Typology now: homology and developmental constraints explain evolvability

By linking the concepts of homology and morphological organization to evolvability, this paper attempts to (1) bridge the gap between developmental and phylogenetic approaches to homology and to (2) show that developmental constraints and natural selection are compatible and in fact complementary. I conceive of a homologue as a unit of morphological evolvability, i.e., as a part of an organism that can exhibit heritable phenotypic variation independently of the organism’s other homologues. An account of homology therefore consists in explaining how an organism’s developmental constitution results in different homologues/characters as units that can evolve independently of each other. The explanans of an account of homology is developmental, yet the very explanandum is an evolutionary phenomenon: evolvability in a character-by-character fashion, which manifests itself in phylogenetic patterns as recognized by phylogenetic approaches to homology. While developmental constraints and selection have often been viewed as antagonistic forces, I argue that both are complementary as they concern different parts of the evolutionary process. Developmental constraints, conceived of as the presence of the same set of homologues across phenotypic change, pertain to how heritable variation can be generated in the first place (evolvability), while natural selection operates subsequently on the produced variation.

Phylogeny and evo-devo: characters, homology, and the historical analysis of the evolution of development

The concept of homology continues to attract more and more commentary. In systematic and evolutionary biology the meaning of homology as synapomorphic similarity inherited from a common ancestor has gained wide acceptance over the last three or four decades. In recent years, however, developmental biologists, in particular, have argued for a new approach to, and new definition for, homology that revolves around the desire to make it more process-oriented and more mechanistic. These efforts raise questions about the relationship between developmental and evolutionary biology as well as how the evolution of development is to be studied. It is argued in this paper that this new approach to homology seemingly decouples developmental biology from the study of the evolution of development rather than to facilitate that study. In contrast, applying the notion of historical, phylogenetic homology to developmental data is inherently comparative and therefore evolutionary.     

Growth, function and homology: aspects of dental replacement in toothcombed strepsirhines.

In maturing juvenile lemurs and lorises, it was found that the anteriormost lower deciduous premolar migrates forward and may become associated with the teeth of the toothcomb; this is similar to previous observations on the dentition of indriines. The mesial shift of dp2 appears to be associated with the eruption of P2 but, more importantly, also with replacement of the deciduous by the permanent teeth of the toothcomb--which is a period of functional disruption at the front of the jaw. It is suggested that this growth-related phenomenon should not be confused with other aspects of dental development and eruption which might be indicative of homology.     

Feathers with Ocular Architecture: Implications for Functional and Evolutionary Similarities of Visual Signals and Receptors

Studies of visual receptors typically assume that only functionally similar structures are relevant to the evolution of complex eyes. This approach ignores growing evidence that different functional classes of organs often share structural and developmental patterns that pertain to biological sameness (deep homology). However, the potential relevance of non-receptor structures to eye evolution remains largely unexplored. An “ocular” feather color mechanism is described whose structural and optical features resemble those of chambered, image-forming eyes to a remarkable degree. These similarities include a laterally expanded, domed light receiving surface similar to that of an eye, an encapsulated spongy tissue mass whose coherent light scattering properties in the human-visible (destructive) and ultraviolet (constructive) wavelength ranges resemble those of cornea and lens, intervening spaces such as those with humors, and a laminar pigmented shelf whose structure and optics resemble a mirrored tapetum lucidum found behind many retinas. Fourier analysis and optical principles indicate that ocular structures adhere to the same light-handling properties regardless of higher function (receptor or signal). The extent to which chambered eyes and ocular feathers have evolved independently is surprisingly equivocal. On the one hand, broad differences in the location, composition, and development of chambered eyes and ocular feather signals suggest convergent evolution on an ocular organization. However, some level of evolutionary parallelism (generative homology) between chambered eyes and ocular feathers is implicated by similarities in constructional materials, tissue development, and signal transduction cascades. Structural, optical, and developmental similarities also occur between more primitive eyes and the colored dermal papillae responsible for avian skin ornamentation. Functional constraints on light-handling requirements, coupled with developmental constraints in high-stress environments on the body surface, may enhance the similar evolutionary outcomes in the different functional setting. Regardless of the mechanistic details, repeated evolution of eye-like structures in different functional settings reveals a biological potential to produce such organs that is much greater than would be inferred from a survey of receptor structures alone.     

Four notions of biological function

I argue that there are at least four different ways in which the term ‘function’ is used in connection with the study of living organisms, namely: (1) function as (mere) activity, (2) function as biological role, (3) function as biological advantage, and (4) function as selected effect. Notion (1) refers to what an item does by itself; (2) refers to the contribution of an item or activity to a complex activity or capacity of an organism; (3) refers to the value for the organism of an item having a certain character rather than another; (4) refers to the way in which a trait acquired and has maintained its current share in the population. The recognition of a separate notion of function as biological advantage solves the problem of the indeterminate reference situation that has been raised against a counterfactual analysis of function, and emphasizes the importance of counterfactual comparison in the explanatory practice of organismal biology. This reveals a neglected problem in the philosophy of biology, namely that of accounting for the insights provided by counterfactual comparison.     

