Assessing similarity: on homology,characters and the need for a semantic approach to non‐evolutionary comparative homology

The problem of homology has been a consistent source of controversy at the heart of systematic biology, as has the step of morphological character analysis in phylogenetics. Based on a clear epistemic framework and a characterization of “characters” as diagnostic evidence units for the recognition of not directly identifiable entities, I discuss the ontological definition and empirical recognition criteria of phylogenetic, developmental and comparative homology, and how these three accounts of homology each contribute to an understanding of the overall phenomenon of homology. I argue that phylogenetic homologies are individuals or historical kinds that require comparative homology for identification. Developmental homologies are natural kinds that ultimately rest on phylogenetic homologies and also require comparative homology for identification. Comparative homologies on the other hand are anatomical structural kinds that are directly identifiable. I discuss pre‐Darwinian comparative homology concepts and their problem of invoking non‐material forces and involving the a priori assumption of a stable positional reference system. Based on Young's concept of comparative homology, I suggest a procedure for recognizing comparative homologues that lacks these problems and that utilizes a semantic framework. This formal conceptual framework provides the much needed semantic transparency and computer‐parsability for documenting, communicating and analysing similarity propositions. It provides an essential methodological framework for generalizing over individual organisms and identifying and demarcating anatomical structural kinds, and it provides the missing link to the logical chain of identifying phylogenetic homology. The approach substantially increases the analytical accessibility of comparative research and thus represents an important contribution to the theoretical and methodological foundation of morphology and comparative biology.     

Parts and Theories in Compositional Biology

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend the use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict.     

The future of DNA-DNA hybridization studies

Summary This article draws on many vertebrate examples to assess the future of DNA-DNA hybridization studies. I first discuss whether applications of the method have reached the point of diminishing returns, or rather the start of a great leap forward, in our evolutionary understanding. Vertebrate groups whose relationships are especially likely to be illuminated include parrots, pigeons, bats, pinnipeds, mammalian carnivores, frogs, and rodents. There are at least two reasons why classifications based on DNA-DNA hybridization may prove to differ from classifications based on particular character, whether these be noncoding DNA sequences or protein sequences or anatomical characters. Because evolutionary relationships can now be deduced independently of anatomical characters, this should permit a renaissance in comparative anatomical studies of adaptation. The origin of major functional shifts from changes in a small fraction of the genome is illustrated by polar bears, sea otters, warblers, vultures, and especially by humans.     

Astroglial heterogeneity closely reflects the neuronal-defined anatomy of the adult murine CNS

Astroglia comprise an extremely morphologically diverse cell type that have crucial roles in neural development and function. Nonetheless, distinct regions of the CNS have traditionally been defined by the phenotypic characteristics and connectivity of neuros. In a complementary fashion, we present evidence that discrete regions of the adult CNS can be delineated based solely on the morphology, density and proliferation rates of astroglia. We used transgenic hGFAP-GFP mice in which robust expression of GFP in adult astroglia enables detailed morphological characterization of this diversely heterogeneous cell population with 3D confocal microscopy. By using three complementary methods for labeling adult astroglia (hGFAP-GFP expression, and GFAP and S100beta immunostaining), we find that there is a remarkably diverse, regionally stereotypical array of astroglial morphology throughout the CNS, and that discrete anatomical regions can be defined solely on the morphology of astroglia within that region. Second, we find that the density of astroglia varies dramatically across the CNS, and that astroglial density effectively delineates even the sub-regions of complex structures, such as the thalamus. We also find that regional astroglial density varies depending on how astroglia are labeled. To quantify and illustrate these broad differences in astroglial density, we generated an anatomical density atlas of the CNS. Third, the proliferation rate, or mitotic index, of astroglia in the adult CNS also effectively defines anatomical regions. These differences are present regardless of the astroglial-labeling method used. To supplement our atlas of astroglial density we generated an atlas of proliferation density for the adult CNS. Together, these studies demonstrate that the morphology, density and proliferation rate of astroglia can independently define the discrete cytoarchitecture of the adult mammalian CNS, and support the concept that regional astroglial heterogeneity reflects important molecular and functional differences between distinct classes of astroglia, much like the long-accepted heterogeneity of neuronal populations.     

A critique of the principle of cognitive simplicity in comparative cognition

A widespread assumption in experimental comparative (animal) cognition is that, barring compelling evidence to the contrary, the default hypothesis should postulate the simplest cognitive ontology (mechanism, process, or structure) consistent with the animal’s behavior. I call this assumption the principle of cognitive simplicity (PoCS). In this essay, I show that PoCS is pervasive but unjustified: a blanket preference for the simplest cognitive ontology is not justified by any of the available arguments. Moreover, without a clear sense of how cognitive ontologies are to be carved up at the joints—and which tools are appropriate for the job—PoCS rests on shaky conceptual ground.     

