Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history.

Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their demographic histories and distributions of fitness effects (DFE) of mutations. Here, we infer the demographic histories and DFEs for amino-acid changing mutations of 39 of the most prevalent and abundant commensal gut microbial species found in Westernized individuals over timescales exceeding human generations. Some species display contractions in population size and others expansions, with several of these events coinciding with several key historical moments in human history.

Parasitoid avoidance of intraguild predation drives enemy complementarity in a multi-trophic ecological network.

How consumer diversity determines consumption efficiency is a central issue in ecology. In the context of predation and biological control, this relationship concerns predator diversity and predation efficiency. Reduced predation efficiency can result from different predator taxa eating each other in addition to their common prey (interference due to intraguild predation).

Revealing trends in measles immunity during periods of varying measles circulation in Madagascar.

Estimating the durability of immunity from vaccination is complicated by unreported re-vaccination, and unobserved natural infection or reexposure, which could result in overestimation of protection longevity. We tested serial cross-sectional serum samples from 2005 to 2015 (N=2,530) for IgG to examine measles seroprevalence, spatiotemporal patterns of titers across regions and antibody dynamics among children aged 1-9 years who grew up during varying measles circulation in Madagascar under a one-dose vaccination schedule. We found that measles seroprevalence has generally decreased over this time period.

More than a token photo: humanizing scientists enhances student engagement.

Despite broad consensus that highlighting counter-stereotypical scientist role models in educational materials promotes equity and success, the specific elements that make these materials effective remain untested. Are pictures of counter-stereotypical scientists enough to communicate to students that scientists come from a variety of backgrounds, or is additional information required? To parse the effects of including visual depictions and humanizing information about scientists featured in biology course materials, we distributed three randomized versions of assignments over several academic terms across 36 undergraduate institutions ( > 3700 students). We found that including humanizing information about scientists was key to increasing student engagement with the biology course materials.

Submarine groundwater discharge drives both direct and indirect effects on organismal and community metabolism on coral reefs.

Coral reefs experience numerous environmental gradients affecting organismal physiology and species biodiversity, which ultimately impact community metabolism. This study shows that submarine groundwater discharge (SGD), a common natural environmental gradient in coastal ecosystems associated with decreasing temperatures, salinity and pH with increasing nutrients, has both direct and indirect effects on coral reef community metabolism by altering individual growth rates and community composition. Our data revealed that SGD exposure hindered the growth of two algae, and by 67 and 200%, respectively, and one coral, by 20%.

Protein quality control is a master modulator of molecular evolution in bacteria.

The bacterial protein quality control (PQC) network comprises a set of genes that promote proteostasis (proteome homeostasis) through proper protein folding and function via chaperones, proteases, and a protein translational machinery. It participates in vital cellular processes and influences organismal development and evolution. In this review, we examine the mechanistic bases for how the bacterial PQC network influences molecular evolution.

Supercooling tolerance in the Mexican lizard Barisia imbricata (Squamata: Anguidae).

Environmental temperature impacts the physiological processes of reptiles, determines their hours of activity per day, and may constrain their ability to meet critical ecological requirements. When environmental temperatures reach freezing, a few lizard species exhibit two mechanisms (supercooling and freezing tolerance) to survive freezing, and these two processes depend on cryoprotective molecules, such as glucose. Organisms produce high glucose concentrations to reach lower than normal crystallisation points, and this blood glucose concentration can double after freezing.

Causal Inference With Observational Data and Unobserved Confounding Variables.

Experiments have long been the gold standard for causal inference in Ecology. As Ecology tackles progressively larger problems, however, we are moving beyond the scales at which randomised controlled experiments are feasible. To answer causal questions at scale, we need to also use observational data -something Ecologists tend to view with great scepticism.

Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics.

Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic relationships of fossil taxa. However, the enamelome is based on only about 10 genes, whose protein products undergo fragmentation in vivo and post mortem.

Critical reproductive behaviors in Scaled Quail and Northern Bobwhite are affected by thermal variability and mean temperature.

Animals can respond differently to shifting thermal variability versus thermal averages, both of which are changing due to climate warming. How these thermal variables affect parental care behaviors can reveal the ability of parents to modify their behaviors to meet the competing demands of their offspring's thermal needs and self-maintenance, which becomes critical in suboptimal thermal conditions. Further, the time frame used to examine the interplay between temperature and behavioral shifts (e.

Impacts of Weather Anomalies and Climate on Plant Disease.

Predicting the effects of climate change on plant disease is critical for protecting ecosystems and food production. Here, we show how disease pressure responds to short-term weather, historical climate and weather anomalies by compiling a global database (4339 plant-disease populations) of disease prevalence in both agricultural and wild plant systems. We hypothesised that weather and climate would play a larger role in disease in wild versus agricultural plant populations, which the results supported.

Unfriendly neighbors: When facilitation does not contribute to restoration success in tidal marsh.

Large-scale restoration projects are an exciting and often untapped opportunity to use an experimental approach to inform ecosystem management and test ecological theory. In our $10M tidal marsh restoration project, we installed over 17,000 high marsh plants to increase cover and diversity, using these plantings in a large-scale experiment to test the benefits of clustering and soil amendments across a stress gradient. Clustered plantings have the potential to outperform widely spaced ones if plants alter conditions in ways that decrease stress for close neighbors.

Wood-loving magic mushrooms from Australia are saprotrophic invaders in the Northern Hemisphere.

