what is serial homology biology

Here, we restricted reasoning across development because of the widely recognized disconnect between homology at different levels of biological organization: homology at one level does not necessitate homology at another (Striedter and Northcutt 1991; Roth 1994; Abouheif et al. Panganiban G., Irvine S.M., Lowe C., Roehl H., Corley L.S., Sherbon B., Grenier J.K., Fallon J.F., Kimble J., Walker M., Wray G.A., Swalla B.J., Martindale M.Q., Carroll S.B.. 13. 2007b). As its name states, REA models a homology annotation as a reciprocal pair of axioms. et al. Serial homology, a type of iterative homology, is the historical and developmental relationship among segmented or, more generally, iterated, structures within an organism, for example, across the various appendages of crustacea, the vertebrae of vertebrates, and the arms of a starfish (Roth 1984). Abouheif E., Akam M., Dickinson W.J., Holland P.W., Meyer A., Patel N.H., Raff R.A., Roth V.L., Wray G.A.. Drosophila Most often these properties involve structural criteria but developmental and functional ones are employed, too. The all-some semantics entail that a given instance of humerus is part of one specific forelimb; it is not part of every instance of forelimb. The particular gene in charge of making sure the haltere develops properly, and not into a wing or something else, is called Ubx. 1997). As mentioned, previous expression analyses for wing marker genes in non-insect arthropods 2012). The philosophy of biology. The OWL expressions for these competency questions are provided in Supplementary material S4 available on Dryad at https://doi.org/10.5061/dryad.0373j7r and also in the homology demonstration file (see Software and Data Availability section). In contrast, the segments outside of the thorax do not have The impressively exaggerated treehopper helmet was shown to have expression of They do not expect the query to return the superclass of the search term (hindlimb), structures for parts (e.g., humerus, femur) of the serial homologs, historical homologs (e.g., pectoral fin) of the serial homologs, or developmental precursors (e.g., hindlimb bud, forelimb bud) of the serial homologs. Dependent on the level of comparison four types of homology are defined: (1) Iterative ( = serial = homonomy), (2) ontogenetic, (3) di- or polymorphic, and (4) supraspecific homology. In contrast, there is no ventral appendage in the abdominal segments of 1997. Bone of the dorsal hyoid arch, references some bone in a region and is not more informative than an ontological parent class expression such as endochondral bone that is part of or derived from the hyoid arch skeleton. That is, in the binary representation, the homologs are also connected to a more general anatomical class, but there it is implied by the structure of the ontology and is thus not necessarily an evolutionary concept. Myriapoda (millipedes and centipedes) is another taxon that may provide interesting insights in regard to identifying tissues homologous to insect wings. 2007a). An illustration of such reasoning is provided by the OntoTrace tool, which can directly extract or infer the presence or absence of anatomical entities across all studies in the KB for a user-specified set of anatomical entities and taxa; these can then be aggregated into an aligned matrix for downstream analysis (Dececchi et al. 32. Through this outcome, we can conclude that there are no leg serial homologs in the ap) Enabling individualized selection of homology relationships would alter the reasoning and thus the derivative products of knowledgebases. 2009; Dahdul et al. Furthermore, in both studies, these 1997. Reasoning with the REA model is much more scalable. 2 and Table 4). and transmitted securely. pleura): The lateral portion of insect thoracic and abdominal segments that consists of several pleural plates. There are two evo-devo concepts that are crucial for the identification of serially homologous structures in insects: marker genes and Hox region selector genes. Kazakov Y., Krtzsch M., Simank F.. Integrating phenotype ontologies across multiple species. In the first mode (Hox action 1), the marker gene expression is often kept among the modified serially homologous structures. 44, 7.13C: Homologs, Orthologs, and Paralogs - Biology LibreTexts Two instances related by a subproperty can be inferred to be also related by the parent property. 