On the Origin of Complex Adaptive Traits: Progress Since the Darwin Versus Mivart Debate

Evolutionary paths toward multi-level convergence of lactic acid bacteria in fructose-rich environments

Convergence provides clues to unveil the non-random nature of evolution. Intermediate paths toward convergence inform us of the stochasticity and the constraint of evolutionary processes. Although previous studies have suggested that substantial constraints exist in microevolutionary paths, it remains unclear whether macroevolutionary convergence follows stochastic or constrained paths. Here, we performed comparative genomics for hundreds of lactic acid bacteria (LAB) species, including clades showing a convergent gene repertoire and sharing fructose-rich habitats. By adopting phylogenetic comparative methods we showed that the genomic convergence of distinct fructophilic LAB (FLAB) lineages was caused by parallel losses of more than a hundred orthologs and the gene losses followed significantly similar orders. Our results further suggested that the loss of adhE, a key gene for phenotypic convergence to FLAB, follows a specific evolutionary path of domain architecture decay and amino acid substitutions in multiple LAB lineages sharing fructose-rich habitats. These findings unveiled the constrained evolutionary paths toward the convergence of free-living bacterial clades at the genomic and molecular levels.

Evolutionary dependence of host type and chasmothecial appendage morphology in obligate plant parasites belonging to Erysipheae (powdery mildew, Erysiphaceae)

Evolutionary relationships between the morphological and ecological traits of fungi are poorly understood. The appendages of chasmothecia, which are sexual reproductive organs of Erysiphaceae, are considered to play a crucial role in the overwintering strategies of these fungi on host plants. Previous studies suggested that both the host type and appendage morphology evolved at the same nodes and transitioned from complex appendages on deciduous hosts to simple appendages on herb/evergreen hosts. However, the evolutionary dependence between host type and appendage morphology remains unproven owing to the limited species data used in analyses. To elucidate the evolutionary relationship between host type and appendage morphology, we used phylogenetic comparative methods (PCMs) to investigate the state transition, ancestral state, evolutionary dependence, and contingent evolution within Erysipheae, the largest and most diverse tribe in Erysiphaceae. Our PCMs, based on a comprehensive data set of Erysipheae, revealed that the most ancestral states were deciduous host types and complex appendages. From these ancestral states, convergent evolution toward the herb/evergreen host types and simple appendages occurred multiple times at the same nodes. For the first time in Erysiphaceae, we detected an evolutionary dependence between host type and appendage morphology. This is one of the few examples in which evolutionary dependence between host phenology and morphological traits in plant-parasitic fungi was demonstrated using PCMs. Appendage simplification on herb/evergreen hosts and complications on deciduous hosts can be reasonably explained by the functional advantages of each appendage type in different overwintering strategies. These expected appendage functions can explain approximately 90% of host type and appendage morphology combinations observed in the analyzed taxa. However, our results also highlighted the occurrence of evolutionary shifts that deviate from the expected advantages of each appendage morphology. These seemingly irrational shifts might be interpretable from the flexibility of overwintering strategies and quantification of appendage functions.

Determination of genomic regions associated with early storage root formation and bulking in cassava

Early cassava storage root formation and bulking is a medium of escape that farmers and processors tend to adopt in cases of abiotic and biotic stresses like drought, flood, and destruction by domestic animals. In this study, 220 cassava genotypes from the International Institute of Tropical Agriculture (IITA), National Root Crops Research Institute (NRCRI), International Center for Tropical Agriculture (CIAT), local farmers (from farmer's field), and NextGen project were evaluated in three locations (Umudike, Benue, and Ikenne). The trials were laid out using a split plot in a randomized incomplete block design (alpha lattice) with two replications in 2 years. The storage roots for each plant genotype were sampled or harvested at 3, 6, 9, and 12 month after planting (MAP). All data collected were analyzed using the R-statistical package. The result showed moderate to high heritability among the traits, and there were significant differences (p< 0.05) among the performances of the genotypes. The genome-wide association mapping using the BLINK model detected 45 single-nucleotide polymorphism (SNP) markers significantly associated with the four early storage root bulking and formation traits on Chromosomes 1, 2, 3, 4, 5, 6, 8, 9, 10, 13, 14, 17, and 18. A total of 199 putative candidate genes were found to be directly linked to early storage root bulking and formation. The functions of these candidate genes were further characterized to regulate i) phytohormone biosynthesis, ii) cellular growth and development, and iii) biosynthesis of secondary metabolites for accumulation of starch and defense. Genome-wide association study (GWAS) also revealed the presence of four pleiotropic SNPs, which control starch content, dry matter content, dry yield, and bulking and formation index. The information on the GWAS could be used to develop improved cassava cultivars by breeders. Five genotypes (W940006, NR090146, TMS982123, TMS13F1060P0014, and NR010161) were selected as the best early storage root bulking and formation genotypes across the plant age. These selected cultivars should be used as sources of early storage root bulking and formation in future breeding programs.

