Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales)

Genome sizes of plants have long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to further test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes, Arabidopsis thaliana—chosen as the model plant system for this reason—as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we confirm correlation between genome size and TE content, however, we are unable to reconstruct phylogenetic relationships and do not detect any shift in TE abundance associated with WGD.

Survival Sounds in Insects: Diversity, Function, and Evolution

Insect defense sounds have been reported for centuries. Yet, aside from the well-studied anti-bat sounds of tiger moths, little is understood about the occurrence, function, and evolution of these sounds. We define a defense sound as an acoustic signal (air- or solid-borne vibration) produced in response to attack or threat of attack by a predator or parasitoid and that promotes survival. Defense sounds have been described in 12 insect orders, across different developmental stages, and between sexes. The mechanisms of defensive sound production include stridulation, percussion, tymbalation, tremulation, and forced air. Signal characteristics vary between species, and we discuss how morphology, the intended receiver, and specific functions of the sounds could explain this variation. Sounds can be directed at predators or non-predators, and proposed functions include startle, aposematism, jamming, and alarm, although experimental evidence for these hypotheses remains scant for many insects. The evolutionary origins of defense sounds in insects have not been rigorously investigated using phylogenetic methodology, but in most cases it is hypothesized that they evolved from incidental sounds associated with non-signaling behaviors such as flight or ventilatory movements. Compared to our understanding of visual defenses in insects, sonic defenses are poorly understood. We recommend that future investigations focus on testing hypotheses explaining the functions and evolution of these survival sounds using predator-prey experiments and comparative phylogenetics.

Comparative Phylogenetics of Papilio Butterfly Wing Shape and Size Demonstrates Independent Hindwing and Forewing Evolution

The complex forces that shape butterfly wings have long been a subject of experimental and comparative research. Butterflies use their wings for flight, camouflage, mate recognition, warning, and mimicry. However, general patterns and correlations among wing shape and size evolution are still poorly understood. We collected geometric morphometric measurements from over 1400 digitized museum specimens of Papilio swallowtails and combined them with phylogenetic data to test two hypotheses: 1) forewing shape and size evolve independently of hindwing shape and size and 2) wing size evolves more quickly than wing shape. We also determined the major axes of wing shape variation and discovered that most shape variability occurs in hindwing tails and adjacent areas. We conclude that forewing shape and size are functionally and biomechanically constrained, whereas hindwings are more labile, perhaps in response to disruptive selective pressure for Batesian mimicry or against predation. The development of a significant, re-usable, digitized data resource will enable further investigation on tradeoffs between flight performance and ecological selective pressures, along with the degree to which intraspecific, local-scale selection may explain macroevolutionary patterns. [Batesian mimicry; Lepidoptera; geometric morphometrics; museum specimens.]

PARAMO: A Pipeline for Reconstructing Ancestral Anatomies Using Ontologies and Stochastic Mapping

Comparative phylogenetics has been largely lacking a method for reconstructing the evolution of phenotypic entities that consist of ensembles of multiple discrete traits—entire organismal anatomies or organismal body regions. In this study, we provide a new approach named PARAMO (PhylogeneticAncestralReconstruction ofAnatomy byMappingOntologies) that appropriately models anatomical dependencies and uses ontology-informed amalgamation of stochastic maps to reconstruct phenotypic evolution at different levels of anatomical hierarchy including entire phenotypes. This approach provides new opportunities for tracking phenotypic radiations and evolution of organismal anatomies.

PARAMO pipeline: reconstructing ancestral anatomies using ontologies and stochastic mapping

ABSTRACTComparative phylogenetics has been largely lacking a method for reconstructing the evolution of phenotypic entities that consist of ensembles of multiple discrete traits – entire organismal anatomies or organismal body regions. In this study, we provide a new approach named PARAMO (Phylogenetic Ancestral Reconstruction of Anatomy by Mapping Ontologies) that appropriately models anatomical dependencies and uses ontology-informed amalgamation of stochastic maps to reconstruct phenotypic evolution at different levels of anatomical hierarchy including entire phenotypes. This approach provides new opportunities for tracking phenotypic radiations and evolution of organismal anatomies.

Evolutionary Transitions in Mode of Development

In the large body of literature on ecological and evolutionary mechanisms underlying transitions between planktotrophy and lecithotrophy, the focus has typically covered long evolutionary timescales; that is, evolution of complex larval traits is generally discussed in the context of phylogenetic patterns detectable at the level of families, classes, or phyla. An analytical approach incorporating comparative phylogenetics is increasingly used to address these long-view questions. Here, we discuss what has been learned from taking a comparative phylogenetic approach and the limitations of this approach. We propose that approaches based on a closer view—that is, analyses that focus on genetic, morphological, and functional variation among individuals, populations, or closely related congeners—have greater potential to answer questions about mechanisms underlying the loss and regain of major complex characters such as feeding larvae.