@article {163323, title = {Bottleneck size drives the evolution of cooperative traits in an aggregative multicellular myxobacterium.}, journal = {PLoS Biol}, volume = {24}, year = {2026}, month = {2026 Jan}, pages = {e3003499}, abstract = {

Repeated population bottlenecks influence the evolution and maintenance of cooperation. However, it remains unclear whether bottlenecks select all cooperative traits expressed by an organism or only a subset of them. Myxococcus xanthus, a social bacterium, displays multiple cooperative traits, including growth, predation, sporulation in multicellular fruiting bodies, and germination. Using laboratory evolution experiments, we investigated the effect of repeated stringent versus relaxed population bottlenecks on the evolution of these four cooperative traits when they were all under selection. We found that only fruiting body formation and growth were positively selected under the stringent regimen, while the other two traits were selected against. The pattern was reversed in the relaxed regimen. Populations propagated under the relaxed regimen also exhibited greater fitness across the entire\ life cycle\ and maintained higher trait variations, including coexistence of cooperative and exploitative strategies. Genomic analyses identified mutations in σ54 interacting protein and DNA binding response regulator protein associated with adaptations in stringent and relaxed regimens, respectively. Furthermore, similar trade-offs, for example, between sporulation and germination, are also seen among natural populations of M. xanthus. Overall, we demonstrate that different bottleneck sizes drive the evolution of cooperative life history traits in distinct ways, often via trade-offs that constrain their joint optimization.

}, keywords = {Bacterial Proteins, Biological Evolution, Mutation, Myxococcus xanthus, Selection, Genetic, Spores, Bacterial}, issn = {1545-7885}, doi = {10.1371/journal.pbio.3003499}, url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003499}, author = {Kalathera, Jyotsna and Jaiswal, Prakhar and Mandal, Neha and Patel, Vishwa and Guttal, Vishwesha and Krishna, Sandeep and Pande, Samay} } @article {160485, title = {Founders predict trait evolution and population performance after evolutionary rescue in the red flour beetle.}, journal = {Proc Natl Acad Sci U S A}, volume = {122}, year = {2025}, month = {2025 Sep 09}, pages = {e2506244122}, abstract = {

Evolutionary rescue helps populations survive environmental change, but the phenotypic and demographic factors associated with rescue dynamics and its long-term effects remain unclear. We experimentally evolved 10 wild-collected populations of flour beetles from across India in a suboptimal corn resource for 70 generations (\>5 y), collecting \>10,000 population census points book-ended by measurements of fitness-related traits for 30 experimental lines. Despite clear ancestral trait differences, all lines showed highly parallel evolutionary rescue within 20 generations. Long-term average population size varied across source populations and was positively correlated with ancestral development rate, which increased convergently across populations and emerged as the single best predictor of population performance during and after evolutionary rescue. Notably, specific demographic events during rescue (such as the rate of population decline and recovery) were uncorrelated both with ancestral trait distributions and post-rescue adaptation. Our results support prior work showing founder traits as key predictors of adaptation, and highlight their role in long-term adaptation and trait evolution following evolutionary rescue.

}, keywords = {Adaptation, Physiological, Animals, Biological Evolution, Coleoptera, India, Phenotype, Population Density, Population Dynamics}, issn = {1091-6490}, doi = {10.1073/pnas.2506244122}, author = {Ravi Kumar, Vrinda and Buddh, Shyamsunder and Singhal, Shivansh and Prakash, Arun and Agashe, Deepa} } @article {160479, title = {Global selection on insect antipredator coloration.}, journal = {Science}, volume = {389}, year = {2025}, month = {2025 Sep 25}, pages = {1336-1341}, abstract = {

Natural selection has repeatedly led to the evolution of two alternative antipredator color strategies-camouflage to avoid detection and aposematism to advertise unprofitability-but we lack understanding of how ecological context favors one strategy over the other. We conducted a globally replicated predation experiment at 21 sites on six continents to test how predator community, prey community, and visual environment influenced the predation risk of 15,018 artificial paper "moth" prey with cryptic or warning coloration. Results indicated that aposematic strategies fare better in environments with low predation intensity, whereas camouflage strategies are advantaged when other camouflaged prey species are rare and when light levels are low. This study demonstrates how multiple mechanisms shape antipredator strategies, helping to explain the evolution and global distribution of camouflaged and aposematic animals.