How to be an anti-reductionist about developmental biology: Response to Laubichler and Wagner

Alexander Rosenberg recently claimed (1997) that developmental biology is currently being reduced to molecular biology. cite several concrete biological examples that are intended to impugn Rosenberg's claim. I first argue that although Laubichler and Wagner's examples would refute a very strong reductionism, a more moderate reductionism would escape their attacks. Next, taking my cue from the antireductionist's perennial stress on the importance of spatial organization, I describe one form an empirical finding that refutes this moderate reductionism would take. Finally, I point out an actual example, anterior-posterior axis determination in the chick, that challenges the reductionist's belief that all developmental regularities can be explained by molecular biology. In short, I argue that Rosenberg's position can be saved from Laubichler and Wagner's criticisms and putative counter-examples, but it would not survive a different kind of counter-example.     

Homology and homocracy revisited: gene expression patterns and hypotheses of homology

Homocracy, a term referring to shared regulatory gene expression patterns between organs in different animals, was introduced recently in order to prevent inappropriate inference of organ homology based on gene expression data. Non-homologous structures expressing homologous genes, and homologous structures expressing non-homologous genes illustrate that gene expression data is not sufficient on its own to identify morphological homology. However, gene expression data might be useful in testing hypotheses of organ homology, because parsimony can be applied on changes in the relation between expression of orthologous regulatory genes and the formation of homologous organs. A method of testing organ homology hypotheses with respect to change in regulatory gene expression required within a particular phylogenetic context is presented.Edited by R.J. Sommer     

临床分离耐甲氧西林溶血性葡萄球菌的SCCmec分型及同源性分析

目的了解临床分离耐甲氧西林溶血性葡萄球菌（MRSH）的SCCmec基因型别及相同SCCmec型别菌株的同源性。方法多重PCR进行SCCmec分型,ERIC-PCR法对相同SCCmec型别菌株进行同源性分析。结果83株临床分离MRSH菌株中,SCCmecI型有23株（27．7％）,SCCmecⅡ型有10株（12．1％）,SCCmecm型有24株（28．9％）,SCCmecIV型有1株（1．2％）,I、Ⅱ混合型有8株（9．6％）,I、Ⅲ混合型有6株（7．2％）,Ⅱ、11混合型有5株（6．0％）,I、Ⅱ、Ⅲ混合型有3株（3．6％）,未分型3株（3．6％）。ERIC—PCR结果显示,23株SCCmecI型分为11型,其中A型5株,B型5株,C型3株,其余8株各为1型,2株未分型;10株SCCmecⅡ型分为6型,其中D型4株,E型2株,3株各为1型,1株未分型;24株SCCmecm型分为9型,其中F型11株,G型2株,H型2株,I型2株,5株各为1型,2株未分型。结论临床分离MRSH中,SCCmecI、Ⅲ型为多,部分菌株呈混合型别;相同SCCmec型别的部分菌株之间可能存在克隆传播。     

Interspecies homology of nodule development genes in Rhizobium and Bradyrhizobium spp.

Abstract DNA fragments representatives of ndv A and ndv B have been used as probes against genomic DNAs from different Rhizobium and Bradyrhizobium species. ndv A and ndv B homologues were found in all species, indicating extensive conservation of these genes. All Rhizobium species show chromosomal localization of ndv A and ndv B homologues.     

The fungal cell wall: Modern concepts of its composition and biological function

This review deals with the cell wall (CW), a poorly known surface structure of the cell of mycelial fungi. Data are presented concerning (i) isolation techniques and purity control methods securing the absence of the cytoplasm content in the CW fraction and (ii) the chemical composition of the CW. The structural (backbone) and intrastructural components of the CW, such as aminopolysaccharides, α- and β-glucans, proteins, lipids, uronic acids, hydrophobins, sporopollenin, and melanins, are discussed in detail. Special attention is given to chitin and its novel function in terms of protecting the cells from stress as well as to the differences of this fungal aminopolysaccharide from the chitin of algae and Arthropoda. The apical growth of hyphae and the involvement of special microvesicles in morphogenesis of a fungal cell are discussed. Data on the enzymes involved in CW synthesis and lysis are presented. In conclusion, the functional role of the fungal CW is discussed in juxtaposition to the surface structures of higher eukaryotes.     

