On the necessity of an archetypal concept in morphology: With special reference to the concepts of “structure” and “homology”

Morphological elements, or structures, are sorted into four categories depending on their level of anatomical isolation and the presence or absence of intrinsically identifying characteristics. These four categories are used to highlight the difficulties with the concept of structure and our ability to identify or define structures. The analysis is extended to the concept of homology through a discussion of the methodological and philosophical problems of the current concept of homology. It is argued that homology is fundamentally a similarity based concept rather than a phylogenetic concept, and a proposal is put forth to return to a comparative context for homology. It is shown that for both the concepts of structure and homology ana priori assumption of stable underlying patterns (i.e. archetypes) is essential.     

Using genetic networks and homology to understand the evolution of phenotypic traits

Homology can have different meanings for different kinds of biologists. A phylogenetic view holds that homology, defined by common ancestry, is rigorously identified through phylogenetic analysis. Such homologies are taxic homologies (=synapomorphies). A second interpretation, "biological homology" emphasizes common ancestry through the continuity of genetic information underlying phenotypic traits, and is favored by some developmental geneticists. A third kind of homology, deep homology, was recently defined as "the sharing of the genetic regulatory apparatus used to build morphologically and phylogenetically disparate features." Here we explain the commonality among these three versions of homology. We argue that biological homology, as evidenced by a conserved gene regulatory network giving a trait its "essential identity" (a Character Identity Network or "ChIN") must also be a taxic homology. In cases where a phenotypic trait has been modified over the course of evolution such that homology (taxic) is obscured (e.g. jaws are modified gill arches), a shared underlying ChIN provides evidence of this transformation. Deep homologies, where molecular and cellular components of a phenotypic trait precede the trait itself (are phylogenetically deep relative to the trait), are also taxic homologies, undisguised. Deep homologies inspire particular interest for understanding the evolutionary assembly of phenotypic traits. Mapping these deeply homologous building blocks on a phylogeny reveals the sequential steps leading to the origin of phenotypic novelties. Finally, we discuss how new genomic technologies will revolutionize the comparative genomic study of non-model organisms in a phylogenetic context, necessary to understand the evolution of phenotypic traits.     

Deep homology: A view from systematics

Over the past decade, it has been discovered that disparate aspects of morphology – often of distantly related groups of organisms – are regulated by the same genetic regulatory mechanisms. Those discoveries provide a new perspective on morphological evolutionary change. A conceptual framework for exploring these research findings is termed ‘deep homology’. A comparative framework for morphological relations of homology is provided that distinguishes analogy, homoplasy, plesiomorphy and synapomorphy. Four examples – three from plants and one from animals – demonstrate that homologous developmental mechanisms can regulate a range of morphological relations including analogy, homoplasy and examples of uncertain homology. Deep homology is part of a much wider range of phenomena in which biological (genes, regulatory mechanisms, morphological traits) and phylogenetic levels of homology can both be disassociated. Therefore, to understand homology, precise, comparative, independent statements of both biological and phylogenetic levels of homology are necessary.     

Morphological criteria for recognising homology in isolated skeletal elements: comparison of traditional and morphometric approaches in conodonts

