The exact meaning of the term systems biology is debated, yet most biologists agree that it refers to the study of organismal properties that cannot be reduced to the functions of single genes or other individual components. That is, systems biology is about the traits\u2014be they physiological, developmental, or behavioral\u2014that arise out of interactions between components. Some systems biologists emphasize not the subject matter of the field, but instead the methodology, which combines experimental perturbations with high-throughput quantitative measurements and mathematical modeling. The goal is to understand how complex biological systems achieve function through iterative cycles of data gathering and model-based prediction. Evolutionary biology intersects with systems biology in two ways. First, evolution provides a means of understanding the current structure and function of biological systems. For example, many studies have found that networks of biological interactions do not have topologies consistent with random connections between pairs of components. The departures from random expectation must have evolutionary explanations, and both adaptive and nonadaptive explanations have been proposed and debated. Second, systems biology holds the promise of replacing unrealistically simple representations of the mapping between genotype and phenotype \u2014a key element of all evolutionary models\u2014with more meaningful ones. Thus, systems biology can expand and enrich our understanding of complex-trait evolution. This article aims to provide entry points into the literature of evolutionary systems biology from its historical roots to its current incarnations. Particular attention is paid to the organizational features and functional properties of complex biological systems. System organization is typically investigated in terms of networks of interacting components, such as genes or proteins. Organizational features of interest range from the global level of overall network topology to the local level of modules and regulatory motifs. Functional properties of interest include modularity, evolvability, and robustness to perturbations, such as environmental fluctuations and mutations. The field of evolutionary systems biology spans a range of organisms and analytical approaches, addresses a range of questions, and, indeed, has several alternative definitions. The works compiled here were chosen to reflect this diversity, to highlight major developments and insights, and to enable more extensive forays into the literature.<\/p>","DOI":"10.1093\/obo\/9780199941728-0010","type":"reference-entry","created":{"date-parts":[[2014,2,20]],"date-time":"2014-02-20T16:36:38Z","timestamp":1392914198000},"source":"Crossref","is-referenced-by-count":0,"title":["Systems Biology"],"prefix":"10.1093","member":"286","published-online":{"date-parts":[[2014,1,13]]},"container-title":["Evolutionary Biology"],"original-title":["Systems Biology"],"language":"en","deposited":{"date-parts":[[2022,9,24]],"date-time":"2022-09-24T08:25:48Z","timestamp":1664007948000},"score":8.375939,"resource":{"primary":{"URL":"https:\/\/oxfordbibliographies.com\/view\/document\/obo-9780199941728\/obo-9780199941728-0010.xml"}},"issued":{"date-parts":[[2014,1,13]]},"ISBN":["9780199941728"],"references-count":0,"URL":"https:\/\/doi.org\/10.1093\/obo\/9780199941728-0010","published":{"date-parts":[[2014,1,13]]}},{"indexed":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T03:20:37Z","timestamp":1715311237878},"reference-count":0,"publisher":"Oxford University Press","isbn-type":[{"value":"9780199941728","type":"electronic"}],"content-domain":{"domain":[],"crossmark-restriction":false},"abstract":"
Evolutionary developmental biology, or evo-devo, is the study of the reciprocal relationships between ontogenetic development and evolutionary processes. This still relatively new research field, of roughly four decades, is highly heterogeneous and based on a variety of different approaches and interpretations of evo-devo as a research field. Broadly conceived forms of evo-devo, in which nearly every comparative-embryological or developmental-genetic approach is presumed to have evolutionary significance, intersect with more specialized practices that are characterized by the explicit evolutionary questions they attempt to answer. In this bibliographic survey we focus on the latter. These works explore an interconnected set of two principal scientific problems: How do the mechanisms of individual