}, keywords = {Animals, Biological Evolution, Biological Mimicry, Color, Ecosystem, Insecta, Pigmentation, Predatory Behavior, Selection, Genetic}, issn = {1095-9203}, doi = {10.1126/science.adr7368}, author = {Medina, Iliana and Exnerov{\'a}, Alice and Da{\v n}kov{\'a}, Kl{\'a}ra and Penacchio, Olivier and Sherratt, Tom N and Albrecht, Tom{\'a}{\v s} and Baidya, Sarika and Bosque, Renan Janke and Brown, H{\'e}lo{\"\i}se and Burdfield-Steel, Emily and Cain, Kristal E and Cez{\'a}rio, Rodrigo Roucourt and Chiari, Ylenia and Esquivel, Carolina and Ferreira, Rhainer Guillermo and Franklin, Amanda M and Garvey, Aloise and Guchu, Samuel and Hastings, Brandon T and Hotov{\'a}-Sv{\'a}dov{\'a}, Kate{\v r}ina and Hwang, Yerin and Kang, Changku and Kasaya, John and Kelley, Jennifer and Kim, Yongsu and Kunte, Krushnamegh and Daetto-Liberato, Felipe and Loeffler-Henry, Karl and Lopez, Vinicius Marques and MacKay-Dietrich, Claire and Mappes, Johanna and De M{\'a}rsico, Mar{\'\i}a Cecilia and Nawge, Viraj and Njoroge, Peter and Nokelainen, Ossi and Pal, Arka and Paul, Archan and Posont, Robert and Ra{\v s}ka, Jan and Reboreda, Juan Carlos and Rojas Ripari, Juan Manuel and Rowland, Hannah M and Sabio, Maria de Las Nieves and Salazar, Camilo and Salgado-Roa, Fabian C and Stephens-C{\'a}rdenas, Steve A and Szab{\'o}, Anita and Mongui Torres, Juan Pablo and Troscianko, Jolyon and Truhl{\'a}{\v r}ov{\'a}, Marie and Umbers, Kate D L and Venton, Molly and Vitasovich, Makenzie and Wang, Lu-Yi and Weil, Sarah-Sophie and Allen, William L} } @article {125200, title = {The layered costs and benefits of translational redundancy.}, journal = {Elife}, volume = {12}, year = {2023}, month = {2023 Mar 02}, abstract = {

The rate and accuracy of translation hinges upon multiple components - including transfer RNA (tRNA) pools, tRNA modifying enzymes, and rRNA molecules - many of which are redundant in terms of gene copy number or function. It has been hypothesized that the redundancy evolves under selection, driven by its impacts on growth rate. However, we lack empirical measurements of the fitness costs and benefits of redundancy, and we have poor a understanding of how this redundancy is organized across components. We manipulated redundancy in multiple translation components of by deleting 28 tRNA genes, 3 tRNA modifying systems, and 4 rRNA operons in various combinations. We find that redundancy in tRNA pools is beneficial when nutrients are plentiful and costly under nutrient limitation. This nutrient-dependent cost of redundant tRNA genes stems from upper limits to translation capacity and growth rate, and therefore varies as a function of the maximum growth rate attainable in a given nutrient niche. The loss of redundancy in rRNA genes and tRNA modifying enzymes had similar nutrient-dependent fitness consequences. Importantly, these effects are also contingent upon interactions across translation components, indicating a layered hierarchy from copy number of tRNA and rRNA genes to their expression and downstream processing. Overall, our results indicate both positive and negative selection on redundancy in translation components, depending on a species{\textquoteright} evolutionary history with feasts and famines.

