Integrative Organismal Biology最新文献

{"title":"AutoBend: An Automated Approach for Estimating Intervertebral Joint Function from Bone-Only Digital Models.","authors":"K E Jones,&nbsp;R J Brocklehurst,&nbsp;S E Pierce","doi":"10.1093/iob/obab026","DOIUrl":"https://doi.org/10.1093/iob/obab026","url":null,"abstract":"<p><p>Deciphering the biological function of rare or extinct species is key to understanding evolutionary patterns across the tree of life. While soft tissues are vital determinants of joint function, they are rarely available for study. Therefore, extracting functional signals from skeletons, which are more widely available via museum collections, has become a priority for the field of comparative biomechanics. While most work has focused on the limb skeleton, the axial skeleton plays a critical role in body support, respiration, and locomotion, and is therefore of central importance for understanding broad-scale functional evolution. Here, we describe and experimentally validate AutoBend, an automated approach to estimating intervertebral joint function from bony vertebral columns. AutoBend calculates osteological range of motion (oROM) by automatically manipulating digitally articulated vertebrae while incorporating multiple constraints on motion, including both bony intersection and the role of soft tissues by restricting excessive strain in both centrum and zygapophyseal articulations. Using AutoBend and biomechanical data from cadaveric experiments on cats and tegus, we validate important modeling parameters required for oROM estimation, including the degree of zygapophyseal disarticulation, and the location of the center of rotation. Based on our validation, we apply a model with the center of rotation located within the vertebral disk, no joint translation, around 50% strain permitted in both zygapophyses and disks, and a small amount of vertebral intersection permitted. Our approach successfully reconstructs magnitudes and craniocaudal patterns of motion obtained from <i>ex vivo</i> experiments, supporting its potential utility. It also performs better than more typical methods that rely solely on bony intersection, emphasizing the importance of accounting for soft tissues. We estimated the sensitivity of the analyses to vertebral model construction by varying joint spacing, degree of overlap, and the impact of landmark placement. The effect of these factors was small relative to biological variation craniocaudally and between bending directions. We also present a new approach for estimating joint stiffness directly from oROM and morphometric measurements that can successfully reconstruct the craniocaudal patterns, but not magnitudes, derived from experimental data. Together, this work represents a significant step forward for understanding vertebral function in difficult-to-study (e.g., rare or extinct) species, paving the way for a broader understanding of patterns of functional evolution in the axial skeleton.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab026"},"PeriodicalIF":1.5,"publicationDate":"2021-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8514422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39527610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differences in Mate Pairings of Hatchery- and Natural-Origin Coho Salmon Inferred from Offspring Genotypes.","authors":"H L Auld,&nbsp;D P Jacobson,&nbsp;A C Rhodes,&nbsp;M A Banks","doi":"10.1093/iob/obab020","DOIUrl":"https://doi.org/10.1093/iob/obab020","url":null,"abstract":"<p><p>Captive breeding can affect how sexual selection acts on subsequent generations. One context where this is important is in fish hatcheries. In many salmon hatcheries, spawning is controlled artificially and offspring are reared in captivity before release into the wild. While previous studies have suggested that hatchery- and natural-origin fish may make different mate choice decisions, it remains to be determined how hatchery fish may be making different mate choice decisions compared with natural-origin fish at a genetic level. Using genotyping-by-sequencing, we identify single-nucleotide polymorphisms (SNPs) associated with variation in mate pairings from a natural context involving hatchery- and natural-origin coho salmon (<i>Oncorhynchus kisutch</i>). In both natural-origin and hatchery mate pairs, we observed more SNPs with negative assortment than positive assortment. However, only 3% of the negative assortment SNPs were shared between the two mating groups, and 1% of the positive assortment SNPs were shared between the two mating groups, indicating divergence in mating cues between wild and hatchery-raised salmon. These findings shed light on mate choice in general and may have important implications in the conservation management of species as well as for improving other captive breeding scenarios. There remains much to discover about mate choice in salmon and research described here reflects our intent to test the potential of ongoing advances in population genomics to develop new hatchery practices that may improve the performance of hatchery offspring, lessening the differences and thus potential impacts upon wild stocks.