development evolve, and how do the properties of developmental systems that characterize organismal lineages influence their further evolution? Within each of these larger areas, a host of more detailed questions can be defined, and, in pursuing them, evo-devo addresses many empirical and conceptual issues that pertain to the emergence of complex phenotypes as well as the evolving interactions of development with population-level processes and the environment. The theoretical consequences of these kinds of investigations have a significant impact on how organismal evolution is conceptualized today. Thus, the publications listed herein were chosen for their specific evo-devo content and their capacity to bridge the empirical and theoretical dimensions. Recent works are favored, but foundational classics of individual subject areas are also cited. Besides the general parts, our survey contains sixteen thematic sections that cover the most important areas of evo-devo research. For each of these sections, we were permitted to list up to ten publications. Of course, this cannot do justice to all the excellent work in the field. Therefore, we attempted to highlight publications that are representative of the selected areas and address crucial conceptual aspects. Since even this criterion is a highly subjective one, we ask all those whose work could not be included for their understanding. In addition to providing an introduction to the characteristic themes of evo-devo, we have aimed for a suitability of this survey as a comprehensive resource for the teaching of evo-devo to advanced undergraduate and graduate students.<\/p>","DOI":"10.1093\/obo\/9780199941728-0138","type":"reference-entry","created":{"date-parts":[[2021,8,24]],"date-time":"2021-08-24T07:18:09Z","timestamp":1629789489000},"source":"Crossref","is-referenced-by-count":0,"title":["Evolutionary Developmental Biology"],"prefix":"10.1093","member":"286","published-online":{"date-parts":[[2021,8,25]]},"container-title":["Evolutionary Biology"],"original-title":["Evolutionary Developmental 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Biol."},{"key":"10.1016\/j.celrep.2023.112110_bib22","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1016\/j.cell.2017.09.026","article-title":"Cohesin loss eliminates all loop domains","volume":"171","author":"Rao","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2023.112110_bib23","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1016\/j.cell.2017.05.004","article-title":"Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization","volume":"169","author":"Nora","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2023.112110_bib24","doi-asserted-by":"crossref","first-page":"2038","DOI":"10.1016\/j.celrep.2016.04.085","article-title":"formation of chromosomal domains by loop extrusion","volume":"15","author":"Fudenberg","year":"2016","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2023.112110_bib25","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1186\/s13059-020-02108-x","article-title":"Spatial patterns of CTCF sites define the anatomy of TADs and their boundaries","volume":"21","author":"Nanni","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2023.112110_bib26","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.ajhg.2021.01.001","article-title":"Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability","volume":"108","author":"McArthur","year":"2021","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.celrep.2023.112110_bib27","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1009346","article-title":"Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors","volume":"17","author":"Jefferys","year":"2021","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.celrep.2023.112110_bib28","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1016\/j.cell.2021.12.011","article-title":"Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses","volume":"185","author":"Einkauf","year":"2022","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2023.112110_bib29","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1172\/JCI124291","article-title":"Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy","volume":"129","author":"Einkauf","year":"2019","journal-title":"J.\u00a0Clin. 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Med."},{"key":"10.1016\/j.celrep.2023.112110_bib52","doi-asserted-by":"crossref","DOI":"10.1038\/srep24157","article-title":"Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4(+) T\u00a0cells","volume":"6","author":"Kok","year":"2016","journal-title":"Sci. Rep."