}, keywords = {Biological Evolution, Cost-Benefit Analysis, Escherichia coli, Exercise, Gene Dosage}, issn = {2050-084X}, doi = {10.7554/eLife.81005}, author = {Raval, Parth K and Ngan, Wing Yui and Gallie, Jenna and Agashe, Deepa} } @article {121923, title = {The tempo and mode of character evolution in the assembly of mimetic communities.}, journal = {Proc Natl Acad Sci U S A}, volume = {120}, year = {2023}, month = {2023 Jan 03}, pages = {e2203724120}, abstract = {

Multitrait adaptive evolution is shaped by factors such as phylogenetic and functional constraints as well as the intensity and direction of selection. The tempo and mode of such multitrait evolution can differentially impact the assembly of biological communities. Batesian mimicry, in which undefended prey gain a fitness advantage by evolving a resemblance to aposematic models, involves adaptive evolution of multiple traits such as color patterns and flight morphology. To elucidate the evolutionary mechanisms of such multitrait adaptations, we evaluated the tempo and mode of adaptive convergence in flight morphology and color patterns in mimetic butterfly communities. We found that compared with Batesian mimics or nonmimetic sister species, models showed significantly faster rates of aposematic trait evolution, creating adaptive peaks for mimicry. At the community level, the degree of mimetic resemblance between mimics and models was positively correlated with the rate of character evolution, but independent of phylogenetic relatedness. Monomorphic mimics and female-limited mimics converged on the color patterns of models to a similar degree, showing that there were no constraints on mimetic trait evolution with respect to sex-specific selections. Convergence was driven by the greater lability of color patterns, which evolved at significantly faster rates than the phylogenetically conserved flight morphological traits, indicating that the two traits evolve under differential selection pressures and/or functional and genetic constraints. These community-wide patterns show that during the assembly of a community, the tempo of adaptive evolution is nonlinear, and specific to the underlying functional relationships and key traits that define the community.

}, keywords = {Animals, Biological Evolution, Biological Mimicry, Biota, Butterflies, Excipients, Female, Male, Phylogeny, Predatory Behavior}, issn = {1091-6490}, doi = {10.1073/pnas.2203724120}, author = {Basu, Dipendra Nath and Bhaumik, Vaishali and Kunte, Krushnamegh} } @article {137346, title = {A theoretical perspective on Waddington{\textquoteright}s genetic assimilation experiments.}, journal = {Proc Natl Acad Sci U S A}, volume = {120}, year = {2023}, month = {2023 Dec 19}, pages = {e2309760120}, abstract = {

Genetic assimilation is the process by which a phenotype that is initially induced by an environmental stimulus becomes stably inherited in the absence of the stimulus after a few generations of selection. While the concept has attracted much debate after being introduced by C. H. Waddington 70 y ago, there have been few experiments to quantitatively characterize the phenomenon. Here, we revisit and organize the results of Waddington{\textquoteright}s original experiments and follow-up studies that attempted to replicate his results. We then present a theoretical model to illustrate the process of genetic assimilation and highlight several aspects that we think require further quantitative studies, including the gradual increase of penetrance, the statistics of delay in assimilation, and the frequency of unviability during selection. Our model captures Waddington{\textquoteright}s picture of developmental paths in a canalized landscape using a stochastic dynamical system with alternative trajectories that can be controlled by either external signals or internal variables. It also reconciles two descriptions of the phenomenon-Waddington{\textquoteright}s, expressed in terms of an individual organism{\textquoteright}s developmental paths, and that of Bateman in terms of the population distribution crossing a hypothetical threshold. Our results provide theoretical insight into the concepts of canalization, phenotypic plasticity, and genetic assimilation.