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab020"},"PeriodicalIF":1.5,"publicationDate":"2021-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8363981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39324301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Scaling and Structural Properties of Juvenile Bull Kelp (<i>Nereocystis luetkeana</i>).","authors":"Katie A Dobkowski,&nbsp;Stephanie B Crofts","doi":"10.1093/iob/obab022","DOIUrl":"https://doi.org/10.1093/iob/obab022","url":null,"abstract":"<p><p>Bull kelp (<i>Nereocystis luetkeana</i>), the only canopy-forming kelp in the Salish Sea, provides primary production in the nearshore subtidal environment and serves as an important habitat for economically and ecologically important species. An annual species, each year juvenile bull kelp sporophytes must grow from the hydrodynamically more benign benthos to the water column, where they experience substantial drag at the surface. Because of the differences in morphology and ecology across life stages, and the fact that previous work has focused mainly on adult bull kelp, we tested whether morphology and structural properties change with stipe length, investigating scaling of both juvenile (stipe length < 40 cm) and mature (stipe length > 40 cm) kelp, and testing how juvenile stipes fail. Juvenile bull kelp grow proportionally (isometric growth) when young, but lengthen more quickly than would be predicted by bulb size (negative allometry) at maturity. Based on our data, the predicted breakpoint between isometric and allometric growth occurred at about 33 cm, likely approximately one to two weeks of growth. Cross-sectional area of the stipe, force to failure, work to failure, and stiffness (Young's modulus) all grow more slowly than would be predicted based on length, while maximum stress and toughness increase more quickly than predicted. There is no change in extensibility over the size range we tested, suggesting that this material property does not change with stipe length. The differences in biomechanics between juvenile and adult kelp are likely a response to the varied hydrodynamic environments experienced during the annual life cycle, which highlights the importance of studying organisms across life stages.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab022"},"PeriodicalIF":1.5,"publicationDate":"2021-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8363980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39324302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Increasing Viscosity Helps Explain Locomotor Control in Swimming <i>Polypterus senegalus</i>.","authors":"K Lutek,&nbsp;E M Standen","doi":"10.1093/iob/obab024","DOIUrl":"https://doi.org/10.1093/iob/obab024","url":null,"abstract":"<p><p>Locomotion relies on the successful integration of sensory information to adjust brain commands and basic motor rhythms created by central pattern generators. It is not clearly understood how altering the sensory environment impacts control of locomotion. In an aquatic environment, mechanical sensory feedback to the animal can be readily altered by adjusting water viscosity. Computer modeling of fish swimming systems shows that, without sensory feedback, high viscosity systems dampen kinematic output despite similar motor control input. We recorded muscle activity and kinematics of six <i>Polypterus senegalus</i> in four different viscosities of water from 1 cP (normal water) to 40 cP. In high viscosity, <i>P. senegalus</i> exhibit increased body curvature, body wave speed, and body and pectoral fin frequency during swimming. These changes are the result of increased muscle activation intensity and maintain voluntary swimming speed. Unlike the sensory-deprived model, intact sensory feedback allows fish to adjust swimming motor control and kinematic output in high viscous water but maintain typical swimming coordination.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab024"},"PeriodicalIF":1.5,"publicationDate":"2021-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8414443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39410282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to: A Global Synthesis of the Correspondence Between Epizoic Barnacles and Their Sea Turtle Hosts.","authors":"","doi":"10.1093/iob/obab018","DOIUrl":"https://doi.org/10.1093/iob/obab018","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/iob/obab002.].</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab018"},"PeriodicalIF":1.5,"publicationDate":"2021-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8331848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39280953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Including Distorted Specimens in Allometric Studies: Linear Mixed Models Account for Deformation.","authors":"B M Wynd,&nbsp;J C Uyeda,&nbsp;S J Nesbitt","doi":"10.1093/iob/obab017","DOIUrl":"https://doi.org/10.1093/iob/obab017","url":null,"abstract":"<p><p>Allometry-patterns of relative change in body parts-is a staple for examining how clades exhibit scaling patterns representative of evolutionary constraint on phenotype, or quantifying patterns of ontogenetic growth within a species. Reconstructing allometries from ontogenetic series is one of the few methods available to reconstruct growth in fossil specimens. However, many fossil specimens are deformed (twisted, flattened, and displaced bones) during fossilization, changing their original morphology in unpredictable and sometimes undecipherable ways. To mitigate