},{"key":"10.1016\/j.celrep.2023.112110_bib53","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: automating chromatin-state discovery and characterization","volume":"9","author":"Ernst","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2023.112110_bib54","doi-asserted-by":"crossref","first-page":"2478","DOI":"10.1038\/nprot.2017.124","article-title":"Chromatin-state discovery and genome annotation with ChromHMM","volume":"12","author":"Ernst","year":"2017","journal-title":"Nat. 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Methods Protoc."},{"key":"10.1016\/j.celrep.2023.112110_bib56","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.34655","article-title":"Distinct chromatin functional states correlate with HIV latency reactivation in infected primary CD4 T\u00a0cells","volume":"7","author":"Battivelli","year":"2018","journal-title":"Elife"},{"key":"10.1016\/j.celrep.2023.112110_bib57","doi-asserted-by":"crossref","DOI":"10.1126\/science.aal3222","article-title":"An environment-dependent transcriptional network specifies human microglia identity","volume":"356","author":"Gosselin","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.celrep.2023.112110_bib58","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/1742-4690-10-67","article-title":"HIV-1 transcription and latency: an update","volume":"10","author":"Van Lint","year":"2013","journal-title":"Retrovirology"},{"key":"10.1016\/j.celrep.2023.112110_bib59","doi-asserted-by":"crossref","first-page":"874","DOI":"10.1016\/j.neuron.2020.06.008","article-title":"An activity-mediated transition in transcription in early postnatal neurons","volume":"107","author":"Stroud","year":"2020","journal-title":"Neuron"},{"key":"10.1016\/j.celrep.2023.112110_bib60","doi-asserted-by":"crossref","first-page":"2042","DOI":"10.1016\/j.celrep.2016.10.061","article-title":"A compendium of chromatin contact maps reveals spatially active regions in the human genome","volume":"17","author":"Schmitt","year":"2016","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2023.112110_bib61","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1182\/blood.2020005780","article-title":"Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis","volume":"137","author":"Qi","year":"2021","journal-title":"Blood"},{"key":"10.1016\/j.celrep.2023.112110_bib62","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1016\/j.cell.2016.09.037","article-title":"Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters","volume":"167","author":"Javierre","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2023.112110_bib63","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1016\/j.cell.2017.09.043","article-title":"Multiscale 3D genome rewiring during mouse neural development","volume":"171","author":"Bonev","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2023.112110_bib64","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1186\/s13059-019-1893-y","article-title":"OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries","volume":"20","author":"An","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.celrep.2023.112110_bib65","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1086\/510915","article-title":"Recurrent HIV-1 integration at the BACH2 locus in resting CD4+ T\u00a0cell populations during effective highly active antiretroviral therapy","volume":"195","author":"Ikeda","year":"2007","journal-title":"J.\u00a0Infect. Dis."},{"key":"10.1016\/j.celrep.2023.112110_bib66","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/nsmb.3328","article-title":"Position effects influence HIV latency reversal","volume":"24","author":"Chen","year":"2017","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.celrep.2023.112110_bib67","doi-asserted-by":"crossref","first-page":"4025","DOI":"10.1083\/jcb.201807108","article-title":"Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler","volume":"217","author":"Chen","year":"2018","journal-title":"J.\u00a0Cell Biol."