Abstract: Accurate hypotheses of primary homology are fundamental to many aspects of the systematics and palaeobiology of fossils. They are particularly critical for conodonts: virtually all areas of conodont research are underpinned by homology, yet the majority of conodont taxa are found only as disarticulated skeletal elements, and hypotheses of element homology are inferred from morphological comparisons with complete skeletons. This can cause problems in taxa where more than one location within the conodont skeleton is occupied by elements with similar morphology. In such cases, morphological comparisons can yield equivocal or erroneous hypotheses of homology of isolated elements. The Eramosa Lagerstätte of Ontario (Silurian, Wenlock) preserves both isolated skeletal elements and articulated conodont skeletons. The latter provide a topological context within which to test hypotheses of element homology and allow blind testing of qualitative discrimination of elements. When applied to P₁ and P₂ elements of Wurmiella excavata, this revealed inaccuracy and inconsistency in distinguishing these P element types. Standardised morphometric protocols were used to further test the efficacy of those characters used in traditional qualitative identification of P element homology, revealing that, individually, none of these characters provides an effective discriminator between P element types. Principal components and discriminant function analyses of ten ‘traditional’ morphological variables combined can distinguish P₁ from P₂ elements with a similar success rate to expert identification. Eigenshape and elliptic Fourier analyses of element outlines proved less effective at capturing shape differences that allowed for discrimination between P₁ and P₂ elements. Analysis of both traditional and outline data demonstrates that in some individuals P₁ and P₂ elements are morphologically distinct from one another, while in others they are almost indistinguishable. These results demonstrate that although qualitative assessments of homology can be prone to error, especially when undertaken by inexperienced researchers, the morphometric and analytical protocols used here provide effective additional tool for discriminating morphologically similar but non‐homologous elements. These methods thus hold promise of broad application to other conodont taxa where identification of element homology in collections of isolated specimens is problematic.     

The hierarchical basis of serial homology and evolutionary novelty

Given the pervasiveness of gene sharing in evolution and the extent of homology across the tree of life, why is everything not homologous with everything else? The continuity and overlapping genetic contributions to diverse traits across lineages seem to imply that no discrete determination of homology is possible. Although some argue that the widespread overlap in parts and processes should be acknowledged as “partial” homology, this threatens a broad base of presumed comparative morphological knowledge accepted by most biologists. Following a long scientific tradition, we advocate a strategy of “theoretical articulation” that introduces further distinctions to existing concepts to produce increased contrastive resolution among the labels used to represent biological phenomena. We pursue this strategy by drawing on successful patterns of reasoning from serial homology at the level of gene sequences to generate an enriched characterization of serial homology as a hierarchical, phylogenetic concept. Specifically, we propose that the concept of serial homology should be applied primarily to repeated but developmentally individualized body parts, such as cell types, differentiated body segments, or epidermal appendages. For these characters, a phylogenetic history can be reconstructed, similar to families of paralogous genes, endowing the notion of serial homology with a hierarchical, phylogenetic interpretation. On this basis, we propose a five-fold theoretical classification that permits a more fine-grained mapping of diverse trait-types. This facilitates answering the question of why everything is not homologous with everything else, as well as how novelty is possible given that any new character possesses evolutionary precursors. We illustrate the fecundity of our account by reference to debates over insect wing serial homologs and vertebrate paired appendages.     

The language of systematics,and the philosophy of ‘total evidence’

This contribution analyses the primacy of classification over generalization, and the philosophy of total evidence that emerges from the relation of homology to character statements. Primary conjectures of homology are basic character statements, i.e. statements that predicate properties of organisms, properties that are instantiated by those organisms and/or their parts. Secondary conjectures of homology are embedded in a second‐level (metalinguistic) discourse that turns on the coherence or incoherence of those basic character statements relative to a hierarchy. The coherence or incoherence of character statements is a logical relation between statements, not a causal (historical) relation between organisms. The choice of the hypothesis of relationships that is supported by the largest set of coherent basic character statements is based on the empirical presupposition that the properties referred to by the set of coherent character statements are grounded in causally efficacious relations of inheritance and ontogeny, and co‐instantiated because they are inherited through common ancestry (Hennig's auxiliary principle). Unless that empirical presupposition is causally grounded, phylogeny reconstruction is of an inherently probabilistic nature, whether under parsimony or other models of analysis. The causal grounding of a coherent set of character statements typically seeks a link between character statements and causally efficacious generative mechanisms for morphological characters (as is defeasibly indicated by topology and connectivity), or secondary structure information for molecular characters.     

