Integrative and Comparative Biology最新文献_第4页

Moving in an Uncertain World: Robust and Adaptive Control of Locomotion from Organisms to Machine Intelligence. 在不确定的世界中移动：从有机体到机器智能的运动鲁棒和自适应控制》（Robust and Adaptive Control of Locomotion from Organisms to Machine Intelligence）。

IF 2.2 3区生物学

Integrative and Comparative Biology Pub Date : 2024-11-21 DOI: 10.1093/icb/icae121

Jean-Michel Mongeau, Yu Yang, Ignacio Escalante, Noah Cowan, Kaushik Jayaram

{"title":"Moving in an Uncertain World: Robust and Adaptive Control of Locomotion from Organisms to Machine Intelligence.","authors":"Jean-Michel Mongeau, Yu Yang, Ignacio Escalante, Noah Cowan, Kaushik Jayaram","doi":"10.1093/icb/icae121","DOIUrl":"10.1093/icb/icae121","url":null,"abstract":"Whether walking, running, slithering, or flying, organisms display a remarkable ability to move through complex and uncertain environments. In particular, animals have evolved to cope with a host of uncertainties-both of internal and external origin-to maintain adequate performance in an ever-changing world. In this review, we present mathematical methods in engineering to highlight emerging principles of robust and adaptive control of organismal locomotion. Specifically, by drawing on the mathematical framework of control theory, we decompose the robust and adaptive hierarchical structure of locomotor control. We show how this decomposition along the robust-adaptive axis provides testable hypotheses to classify behavioral outcomes to perturbations. With a focus on studies in non-human animals, we contextualize recent findings along the robust-adaptive axis by emphasizing two broad classes of behaviors: (1) compensation to appendage loss and (2) image stabilization and fixation. Next, we attempt to map robust and adaptive control of locomotion across some animal groups and existing bio-inspired robots. Finally, we highlight exciting future directions and interdisciplinary collaborations that are needed to unravel principles of robust and adaptive locomotion.","PeriodicalId":54971,"journal":{"name":"Integrative and Comparative Biology","volume":" ","pages":"1390-1407"},"PeriodicalIF":2.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11579605/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141876694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Building, Maintaining, and (re-)Deploying Genetic Toolkits during Convergent Evolution. 在聚合进化过程中构建、维护和（重新）部署基因工具包。

IF 2.2 3区生物学

Integrative and Comparative Biology Pub Date : 2024-11-21 DOI: 10.1093/icb/icae114

Todd H Oakley

{"title":"Building, Maintaining, and (re-)Deploying Genetic Toolkits during Convergent Evolution.","authors":"Todd H Oakley","doi":"10.1093/icb/icae114","DOIUrl":"10.1093/icb/icae114","url":null,"abstract":"A surprising insight from the advent of genomic sequencing was that many genes are deeply conserved during evolution. With a particular focus on genes that interact with light in animals, I explore the metaphor of genetic toolkits, which can be operationalized as lists of genes involved in a trait of interest. A fascinating observation is that genes of a toolkit are often used again and again during convergent evolution, sometimes across vast phylogenetic distances. Such a pattern in the evolution of toolkits requires three different stages: (i) origin, (ii) maintenance, and (iii) redeployment of the genes. The functional origins of toolkit genes might often be rooted in interactions with external environments. The origins of light interacting genes in particular may be tied to ancient responses to photo-oxidative stress, inspiring questions about the extent to which the evolution of other toolkits was also impacted by stress. Maintenance of genetic toolkits over long evolutionary timescales requires gene multifunctionality to prevent gene loss when a trait of interest is absent. Finally, the deployment of toolkit genes in convergently evolved traits like eyes sometimes involves the repeated use of similar, ancient genes yet other times involves different genes, specific to each convergent origin. How often a particular gene family is used time and again for the same function may depend on how many possible biological solutions are available. When few solutions exist and the genes are maintained, evolution may be constrained to use the same genes over and over. However, when many different solutions are possible, convergent evolution often takes multiple different paths. Therefore, a focus on genetic toolkits highlights the combination of legacy-plus-innovation that drives the evolution of biological diversity.","PeriodicalId":54971,"journal":{"name":"Integrative and Comparative Biology","volume":" ","pages":"1505-1512"},"PeriodicalIF":2.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141725125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Leeches Predate on Fast-Escaping and Entangling Blackworms by Spiral Entombment. 水蛭通过螺旋缠绕捕食快速逃离和缠绕的黑虫。

IF 2.2 3区生物学

Integrative and Comparative Biology Pub Date : 2024-11-21 DOI: 10.1093/icb/icae118

Harry Tuazon, Samuel David, Kenneth Ma, Saad Bhamla

引用次数: 0

Does Phenotypic Integration Promote Convergent Evolution? 表型整合会促进趋同进化吗？

IF 2.2 3区生物学

Integrative and Comparative Biology Pub Date : 2024-11-21 DOI: 10.1093/icb/icae041