碳青霉烯类耐药肺炎克雷伯菌基因型检测及同源性分析

目的了解福建医科大学附属第一医院耐碳青霉烯类肺炎克雷伯菌（KPC）的耐药基因分型及同源性分布情况。方法收集临床分离的29株KPC,改良Hodge试验检测碳青霉烯酶表型。PCR检测碳青霉烯酶blaKPC、blaIMP-1、blaVIM-1、blaOXA-48及blaNDM-基因;阳性结果进行DNA测序,并进行BLAST比对确定其基因型。采用肠杆菌科基因间重复序列（ERIC—PCR）对KPC进行同源性分析。结果29株KPC中Hodge试验阳性27株,阳性率为93．1％（27／29）。PCR扩增和DNA测序显示28株为blaKPC-2,株为blaIMP-1,未检出blaVIM-2、blaOXA-48和blaNDM-1基因。同源性分析发现KPC主要存在两种型别：28株A1和1株A2。结论blaKPC-2型碳青霉烯酶是该院KPC的主要型别,A1型已在该院流行,应加强院感监测和预防。ERIC—PCR是一种简便、快捷的基因分型技术,适合同源性的初步分型筛查。     

Similarity,parsimony and conjectures of homology: The chelonian shoulder girdle revisited

Much has been written about the definition and recognition of biological homology. Homology is usually defined as similarity inherited from a common ancestor (e.g., papers in Hall, 1994). It is recognised through cladistic analysis: Patterson (1982) and de Pinna (1991) have cogently argued that homology can be equated with synapomorphy (a shared evolutionary novelty uniting a monophyletic group). Such identification involves two stages: first, a possible homology is proposed on the basis of morphological similarity. This similarity might be structural, topological, developmental, or any combination thereof. Next, a cladistic analysis is performed, involving the trait in question and all other informative traits identified. If the trait is congruent with the resultant phylogeny, it is accepted as homologous in all taxa which possess it. If the trait is incongruent with the phylogeny, it is interpreted as homoplasious in certain taxa. This has been termed the test of congruence (Patterson, 1982; de Pinna, 1991). Rieppel (1996) has recently suggested that the test of congruence might be circular, and that as a result certain inferences about the evolution of the chelonian shoulder girdle (Lee, 1996) are poorly substantiated. Here I argue that the test of congruence is not circular, and that the disputed conclusions about the evolution of chelonian shoulder girdle can be defended on the basis of parsimony. More generally, I suggest how considerations of parsimony can and should be used to arbitrate between conflicting conjectures of homology that are both congruent with an accepted phylogeny.     

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.     

Sequence analysis and homology modeling of peroxidase from Medicago sativa

Plant peroxidases are one of the most extensively studied group of enzymes which find applications in the environment, health,pharmaceutical, chemical and biotechnological processes. Class III secretary peroxidase from alfalfa (Medicago sativa) has beencharacterized using bioinformatics approach Physiochemical properties and topology of alfalfa peroxidase were compared withthat of soybean and horseradish peroxidase, two most popular commercially available peroxidase preparations. Lower value ofinstability index as predicted by ProtParam and presence of extra disulphide linkages as predicted by Cys_REC suggested alfalfaperoxidase to be more stable than either of the commercial preparations. Multiple Sequence Alignment (MSA) with otherfunctionally similar proteins revealed the presence of highly conserved catalytic residues. Three dimensional model of alfalfaperoxidase was constructed based on the crystal structure of soybean peroxidase (PDB Id: 1FHF A) by homology modellingapproach. The model was checked for stereo chemical quality by PROCHECH, VERIFY 3D, WHAT IF, ERRAT, 3D MATCH ANDProSA servers. The best model was selected, energy minimized and used to analyze structure function relationship with substratehydrogen peroxide by Autodock 4.0. The enzyme substrate complex was viewed with Swiss PDB viewer and one residue ASP43was found to stabilize the interaction by hydrogen bonds. The results of the study may be a guiding point for further investigationson alfalfa peroxidase.     

Impact of a multimodal exercise program on tibial bone health in adolescents with Development Coordination Disorder: an examination of feasibility and potential efficacy

Objectives:Developmental coordination disorder (DCD) compromises bone health purportedly due to lower levels of physical activity. The potential of an exercise intervention to improve bone health parameters in adolescents with DCD has not previously been studied. This study thus aimed to determine the impact of a multimodal exercise intervention on bone health in this population at-risk of secondary osteoporosis.Methods:Twenty-eight adolescents (17 male, 11 female) aged between 12-17 years (M_age=14.1) with DCD participated in a twice weekly, 13-week generalised multimodal exercise intervention. Peripheral quantitative computed tomography scans of the tibia (4% and 66%) were performed over a six month period. Generalised estimating equations were used to examine the impact of fitness measures on bone parameters over time.Results:An overall improvement trend was observed for bone health, with significant increases at the 66% tibial site for bone mass (4.12% increase, d_cohen=0.23, p=0.010) and cortical area (5.42% increase, η² =12.09, p=0.014). Lower body fitness measures were significantly associated with improvements in bone health parameters, tempered by the degree of motor impairment.Conclusion:A multimodal exercise intervention may be effective in improving bone health of adolescents with DCD. Given the impact of motor impairments, gains may be greater over an extended period of study.