Comparative Dating Of Attine Ant And Lepiotaceous Cultivar Phylogenies Reveals Coevolutionary Synchrony And Discord

The mutualistic symbiosis between fungus-gardening ants and their cultivars has made fundamental contributions to our understanding of the coevolution of complex species interactions. Reciprocal specialization and vertical symbiont cotransmission are thought to promote a pattern of largely synchronous coevolutionary diversification in attines. Here we test this hypothesis by inferring the first time-calibrated multigene phylogeny of the lepiotaceous attine cultivars and comparing it with the recently published fossil-anchored phylogeny of the attine ants. While this comparison reveals some possible cases of synchronous origins of ant and fungal clades, there were a number of surprising asynchronies. For example, leaf-cutter cultivars appear to be significantly younger than the corresponding ant genera. Similarly, a clade of fungi interacting with primitive fungus-gardening ants-thought to be ancestral to the more derived leaf-cutter symbionts-appears instead to be a more recent acquisition from free-living stock. These macroevolutionary patterns are consistent with recent population-level studies suggesting occasional acquisition of novel cultivar types from environmental sources and horizontal transmission of cultivars between different ant species. Horizontal transmission events, even if rare, appear to form loose ecological connections between diffusely coevolving ant and fungus lineages that permit punctuated changes in the topology of the mutualistic ant-fungus interaction network.Integrative Biolog

Allometry of Workers of the Fire Ant, Solenopsis invicta

The relationship between worker body size and the shape of their body parts was explored in the polymorphic ant, Solenopsis invicta. The data consisted of 20 measurements of body parts as well as sums of some of these measurements. Size-free shape variables were created by taking the ratios of relevant measures. After log-transformation, these ratios were regressed against the logarithm of total body length, or against the log of the size of the parent part. Slopes of zero indicated that shape did not change with size, and non-zero slopes signaled a size-related change of shape. Across the range of worker sizes, the head length retained a constant proportion to body length, but relative headwidth increased such that head shape changed from a barrel-profile to a somewhat heart-shaped profile. Antennae became relatively smaller, with the club contributing more to this decline than the other parts. The alinotum became relatively shorter and higher (more humped), and the gaster increased in both relative width and length, and therefore in volume. All three pairs of legs were isometric to body length. The component parts of the legs, with one exception, were isometric to their own total leg length. The body of S. invicta Abbreviation: / HL: head length BL: body length HW1: width across the eyes HW2: width above the eyes HW3: width below the eye

Construction and analysis of a simplified many-body neutrino model

In dense neutrino systems, such as found in the early Universe, or near a supernova core, neutrino flavor evolution is affected by coherent neutrino-neutrino scattering. It has been recently suggested that many-particle quantum entanglement effects may play an essential role in these systems, potentially invalidating the traditional description in terms of a set of single-particle evolution equations. We model the neutrino system by a system of interacting spins, following an earlier work which showed that such a spin system can in some cases be solved exactly. We extend this work by constructing an exact analytical solution to a more general spin system, including initial states with asymmetric spin distribution and, moreover, not necessarily aligned along the same axis. Our solution exhibits a rich set of behaviors, including coherent oscillations and dephasing and a transition from the classical to quantum regimes. We argue that the classical evolution of the spin system captures the entire coherent behavior of the neutrino system, while the quantum effects in the spin system capture some, but not all, of the neutrino incoherent evolution. By comparing the spin and neutrino systems, we find no evidence for the violation of the accepted one-body description, though the argument involves some subtleties not appreciated before. The analysis in this paper may apply to other two-state systems beyond the neutrino field.Comment: 22 pages, 7 figure

Towards dense object tracking in a 2D honeybee hive

From human crowds to cells in tissue, the detection and efficient tracking of multiple objects in dense configurations is an important and unsolved problem. In the past, limitations of image analysis have restricted studies of dense groups to tracking a single or subset of marked individuals, or to coarse-grained group-level dynamics, all of which yield incomplete information. Here, we combine convolutional neural networks (CNNs) with the model environment of a honeybee hive to automatically recognize all individuals in a dense group from raw image data. We create new, adapted individual labeling and use the segmentation architecture U-Net with a loss function dependent on both object identity and orientation. We additionally exploit temporal regularities of the video recording in a recurrent manner and achieve near human-level performance while reducing the network size by 94% compared to the original U-Net architecture. Given our novel application of CNNs, we generate extensive problem-specific image data in which labeled examples are produced through a custom interface with Amazon Mechanical Turk. This dataset contains over 375,000 labeled bee instances across 720 video frames at 2 FPS, representing an extensive resource for the development and testing of tracking methods. We correctly detect 96% of individuals with a location error of ~7% of a typical body dimension, and orientation error of 12 degrees, approximating the variability of human raters. Our results provide an important step towards efficient image-based dense object tracking by allowing for the accurate determination of object location and orientation across time-series image data efficiently within one network architecture.Comment: 15 pages, including supplementary figures. 1 supplemental movie available as an ancillary fil

Interactive web-based visualization and sharing of phylogenetic trees using phylogeny.IO