C Tristan Stayton

{"title":"Does Phenotypic Integration Promote Convergent Evolution?","authors":"C Tristan Stayton","doi":"10.1093/icb/icae041","DOIUrl":"10.1093/icb/icae041","url":null,"abstract":"Phenotypic integration is often perceived as being able to produce convergent evolution in the absence of selection, but specific mechanisms for this process are lacking and a connection has never been empirically demonstrated. A new model of the effect of integration on convergence provides such a mechanism, along with other predictions about the influence of integration on evolutionary patterns. I use simulations and data from three empirical systems-turtle shells, characiform fish, and squirrel mandibles-to investigate the degree to which evolutionary integration is associated with high levels of convergent evolution. Levels of integration were varied in Brownian motion simulations and the resulting amounts of stochastic convergent evolution were quantified. Each empirical system was divided into modules, and the strength of integration, average amount of convergence, phenotypic disparity, and rate of evolution in each module were measured. Results from the simulations and from all three empirical systems converge on a common result: higher levels of phenotypic integration are indeed associated with higher levels of convergence. This is despite a lack of consistent association between the strength of phenotypic integration and evolutionary rate or disparity. The results here are only correlational. Further studies that more closely examine the influence of within-population drivers of evolutionary integration-for example, genetic or developmental integration-on convergence are required before it is possible to definitively establish when phenotypic integration can cause evolutionary convergence. Until then, however, the results of this study strongly suggest that phenotypic integration will often promote convergent evolution.","PeriodicalId":54971,"journal":{"name":"Integrative and Comparative Biology","volume":" ","pages":"1484-1493"},"PeriodicalIF":2.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141071620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc. 利用 PhyloAcc 鉴定快速进化的非编码基因组元素的实用指南和工作流程。

IF 2.2 3区生物学

Integrative and Comparative Biology Pub Date : 2024-11-21 DOI: 10.1093/icb/icae056

Gregg W C Thomas, Patrick Gemmell, Subir B Shakya, Zhirui Hu, Jun S Liu, Timothy B Sackton, Scott V Edwards

{"title":"Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc.","authors":"Gregg W C Thomas, Patrick Gemmell, Subir B Shakya, Zhirui Hu, Jun S Liu, Timothy B Sackton, Scott V Edwards","doi":"10.1093/icb/icae056","DOIUrl":"10.1093/icb/icae056","url":null,"abstract":"Comparative genomics provides ample ways to study genome evolution and its relationship to phenotypic traits. By developing and testing alternate models of evolution throughout a phylogeny, one can estimate rates of molecular evolution along different lineages in a phylogeny and link these rates with observations in extant species, such as convergent phenotypes. Pipelines for such work can help identify when and where genomic changes may be associated with, or possibly influence, phenotypic traits. We recently developed a set of models called PhyloAcc, using a Bayesian framework to estimate rates of nucleotide substitution on different branches of a phylogenetic tree and evaluate their association with pre-defined or estimated phenotypic traits. PhyloAcc-ST and PhyloAcc-GT both allow users to define a priori a set of target lineages and then compare different models to identify loci accelerating in one or more target lineages. Whereas ST considers only one species tree across all input loci, GT considers alternate topologies for every locus. PhyloAcc-C simultaneously models molecular rates and rates of continuous trait evolution, allowing the user to ask whether the two are associated. Here, we describe these models and provide tips and workflows on how to prepare the input data and run PhyloAcc.","PeriodicalId":54971,"journal":{"name":"Integrative and Comparative Biology","volume":" ","pages":"1513-1525"},"PeriodicalIF":2.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11579529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141181588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Physiological Basis of Convergent Evolution in Animal Communication Systems. 动物通讯系统趋同进化的生理学基础。

IF 2.2 3区生物学

Integrative and Comparative Biology Pub Date : 2024-11-21 DOI: 10.1093/icb/icae091