Developmental pathways,homology and homonomy in metameric animals

Following Wagner's (1989) distinction between historical and biological concepts of homology, we analyze homology problems of metameric animals in the light of a biological concept. In identifying homology, we refer to the common informational background which two structures share. Therefore, homology relationships are matters of degree; they are ‘perfect’ only when there is full identity of informational background between the structures under comparison. Homonomy (serial homology) is not fundamentally different from other kinds of homology. We regard the differences between epimorphically and anamorphically developed segments as minor; therefore, the two kinds of segments are largely homologous. The morphogenetic processes giving rise to segmental structures are regarded as not necessarily hierarchical. We contrast the phylogenetic pattern of hierarchically nested homologies with a largely non-hierarchical pattern of homologous structures within the individual organism. This topological difference adds to heterochrony in generating the widespread mismatch of ontogeny and phylogeny.     

DNA-DNA hybridizations among lactic streptococcal temperate and virulent phages belonging to distinct lytic groups

Summary Ten lactic streptococcal temperate phages and eight lactic streptococcal virulent phages classified on the basis of host range were differentiated by DNA-DNA hybridization. Virulent phages were classified in two distinct homology groups and temperate phages in a single one. In both temperate and virulent phages, no correlation was found between DNA homology groups and lytic groups. For most of the virulent phages, no DNA-DNA hybridization occurred with the temperature phages; however, partial sequence homology was found with DNAs from two virulent phages and four temperate phages.     

Evo-devo and the search for homology (“sameness”) in biological systems

Developmental biology and evolutionary studies have merged into evolutionary developmental biology (“evo-devo”). This synthesis already influenced and still continues to change the conceptual framework of structural biology. One of the cornerstones of structural biology is the concept of homology. But the search for homology (“sameness”) of biological structures depends on our favourite perspectives (axioms, paradigms). Five levels of homology (“sameness”) can be identified in the literature, although they overlap to some degree: (i) serial homology (homonomy) within modular organisms, (ii) historical homology (synapomorphy), which is taken as the only acceptable homology by many biologists, (iii) underlying homology (i.e., parallelism) in closely related taxa, (iv) deep evolutionary homology due to the “same” master genes in distantly related phyla, and (v) molecular homology exclusively at gene level. The following essay gives emphasis on the heuristic advantages of seemingly opposing perspectives in structural biology, with examples mainly from comparative plant morphology. The organization of the plant body in the majority of angiosperms led to the recognition of the classical root–shoot model. In some lineages bauplan rules were transcended during evolution and development. This resulted in morphological misfits such as the Podostemaceae, peculiar eudicots adapted to submerged river rocks. Their transformed “roots” and “shoots” fit only to a limited degree into the classical model which is based on either–or thinking. It has to be widened into a continuum model by taking over elements of fuzzy logic and fractal geometry to accommodate for lineages such as the Podostemaceae.     

Expression, purification, and characterization of thymidylate synthase from Lactococcus lactis.

The thymidylate synthase (TS) gene from Lactococcus lactis has been highly expressed in Escherichia coli. The TS protein was purified by sequential chromatography on Q-Sepharose and phenyl-Sepharose. Six grams of cell pellet yielded 140 mg of homogeneous TS. TS is a highly conserved enzyme, and several of the conserved amino acid residues that have been implicated in catalytic function are altered in L. lactis TS. By use of a 3-dimensional homology model, we have predicted covariant changes that might compensate for these differences. With the large amounts of L. lactis TS now available, studies can be pursued to understand the structure-function relationships of this enzyme compared to other TSs and to confirm the presumed roles of the compensatory changes predicted in the homology model.     