Traditional static publication formats make visualization, exploration, and sharing of massive phylogenetic trees difficult. A phylogenetic study often involves hundreds of taxa, and the resulting tree has to be split across multiple journal pages, or be shrunk onto one, which jeopardizes legibility. Furthermore, additional data layers, such as species-specific information or time calibrations are often displayed in separate figures, making the entire picture difficult for readers to grasp. Web-based technologies, such as the Data Driven Document (D3) JavaScript library, were created to overcome such challenges by allowing interactive displays of complex data sets. The new phylogeny.IO web server (https://phylogeny.io) overcomes this issue by allowing users to easily import, annotate, and share interactive phylogenetic trees. It allows a range of static (e.g. such as shapes and colors) and dynamic (e.g. pop-up text and images) annotations. Annotated trees can be saved on the server for subsequent modification or they may be shared as IFrame HTML objects, easily embeddable in any web page. The principal goal of phylogeny.IO is not to produce publication-ready figures, but rather to provide a simple and intuitive annotation interface that allows easy and rapid sharing of figures in blogs, lecture notes, press releases, etc

Genes associated with ant social behavior show distinct transcriptional and evolutionary patterns

Studies of the genetic basis and evolution of complex social behavior emphasize either conserved or novel genes. To begin to reconcile these perspectives, we studied how the evolutionary conservation of genes associated with social behavior depends on regulatory context, and whether genes associated with social behavior exist in distinct regulatory and evolutionary contexts. We identified modules of co-expressed genes associated with age-based division of labor between nurses and foragers in the ant Monomorium pharaonis, and we studied the relationship between molecular evolution, connectivity, and expression. Highly connected and expressed genes were more evolutionarily conserved, as expected. However, compared to the rest of the genome, forager-upregulated genes were much more highly connected and conserved, while nurse-upregulated genes were less connected and more evolutionarily labile. Our results indicate that the genetic architecture of social behavior includes both highly connected and conserved components as well as loosely connected and evolutionarily labile components.It was funded by University of Pennsylvania with grant name: University Research Foundation grant

Comparative transcriptomics of social insect queen pheromones

Queen pheromones are chemical signals that mediate reproductive division of labor in eusocial animals. Remarkably, queen pheromones are composed of identical or chemically similar compounds in some ants, wasps and bees, even though these taxa diverged > 150MYA and evolved queens and workers independently. Here, we measure the transcriptomic consequences of experimental exposure to queen pheromones in workers from two ant and two bee species (genera: Lasius, Apis, Bombus), and test whether they are similar across species. Queen pheromone exposure affected transcription and splicing at many loci. Many genes responded consistently in multiple species, and the set of pheromone-sensitive genes was enriched for functions relating to lipid biosynthesis and transport, olfaction, production of cuticle, oogenesis, and histone (de)acetylation. Pheromone-sensitive genes tend to be evolutionarily ancient, positively selected, peripheral in the gene coexpression network, hypomethylated, and caste-specific in their expression. Our results reveal how queen pheromones achieve their effects, and suggest that ants and bees use similar genetic modules to achieve reproductive division of labor.Peer reviewe

Using experimental evolution and next-generation sequencing to teach bench and bioinformatic skills

PrePrints 2 Abstract Advances in sequencing technology have exponentially increased data-generating capabilities, 15 and data analysis has now become the major hurdle in many research programs. As sequencing tools become more accessible and automated, experimental design and data analysis skills become the key factors in determining the success of a study. However, proper bioinformatic analysis also relies on a deep understanding of laboratory workflow, in order to prevent biases in the data. This is particularly true if commercial kits are used, as proprietary reagents 20 frequently obfuscate underlying reactions and their conditions. Here we present a training module that seamlessly combines laboratory components (experimental evolution of T5 bacteriophage resistance by Escherichia coli, and library preparation), with bioinformatic analysis of the resulting data. Students conduct a simple genetic variant discovery experiment in the course of about a week. The module uses mature Illumina chemistry for both library 25 preparation and sequencing, though it can be modified for use with any sequencing platform

Integrating host plant phylogeny, plant traits, intraspecific competition and repeated measures using a phylogenetic mixed model of field behaviour by polyphagous herbivores, the leaf-cutting ants

Herbivores use a wide range of factors to choose their host, including their own physiological states, physical characteristics of plants and the degree of competition. Field observations of herbivores in their native habitats provide a means for simultaneously estimating the relative importance of these factors, but statistical analysis of all these factors may be challenging. Here we used a 7-week dataset of leaf-cutting ant (Atta cephalotes) foraging in a diverse Neotropical arboretum containing 193 tree species (822 trees) to examine the relative role of tree phylogeny, territoriality and tree functional characteristics using a phylogenetic generalized least squares (PGLS) model. We observed that 54 tree species (117 trees) were foraged by the ants. This pattern was not random, but reflected known features of leaf-cutting ant foraging behaviour, such as a preference for larger trees and the decreased likelihood of foraging at the periphery of a colony\u27s territory. However, random effects such as tree phylogeny, the identity of individual trees and colony-specific effects explained most of the variation in foraging data. A significant phylogenetic effect on foraging likelihood (lambda = 0.28), together with repeated measures of foraging on the same tree species, allowed estimation of relative palatability for each plant species. PGLS models can be flexibly scaled to include other covariates for even more complex investigation of foraging behaviour, and the link function can be modified to include the amount of plants foraged. As a result, PGLS can be used as a flexible framework for the study of LCA foraging