Biology subjects

Mehta, R. S.

Publications and source records attributed to Mehta, R. S..

5 recordsLinked to original sources

bioRxiv2022

50 shades of greenbeard: Robust evolution of altruism based on similarity of complex phenotypes

We study the evolution of altruistic behavior under a model where individuals choose to cooperate by comparing a set of continuous phenotype tags. Individuals play a donation game and only donate to other individuals that are sufficiently similar to themselves in a multidimensional phenotype space. We find the generic maintenance of robust altruism when phenotypes are multidimensional. Selection for altruism is driven by the coevolution of individual strategy and phenotype; altruism levels shape the distribution of individuals in phenotype space. Low donation rates induce a phenotype distribution that renders the population vulnerable to the invasion of altruists, whereas high donation rates prime a population for cheater invasion, resulting in cyclic dynamics that maintain substantial levels of altruism. Altruism is therefore robust to invasion by cheaters in the long term in this model. Furthermore, the shape of the phenotype distribution in high phenotype dimension--which is potentially more biologically relevant than low phenotype dimension--allows altruists to better resist the invasion by cheaters, and as a result the amount of donation increases with increasing phenotype dimension. We also generalize previous results in the regime of weak selection to two competing strategies in continuous phenotype space, and show that success under weak selection is crucial to success under strong selection in our model. Our results support the viability of a simple similarity-based mechanism for altruism in a well-mixed population.

evolutionary biology↗

bioRxiv2022

Detecting patterns of accessory genome coevolution in bacterial species using data from thousands of bacterial genomes

Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes that we call a "coevolution score". The method is based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. This approach avoids the need for an accurate phylogenetic tree and allows very large datasets to be analyzed for signatures of recent coevolution. We apply our method to all of the more than 3 million pairs of genes from the entire annotated Staphylococcus aureus accessory genome of 2,756 annotated genes using a database of over 40,000 whole genomes. We find many pairs of genes that that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of dozens of rapidly coevolving genes, primarily consisting of genes involved in metal resistance, virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. Our results reflect the fact that the evolution of many bacterial pathogens since the middle of the twentieth century has largely been driven by antibiotic resistance gene gain, and in the case of S. aureus the SCCmec complex is the most prominent of these elements driving the evolution of resistance. The frequent coincidence of these gene gain or loss events suggests that S. aureus switch between antibiotic-resistant niches and antibiotic-susceptible ones. While we focus on gene gain and loss, our method can also detect genes which tend to acquire substitutions in tandem or, in datasets that include phenotypic information, genotype-phenotype or phenotype-phenotype coevolution.

genomics↗

bioRxiv2021

The probability of joint monophyly of all species in an arbitrary species tree.

Monophyly is a feature of a set of genetic lineages in which every lineage in the set is more closely related to all other members of the set than it is to any lineage outside the set. Multiple sets of lineages that are separately monophyletic are said to be reciprocally monophyletic, or jointly monophyletic. The prevalence of reciprocal monophyly, or joint monophyly, has been used to evaluate phylogenetic and phylogeographic hypotheses, as well as to delimit species. These applications often make use of a probability of joint monophyly under models of gene lineage evolution. Studies in coalescent theory have computed this joint monophyly probability for small numbers of separate groups in arbitrary species trees, and for arbitrary numbers of separate groups in trivial species trees. Here, generalizing existing results on monophyly probabilities under the multispecies coalescent, we derive the probability of joint monophyly for arbitrary numbers of separate groups in arbitrary species trees. We illustrate how our result collapses to previously examined cases. We also study the effect of tree height, sample size, and number of species on the probability of joint monophyly. The result also enables computation of relatively simple lower and upper bounds on the joint monophyly probability. Our results expand the scope of joint monophyly calculations beyond small numbers of species, subsuming past formulas that have been used in simpler cases.

evolutionary biology↗

bioRxiv2021

Diet-derived metabolites and mucus link the gut microbiome to fever after cytotoxic cancer treatment

Not all cancer patients with severe neutropenia develop fever, and the fecal microbiome may play a role. In neutropenic hematopoietic cell transplant patients (n=119), 63 (53%) developed a subsequent fever and had increased fecal Akkermansia muciniphila, a mucus-degrading bacteria (p=0.006, corrected for multiple comparisons). In mouse models, two therapies, irradiation and melphalan, similarly expanded A. muciniphila. Dietary restriction of unirradiated mice also expanded A. muciniphila and thinned the colonic mucus layer. Azithromycin treatment depleted A. muciniphila and preserved colonic mucus. Dietary restriction raised colonic luminal pH and reduced acetate, propionate, and butyrate. Culturing A. muciniphila with lower pH and increased propionate prevented utilization of mucin. Treating irradiated mice with azithromycin or propionate preserved the mucus layer, lessened hypothermia, and reduced inflammatory cytokines in the colon. These results suggest that diet, metabolites and colonic mucus link the microbiome to neutropenic fever, and could guide future microbiome-based preventive strategies.

microbiology↗

bioRxiv2020

The Azolla fern symbiosis sexual reproduction requires far-red light and involves responsive CMADS1 homologue, miR319-controlled GAMYB, miR529 in the fern and transporters in the symbiont

Azolla ferns and the filamentous cyanobacteria Nostoc azollae constitute a model symbiosis that enabled colonization of the water surface with traits highly desirable for development of more sustainable crops: their floating mats capture CO2 and fixate N2 at high rates phototrophically. Their mode of sexual reproduction is heterosporous. Regulation of the transition from vegetative to spore-forming phases in ferns is largely unknown, yet a pre-requisite for Azolla domestication, and of particular interest since ferns represent the sister lineage of seed plants. Far-red light (FR) induced sporocarp formation in A. filiculoides. Sporocarps obtained, when crossed, verified species attribution of Netherlands strains but not Irans Anzali lagoon. FR-responsive transcripts included CMADS1 MIKCC-homologues and miRNA-controlled GAMYB transcription factors in the fern, transporters in N.azollae, and ycf2 in chloroplasts. Loci of conserved miRNA in the fern lineage included miR172, yet FR only induced miR529 and miR535, and reduced miR319 and miR159. Suppression of sexual reproduction in both gametophyte and sporophyte-dominated plant lineages by red light is likely a convergent ecological strategy in open fields as the active control networks in the different lineages differ. MIKCC transcription factor control of flowering and flower organ specification, however, likely originated from the diploid to haploid phase transition in the homosporous common ancestor of ferns and seed plants.

plant biology↗