The notion of homology in current comparative biology

Current notions on homology, and its recognition, causation, and explanation are reviewed in this report. The focus is primarily on concepts because the formulation of precise definitions of homology has contributed little to our understanding of the issue. Different aspects or concepts of homology have been contrasted, currently the most important ones being the distinction between systematic and biological concepts. The systematic concept of homology focuses on common ancestry and on taxa; the biological concept tries to explain patterns of conservatism in evolution by shared developmental constraints. Similarity or correspondence is generally accepted as a primary criterion in the delimitation of homologues, albeit that this criterion is not without practical and theoretical problems. Apart from similarity, the biological concept of homology also stresses developmental individuality of putative homologous structures. Structural and positional aspects of homology can be separated, with positional homology acquiring an independent status. Similarity, topographic relationships, and ontogenetic development cannot be tests of homology. Within the cladistic paradigm, the most decisive test of homology is that of congruence; proponents of the biological-homology concept have been less concerned with test implications. Adopting a hierarchical view of nature suggests that characters have to be homologized at their appropriate level of organization. A taxic or systematic approach to homology has precedence over a transformational or biological approach. Nevertheless, pattern analysis and process explanations are not independent of each other.     

The female orgasm and the homology concept in evolutionary biology

The definition of homology and its application to reproductive structures, external genitalia, and the physiology of sexual pleasure has a tortuous history. While nowadays there is a consensus on the developmental homology of genital and reproductive systems, there is no agreement on the physiological translation, or the evolutionary origination and roles, of these structural correspondences and their divergent histories. This paper analyzes the impact of evolutionary perspectives on the homology concept as applied to the female orgasm, and their consequences for the biological and social understanding of female sexuality and reproduction. After a survey of the history of pre-evolutionary biomedical views on sexual difference and sexual pleasure, we examine how the concept of sexual homology was shaped in the new phylogenetic framework of the late 19th century. We then analyse the debates on the anatomical locus of female pleasure at the crossroads of theories of sexual evolution and new scientific discourses in psychoanalysis and sex studies. Moving back to evolutionary biology, we explore the consequences of neglecting homology in adaptive explanations of the female orgasm. The last two sections investigate the role played by different articulations of the homology concept in evolutionary developmental explanations of the origin and evolution of the female orgasm. These include the role of sexual, developmental homology in the byproduct hypothesis, and a more recent hypothesis where a phylogenetic, physiological concept of homology is used to account for the origination of the female orgasm. We conclude with a brief discussion on the social implications for the understanding of female pleasure derived from these different homology frameworks.     

Uncover the conserved property underlying sequence‐distant and structure‐similar proteins

It is widely accepted that a protein's sequence determines its structure. The surprising finding that proteins of distant sequence can adopt similar 3D structures has raised interesting questions regarding underlying conserved properties that are essential for protein folding and stability. Uncovering the conserved properties may shed light on the folding mechanism of proteins and help with the development of computational tools for protein structure prediction. We compiled and analyzed a structure pair dataset of 66 high‐resolution and low sequence identity (16–38%) soluble proteins. Structure deviation for each pair was confirmed by calculating its C_α SiMax value and comparing its potential energy per residue. Analysis of favorable inter‐residue interactions for each structure pair indicated that the average number of inter‐residue interactions within each structure represents a conserved feature of homologous structures of distant sequence. Detailed comparison of individual types of interactions showed that the average number of either hydrophobic or hydrogen bonding interactions remains unchanged for each structure pair. These findings should be of help to improving the quality of homology models based on templates of low sequence identity, thus broadening the application of homology modeling techniques for protein studies. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 340–347, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Myriapod metamerism and arthropod segmentation

Outstanding progress in understanding segmentation of tracheate arthropods (Atelocerata), i.e. Chilopoda, Diplopoda, Pauropoda, Symphyla and Insecta, has been gained through experimental studies carried out on a single, very derivative organism, i.e. Drosophila. We stress the need for a broader comparative approach. We have studied the segmental structure of the trunk in geophilomorph centipedes, where we can identify morphogenetic units of two, four, eight or 16 segments. Accordingly, we sketch an improved model for arthropod segmentation, with the following initial steps: (a) biochemical marking of a very few repetitive units (eosegments); (b) iterative duplications of this first periodicity, until the embryo acquires an array of biochemical markings matching the whole number of segments of the future larva or juvenile specimen; (c) transpatterning, stabilization and interpretation of this 'segmental' arrangement; (d) possible repatterning, to give a final repetitive pattern we define as metasegmental. Finally, we express some doubt about the homology between annelid and arthropod segmentation.     