22. Anatomy ontologies are formal graph representations of anatomical structures and the relationships among them. As discussed above in Logical models of homology assertions, the REA model is amenable to more efficient reasoning, such as with the ELK reasoner. More formally, if specifically, entity A occurring in taxon X is homologous to entity B occurring in taxon Y, we substitute A with the class expression A and in_taxon some X (i.e., those instances of A that are in some instance of taxon X) and B with B and in_taxon some Y (here using the REA model): Here, X and Y are terms from a taxonomy ontology, for example, Vertebrate Taxonomy Ontology (VTO; Midford et al. This is driven in part by requiring a model that works smoothly with ontologies developed as part of the broad biological OBO library, which includes the Uberon anatomy ontology. FOIA Here, we introduce two alternative logical models for homology: Reciprocal Existential Axioms (REA) and Ancestral Value Axioms (AVA; Table 1). : Alternative requirements for Vestigial, Scalloped, and Dmef2 during muscle differentiation in, The Vestigial and Scalloped proteins act together to directly regulate wing-specific gene expression in, Integration of positional signals and regulation of wing formation and identity by. A) Dorsal/tergal wing serial homologs. Subclassalso Subtype. A term in an ontology that narrows down another (parent) term. It will be interesting to investigate how much of the gene regulatory network operating in these tissues is shared with insect wings. Bethesda, MD 20894, Web Policies Over a century of investigations into this question have resulted in two prominent hypotheses on the evolutionary origin of insect wings: the tergal hypothesis and the pleural hypothesis. REA returned no results from a query for serial homologs of hind flipper. The same AVA query returned all expected results and additionally phenotypes for the search term itself (hind flipper) and its superclass (hindlimb; Fig. Because Serial homology is a special type of homology, defined by Owen as "representative or repetitive relation in the segments of the same organism." [1] Ernst Haeckel preferred the term "homotypy" for the same phenomenon. Evolution of homeotic gene regulation and function in flies and butterflies. 2012), the definitions of classes focus on some re-identifiable property or properties that members of the classes have in common; they do not include criteria of homology. These results are consistent with OWL entailments of the respective models. Is Travillian R., Malone J., Pang C., Hancock J., Holland P.W.H., Schofield P., Parkinson H.. Expert curators use this term across vertebrates without restricting the semantics to different taxonomic groups. sterna): The large ventral plate of insect thoracic and abdominal segments. Although considerable research and thought has been applied to understanding how homology can be identified and further codified, including suggestions for a semantic framework (Vogt 2017, 2018a,b), general expectations for a semantic model have not been previously formalized. Several leg branches (homologous to a pleural lineage) in the brine shrimp and the crayfish have been shown to express some wing marker genes vg-positive epidermal tissues followed by Hox transformation studies to test whether the identified tissues transform into wings. We thank Nipam Patel for the opportunity to contribute this review, and Ehab Abouheif and Gnter Wagner for providing us with valuable comments to improve our manuscript. Note that this file is intended to be used in conjunction with referenced ontologies (e.g., Uberon) and includes only the homology axioms, not metadata for individual terms such as label and definition. 3, For example, a user query to paired limb/fin would return paired fin and limb (Fig. 33. You must there are over 200,000 words in our free online dictionary, but you are looking for one that's only in the Merriam-Webster Unabridged Dictionary. Another example of limiting homology inference on the basis of biological knowledge comes from developmental biology. In ECO, NAS is a type of author statement without traceable support that is used in a manual assertion. For example, it has been reported that wing tissue arises at a lateral (pleural) position and migrates dorsally to merge into the tergolateral margin during the nymphal stages in a dragonfly, which may support the pleural (or perhaps dual?) Though not comprehensive, because the literature in the area of fin/limb evolution is substantial and homology statements specific to many taxonomic groups were not extracted (e.g., between urodele and anuran amphibians), many of the well-known and controversial homologies across fishes and amphibians were captured. What is a homology in biology? (with examples) - science - 2023 Jackson L.M., Fernando P.C., Hanscom J.S., Balhoff J.P., Mabee P.M.. REA is designed to fit within the OWL EL profile. vg-positive epidermal tissues that contribute to adult morphology By studying the molecular and developmental mechanisms that orchestrate the differentiation of wing serial homologs from wings (and vice versa), we will be able to identify the mechanisms that are operating uniquely in the winged segments. Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 5 Figure 1). Despite the volume of literature on homology, an . 