Homology and misdirection

Hennig (1966) recognized symplesiomorphies as homologies, and that view is logically correct under the concept of homology (homogeny) prevalent among evolutionists since 1870. Nelson and Platnick (1981) instead wanted homology to exclude symplesiomorphies for reasons that they never made clear but which certainly included opposition to Hennig. They and some of their followers, most recently Platnick (2013) and Brower and de Pinna (2013), have continued to advocate that anti‐Hennigian position, often under the slogan “homology equals synapomorphy,” while ironically passing themselves off as cladists and often using ambiguous or falsified citations to pretend that legitimate phylogeneticists think likewise. Such authors have seldom shown much concern for accuracy or logic, with the result that a great deal of print has been wasted. Those problems can be avoided simply by maintaining a Hennigian view and so discarding the purported equivalence of homology and synapomorphy.     

Homology in Development and the Development of the Homology Concept

Homology is a central concept for Developmental Evolution. HereI argue that homology should be explained within the referenceprocesses of development and evolution; development becauseit is the proximate cause of morphological characters and evolutionbecause it deals with organic transformations and stability.This was already recognized by Hans Spemann in 1915. In a seminalessay "A history and critique of the homology concept" Spemannanalyzed the history and present problems of the homology concept.Here I will continue Spemann's project and analyze some of the20th century contributions to homology. I will end with a fewreflections about the connections between developmental processesand homology and conclude that developmental processes are inherentin (i) the assessment of homology, (ii) the explanation of homology,(iii) the origin of evolutionary innovations (incipient homologues),and (iv) can be considered homologous themselves.     

Homology and logical fallacy

The meaning of homology, is analyzed in a phylogenetic context. The notion of homology is unequivocal only if tied to recency of common ancestry, i.e. to the concept of monophyly. Processual analysis of the biological causes of similarity cannot provide guidance in the search for relations of homology. Instead, it is the reconstruction of the taxic hierarchy based on homology and congruence which provides guidance in the search for underlying causes of similarity. Pattern reconstruction is shown to have logical precedence over process explanations.     

Homology thinking

This paper explores an important type of biological explanation called ‘homology thinking.’ Homology thinking explains the properties of a homologue by citing the history of a homologue. Homology thinking is significant in several ways. First, it offers more detailed explanations of biological phenomena than corresponding analogy explanations. Second, it provides an important explanation of character similarity and difference. Third, homology thinking offers a promising account of multiple realizability in biology.     

基因间的同源关系

同源是指从共同祖先的特性遗传下来的通常带有分歧的两个特征之间的关系。同源概念组成了进化基因组学的基础并对功能基因组学有巨大作用,但基于对同源概念的不准确理解,当前对其有诸多模糊表述,因此了解其确切含义具有重要意义。本文就同源、直系同源和旁系同源的概念和性质进行综述。     

基因间的同源关系

同源是指从共同祖先的特性遗传下来的通常带有分歧的两个特征之间的关系。同源概念组成了进化基因组学的基础并对功能基因组学有巨大作用,但基于对同源概念的不准确理解,当前对其有诸多模糊表述,因此了解其确切含义具有重要意义。本文就同源、直系同源和旁系同源的概念和性质进行综述。     

Homology and homoeomorphy in ostracod limbs

The functional modifications of myodocopan and podocopan ostracod limbs constitute a rich data set with which to carry out phylogenetic analyses, but efforts are hindered by lack of consensus on homologies. Homoeomorphy presents particular difficulties; for example, the furca is post-anal in Myodocopa but pre-anal in Podocopa, suggesting homoeomorphy, not homology. Homoeomorphies also exist between ostracod appendages and those of other Crustacea, for example the oral cone and styliform mandibulae of Paradoxostomatidae (Ostracoda) and Siphonostomatoida (Copepoda), both adaptations to commensal or parasitic lifestyles. Such clear manifestations of homoeomorphy, arising independently in different lineages as a result of similar functional requirements imposed on plesiomorphic appendage structures, warn of the possibility of more subtle examples which, if unrecognized, would lead to misinterpretations of character states used in phylogenetic analysis. For instance, the branchial plates found on third, fourth and fifth limbs of podocopans may not be homologous with the branchial plates on the fifth and sixth limbs of myodocopans. Limb homologies of podocopan ostracods (primarily as represented by various podocopid taxa) are investigated. Evidence is presented, based on studies of morphology and musculature, that podocopid branchial plates are exopodites (arising from the basis), while those of myodocopans are epipodites (arising from the coxa or precoxa). In Podocopida, moreover, the protopodites of post-mandibular limbs appear to be undifferentiated, comprising only a basis, while those of Myodocopa clearly exhibit a basis, coxa and often a precoxa. These differences argue against monophyly of the Ostracoda. The absence of epipodites, combined with the lack of a coxa in post-mandibular limbs, is potentially indicative of closer affinities between podocopans and Cambrian stem-group crustaceans (including Phosphatocopida) than between podocopans and myodocopans. The possible derivation of podocopid third, fourth and fifth limbs from a stem-group crustacean limb is demonstrated. The hypothesis is advanced that podocopan ostracods (represented today by Podocopida, Platycopida and Palaeocopida) are derived from much nearer the base of the crown-group Crustacea than myodocopans.     