膜联蛋白AnxB1序列缺失突变体的结构模建及活性分析

为获得低分子量、低免疫原性的膜联蛋白AnxB1的序列缺失突变体 ,以AnxB1C端的 4个内部同源结构域为基础 ,模拟构建了 4个突变体群 .利用同源模建的方法对各突变体进行结构模建和分子优化 ,最后选择 4个结构最为合理的突变体在大肠杆菌GST融合表达系统中表达 .结果显示 :GST M3和GST M4均表达出较强的抗凝血活性 ,且免疫原性也降低为原来的 1 2 ,为进一步构建兼具抗凝、溶栓双重功能的靶向性溶栓药物奠定了基础 .     

The ontogeny and homology of the Weberian apparatus in the zebrafish Danio rerio (Ostariophysi: Cypriniformes)

The ontogeny of the Weberian apparatus was examined in the zebrafish, Danio rerio , using both cleared and stained specimens and histology. Over 300 individuals from four independent zebrafish lineages, ranging in size from 3 to 28 mm TL, were examined for this study. Results provide a basic understanding of the development of the Weberian apparatus in the wild-type zebrafish. Our results, in conjunction with those already published, point to substantial variation in the development of the Weberian apparatus among otophysans and new interpretations of the homology of certain ossicles (e.g. tripus and claustrum). Hypotheses of homology among various Weberian ossicles are considered and represent an important step in understanding the evolution of sound transmission in ostariophysan fishes.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 241–254.     

鸡MyD88-TIR的同源模建

髓样分化因子(MyD88)是Toll受体(TLR)信号通路中的一个关键接头分子,在传递信息和介导炎症反应中具有重要的作用。对鸡MyD88(Myeloid differentiation primary response protein MyD88)的TIR(Toll-interleukin1-resistance)区域进行同源建模,并评估其可用性,为进一步研究MyD88与TLR(Toll receptor)相互作用的原理奠定基础。通过结构域分析、模板相似性搜索和序列比对、初始建模、精修和动力学优化,立体化学结构和能量合理性评估,获得未知三维结构的鸡MyD88-TIR三维模型。结果表明,鸡MyD88包含DEATH和TIR两个结构域,所模拟的MyD88-TIR三维模型二面角构象和氨基酸能量分布以及主侧链立体化学特性合理。     

Defining parameters for homology-tolerant database searching.

De novo interpretation of tandem mass spectrometry (MS/MS) spectra provides sequences for searching protein databases when limited sequence information is present in the database. Our objective was to define a strategy for this type of homology-tolerant database search. Homology searches, using MS-Homology software, were conducted with 20, 10, or 5 of the most abundant peptides from 9 proteins, based either on precursor trigger intensity or on total ion current, and allowing for 50%, 30%, or 10% mismatch in the search. Protein scores were corrected by subtracting a threshold score that was calculated from random peptides. The highest (p < .01) corrected protein scores (i.e., above the threshold) were obtained by submitting 20 peptides and allowing 30% mismatch. Using these criteria, protein identification based on ion mass searching using MS/MS data (i.e., Mascot) was compared with that obtained using homology search. The highest-ranking protein was the same using Mascot, homology search using the 20 most intense peptides, or homology search using all peptides, for 63.4% of 112 spots from two-dimensional polyacrylamide gel electrophoresis gels. For these proteins, the percent coverage was greatest using Mascot compared with the use of all or just the 20 most intense peptides in a homology search (25.1%, 18.3%, and 10.6%, respectively). Finally, 35% of de novo sequences completely matched the corresponding known amino acid sequence of the matching peptide. This percentage increased when the search was limited to the 20 most intense peptides (44.0%). After identifying the protein using MS-Homology, a peptide mass search may increase the percent coverage of the protein identified.