Magic mushrooms are fungi that produce psilocybin, an entheogen with long-term cultural use and a breakthrough compound for treatment of mental health disorders. Fungal populations separated by geography are candidates for allopatric speciation, yet species connectivity typically persists because there is minimal divergence at functional parts of mating compatibility genes. We studied whether connectivity is maintained across populations of a widespread species complex of magic mushrooms that has infiltrated the Northern Hemisphere from a hypothesised centre of origin in Australasia.

Fungal Planet description sheets: 1697-1780.

Novel species of fungi described in this study include those from various countries as follows: , from accumulated snow sediment sample. , on leaf spots of . , on submerged decaying wood in sea water, on , as endophyte from healthy leaves of .

From spots to stripes: Evolution of pigmentation patterns in monkeyflowers via modulation of a reaction-diffusion system and its prepatterns.

The reaction-diffusion (RD) system is widely assumed to account for many complex, self-organized pigmentation patterns in natural organisms. However, the specific configurations of such RD networks and how RD systems interact with positional information (i.e.

Species-habitat networks reveal conservation implications that other community analyses do not detect.

Grassland restoration is an important conservation intervention supporting declining insect pollinators in threatened calcareous grassland landscapes. While the success of restoration is often quantified using simple measures of diversity or similarity to target communities, these measures do not capture all fundamental aspects of community reconstruction. Here, we develop species-habitat networks that aim to define habitat-level foraging dependencies of pollinators across restored grassland landscapes and compare their value to these more conventional measures of community restoration.

A juvenile spinner shark in southern New England: A rare visitor or a sign of change?

A juvenile spinner shark, Carcharhinus brevipinna, was captured and released in the coastal waters of Rhode Island, USA, where range delineations based on historic records of spinner sharks and the species' congener, the blacktip shark, Carcharhinus limbatus, are plagued by misidentification. The shark in question was within the size range of neonates for C. brevipinna and bore a partially healed umbilical wound.

Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.

Bacterial cellulose (BC) holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges in bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships.

Chemical signals and social structures strengthen sexual isolation in Drosophila pseudoobscura.

Species that coexist in hybrid zones sexually isolate through reproductive character displacement, a mechanism that favours divergence between species. In Drosophila, behavioural and physiological traits discourage heterospecific mating between species. Recently, social network analysis revealed flies produce strain-specific and species-specific social structures.

The population dynamics of clustered consumer-resource spatial patterns: Insights from the demographics of a Turing mechanism.

In ecology, Alan Turing's proposed activation-inhibition mechanism has been abstracted as corresponding to several ecological interaction types to explain pattern formation in ecosystems. Consumer-resource interactions have strong theoretical arguments linking them to both the Turing mechanism and pattern formation, but there is little empirical support to demonstrate these claims. Here, we connect several lines of evidence to support the proposition that consumer-resource interactions can create empirically observed spatial patterns through a mechanism similar to Turing's theory.

Similar Conditions With Opposite Effects: Predation-Risk Effects on Prey Abundance Are Highly Contingent.

Experiments have shown that predation-risk effects on prey fitness can be highly contingent on environmental conditions, suggesting a potential difficulty in generalizing risk effects on prey abundance in natural settings. Rather than study the influence of a particular controlled factor, we examine the problem with a novel approach. We examined the influence of risk effects in multiple experiments performed under similar study conditions.

Punctuated versus gradual shifts in the multivariate evolutionary process: a test with paired radiations of scincid lizards.

As lineages become separated in time, they are expected to accumulate mutational (or developmental-genetic) differences that influence the macroevolutionary trajectories of those lineages even under similar environmental conditions. Here, we compare the dynamics of phenotypic evolution in radiations of scincid lizards from Australia and Madagascar that are separated by more than 100 million years of independent evolution and show rampant phenotypic parallelism. We collected linear measurements of the skull, limbs, and limb girdles from micro-CT scans of 94 Australian and 29 Malagasy species.

Strengthening serological studies: the need for greater geographical diversity, biobanking, and data-accessibility.

Serological studies uniquely strengthen infectious disease surveillance, expanding prevalence estimates to encompass asymptomatic infections, and revealing the otherwise inapparent landscape of immunity, including who is and is not susceptible to infection. They are thus a powerful complement to often incomplete epidemiological and public health measures (administrative measures of vaccination coverage, incidence estimates, etc.).

Decoding the blueprint of receptor binding by filoviruses through large-scale binding assays and machine learning.

Evidence suggests that bats are important hosts of filoviruses, yet the specific species involved remain largely unidentified. Niemann-Pick C1 (NPC1) is an essential entry receptor, with amino acid variations influencing viral susceptibility and species-specific tropism. Herein, we conducted combinatorial binding studies with seven filovirus glycoproteins (GPs) and NPC1 orthologs from 81 bat species.

Application of the DRASTIC Model to Assess the Vulnerability of Groundwater Contamination Near Zaporizhzhia Nuclear Power Plant, Ukraine.

Russia's invasion of Ukraine continues to have a devastating effect on the well-being of Ukrainians and their environment. We evaluated a major environmental hazard caused by the war: the potential for groundwater contamination in proximity to the Zaporizhzhia Nuclear Power Plant (NPP). We quantified groundwater vulnerability with the DRASTIC index, which was originally developed by the United States Environmental Protection Agency and has been used at various locations worldwide to assess relative pollution potential.