形态性状、分子性状与同源性

“同源性(homology)”是生物学中最基本的概念之一。近年来, 随着分子生物学、生物信息学、发育生物学以及进化发育遗传学等学科的快速发展, 同源性一词在形态性状的比较、核苷酸和氨基酸序列的分析以及探讨形态性状进化的分子机制等方面都有广泛应用。然而, 由于不同的研究者对同源性概念的理解有所不同, 在实际应用中难免会出现不恰当使用“同源性”一词并得出错误结论的情况。本文从不同的角度介绍了如何对同源性进行判断以及影响同源性判断的因素。并指出正确理解同源性这一概念的含义, 以及通过综合各方面的证据对同源性进行推断对于揭示基因型和表型的进化以及二者之间的关系非常重要。     

Morphogenesis and Homology in Arthropod Limbs

Arthropods exhibit highly diverse limb morphologies rangingfrom unbranched walking legs to multibranched swimming paddles.Understanding morphogenesis in structurally diverse limbs canbe useful for ascertaining homologies between limbs. Structurallysimilar limbs have been produced by different evolutionary modificationsof morphogenesis in certain cases. Whereas it is easy to supportthe claim that whole arthropod limbs are homologous structures,I demonstrate that it is not always possible to draw well-foundedhomologies between parts of different limbs. This result isimportant with regard to general models of appendage developmentand evolution in arthropods because it clarifies contradictoryexplanations based exclusively on gene expression data.     

Homology in classical and molecular biology

Hypotheses of homology are the basis of comparative morphology and comparative molecular biology. The kinds of homologous and nonhomologous relations in classical and molecular biology are explored through the three tests that may be applied to a hypothesis of homology: congruence, conjunction, and similarity. The same three tests apply in molecular comparisons and in morphology, and in each field they differentiate eight kinds of relation. These various relations are discussed and compared. The unit or standard of comparison differs in morphology and in molecular biology; in morphology it is the adult or life cycle, but with molecules it is the haploid genome. In morphology the congruence test is decisive in separating homology and nonhomology, whereas with molecular sequence data similarity is the decisive test. Consequences of this difference are that the boundary between homology and nonhomology is not the same in molecular biology as in morphology, that homology and synapomorphy can be equated in morphology but not in all molecular comparisons, and that there is no detected molecular equivalent of convergence. Since molecular homology may reflect either species phylogeny or gene phylogeny, there are more kinds of homologous relation between molecular sequences than in morphology. The terms paraxenology and plerology are proposed for two of these kinds--respectively, the consequence of multiple xenology and of gene conversion.     

Homology,limbs, and genitalia

SUMMARY Similarities in genetic control between the main body axis and its appendages have been generally explained in terms of genetic co-option. In particular, arthropod and vertebrate appendages have been explained to invoke a common ancestor already provided with patterned body outgrowths or independent recruitment in limb patterning of genes or genetic cassettes originally used for purposes other than axis patterning. An alternative explanation is that body appendages, including genitalia, are evolutionarily divergent duplicates (paramorphs) of the main body axis. However, are all metazoan limbs and genitalia homologous? The concept of body appendages as paramorphs of the main body axis eliminates the requirement for the last common ancestor of limb-bearing animals to have been provided with limbs. Moreover, the possibility for an animal to express complex organs ectopically demonstrates that positional and special homology may be ontogenetically and evolutionarily uncoupled. To assess the homology of animal genitalia, we need to take into account three different sets of mechanisms, all contributing to their positional and/or special homology and respectively involved (1) in the patterning of the main body axis, (2) in axis duplication, followed by limb patterning mechanisms diverging away from those still patterning the main body axis (axis paramorphism), and (3) in controlling the specification of sexual/genital features, which often, but not necessarily, come into play by modifying already developed and patterned body appendages. This analysis demonstrates that a combinatorial approach to homology helps disentangling phylogenetic and ontogenetic layers of homology.     

Homology between prokaryotic and eukaryotic ribonucleases

Summary There is homology between the amino acid sequences of the extracellular ribonucleases T1 and St, from the eukaryoteAspergillus oryzae and the prokaryoteStreptomyces erythreus, respectively. Together with other extracellular ribonucleases homologous to each, these enzymes make up a family of interest to evolutionary biology and useful in studies of protein structure and function.     

Homology and the origin of correspondence

Homology is a natural kind term and a precise account of what homologyis has to come out of theories about the role of homologues in evolution anddevelopment. Definitions of homology are discussed with respect to the questionas to whether they are able to give a non-circular account of thecorrespondenceor sameness referred to by homology. It is argued that standard accounts tiehomology to operational criteria or specific research projects, but are not yetable to offer a concept of homology that does not presuppose a version ofhomology or a comparable notion of sameness. This is the case for phylogeneticdefinitions that trace structures back to the common ancestor as well as fordevelopmental approaches such as Wagner's biological homology concept. Incontrast, molecular homology is able to offer a definition of homology in genesand proteins that explicates homology by reference to more basic notions.Molecular correspondence originates by means of specific features of causalprocesses. It is speculated that further understanding of morphogenesis mightenable biologists to give a theoretically deeper definition of homology alongsimilar lines: an account which makes reference to the concrete mechanisms thatoperate in organisms.     