18, and these ventral appendages can transform into one another upon various Hox mutations (including both gain-of-function and loss-of-function (LOF) mutations) vg appears to be the only gene whose expression can induce ectopic wing structures in government site. vg dependency of this tissue has yet to be tested, given that the treehopper helmet is an expansion of the prothoracic tergum Comparison of the REA and the AVA homology model. The https:// ensures that you are connecting to the The anatomy ontologies and reasoning capabilities of the Phenoscape Knowledgebase (hereafter, the KB) provide the core framework for automatically extracting the basic data desired at the outset of a comparative anatomical study, namely all of the published data for a set of anatomical structures in a focal taxon. A) bristletail tergal edge, cockroach lateral pronotum, beetle T1 carinated margin, beetle pupal gin-trap, and treehopper helmet and ( Assertions about homology in the literature sometimes also take the form of rejecting or discounting a homology relationship between structures. while serving at the U.S. National Science Foundation. An official website of the United States government. Is Many of the genes in this class encode transcription factors. Additional evidence for the presence of wing serial homologs in non-winged segments comes from the outcome of the abdominal Hox gene analysis in beetles. vg-dependent epidermal tissues were found in non-winged segments in beetles. 22, To relate two anatomical terms as historically homologous, we used the relation in historical homology relationship with (RO:HOM0000007) from the OBO Relations Ontology (RO; http://purl.obolibrary.org/obo/ro.owl), which is defined as: Homology that is defined by common descent. Serially homologous structures were related using the relation in serial homology relationship with (RO:HOM0000027), which is defined as: Iterative homology that involves structures arranged along the main body axis. These relations are derived from the HOM; http://purl.obolibrary.org/obo/hom.owl), which contains 66 classes representing concepts related to organismal similarity, including homology and homoplasy. 41, Both REA and AVA returned the expected phenotypes; AVA additionally returned phenotypes for the search term itself (pectoral fin) and its subtype (archipterygial fin; Fig. Although in many cases, it may suffice for a user to query for serial homologs by using a shared parent term (e.g., a query for vertebra returns vertebra 1, vertebra 2, vertebra 3, etc. Such a research program would be enhanced by the ability to conduct taxonomically broad similarity searches in a knowledgebase such as the one used here. 14. Even where there is a single robust phylogeny, there may not be a named taxon class or other identifier that corresponds to the last common ancestor. 18. Thus, it is critical to assess the ability of a tissue to transform into the wing upon Hox mutation before determining whether the tissue is a wing serial homolog. A summary of the history of the wing origin debate and an overall perspective on how the application of evo-devo approaches to this question can lead to new insights on the evolutionary origin of insect wings have previously been reviewed Subgraphs of paired fin and limb terms showing terms pertaining to competency questions 14 on historical homology. Nine of these 10 classes are relevant to the fin/limb collection of homology assertions assembled here: paired limb/fin bud UBERON:000435; limb/fin segment UBERON:0010538; paired limb/fin cartilage UBERON:0007389; paired limb/fin skeleton UBERON:0011582; pelvic appendage UBERON:000470; paired limb/fin UBERON:0004708; pectoral appendage UBERON:0004710; paired limb/fin field UBERON:0005732, and bone of free limb or fin UBERON:0004375. Along the same line, transcriptome comparison between wings and wing serial homologs will allow us to comprehensively identify genes expressed differentially between these tissues. "Serial homology," a type of iterative homology, is the historical and developmental relationship among segmented or, more generally, iterated, structures within an organism, for example, across the various appendages of crustacea, the vertebrae of vertebrates, and the arms of a starfish . This has been aided considerably by computer-based analysis, which is enabled by the standardization of genomic data. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This work lays the foundation for homology reasoning to be incorporated into other ontology-based tools, such as those that enable synthetic supermatrix construction and candidate gene discovery. In addition, the AVA model also returned the specified query term and any subtypes, because the query term is itself a descendant of the ancestral structure in the model. The linguistic problem of morphology: structure versus homology and the standardization of morphological data, 1,2,3 = 2,3,4: a solution to the problem of the homology of the digits in the avian hand, http://creativecommons.org/licenses/by/4.0/, https://github.com/phenoscape/phenoscape-owl-tools, https://github.com/phenoscape/homology-annotations-demo, OWL 2 Web Ontology Language Profiles 2012, https://www.w3.org/TR/owl2-manchester-syntax/, http://purl.org/phenoscape/demo/phenoscape_homology.owl, https://wiki.phenoscape.org/wiki/Acknowledgments. For example, some might desire homology reasoning to lead to the conclusion that the developmental precursors of homologous structures are themselves homologs. vHOG describes structures with historical homology relations between model vertebrate species. 