},{"key":"10.1016\/j.celrep.2023.112110_bib68","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1038\/nrg.2016.147","article-title":"Organization and function of the 3D\u00a0genome","volume":"17","author":"Bonev","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.celrep.2023.112110_bib69","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2021.633762","article-title":"Utilization of host cell chromosome conformation by viral pathogens: knowing when to hold and when to fold","volume":"12","author":"Majumder","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1016\/j.celrep.2023.112110_bib70","doi-asserted-by":"crossref","first-page":"3054","DOI":"10.1073\/pnas.1423199113","article-title":"The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome","volume":"113","author":"Satou","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2023.112110_bib71","doi-asserted-by":"crossref","first-page":"3190","DOI":"10.1093\/nar\/gkac107","article-title":"Role of the cellular factor CTCF in the regulation of bovine leukemia virus latency and three-dimensional chromatin organization","volume":"50","author":"Bellefroid","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2023.112110_bib72","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1016\/j.molcel.2016.05.018","article-title":"Chromatin domains: the unit of chromosome organization","volume":"62","author":"Dixon","year":"2016","journal-title":"Mol. 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This chapter explores polar marine biology. Polar ecosystems are influenced by strong seasonality, especially of ice cover. Also, a diverse phytoplankton assemblage fuels the polar food webs. Carnivores exert top-down effects, so overfishing of carnivores has had strong effects on polar food webs. The chapter considers the impact of climate change and ocean warming on the organization of polar ecosystems. It examines the food webs and the impact of climate change within Arctic marine systems and Antarctic marine systems. Global climate change is decreasing summer ice cover in the Arctic, so major changes are occurring in sea temperature and the organization of benthic communities.<\/p>","DOI":"10.1093\/hesc\/9780197543504.003.0026","type":"book-chapter","created":{"date-parts":[[2023,9,15]],"date-time":"2023-09-15T11:37:56Z","timestamp":1694777876000},"source":"Crossref","is-referenced-by-count":0,"title":["Polar Marine Biology"],"prefix":"10.1093","author":[{"given":"Jeffrey S.","family":"Levinton","sequence":"first","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2023,8,31]]},"container-title":["Marine Biology"],"original-title":["Polar Marine Biology"],"language":"en","link":[{"URL":"https:\/\/www.oxfordsciencetrove.com\/display\/10.1093\/hesc\/9780197543504.001.0001\/isbn-9780197543504-book-part-19","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,6]],"date-time":"2024-02-06T08:31:27Z","timestamp":1707208287000},"score":8.092086,"resource":{"primary":{"URL":"https:\/\/www.oxfordsciencetrove.com\/view\/10.1093\/hesc\/9780197543504.001.0001\/isbn-9780197543504-book-part-19"}},"issued":{"date-parts":[[2021,7,15]]},"ISBN":["9780197543504","9780197661864"],"references-count":0,"URL":"https:\/\/doi.org\/10.1093\/hesc\/9780197543504.003.0026","published":{"date-parts":[[2021,7,15]]}},{"indexed":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T07:15:13Z","timestamp":1765610113653},"reference-count":0,"publisher":"Oxford University Press","isbn-type":[{"value":"9780199941728","type":"electronic"}],"content-domain":{"domain":[],"crossmark-restriction":false},"abstract":"
Philosophy of evolutionary biology is a major subfield of philosophy of biology concerned with the methods, conceptual foundations, and implications of evolutionary biology. It also concerns relationships between evolutionary biology and neighboring fields, such as biochemistry, genetics, cell and molecular biology, developmental biology, and ecology. Initially, many of the questions of central concern to philosophy of biology grew out of general philosophy of science. For instance, one long-standing debate in philosophy of science concerns the matter of what is distinctive of scientific inquiry. Various criteria have been proposed, and much of the early work in philosophy of biology concerned whether evolutionary biology meets these criteria. Another long-standing debate in philosophy of science concerns whether there is any legitimate role for values in science. The study of the evolution of human behavior and cognition has been scrutinized as an instance of both potentially pernicious and positive influence of values in science. More recently, philosophers of biology both collaborate with and draw upon evolutionary biology to either address broader philosophical concerns, such as the nature of consciousness, or engage directly with debates internal to evolutionary biology. For example, philosophers have engaged in conceptual and methodological debates within evolutionary biology over the appropriate