形态性状、分子性状与同源性

“同源性（homology）”是生物学中最基本的概念之一。近年来,随着分子生物学、生物信息学、发育生物学以及进化发育遗传学等学科的快速发展,同源性一词在形态性状的比较、核苷酸和氨基酸序列的分析以及探讨形态性状进化的分子机制等方面都有广泛应用。然而,由于不同的研究者对同源性概念的理解有所不同,在实际应用中难免会出现不恰当使用“同源性”一词并得出错误结论的情况。本文从不同的角度介绍了如何对同源性进行判断以及影响同源性判断的因素。并指出正确理解同源性这一概念的含义,以及通过综合各方面的证据对同源性进行推断对于揭示基因型和表型的进化以及二者之间的关系非常重要。     

Homology search for genes

MOTIVATION: Life science researchers often require an exhaustive list of protein coding genes similar to a given query gene. To find such genes, homology search tools, such as BLAST or PatternHunter, return a set of high-scoring pairs (HSPs). These HSPs then need to be correlated with existing sequence annotations, or assembled manually into putative gene structures. This process is error-prone and labor-intensive, especially in genomes without reliable gene annotation. RESULTS: We have developed a homology search solution that automates this process, and instead of HSPs returns complete gene structures. We achieve better sensitivity and specificity by adapting a hidden Markov model for gene finding to reflect features of the query gene. Compared to traditional homology search, our novel approach identifies splice sites much more reliably and can even locate exons that were lost in the query gene. On a testing set of 400 mouse query genes, we report 79% exon sensitivity and 80% exon specificity in the human genome based on orthologous genes annotated in NCBI HomoloGene. In the same set, we also found 50 (12%) gene structures with better protein alignment scores than the ones identified in HomoloGene. AVAILABILITY: The Java implementation is available for download from http://www.bioinformatics.uwaterloo.ca/software.     

Homology across inheritance systems

Recent work on inheritance systems can be divided into inclusive conceptions, according to which genetic and non-genetic inheritance are both involved in the development and transmission of nearly all animal behavioral traits, and more demanding conceptions of what it takes for non-genetic resources involved in development to qualify as a distinct inheritance system. It might be thought that, if a more stringent conception is adopted, homologies could not subsist across two distinct inheritance systems. Indeed, it is commonly assumed that homology relations cannot survive a shift between genetic and cultural inheritance systems, and substantial reliance has been placed on that assumption in debates over the phylogenetic origins of hominin behavioral traits, such as male-initiated intergroup aggression. However, in the homology literature it is widely accepted that a trait can be homologous—that is, inherited continuously in two different lineages from a single common ancestor—despite divergence in the mechanisms involved in the trait’s development in the two lineages. In this paper, we argue that even on an extremely stringent understanding of what it takes for developmental resources to form a separate inheritance system, homologies can nonetheless subsist across shifts between distinct inheritance systems. We argue that this result is a merit of this way of characterizing what it is to be an inheritance system, that it has implications for adjudicating between alternative accounts of homology, and that it offers an important cautionary lesson about how (not) to reason with the homology concept, particularly in the context of cultural species.     

Homology and the hierarchy of biological systems

Homology is the similarity between organisms due to common ancestry. Introduced by Richard Owen in 1843 in a paper entitled "Lectures on comparative anatomy and physiology of the invertebrate animals", the concept of homology predates Darwin's "Origin of Species" and has been very influential throughout the history of evolutionary biology. Although homology is the central concept of all comparative biology and provides a logical basis for it, the definition of the term and the criteria of its application remain controversial. Here, I will discuss homology in the context of the hierarchy of biological organization. I will provide insights gained from an exemplary case study in evolutionary developmental biology that indicates the uncoupling of homology at different levels of biological organization. I argue that continuity and hierarchy are separate but equally important issues of homology.     

Homology, biogeography and areas of endemism

Hypotheses of biogeographic homology constitute the basis of historical biogeography. Primary biogeographic homology refers to a conjecture on a common biogeographic history, and secondary biogeographic homology refers to the cladistic test of the formerly recognized homology. Panbiogeography deals with the former, through the recognition of generalized tracks and areas of endemism, whereas cladistic biogeography deals with the latter, through the generation of general area cladograms. A historical biogeographic analysis may include both approaches, in a two‐stage analysis.     

Homology of delta crystallin and argininosuccinate lyase

1. Delta crystallin, a major lens protein characteristic of birds and reptiles, is homologous to argininosuccinate lyase; 57% of the residues in chicken delta crystallin and human lyase are identical. 2. Even more similar (62% identical residues) to the human lyase is the sequence translated from the presumably inactive delta-2 gene of the delta crystallin locus. 3. As both delta crystallin and lyase are synthesized in birds only during the embryonic and juvenile stages, the persistence of delta crystallin in the adult lens appears to be paedomorphic. 4. Possible correlations of the origins of delta crystallin with other events in sauropsid evolution are proposed.