against post burial changes, paleontologists typically remove clearly distorted measurements from analyses. However, this can potentially remove evidence of individual variation and limits the number of samples amenable to study, which can negatively impact allometric reconstructions. Ordinary least squares (OLS) regression and major axis regression are common methods for estimating allometry, but they assume constant levels of residual variation across specimens, which is unlikely to be true when including both distorted and undistorted specimens. Alternatively, a generalized linear mixed model (GLMM) can attribute additional variation in a model (e.g., fixed or random effects). We performed a simulation study based on an empirical analysis of the extinct cynodont, <i>Exaeretodon argentinus</i>, to test the efficacy of a GLMM on allometric data. We found that GLMMs estimate the allometry using a full dataset better than simply using only non-distorted data. We apply our approach on two empirical datasets, cranial measurements of actual specimens of <i>E. argentinus</i> (<i>n</i> = 16) and femoral measurements of the dinosaur <i>Tawa hallae</i> (<i>n</i> = 26). Taken together, our study suggests that a GLMM is better able to reconstruct patterns of allometry over an OLS in datasets comprised of extinct forms and should be standard protocol for anyone using distorted specimens.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab017"},"PeriodicalIF":1.5,"publicationDate":"2021-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/iob/obab017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39299403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wing Shape in Waterbirds: Morphometric Patterns Associated with Behavior, Habitat, Migration, and Phylogenetic Convergence.","authors":"Stephanie L Baumgart,&nbsp;Paul C Sereno,&nbsp;Mark W Westneat","doi":"10.1093/iob/obab011","DOIUrl":"https://doi.org/10.1093/iob/obab011","url":null,"abstract":"<p><p>Wing shape plays a critical role in flight function in birds and other powered fliers and has been shown to be correlated with flight performance, migratory distance, and the biomechanics of generating lift during flight. Avian wing shape and flight mechanics have also been shown to be associated with general foraging behavior and habitat choice. We aim to determine if wing shape in waterbirds, a functionally and ecologically diverse assemblage united by their coastal and aquatic habitats, is correlated with various functional and ecological traits. We applied geometric morphometric approaches to the spread wings of a selection of waterbirds to search for evolutionary patterns between wing shape and foraging behavior, habitat, and migratory patterns. We found strong evidence of convergent evolution of high and low aspect ratio wing shapes in multiple clades. Foraging behavior also consistently exhibits strong evolutionary correlations with wing shape. Habitat, migration, and flight style, in contrast, do not exhibit significant correlation with wing shape in waterbirds. Although wing shape is critical to aerial flight function, its relationship to habitat and periodic locomotor demands such as migration is complex.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab011"},"PeriodicalIF":1.5,"publicationDate":"2021-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/iob/obab011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39302811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metamorphosis Imposes Variable Constraints on Genome Expansion through Effects on Development","authors":"Rachel L Mueller, C. Cressler, Rachel S Schwarz, Rebecca A Chong, Marguerite A Butler","doi":"10.1101/2021.05.05.442795","DOIUrl":"https://doi.org/10.1101/2021.05.05.442795","url":null,"abstract":"Genome size varies ~ 100,000-fold across eukaryotes and has long been hypothesized to be influenced by metamorphosis in animals. Transposable element accumulation has been identified as a major driver of increase, but the nature of constraints limiting the size of genomes has remained unclear, even as traits such as cell size and rate of development co-vary strongly with genome size. Salamanders, which possess diverse metamorphic and non-metamorphic life histories, have the largest vertebrate genomes — 3 to 40 times that of humans — as well as the largest range of variation in genome size. We tested 13 biologically-inspired hypotheses exploring how the form of metamorphosis imposes varying constraints on genome expansion in a broadly representative phylogeny containing 118 species of salamanders. We show that metamorphosis during which animals undergo the most extensive and synchronous remodeling imposes the most severe constraint against genome expansion, with the severity of constraint decreasing with reduced extent and synchronicity of remodeling. More generally, our work demonstrates the potential for broader interpretation of phylogenetic comparative analysis in exploring the balance of multiple evolutionary pressures shaping phenotypic evolution.","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":"5 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43537532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of Intertidal Position on Metabolism and Behavior in the Acorn Barnacle, <i>Balanus glandula</i>.","authors":"Kali M Horn,&nbsp;Michelle