Convergence in carnivorous pitcher plants reveals a mechanism for composite trait evolution

Composite traits involve multiple components that, only when combined, gain a new synergistic function. Thus, how they evolve remains a puzzle. We combined field experiments, microscopy, chemical analyses, and laser Doppler vibrometry with comparative phylogenetic analyses to show that two carnivorous Nepenthes pitcher plant species independently evolved similar adaptations in three distinct traits to acquire a new, composite trapping mechanism. Comparative analyses suggest that this new trait arose convergently through "spontaneous coincidence" of the required trait combination, rather than directional selection in the component traits. Our results indicate a plausible mechanism for composite trait evolution and highlight the importance of stochastic phenotypic variation as a facilitator of evolutionary novelty.

Phenotypic systems biology for organisms: Concepts, methods and case studies

Design principles of phenotypes in organisms are fundamental issues in physical biology. So far, understanding "systems" of living organisms have been chiefly promoted by understanding the underlying biomolecules such as genes and proteins, and their intra- and inter-relationships and regulations. After a long period of sophistication, biophysics and molecular biology have established a general framework for understanding 'molecular systems' in organisms without regard to species, so that the findings of fly studies can be applied to mouse studies. However, little attention has been paid to exploring "phenotypic systems" in organisms, and thus its general framework remains poorly understood. Here I review concepts, methods, and case studies using butterfly and moth wing patterns to explore phenotypes as systems. First, I present a unifying framework for phenotypic traits as systems, termed multi-component systems. Second, I describe how to define components of phenotypic systems, and also show how to quantify interactions among phenotypic parts. Subsequently, I introduce the concept of the macro-evolutionary process, which illustrates how to generate complex traits. In this point, I also introduce mathematical methods, "phylogenetic comparative methods", which provide stochastic processes along molecular phylogeny as bifurcated paths to quantify trait evolution. Finally, I would like to propose two key concepts, macro-evolutionary pathways and genotype-phenotype loop (GP loop), which must be needed for the next directions. I hope these efforts on phenotypic biology will become one major target in biophysics and create the next generations of textbooks. This review article is an extended version of the Japanese article, Biological Physics in Phenotypic Systems of Living Organisms, published in SEIBUTSU-BUTSURI Vol. 61, p. 31-35 (2021).

Lifestyle Evolution Analysis by Binary-State Speciation and Extinction (BiSSE) Model

Phylogenetic comparative methods (PCMs) combine statistics and evolutionary models to infer the dynamics of trait evolution and diversification that underlie the observed phylogeny. While PCMs have been used to study macro-evolutionary processes and evolutionary transitions of macroorganisms, their application to microbes is still limited. With the abundance of publicly available genomic and trait character data for diverse microbes nowadays, applications of PCMs on these data can provide insights into the fundamental principles that govern microbial evolution. Here, we introduce the Binary-State Speciation and Extinction (BiSSE) model, which is a relatively simple yet powerful approach for analyzing trait evolution. We begin by explaining the theoretical background and intuition behind the BiSSE model. Then, R commands for running the BiSSE model are presented. Finally, we introduce a case study that successfully applied the BiSSE model to investigate generalist and specialist microbial lifestyle evolution.

