computationally reconstructed decaying G. buphthalma beetles sampled from the wild using experimentally-derived life history data, i.e. emergence times, sex ratios, and fecundity measurements. Through agent-based modeling, we show that nematode coexistence is possible over a wide range of scenarios. This work provides a unique experimental and computational framework to synthesize various approaches to metacommunity and species succession theories.

ecology↗

EBAX-1/ZSWIM8 destabilizes miRNAs resulting in transgenerational memory of a predatory trait

Environmental influences on traits and associated transgenerational epigenetic inheritance have widespread implications, but remain controversial and underlying mechanisms poorly understood. We introduce long-term environmental induction experiments on alternative diets in Pristionchus pacificus, a nematode exhibiting mouth-form plasticity including predation, by propagating 110 isogenic lines for 101 generations with associated food-reversal experiments. We found dietary induction and subsequent transgenerational memory of the predatory morph and identified a role of ubiquitin ligase EBAX-1/ZSWIM8 in this process. Ppa-ebax-1 mutants have no memory and Ppa-EBAX-1 destabilizes the clustered microRNA family miR-2235a/miR-35. Deletions of a cluster of 44 identical miR-2235a copies resulted in precocious and extended transgenerational inheritance of the predatory morph. These findings indicate that EBAX-1/ZSWIM8 destabilizes miRNAs resulting in transgenerational memory, suggesting a role for target-directed miRNA degradation.

genetics↗

Inferring the selective history of CNVs using a maximum likelihood model

Copy number variations (CNVs) - structural variations generated by deletion and/or duplication that result in change in DNA dosage - are prevalent in nature. CNVs can drastically affect the phenotype of an organism and have been shown to be both involved in genetic disorders and be used as raw material in adaptive evolution. Unlike single-nucleotide variations, the often large and varied effects of CNVs on phenotype hinders our ability to infer their selective advantage based on the population genetics data. Here, we present a likelihood-based approach, dubbed PoMoCNV, that estimates the evolutionary parameters of CNVs based on population genetics data. As a case study, we analyze the genomics data of 40 strains of Caenorhabditis elegans, representing four different populations. We take advantage of the data on chromatin accessibility to interpret the evolutionary parameters of CNVs inferred by PoMoCNV. We further test the reliability of PoMoCNV by estimating the evolutionary parameters of CNVs for mutation-accumulation experiments in C. elegans with varying levels of genetic drift. SignificanceInferring the evolutionary parameters of copy number variations (CNVs) based on population genetics data is crucial to understand their role in evolution. However, given the diversity in the size and effects of CNVs, such inference poses a challenge. We developed a likelihood-based approach called PoMoCNV to address this issue.

bioinformatics↗

Genetic drift promotes and recombination hinders speciation on a holey fitness landscape

Dobzhansky and Muller proposed a general mechanism through which microevolution, the substitution of alleles within populations, can cause the evolution of reproductive isolation between populations and, therefore, macroevolution. As allopatric populations diverge, many combinations of alleles differing between them have not been tested by natural selection and may thus be incompatible. Such genetic incompatibilities often cause low fitness in hybrids between species. Furthermore, the number of incompatibilities grows with the genetic distance between diverging populations. However, what determines the rate and pattern of accumulation of incompatibilities remains unclear. We investigate this question by simulating evolution on holey fitness landscapes on which genetic incompatibilities can be identified unambiguously. We find that genetic incompatibilities accumulate more slowly among genetically robust populations and identify two determinants of the accumulation rate: recombination rate and population size. In large populations with abundant genetic variation, recombination selects for increased genetic robustness and, consequently, incompatibilities accumulate more slowly. In small populations, genetic drift interferes with this process and promotes the accumulation of genetic incompatibilities. Our results suggest a novel mechanism by which genetic drift promotes and recombination hinders speciation. Author summaryAs geographically isolated populations evolve, genetic incompatibilities accumulate between them. Eventually, these incompatibilities may cause the populations to become different species. What determines how quickly species are formed in this way remains unclear. We investigate this question using computer simulations and find that genetic incompatibilities accumulate more slowly among populations with individuals that are robust to genetic perturbations. We identify two factors that influence the accumulation rate via their effects on genetic robustness: the size of the populations and how much recombination takes place in them. Small populations with rare recombination accumulate incompatibilities more quickly.

evolutionary biology↗

Experimental and theoretical support for costs of plasticity and phenotype in a nematode cannibalistic trait