}, keywords = {Adaptation, Physiological, Biological Evolution, Epigenesis, Genetic, Models, Genetic, Penetrance, Phenotype}, issn = {1091-6490}, doi = {10.1073/pnas.2309760120}, author = {Raju, Archishman and Xue, BingKan and Leibler, Stanislas} } @article {112957, title = {The thermal niche and phylogenetic assembly of evergreen tree metacommunities in a mid-to-upper tropical montane zone.}, journal = {Proc Biol Sci}, volume = {289}, year = {2022}, month = {2022 Jun 29}, pages = {20220038}, abstract = {

Frost and freezing temperatures have posed an obstacle to tropical woody evergreen plants over evolutionary time scales. Thus, along tropical elevation gradients, frost may influence woody plant community structure by filtering out lowland tropical clades and allowing extra-tropical lineages to establish at higher elevations. Here we assess the extent to which frost and freezing temperatures influence the taxonomic and phylogenetic structure of naturally patchy evergreen forests (locally known as ) along a mid-upper montane elevation gradient in the Western Ghats, India. Specifically, we examine the role of large-scale macroclimate and factors affecting local microclimates, including patch size and distance from edge, in driving metacommunity structure. We find that the metacommunity shows phylogenetic overdispersion with elevation, with greater representation of extra-tropical lineages above 2000 m, and marked turnover in taxonomic composition of woody communities near the frost-affected forest edge above 2000 m, from those below 2000 m. Both minimum winter temperature and patch size were equally important in determining metacommunity structure, with plots inside very large dominated by older tropical lineages, with many endemics. Phylogenetic overdispersion in the upper montane metacommunity thus resulted from tropical lineages persisting in the interiors of large closed frost-free where their regeneration niche has been preserved over time.

}, keywords = {Biological Evolution, Cold Temperature, Fever, Forests, Phylogeny, Wood}, issn = {1471-2954}, doi = {10.1098/rspb.2022.0038}, author = {Das, Arundhati Abin and Ratnam, Jayashree} } @article {25260, title = {Genetic Structure and Phylogeography of the Leopard Cat (Prionailurus bengalensis) Inferred from Mitochondrial Genomes.}, journal = {J Hered}, volume = {108}, year = {2017}, month = {2017 06 01}, pages = {349-360}, abstract = {

The Leopard cat Prionailurus bengalensis is a habitat generalist that is widely distributed across Southeast Asia. Based on morphological traits, this species has been subdivided into 12 subspecies. Thus far, there have been few molecular studies investigating intraspecific variation, and those had been limited in geographic scope. For this reason, we aimed to study the genetic structure and evolutionary history of this species across its very large distribution range in Asia. We employed both PCR-based (short mtDNA fragments, 94 samples) and high throughput sequencing based methods (whole mitochondrial genomes, 52 samples) on archival, noninvasively collected and fresh samples to investigate the distribution of intraspecific genetic variation. Our comprehensive sampling coupled with the improved resolution of a mitochondrial genome analyses provided strong support for a deep split between Mainland and Sundaic Leopard cats. Although we identified multiple haplogroups within the species{\textquoteright} distribution, we found no matrilineal evidence for the distinction of 12 subspecies. In the context of Leopard cat biogeography, we cautiously recommend a revision of the Prionailurus bengalensis subspecific taxonomy: namely, a reduction to 4 subspecies (2 mainland and 2 Sundaic forms).

}, keywords = {Animals, Asia, Southeastern, Biological Evolution, Cytochromes b, DNA, Mitochondrial, Felidae, Genetic Variation, Genetics, Population, Genome, Mitochondrial, Haplotypes, Phylogeography, Sequence Analysis, DNA}, issn = {1465-7333}, doi = {10.1093/jhered/esx017}, author = {Patel, Riddhi P and Wutke, Saskia and Lenz, Dorina and Mukherjee, Shomita and Ramakrishnan, Uma and Veron, G{\'e}raldine and Fickel, J{\"o}rns and Wilting, Andreas and F{\"o}rster, Daniel W} }