Moss mimesis par excellence: integrating previous and new data on the life history and larval ecomorphology of long-bodied craneflies (Diptera: Cylindrotomidae: Cylindrotominae)

Different physical structures play a central role in animal camouflage. However, in evolutionary studies of mimicry, the ecological and evolutionary significance of such structures has been poorly investigated. Larvae of long-bodied craneflies, Cylindrotominae, are all obligate herbivores and resemble plants. They are distinctively characterized by possessing numerous elongated cuticular lobes on the integument. A comprehensive overview of the biology and morphology of cylindrotomids, particularly their larval stages, is laid out, providing original data on nine species. To explore the ecological background of moss resemblance, host-plants of most examined species are clarified, revealing that terrestrial moss-feeding species tend to use specific groups of mosses, either belonging to Bryales or Hypnales. However, the evolution of cryptic forms remains paradoxical, due to the apparent absence of visual predators. Based on histological examinations, extensive internal musculatures within the cuticular lobes on the lateral side are discovered, shedding new light on their function in locomotion. Traditional functional explanations for these lobes, particularly as devices for respiration, locomotion and attachment, are challenged. This study promotes our understanding of the ecomorphology of mimicry devices, which is an angle often dismissed in evolutionary studies of mimicry.

Multi-level convergence of complex traits and the evolution of bioluminescence

Evolutionary convergence provides natural opportunities to investigate how, when, and why novel traits evolve. Many convergent traits are complex, highlighting the importance of explicitly considering convergence at different levels of biological organization, or 'multi-level convergent evolution'. To investigate multi-level convergent evolution, we propose a holistic and hierarchical framework that emphasizes breaking down traits into several functional modules. We begin by identifying long-standing questions on the origins of complexity and the diverse evolutionary processes underlying phenotypic convergence to discuss how they can be addressed by examining convergent systems. We argue that bioluminescence, a complex trait that evolved dozens of times through either novel mechanisms or conserved toolkits, is particularly well suited for these studies. We present an updated estimate of at least 94 independent origins of bioluminescence across the tree of life, which we calculated by reviewing and summarizing all estimates of independent origins. Then, we use our framework to review the biology, chemistry, and evolution of bioluminescence, and for each biological level identify questions that arise from our systematic review. We focus on luminous organisms that use the shared luciferin substrates coelenterazine or vargulin to produce light because these organisms convergently evolved bioluminescent proteins that use the same luciferins to produce bioluminescence. Evolutionary convergence does not necessarily extend across biological levels, as exemplified by cases of conservation and disparity in biological functions, organs, cells, and molecules associated with bioluminescence systems. Investigating differences across bioluminescent organisms will address fundamental questions on predictability and contingency in convergent evolution. Lastly, we highlight unexplored areas of bioluminescence research and advances in sequencing and chemical techniques useful for developing bioluminescence as a model system for studying multi-level convergent evolution.

Modern termites inherited the potential of collective construction from their common ancestor

Animal collective behaviors give rise to various spatial patterns, such as the nests of social insects. These structures are built by individuals following a simple set of rules, slightly varying within and among species, to produce a large diversity of shapes. However, little is known about the origin and evolution of the behavioral mechanisms regulating nest structures. In this study, we discuss the perspective of inferring the evolution of collective behaviors behind pattern formations using a phylogenetic framework. We review the collective behaviors that can be described by a single set of behavioral rules, and for which variations of the environmental and behavioral parameter values produce diverse patterns. We propose that this mechanism could be at the origin of the pattern diversity observed among related species, and that, when they are placed in the proper conditions, species have the behavioral potential to form patterns observed in related species. The comparative analysis of shelter tube construction by lower termites is consistent with this hypothesis. Although the use of shelter tubes in natural conditions is variable among species, most modern species have the potential to build them, suggesting that the behavioral rules for shelter tube construction evolved once in the common ancestor of modern termites. Our study emphasizes that comparative studies of behavioral rules have the potential to shed light on the evolution of collective behaviors.

