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1. Effect of environmental signals on growth and development in mosses

   https://doi.org/10.1093/jxb/erac138  

   Mohanasundaram, Boominathan; Pandey, Sona; Petraglia, ed., Alessandro (April 2022, Journal of Experimental Botany)

   Abstract Plants perceive a multitude of environmental signals and stresses, and integrate their response to them in ways that culminate in modified phenotypes, optimized for plant survival. This ability of plants, known as phenotypic plasticity, is found throughout evolution, in all plant lineages. For any given environment, the specifics of the response to a particular signal may vary depending on the plants’ unique physiology and ecological niche. The bryophyte lineage, including mosses, which diverged from the vascular plants ~450–430 million years ago, represent a unique ecological and phylogenetic group in plant evolution. Several aspects of the moss life cycle, their morphology including the presence of specialized tissue types and distinct anatomical features, gene repertoires and networks, as well as the habitat differ significantly from those of vascular plants. To evaluate the outcomes of these differences, we explore the phenotypic responses of mosses to environmental signals such as light, temperature, CO2, water, nutrients, and gravity, and compare those with what is known in vascular plants. We also outline knowledge gaps and formulate testable hypotheses based on the contribution of anatomical and molecular factors to specific phenotypic responses. 

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2. Evolution and strain diversity advance exploration of Candida albicans biology

   https://doi.org/10.1128/msphere.00641-23  

   Anderson, Matthew Z; Dietz, Siobhan M (August 2024, mSphere)

   Mitchell, Aaron P (Ed.)

   ABSTRACT Fungi were some of the earliest organismal systems used to explore mutational processes and its phenotypic consequences on members of a species. Yeasts that cause significant human disease were quickly incorporated into these investigations to define the genetic and phenotypic drivers of virulence. AmongCandidaspecies,Candida albicanshas emerged as a model for studying genomic processes of evolution because of its clinical relevance, relatively small genome, and ability to tolerate complex chromosomal changes. Here, we describe major recent findings that used evolution of strains from defined genetic backgrounds to delineate mutational and adaptative processes and include how nascent exploration into naturally occurring variation is contributing to these conceptual frameworks. Ultimately, efforts to discern adaptive mechanisms used byC. albicanswill continue to divulge new biology and can better inform treatment regimens for the increasing prevalence of fungal disease. 

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3. Understanding Organismal Capacity to Respond to Anthropogenic Change: Barriers and Solutions

   https://doi.org/10.1093/icb/icab162  

   Gabor, Caitlin R; Kivlin, Stephanie N; Hua, Jessica; Bickford, Nate; Reiskind, Martha O; Wright, Timothy F (July 2021, Integrative and Comparative Biology)

   null (Ed.)

   Synopsis Global environmental changes induced by human activities are forcing organisms to respond at an unprecedented pace. At present we have only a limited understanding of why some species possess the capacity to respond to these changes while others do not. We introduce the concept of multidimensional phenospace as an organizing construct to understanding organismal evolutionary responses to environmental change. We then describe five barriers that currently challenge our ability to understand these responses: (1) Understanding the parameters of environmental change and their fitness effects, (2) Mapping and integrating phenotypic and genotypic variation, (3) Understanding whether changes in phenospace are heritable, (4) Predicting consistency of genotype to phenotype patterns across space and time, and (5) Determining which traits should be prioritized to understand organismal response to environmental change. For each we suggest one or more solutions that would help us surmount the barrier and improve our ability to predict, and eventually manipulate, organismal capacity to respond to anthropogenic change. Additionally, we provide examples of target species that could be useful to examine interactions between phenotypic plasticity and adaptive evolution in changing phenospace. 

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4. Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies

   https://doi.org/10.1093/sysbio/syac022  

   Porto, Diego S.; Dahdul, Wasila M.; Lapp, Hilmar; Balhoff, James P.; Vision, Todd J.; Mabee, Paula M.; Uyeda, Josef (March 2022, Systematic Biology)

   Abstract Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent “parts”, but instead a set of dependent and hierarchically nested entities resulting from ontogeny and phylogeny. How do we make sense of these dependent and at times redundant characters? One promising approach is using ontologies—structured controlled vocabularies that summarize knowledge about different properties of anatomical entities, including developmental and structural dependencies. Here, we assess whether evolutionary patterns can explain the proximity of ontology-annotated characters within an ontology. To do so, we measure phylogenetic information across characters and evaluate if it matches the hierarchical structure given by ontological knowledge—in much the same way as across-species diversity structure is given by phylogeny. We implement an approach to evaluate the Bayesian phylogenetic information (BPI) content and phylogenetic dissonance among ontology-annotated anatomical data subsets. We applied this to data sets representing two disparate animal groups: bees (Hexapoda: Hymenoptera: Apoidea, 209 chars) and characiform fishes (Actinopterygii: Ostariophysi: Characiformes, 463 chars). For bees, we find that BPI is not substantially explained by anatomy since dissonance is often high among morphologically related anatomical entities. For fishes, we find substantial information for two clusters of anatomical entities instantiating concepts from the jaws and branchial arch bones, but among-subset information decreases and dissonance increases substantially moving to higher-level subsets in the ontology. We further applied our approach to address particular evolutionary hypotheses with an example of morphological evolution in miniature fishes. While we show that phylogenetic information does match ontology structure for some anatomical entities, additional relationships and processes, such as convergence, likely play a substantial role in explaining BPI and dissonance, and merit future investigation. Our work demonstrates how complex morphological data sets can be interrogated with ontologies by allowing one to access how information is spread hierarchically across anatomical concepts, how congruent this information is, and what sorts of processes may play a role in explaining it: phylogeny, development, or convergence. [Apidae; Bayesian phylogenetic information; Ostariophysi; Phenoscape; phylogenetic dissonance; semantic similarity.] 

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5. Chimeric dihydrofolate reductases display properties of modularity and biophysical diversity

   https://doi.org/10.1002/pro.3646  

   Rodrigues, João V.; Ogbunugafor, C. Brandon; Hartl, Daniel L.; Shakhnovich, Eugene I. (May 2019, Protein Science)

   Abstract While reverse genetics and functional genomics have long affirmed the role of individual mutations in determining protein function, there have been fewer studies addressing how large‐scale changes in protein sequences, such as in entire modular segments, influence protein function and evolution. Given how recombination can reassort protein sequences, these types of changes may play an underappreciated role in how novel protein functions evolve in nature. Such studies could aid our understanding of whether certain organismal phenotypes related to protein function—such as growth in the presence or absence of an antibiotic—are robust with respect to the identity of certain modular segments. In this study, we combine molecular genetics with biochemical and biophysical methods to gain a better understanding of protein modularity in dihydrofolate reductase (DHFR), an enzyme target of antibiotics also widely used as a model for protein evolution. We replace an integral α‐helical segment ofEscherichia coliDHFR with segments from a number of different organisms (many nonmicrobial) and examine how these chimeric enzymes affect organismal phenotypes (e.g., resistance to an antibiotic) as well as biophysical properties of the enzyme (e.g., thermostability). We find that organismal phenotypes and enzyme properties are highly sensitive to the identity of DHFR modules, and that this chimeric approach can create enzymes with diverse biophysical characteristics. 

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