Nigel K Anderson, Doris Preininger, Matthew J Fuxjager

{"title":"Physiological Basis of Convergent Evolution in Animal Communication Systems.","authors":"Nigel K Anderson, Doris Preininger, Matthew J Fuxjager","doi":"10.1093/icb/icae091","DOIUrl":"10.1093/icb/icae091","url":null,"abstract":"To humans, the diverse array of display behaviors that animals use for communication can easily seem peculiar or bizarre. While ample research delves into the evolutionary principles that shape these signals' effectiveness, little attention is paid to evolutionary patterning of signal design across taxa, particularly when it comes to the potential convergent evolution of many elaborate behavioral displays. By taking a mechanistic perspective, we explore the physiological and neurobiological mechanisms that likely influence the evolution of communication signals, emphasizing the utilization of pre-existing structures over novel adaptations. Central to this investigation are the concepts of perceptual bias and ritualization that we propose contribute to the convergence of elaborate display designs across species. Perceptual bias explains a phenomenon where pre-existing perceptual systems of receivers, used for innate behaviors such as food and predator recognition, select for certain traits of a communication signal from a signaler. Ritualization occurs when traits with no functional role in communication are co-opted through selection and transformed into a new communicative signal. Importantly, susceptibility for ritualization can be brought about through physiological modifications that occurred early in evolutionary time. In this way, perceptual bias can be a selective force that causes the co-option of non-communicative traits into a new communication signal through ritualization involving pre-existing modifications to physiological systems. If the perceptual bias, non-communicative signal, and physiological modifications that increase susceptibility to ritualization are highly conserved, then we may see the convergent evolution of the new communication signal with unrelated taxa facing similar sensory constraints. We explore this idea here using the foot-flagging frog system as a theoretical case study.","PeriodicalId":54971,"journal":{"name":"Integrative and Comparative Biology","volume":" ","pages":"1422-1436"},"PeriodicalIF":2.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Burrowing Constrains the Phenotypic Diversity of Fossorial Crayfish. 穴居限制了螯虾的表型多样性。

IF 2.2 3区生物学

Integrative and Comparative Biology Pub Date : 2024-11-21 DOI: 10.1093/icb/icae067

Emmy M Delekta, Matthew A Kolmann

{"title":"Burrowing Constrains the Phenotypic Diversity of Fossorial Crayfish.","authors":"Emmy M Delekta, Matthew A Kolmann","doi":"10.1093/icb/icae067","DOIUrl":"10.1093/icb/icae067","url":null,"abstract":"Strong selective pressure on phenotype can arise when habitat transitions fundamentally alter the physical media in which animals live, such as the invasion of land by lobe-finned fishes and insects. When environmental gradients differ drastically among habitats and multiple lineages transition between these habitats, we expect phenotypic convergence to be prevalent. One transition where widespread convergence has been observed is the shift from aboveground to subterranean environments in fossorial animals. Subterranean environments are low-light, confined spaces and tend to be hypoxic or anoxic, not to mention that the act of burrowing itself demands morphological specializations for excavation. Research suggests burrowing promotes morphological convergence in crayfish, with non-burrowing forms having a dorsoventrally compressed carapace and long, slender claws (chelae), while primary burrowing forms have a dorsolaterally compressed carapace and shorter, more powerful claws. However, earlier ecomorphological comparisons relied on qualitative rather than quantitative assessments of phenotypic differences. This study tested for convergence in North American crayfishes using a geometric morphometric approach. We photographed the carapace and claw for representative species across 13 North American genera. We hypothesized that crayfishes that occur in similar habitats and exhibit similar burrowing behaviors, would converge in their carapace and claw shapes. We found evidence for convergence in carapace and claw morphologies in burrowing crayfishes. However, claw phenotypes did not converge as strongly as carapace shape, an example of \"imperfect\" or \"incomplete\" convergence we attribute to the multiple competing demands on claw form and function. We argue that nuances in habitat characteristics, like soil type or compaction, make complete convergence unlikely for range- and dispersal-limited fossorial crayfishes.","PeriodicalId":54971,"journal":{"name":"Integrative and Comparative Biology","volume":" ","pages":"1454-1466"},"PeriodicalIF":2.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141307466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Anterior-Posterior Wnt Signaling Network Conservation between Indirect Developing Sea Urchin and Hemichordate Embryos. 间接发育的海胆和半脊柱动物胚胎之间前后Wnt信号网络的保护。

IF 2.2 3区生物学

Integrative and Comparative Biology Pub Date : 2024-11-21 DOI: 10.1093/icb/icae047