2017) for biodiverse species. It includes manually reviewed mappings to species-specific anatomical ontologies; no homology hypotheses are stated within the ontology itself (Niknejad et al. A Logical Model of Homology for Comparative Biology - PMC 2014; Giglio et al. Conserved and unique transcriptional features of pharyngeal arches in vg-dependent epidermal tissues that contribute to the adult morphology in the non-winged segments. Mungall C.J., Gkoutos G.V., Smith C.L., Haendel M.A., Lewis S.E., Ashburner M.. 2014). On the other hand, the same master gene (the second class of marker genes) often orchestrates the development of tissues that are serially homologous to each other; thus, this type of marker gene is useful for investigating the history of the tissue and for identifying serial homologs that are morphologically diverged. Arthropod phylogeny based on eight molecular loci and morphology. Drosophila situation likely does not reflect an ancestral state. Clark-Hachtel and Tomoyasu have proposed that the treehopper helmet is serially homologous to the dorsal (tergal) wing serial homologs but not lateral (pleural) wing serial homologs; therefore, the helmet is partially serially homologous to wings Although a researcher might use these data in a number of different ways, the data required will generally be a matrix of taxa and anatomical phenotypes. This pluralistic approach reflects the multiple ways that comparative morphologists understand and group anatomical structures. In particular, the term serial homology is used for a series of general homologs. 60 2018. Anatomical Network Comparison of Human Upper and Lower, Newborn and Answered: What is meant by serial homology, and | bartleby For example, the hyomandibula in the jaw of fishes is homologous to the stapes, an inner ear bone in mammals, as a bone of the dorsal hyoid arch in vertebrates. 1997). The concept of gaining insights into evolutionary transitional states of wings through wing serial homologs is not new. The classic example is the forelimb, where the same basic arrangement is seen in things as dissimilar as . Fortunately, the situation is much less complicated in insects because of their metameric body plan. In biology, homology is commonly defined as any similarity between structures of organisms in different taxa that . et al. We also recorded statements of homology for which a source of the evidence was cited and for which no evidence or source was explicitly given by annotation with the terms traceable author statement (ECO:0000033) and non-traceable author statement (ECO:0000034), respectively. (i) The first and foremost criticism to the evo-devo approach is its tendency to rely on a limited number of marker genes when identifying certain tissue lineages. In the head segments, these appendages form a series of mouthparts as well as antennae. We systematically sought explicit homology statements between the skeletal elements in actinopterygian fins and sarcopterygian fins and limbs. Drosophila (Hox action 2). Both of the OWL models, we explored represent a homology assertion as a binary relation. (ii) Although several new wing serial homologs have been identified through evo-devo studies, it is far from being able to fully reconstruct a transition series for wing evolution. In initial tests of the reasoning based on homology assertions from the literature, we discovered that homology axioms involving general, i.e., less specific, grouping terms can return unexpected results. Further, they do not expect phenotypes to parts of the homologs serial homolog (e.g., humerus of the forelimb), or their developmental precursor (forelimb bud and forelimb wing bud). 62). Serial homology synonyms, Serial homology pronunciation, Serial homology translation, English dictionary definition of Serial homology. Drosophila as an example to discuss how we can apply the above-mentioned evo-devo concept to the identification of serially homologous structures. 46. To date, reasoning performed in the KB using anatomy ontologies has not explicitly incorporated homology. Niknejad A., Comte A., Parmentier G., Roux J., Bastian F.B., Robinson-Rechavi M.. Here, we formalize the biological expectations for homology reasoning and evaluate the consequences of applying formal homology relationships between anatomical structures in an anatomy ontology, using the skeletal elements of the fins and limbs of vertebrates as an example. Consensus concerning the homology of many structures may never be achieved, as different lines of evidence can point in opposing directions. The Anatomical Record Bone Biology Free Access Comments on the Serial Homology and Homologues of Vertebral Lateral Projections in Crocodylia (Eusuchia) Lucy Gomes de Souza First published: 07 March 2018 https://doi.org/10.1002/ar.23802 Citations: 8 Souza - Crocodylia serial homology For example, in regard to the wing serial homologs of tergal origin, they can be lateral expansions of dorsal body wall or an elaborated helmet in T1, gin-traps (modified body wall) in the abdomen, and wings in T2 and T3. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry) and serial homology (the similarity of repeated .
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