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1. Functional coupling in the evolution of suction feeding and gill ventilation of sculpins (Perciformes: Cottoidei)

   https://doi.org/10.1093/icb/icz022  

   Farina, S. C.; Knope, M. L.; Corn, K. A.; Summers, A. P.; Bemis, W. E. (April 2019, Integrative and Comparative Biology)

   Abstract Suction feeding and gill ventilation in teleosts are functionally coupled, meaning that there is an overlap in the structures involved with both functions. Functional coupling is one type of morphological integration, a term that broadly refers to any covariation, correlation, or coordination among structures. Suction feeding and gill ventilation exhibit other types of morphological integration, including functional coordination (a tendency of structures to work together to perform a function) and evolutionary integration (a tendency of structures to covary in size or shape across evolutionary history). Functional coupling, functional coordination, and evolutionary integration have each been proposed to limit morphological diversification to some extent. Yet teleosts show extraordinary cranial diversity, suggesting that there are mechanisms within some teleost clades that promote morphological diversification, even within the highly integrated suction feeding and gill ventilatory systems. To investigate this, we quantified evolutionary integration among four mechanical units associated with suction feeding and gill ventilation in a diverse clade of benthic, primarily suction-feeding fishes (Cottoidei; sculpins and relatives). We reconstructed cottoid phylogeny using molecular data from 108 species, and obtained 24 linear measurements of four mechanical units (jaws, hyoid, opercular bones, and branchiostegal rays) from micro-CT reconstructions of 44 cottoids and 1 outgroup taxon. We tested for evolutionary correlation and covariation among the four mechanical units using phylogenetically corrected principal component analysis to reduce the dimensionality of measurements for each unit, followed by correlating phylogenetically independent contrasts and computing phylogenetic generalized least squares models from the first principle component axis of each of the four mechanical units. The jaws, opercular bones, and branchiostegal rays show evolutionary integration, but the hyoid is not positively integrated with these units. To examine these results in an ecomorphological context, we used published ecological data in phylogenetic ANOVA models to demonstrate that the jaw is larger in fishes that eat elusive or grasping prey (e.g., prey that can easily escape or cling to the substrate) and that the hyoid is smaller in intertidal and hypoxia-tolerant sculpins. Within Cottoidei, the relatively independent evolution of the hyoid likely has reduced limitations on morphological evolution within the highly morphologically integrated suction feeding and gill ventilatory systems. 

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2. Disentangling Mechanical and Sensory Modules in the Radiation of Noctilionoid Bats

   https://doi.org/10.1086/725368  

   Mutumi, Gregory L.; Hall, Ronald P.; Hedrick, Brandon P.; Yohe, Laurel R.; Sadier, Alexa; Davies, Kalina T.; Rossiter, Stephen J.; Sears, Karen E.; Dávalos, Liliana M.; Dumont, Elizabeth R. (August 2023, The American Naturalist)

   With diverse mechanical and sensory functions, the vertebrate cranium is a complex anatomical structure whose shifts between modularity and integration, especially in mechanical func- tion, have been implicated in adaptive diversification. Yet how me- chanical and sensory systems and their functions coevolve, as well as how their interrelationship contributes to phenotypic disparity, remain largely unexplored. To examine the modularity, integration, and evolutionary rates of sensory and mechanical structures within the head, we analyzed hard and soft tissue scans from ecologically diverse bats in the superfamily Noctilionoidea, a clade that ranges from insectivores and carnivores to frugivores and nectarivores. We identified eight regions that evolved in a coordinated fashion, thus recognizable as evolutionary modules: five associated with bite force and three linked to olfactory, visual, and auditory systems. Interrelationships among these modules differ between Neotropical leaf-nosed bats (family Phyllostomidae) and other noctilionoids. Consistent with the hypothesis that dietary transitions begin with changes in the capacity to detect novel food items followed by adap- tations to process them, peak rates of sensory module evolution pre- date those of some mechanical modules. We propose that the co- evolution of structures influencing bite force, olfaction, vision, and hearing constituted a structural opportunity that allowed the phyllostomid ancestor to take advantage of existing ecological op- portunities and contributed to the clade’s remarkable radiation. 