Jennifer L Fenner, Callum Newberry, Callie Todd, Ryan C Range

{"title":"Anterior-Posterior Wnt Signaling Network Conservation between Indirect Developing Sea Urchin and Hemichordate Embryos.","authors":"Jennifer L Fenner, Callum Newberry, Callie Todd, Ryan C Range","doi":"10.1093/icb/icae047","DOIUrl":"10.1093/icb/icae047","url":null,"abstract":"How animal body plans evolved and diversified is a major question in evolutionary developmental biology. To address this question, it is important to characterize the exact molecular mechanisms that establish the major embryonic axes that give rise to the adult animal body plan. The anterior-posterior (AP) axis is the first axis to be established in most animal embryos, and in echinoderm sea urchin embryos its formation is governed by an integrated network of three different Wnt signaling pathways: Wnt/β-catenin, Wnt/JNK, and Wnt/PKC pathways. The extent to which this embryonic patterning mechanism is conserved among deuterostomes, or more broadly in metazoans, is an important open question whose answers could lead to a deeper appreciation of the evolution of the AP axis. Because Ambulacrarians (echinoderms and hemichordates) reside in a key phylogenetic position as the sister group to chordates, studies in these animals can help inform on how chordate body plans may have evolved. Here, we assayed the spatiotemporal gene expression of a subset of sea urchin AP Wnt patterning gene orthologs in the hemichordate, Schizocardium californicum. Our results show that positioning of the anterior neuroectoderm (ANE) to a territory around the anterior pole during early AP formation is spatially and temporally similar between indirect developing hemichordates and sea urchins. Furthermore, we show that the expression of wnt8 and frizzled5/8, two known drivers of ANE patterning in sea urchins, is similar in hemichordate embryos. Lastly, our results highlight divergence in embryonic expression of several early expressed Wnt genes (wnt1, wnt2, and wnt4). These results suggest that expression of the sea urchin AP Wnt signaling network is largely conserved in indirect developing hemichordates setting the foundation for future functional studies in S. californicum.","PeriodicalId":54971,"journal":{"name":"Integrative and Comparative Biology","volume":" ","pages":"1214-1225"},"PeriodicalIF":2.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11579615/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141071584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Acquisition of polymorphism in the chordate doliolids. 脊索动物中多态性的获得。

IF 2.2 3区生物学

Integrative and Comparative Biology Pub Date : 2024-11-21 DOI: 10.1093/icb/icae101

C J Pickett, Joseph Ryan, Bradley Davidson

{"title":"Acquisition of polymorphism in the chordate doliolids.","authors":"C J Pickett, Joseph Ryan, Bradley Davidson","doi":"10.1093/icb/icae101","DOIUrl":"10.1093/icb/icae101","url":null,"abstract":"In polymorphic organisms, a single genome is deployed to program numerous, morphologically distinct body plans within a colony. This complex life history trait has evolved independently within a limited subset of animal taxa. Reconstructing the underlying genetic, cellular, and developmental changes that drove the emergence of polymorphic colonies represents a promising avenue for exploring diversifying selection and resulting impacts on developmental gene regulatory networks. Doliolids are the only polymorphic chordate, deploying a single genome to program distinct morphs specialized for locomotion, feeding, asexual, or sexual reproduction. In this review, we provide a detailed summary of doliolid anatomy, development, taxonomy, ecology, life history, and the cellular basis for doliolid polymorphism. In order to frame the potential evolutionary and developmental insights that could be gained by studying doliolids, we provide a broader overview of polymorphism. We then discuss how comparative studies of polymorphic cnidarians have begun to illuminate the genetic basis of this unusual and complex life history strategy. We then provide a summary of life history divergence in the chordates, particularly among doliolids and their polymorphic cousins, the salps and pyrosomes.","PeriodicalId":54971,"journal":{"name":"Integrative and Comparative Biology","volume":" ","pages":"1255-1268"},"PeriodicalIF":2.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141592191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single-cell Transcriptomic Studies Unveil Potential Nodes of the Notochord Gene Regulatory Network. 单细胞转录组研究揭示脊索基因调控网络的潜在节点

IF 2.2 3区生物学

Integrative and Comparative Biology Pub Date : 2024-11-21 DOI: 10.1093/icb/icae084

Lenny J Negrón-Piñeiro, Anna Di Gregorio

{"title":"Single-cell Transcriptomic Studies Unveil Potential Nodes of the Notochord Gene Regulatory Network.","authors":"Lenny J Negrón-Piñeiro, Anna Di Gregorio","doi":"10.1093/icb/icae084","DOIUrl":"10.1093/icb/icae084","url":null,"abstract":"Transcription factors (TFs) are DNA-binding proteins able to modulate the timing, location, and levels of gene expression by binding to regulatory DNA regions. Therefore, the repertoire of TFs present in the genome of a multicellular organism and the expression of variable constellations of TFs in different cellular cohorts determine the distinctive characteristics of developing tissues and organs. The information on tissue-specific assortments of TFs, their cross-regulatory interactions, and the genes/regulatory regions targeted by each TF is summarized in gene regulatory networks (GRNs), which provide genetic blueprints for the specification, development, and differentiation of multicellular structures. In this study, we review recent transcriptomic studies focused on the complement of TFs expressed in the notochord, a distinctive feature of all chordates. We analyzed notochord-specific datasets available from organisms representative of the three chordate subphyla, and highlighted lineage-specific variations in the suite of TFs expressed in their notochord. We framed the resulting findings within a provisional evolutionary scenario, which allows the formulation of hypotheses on the genetic/genomic changes that sculpted the structure and function of the notochord on an evolutionary scale.","PeriodicalId":54971,"journal":{"name":"Integrative and Comparative Biology","volume":" ","pages":"1194-1213"},"PeriodicalIF":2.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11579531/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141447656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0