Multicomponent structures in camouflage and mimicry in butterfly wing patterns

Understanding how morphological structures are built is essential for appreciating the morphological complexity and divergence of organisms. One representative case of morphological structures is the camouflage and mimicry of butterfly wing patterns. Some previous studies have questioned whether camouflage and mimicry are truly structures, considering that they rely on coloration. Nevertheless, our recent study revealed that the leaf pattern of Kallima inachus butterfly wings evolved through the combination of changes in several pigment components in a block-wise manner; it remains unclear whether such block-wise structures are common in other cases of camouflage and mimicry in butterflies and how they come about. Previous studies focused solely on a set of homologous components, termed the nymphalid ground plan. In the present study, we extended the scope of the description of components by including not only the nymphalid ground plan but also other common components (i.e., ripple patterns, dependent patterns, and color fields). This extension allowed us to analyze the combinatorial building logic of structures and examine multicomponent structures of camouflage and mimicry in butterfly wing patterns. We investigated various patterns of camouflage and mimicry (e.g., masquerade, crypsis, Müllerian mimicry, Batesian mimicry) in nine species and decomposed them into an assembly of multiple components. These structural component analyses suggested that camouflage and mimicry in butterfly wing patterns are built up by combining multiple types of components. We also investigated associations between components and the kinds of camouflage and mimicry. Several components are statistically more often used to produce specific types of camouflage or mimicry. Thus, our work provides empirical evidence that camouflage and mimicry patterns of butterfly wings are mosaic structures, opening up a new avenue of studying camouflage, and mimicry from a structural perspective.

Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato

BACKGROUND

Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important trait from agronomic and biological perspectives. Information about the molecular mechanisms underlying CSRFAB traits is lacking.

RESULTS

Here, as a first step toward understanding the genetic basis of CSRFAB in sweetpotato, we performed a genome-wide association study (GWAS) using phenotypic data from four distinct developmental stages and 33,068 single nucleotide polymorphism (SNP) and insertion-deletion (indel) markers. Based on Bonferroni threshold (p-value < 5 × 10- 7), we identified 34 unique SNPs that were significantly associated with the complex trait of CSRFAB at 150 days after planting (DAP) and seven unique SNPs associated with discontinuous storage root formation and bulking (DCSRFAB) at 90 DAP. Importantly, most of the loci associated with these identified SNPs were located within genomic regions (using Ipomoea trifida reference genome) previously reported for quantitative trait loci (QTL) controlling similar traits. Based on these trait-associated SNPs, 12 and seven candidate genes were respectively annotated for CSRFAB and DCSRFAB traits. Congruent with the contrasting and inverse relationship between discontinuous and continuous storage root formation and bulking, a DCSRFAB-associated candidate gene regulates redox signaling, involved in auxin-mediated lateral root formation, while CSRFAB is enriched for genes controlling growth and senescence.

CONCLUSION

Candidate genes identified in this study have potential roles in cell wall remodeling, plant growth, senescence, stress, root development and redox signaling. These findings provide valuable insights into understanding the functional networks to develop strategies for sweetpotato yield improvement. The markers as well as candidate genes identified in this pioneering research for CSRFAB provide important genomic resources for sweetpotato and other root crops.

Regulatory mechanism predates the evolution of self-organizing capacity in simulated ant-like robots

The evolution of complexity is one of the prime features of life on Earth. Although well accepted as the product of adaptation, the dynamics underlying the evolutionary build-up of complex adaptive systems remains poorly resolved. Using simulated robot swarms that exhibit ant-like group foraging with trail pheromones, we show that their self-organizing capacity paradoxically involves regulatory behavior that arises in advance. We focus on a traffic rule on their foraging trail as a regulatory trait. We allow the simulated robot swarms to evolve pheromone responsiveness and traffic rules simultaneously. In most cases, the traffic rule, initially arising as selectively neutral component behaviors, assists the group foraging system to bypass a fitness valley caused by overcrowding on the trail. Our study reveals a hitherto underappreciated role of regulatory mechanisms in the origin of complex adaptive systems, as well as highlights the importance of embodiment in the study of their evolution.