Developmental plasticity is the ability of a genotype to express multiple phenotypes under different environmental conditions and has been shown to facilitate the evolution of novel traits. However, while the associated cost of plasticity, i.e., the loss in fitness due to the plastic response to environment, and the cost of phenotype, i.e., the loss of fitness due to expressing a fixed phenotype across environments, have been theoretically predicted, empirically such costs remain poorly documented and little understood. Here, we use a plasticity model system, hermaphroditic nematode Pristionchus pacificus, to experimentally measure these costs in wild isolates under controlled laboratory conditions. P. pacificus can develop either a bacterial feeding or predatory mouth morph in response to different external stimuli, with natural variation of mouth-morph ratios between strains. We first demonstrated the cost of phenotype by analyzing fecundity and developmental speed in relation to mouth morphs across the P. pacificus phylogenetic tree. Then, we exposed P. pacificus strains to two distinct microbial diets that induce strain-specific mouth-form ratios. Our results indicate that the plastic strain does shoulder a cost of plasticity, i.e., the diet-induced predatory mouth morph is associated with reduced fecundity and slower developmental speed. In contrast, the non-plastic strain suffers from the cost of phenotype since its phenotype does not change to match the unfavorable bacterial diet, but shows increased fitness and higher developmental speed on the favorable diet. Furthermore, using a stage-structured population model based on empirically-derived life history parameters, we show how population structure can alleviate the cost of plasticity in P. pacificus. The results of the model illustrate the extent to which the costs associated with plasticity and its effect of competition depend on ecological factors. This study provides comprehensive support for the costs of plasticity and phenotype based on empirical and modeling approaches. Impact SummaryA genotype able to express a range of phenotypes in response to environmental conditions, that is to demonstrate developmental plasticity, would be a Darwinian demon, able to infinitely adapt and outcompete those genotypes that require genetic change to express a phenotype fit to an environment. It has been suggested that the absence of such demons in nature is due to the cost of plasticity, i.e., developmental plasticity results in a reduction of biological fitness compared to a genotype that facultatively expresses a phenotype matching the environment. While conceptually simple, measuring the cost of plasticity in nature has proven a major challenge. We use the nematode P. pacificus to measure the cost of plasticity. During its development, P. pacificus can assume one of two possible mouth forms: predatory or non-predatory. The likelihood developing any of these two mouth forms is determined by a gene regulatory network, which itself is affected by a wide range on environmental conditions, including diet. We used two strains of P. pacificus and grew them on two different bacterial diets. The plastic strain was capable of switching from non-predatory to predatory mouth form depending on the diet, while the non-plastic strain could only express the predatory mouth form on either of the diets. By measuring the number eggs laid in both strain on each diet, we show that the plastic response is associated with a reduction in fecundity, thus providing a clear example of the cost of plasticity. We then use a stage-structured model to simulate the population dynamics of the plastic and the non-plastic strains. Our simulation show that the cost of plasticity is highly context dependent and its ecological ramifications can be greatly influenced by biotic and abiotic factors.

evolutionary biology↗

The lottery of spermatogenesis

The causes of male infertility are yet to be fully understood. Here, we propose that male infertility can be partly attributed to the insufficiency of cytoplasmically-inherited proteins in sperms. Using a simple stochastic model of spermatogenesis, we show that in a range of parameters, the proportion of viable sperms can be reduced simply due to stochastic transmission of proteins from spermatogonia to spermatids.

developmental biology↗

A hierarchical approach to model decision making: a study in chemotactic behavior of Escherichia coli

Reducing the complex behavior of living entities to its underlying physical and chemical processes is a formidable task in biology. Complex behaviors can be characterized as decision making: the ability to process the incoming information via an intracellular network and act upon this information to choose appropriate strategies. Motility is one such behavior that has been the focus many modeling efforts in the past. Our aim is to reduce the chemotactic behavior in E. coli to its molecular constituents in order to paint a comprehensive and end-to-end picture of this intricate behavior. We utilize a hierarchical approach, consisting of three layers, to achieve this goal: at the first level, chemical reactions involved in chemotaxis are simulated. In the second level, the chemical reactions give rise to the mechanical movement of six independent flagella. At the last layer, the two lower layers are combined to allow a digital bacterium to receive information from its environment and swim through it with verve. Our results are in concert with the experimental studies concerning the motility of E. coli cells. In addition, we show that our detailed model of chemotaxis is reducible to a non-homogeneous Markov process.

systems biology↗

Making ATP fast and slow: do yeasts play a mixed strategy to metabolise glucose?

The ability of some microorganisms to switch from respiration to fermentation in the presence of oxygen-the so-called Crabtree effect-has been a fascinating subject of study at the theoretical and experimental fronts. Game-theoretical approaches have been routinely used to examine and explain the way a microorganism, such as yeast, would switch between the two ATP-producing pathways, i.e., respiration and fermentation. Here we attempt to explain the switch between respiration and fermentation in yeast by constructing a simple metabolic switch. We then utilise an individual-based model, in which each individual is equipped with all the relevant chemical reactions, to see how cells equipped with such metabolic switch would behave in different conditions. We further investigate our proposed metabolic switch using the game-theoretical approach. Based on this model, we postulate that individuals play a mixed game of glucose metabolism in the population. This approach not only sheds some light in the varieties of metabolic regulations that can be utilised by the individual in the population in competition with others for a common resource, it would also allow a better understanding of the causes of the Warburg effect and similar phenomena observed in nature.

systems biology↗

Noise-driven Cell Differentiation and the Emergence of Organization

One of the major transitions in evolution is the step from unicellularity into the brave new world of multicellularity. To understand this feat, one has to fathom two main characteristics of multicellular organisms: differentiation and self-organization. Any explanation concerning this major transition should involve mechanisms that can simultaneously explain the marvellous intricacies manifest in the aforementioned characteristics, and an account of the evolution of such traits. Here we propose a noise-driven differentiation (NDD) model. The reliance on noise, in place of a more mechanistic approach, makes the NDD model a more suitable approach to explain differentiation and self-organization. Furthermore, our model sheds some light on the possible evolutionary origins of these biological innovations. To test the NDD model, we utilize a model of cell aggregation. The behavior of this model of cell aggregation is in concert with the NDD model.

cell biology↗