E H Fournet,&nbsp;Kaitlin A Liautaud,&nbsp;Lynsey N Morton,&nbsp;Allie M Cyr,&nbsp;Alyse L Handley,&nbsp;Megan M Dotterweich,&nbsp;Kyra N Anderson,&nbsp;Mackenzie L Zippay,&nbsp;Kristin M Hardy","doi":"10.1093/iob/obab010","DOIUrl":"https://doi.org/10.1093/iob/obab010","url":null,"abstract":"<p><p>The intertidal zone is characterized by persistent, tidally-driven fluctuations in both abiotic (e.g., temperature, oxygen, and salinity) and biotic (e.g., food availability and predation) factors, which make this a physiologically challenging habitat for resident organisms. The relative magnitude and degree of variability of environmental stress differ between intertidal zones, with the most extreme physiological stress often being experienced by organisms in the high intertidal. Given that so many of the constantly shifting parameters in this habitat are primary drivers of metabolic rate (e.g., temperature, [O₂], and food availability), we hypothesized that sessile conspecifics residing in different tidal zones would exhibit distinct \"metabolic phenotypes,\" a term we use to collectively describe the organisms' baseline metabolic performance and capacity. To investigate this hypothesis, we collected acorn barnacles (<i>Balanus glandula</i>) from low, mid, and high intertidal positions in San Luis Obispo Bay, CA, and measured a suite of biochemical (whole-animal citrate synthase (CS) and lactate dehydrogenase (LDH) activity, and aerial [D-lactate]), physiological (O₂ consumption rates), morphological (body size), and behavioral (e.g., cirri beat frequency and percentage of time operculum open) indices of metabolism. We found tidal zone-dependent differences in <i>B. glandula</i> metabolism that primarily related to anaerobic capacity, cirral activity patterns, and body size. Barnacles from the low intertidal tended to have a greater capacity for anaerobic metabolism (i.e., increased LDH activity and increased baseline [D-lactate]), have reduced cirral beating activity-and presumably reduced feeding-when submerged, and be smaller in size compared to conspecifics in the high intertidal. We did not, however, see any D-lactate accumulation in barnacles from any tidal height throughout 96 h of air exposure. This trend indicates that the enhanced capacity of low intertidal barnacles for anaerobic metabolism may have evolved to support metabolism during more prolonged episodes of emersion or during events other than emersion (e.g., coastal hypoxia and predation). There were also no significant differences in CS activity or baseline O₂ consumption rates (in air or seawater at 14°C) across tidal heights, which imply that aerobic metabolic capacity may not be as sensitive to tidal position as anaerobic processes. Understanding how individuals occupying different shore heights differ in their metabolic capacity becomes increasingly interesting in the context of global climate change, given that the intertidal zone is predicted to experience even greater extremes in abiotic stress.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab010"},"PeriodicalIF":1.5,"publicationDate":"2021-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/iob/obab010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39221263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regional Tongue Deformations During Chewing and Drinking in the Pig.","authors":"Rachel A Olson,&nbsp;Stéphane J Montuelle,&nbsp;Hannah Curtis,&nbsp;Susan H Williams","doi":"10.1093/iob/obab012","DOIUrl":"https://doi.org/10.1093/iob/obab012","url":null,"abstract":"<p><p>As a muscular hydrostat, the tongue undergoes complex deformations during most oral behaviors, including chewing and drinking. During thesebehaviors, deformations occur in concert with tongue and jaw movements to position and transport the bolus. Moreover, the various parts of the tongue may move and deform at similar timepoints relative to the gape cycle or they may occur at different timepoints, indicating regional biomechanical and functional variation. The goal of this study is to quantify tongue deformations during chewing and drinking in pigs by characterizing intrinsic changes in tongue dimensions (i.e., length and width) across multiple regions simultaneously. Tongue deformations are generally larger during chewing cycles compared to drinking cycles. Chewing and drinking also differ in the timing, relative to the gape cycle, of regional length and width, but not total length, deformations. This demonstrates functional differences in the temporal dynamics of localized shape changes, whereas the global properties of jaw-tongue coordination are maintained. Finally, differences in the trade-off between length and width deformations demonstrate that the properties of a muscular hydrostat are observed at the whole tongue level, but biomechanical variation (e.g., changes in movements and deformations) at the regional level exists. This study provides new critical insights into the regional contributions to tongue deformations as a basis for future work on multidimensional shape changes in soft tissues.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab012"},"PeriodicalIF":1.5,"publicationDate":"2021-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/iob/obab012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39644954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}