conditions for testing hypotheses about adaptation, the units, targets, or levels of selection, mechanisms and measures of inheritance, modes of phylogenetic inference, and classification and systematics. In this category, the line between science and philosophy blurs; participants in many of these debates include both philosophers and biologists. This entry will focus on philosophers\u2019 contributions. To be sure, evolutionary biologists have contributed far more. Please see the Oxford Bibliographies on these topics for scientific contributions to all of these topics. I also urge readers to review the excellent Stanford Encyclopedia of Philosophy entries on topics including but not limited to \u201cEvolution,\u201d \u201cNatural Selection,\u201d \u201cTeleological Notions in Biology,\u201d \u201cUnits and Levels of Selection,\u201d \u201cAdaptationism,\u201d \u201cEvolutionary Genetics,\u201d \u201cEvolutionary Psychology,\u201d and \u201cDevelopmental Biology.\u201d<\/p>","DOI":"10.1093\/obo\/9780199941728-0133","type":"reference-entry","created":{"date-parts":[[2021,4,18]],"date-time":"2021-04-18T14:40:41Z","timestamp":1618756841000},"source":"Crossref","is-referenced-by-count":1,"title":["The Philosophy of Evolutionary Biology"],"prefix":"10.1093","author":[{"given":"Anya","family":"Plutynski","sequence":"first","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2021,4,21]]},"container-title":["Evolutionary Biology"],"original-title":["The Philosophy of Evolutionary Biology"],"language":"en","deposited":{"date-parts":[[2021,9,23]],"date-time":"2021-09-23T19:41:40Z","timestamp":1632426100000},"score":8.081121,"resource":{"primary":{"URL":"https:\/\/oxfordbibliographies.com\/view\/document\/obo-9780199941728\/obo-9780199941728-0133.xml"}},"issued":{"date-parts":[[2021,4,21]]},"ISBN":["9780199941728"],"references-count":0,"URL":"https:\/\/doi.org\/10.1093\/obo\/9780199941728-0133","published":{"date-parts":[[2021,4,21]]}},{"indexed":{"date-parts":[[2023,7,11]],"date-time":"2023-07-11T04:32:22Z","timestamp":1689049942353},"reference-count":0,"publisher":"Egypts Presidential Specialized Council for Education and Scientific Research","issue":"1","content-domain":{"domain":["eij.journals.ekb.eg"],"crossmark-restriction":false},"short-container-title":["\u0625\u0628\u062f\u0627\u0639\u0627\u062a \u062a\u0631\u0628\u0648\u064a\u0629"],"published-print":{"date-parts":[[2023,1,1]]},"DOI":"10.21608\/eji.2023.280845","type":"journal-article","created":{"date-parts":[[2023,7,10]],"date-time":"2023-07-10T11:17:00Z","timestamp":1688987820000},"page":"235-239","update-policy":"http:\/\/dx.doi.org\/10.21608\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["\u00a0\u00a0\u00a0\u00a0\u00a0 smart home\u00a0 \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0"],"prefix":"10.21608","volume":"24","author":[{"given":"Shereen kamel","family":"( Biology)","sequence":"first","affiliation":[]},{"given":"Lilyan Atef \u00a0","family":"( Biology)","sequence":"additional","affiliation":[]},{"given":"Feby Kareem","family":"( Biology)","sequence":"additional","affiliation":[]},{"given":"Merna mourad","family":"( Biology)","sequence":"additional","affiliation":[]},{"given":"Amany saber","family":"\u00a0( Biology)","sequence":"additional","affiliation":[]},{"given":"Esraa Osama","family":"\u00a0( Biology)","sequence":"additional","affiliation":[]}],"member":"9060","published-online":{"date-parts":[[2023,1,1]]},"container-title":["\u0625\u0628\u062f\u0627\u0639\u0627\u062a \u062a\u0631\u0628\u0648\u064a\u0629"],"language":"ar","link":[{"URL":"https:\/\/eij.journals.ekb.eg\/article_280845_4f56f43e8152ea7acd0015eeae655aae.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,10]],"date-time":"2023-07-10T12:37:29Z","timestamp":1688992649000},"score":8.072883,"resource":{"primary":{"URL":"https:\/\/eij.journals.ekb.eg\/article_280845.html"}},"issued":{"date-parts":[[2023,1,1]]},"references-count":0,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,1,1]]},"published-print":{"date-parts":[[2023,1,1]]}},"URL":"https:\/\/doi.org\/10.21608\/eji.2023.280845","ISSN":["2536-9407"],"issn-type":[{"value":"2536-9407","type":"electronic"}],"published":{"date-parts":[[2023,1,1]]}},{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T03:56:07Z","timestamp":1760241367970,"version":"build-2065373602"},"reference-count":0,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2018,1,11]],"date-time":"2018-01-11T00:00:00Z","timestamp":1515628800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"