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3. Evolutionary Integration and Modularity in the Archosaur Cranium

   https://doi.org/10.1093/icb/icz052  

   Felice, Ryan N.; Watanabe, Akinobu; Cuff, Andrew R.; Noirault, Eve; Pol, Diego; Witmer, Lawrence M.; Norell, Mark A.; O'Connor, Patrick M.; Goswami, Anjali (May 2019, Integrative and Comparative Biology)

   Abstract Complex structures, like the vertebrate skull, are composed of numerous elements or traits that must develop and evolve in a coordinated manner to achieve multiple functions. The strength of association among phenotypic traits (i.e., integration), and their organization into highly-correlated, semi-independent subunits termed modules, is a result of the pleiotropic and genetic correlations that generate traits. As such, patterns of integration and modularity are thought to be key factors constraining or facilitating the evolution of phenotypic disparity by influencing the patterns of variation upon which selection can act. It is often hypothesized that selection can reshape patterns of integration, parceling single structures into multiple modules or merging ancestrally semi-independent traits into a strongly correlated unit. However, evolutionary shifts in patterns of trait integration are seldom assessed in a unified quantitative framework. Here, we quantify patterns of evolutionary integration among regions of the archosaur skull to investigate whether patterns of cranial integration are conserved or variable across this diverse group. Using high-dimensional geometric morphometric data from 3D surface scans and computed tomography scans of modern birds (n = 352), fossil non-avian dinosaurs (n = 27), and modern and fossil mesoeucrocodylians (n = 38), we demonstrate that some aspects of cranial integration are conserved across these taxonomic groups, despite their major differences in cranial form, function, and development. All three groups are highly modular and consistently exhibit high integration within the occipital region. However, there are also substantial divergences in correlation patterns. Birds uniquely exhibit high correlation between the pterygoid and quadrate, components of the cranial kinesis apparatus, whereas the non-avian dinosaur quadrate is more closely associated with the jugal and quadratojugal. Mesoeucrocodylians exhibit a slightly more integrated facial skeleton overall than the other grades. Overall, patterns of trait integration are shown to be stable among archosaurs, which is surprising given the cranial diversity exhibited by the clade. At the same time, evolutionary innovations such as cranial kinesis that reorganize the structure and function of complex traits can result in modifications of trait correlations and modularity. 

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4. On understanding causal relationships within the Earth-life sciences

   Dolby, G (December 2021, American Geophysical Union)

   A goal common to several disciplines within earth and life sciences is to understand how earth processes and abiotic conditions shape the diversification and distribution of species on our planet. To develop a mechanistic and detailed understanding of these relationships across taxonomic-geographic settings should inform a set of boundary conditions that describe the geologic and climatic conditions under which new biodiversity is generated along with the organismal traits (e.g., generation time, dispersal ability) that govern why species vary in their evolutionary responses to the same external influences. However, earth and life sciences each encompass a set of highly complex and sometimes nested relationships. This presents a need for new ways to guide the integration of domain knowledge across these complex systems in a way that can generate new hypotheses, facilitate interdisciplinary collaboration, and shape earth-life theory moving forward. Here, I outline the use of causal structures, which are a set of tools to diagram cause-effect relationships at different levels of detail (specification) that include structural equation meta models (SEMMs), causal diagrams (CDs), and structural equation models (SEMs). I will give examples of how to use SEMMs and CDs to detail earth-life relationships, what we can learn from doing so, and pose a way for how we might quantify these relationships. I hope to demonstrate the usefulness and applicability of thinking about earth-life systems within a causal framework, and speculate about temporal dynamics and the potential for abiotic-to-biotic causal thresholds that may occur over time in different earth-life systems. 

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5. Environment‐driven shifts in interindividual variation and phenotypic integration within subnetworks of the mussel transcriptome and proteome

   https://doi.org/10.1111/mec.16452  

   Tanner, Richelle L.; Gleason, Lani U.; Dowd, W. Wesley (April 2022, Molecular Ecology)

   Abstract The environment can alter the magnitude of phenotypic variation among individuals, potentially influencing evolutionary trajectories. However, environmental influences on variation are complex and remain understudied. Populations in heterogeneous environments might exhibit more variation, the amount of variation could differ between benign and stressful conditions, and/or variation might manifest in different ways among stages of the gene‐to‐protein expression cascade or among physiological functions. Here, we explore these three issues by quantifying patterns of inter‐individual variation in both transcript and protein expression levels among California mussels,Mytilus californianusConrad. Mussels were exposed to five ecologically relevant treatments that varied in the mean and interindividual heterogeneity of body temperature. To target a diverse set of physiological functions, we assessed variation within 19 expression subnetworks, including canonical stress‐response pathways and empirically derived coexpression clusters that represent a diffuse set of cellular processes. Variation in expression was particularly pronounced in the treatments with high mean and heterogeneous body temperatures. However, with few exceptions, environment‐dependent shifts of variation in the transcriptome were not reflected in the proteome. A metric of phenotypic integration provided evidence for a greater degree of constraint on relative expression levels (i.e., stronger correlation) within expression subnetworks in benign, homogeneous environments. Our results suggest that environments that are more stressful on average – and which also tend to be more heterogeneous – can relax these expression constraints and reduce phenotypic integration within biochemical subnetworks. Context‐dependent “unmasking” of functional variation may contribute to interindividual differences in physiological phenotype and performance in stressful environments. 

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