Estrogen synthetase (aromatase) immunohistochemistry reveals concordance between avian and rodent limbic systems and hypothalami

During amniote evolution, an early divergence occurred about 300 million years ago between the reptilian lines leading to the appearance of birds (anapsids) and mammals (synapsids). The different functional requirements of these vertebrate groups have involved divergent evolution of their brains. Even superficial examination reveals major anatomical differences between mammalian and avian brains, such as extensive development of the optic lobes and cerebellum in birds and a highly developed cortex in mammals. It has been nearly impossible to identify avian homologs of some mammalian brain regions by standard morphological criteria. This has long frustrated efforts at clarifying hypotheses regarding the anatomical location, field size, and regulation of brain functions shared between these two classes, despite the certainty that the principles of neurobiology apply equally at the cellular level in both groups. In an effort to remove this barrier, we have sought markers of common function that despite apparent anatomical dissimilarity, can allow recognition of homologous brain structures. We illustrate here how comparative analysis of the distribution of the steroid-metabolizing enzyme estrogen synthetase (aromatase) may help to understand the differences and similarities in the limbic system and hypothalamus of birds and mammals.     

ARE PINNIPEDS FUNCTIONALLY DIFFERENT FROM FISSIPED CARNIVORES? THE IMPORTANCE OF PHYLOGENETIC COMPARATIVE ANALYSES

Abstract.— It is widely assumed that adaptations to an aquatic lifestyle are so profound as to produce only obvious differences between pinnipeds and the remaining, largely terrestrial carnivore species ("fissipeds"). Thus, comparative studies of the order Carnivora routinely examine these groups independently. This approach is invalid for two reasons. First, fissipeds are a paraphyletic assemblage, which raises the general issue of when it is appropriate to ignore monophyly as a criterion for inclusion in comparative studies. Second, the claim that most functional characters (beyond a few undoubted characteristic features) are different in pinnipeds and fissipeds has never been quantitatively examined, nor with phylogenetic comparative methods. We test for possible differences between these two groups in relation to 20 morphological, life-history, physiological, and ecological variables. Comparisons employed the method of independent contrasts based on a complete and dated species-level phylogeny of the extant Carnivora. Pinnipeds differ from fissipeds only through evolutionary grade shifts in a limited number of life-history traits: litter weight (vs. gestation length), birth weight, and age of eyes opening (both vs. size). Otherwise, pinnipeds display the same rate of evolution as phylogenetically equivalent fissiped taxa for all variables. Overall functional differences between pinnipeds and fissipeds appear to have been overstated and may be no greater than those among major fissiped groups. Recognition of this fact should lead to a more complete understanding of carnivore biology as a whole through more unified comparative tests. Comparative studies that do not include monophyletic groups for phylogenetically based comparative tests should be reconsidered.     

From Carlquist’s ecological wood anatomy to Carlquist’s Law: why comparative anatomy is crucial for functional xylem biology

All students of xylem structure–function relations need to be familiar with the work of Sherwin Carlquist. He studies xylem through the lens of the comparative method, which uses the appearance of similar anatomical features under similar conditions of natural selection to infer function. “Function” in biology implies adaptation; maximally supported adaptation inferences require experimental and comparative xylem scientists to work with one another. Engaging with comparative inferences of xylem function will, more likely sooner rather than later, bring one to the work of Sherwin Carlquist. To mark his 90th birthday, I highlight just a few examples of his extraordinarily perceptive and general comparative insights. One is “Carlquist’s Law”, the pervasive tendency for vessels to be solitary when background cells are conductive. I cover his pioneering of “ecological” wood anatomy, viewing xylem variation as reflecting the effects of selection across climate and habit variation. Another is the embolism vulnerability–conduit diameter relationship, one of the most widely invoked structure–function relationships in xylem biology. I discuss the inferential richness within the notion of Carlquistian paedomorphosis, including detailed functional inferences regarding ray cell orientation. My final example comes from his very recent work offering the first satisfactory hypothesis accounting for the geographical and histological distribution of scalariform perforation plates as an adaptation, including “Carlquist’s Ratchet”, why scalariform plates are adaptive but do not re-evolve once lost. This extraordinarily rich production over six decades is filled with comparative inferences that should keep students of xylem function busy testing for decades to come.     

Use with caution: Developmental systems divergence and potential pitfalls of animal models

Transgenic animal models have played an important role in elucidating gene functions and the molecular basis development, physiology, behavior, and pathogenesis. Transgenic models have been so successful that they have become a standard tool in molecular genetics and biomedical studies and are being used to fulfill one of the main goals of the post-genomic era: to assign functions to each gene in the genome. However, the assumption that gene functions and genetic systems are conserved between models and humans is taken for granted, often in spite of evidence that gene functions and networks diverge during evolution. In this review, I discuss some mechanisms that generate functional divergence and highlight recent examples demonstrating that gene functions and regulatory networks diverge through time. These examples suggest that annotation of gene functions based solely on mutant phenotypes in animal models, as well as assumptions of conserved functions between species, can be wrong. Therefore, animal models of gene function and human disease may not provide appropriate information, particularly for rapidly evolving genes and systems.     

Testing the ortholog conjecture with comparative functional genomic data from mammals

A common assumption in comparative genomics is that orthologous genes share greater functional similarity than do paralogous genes (the "ortholog conjecture"). Many methods used to computationally predict protein function are based on this assumption, even though it is largely untested. Here we present the first large-scale test of the ortholog conjecture using comparative functional genomic data from human and mouse. We use the experimentally derived functions of more than 8,900 genes, as well as an independent microarray dataset, to directly assess our ability to predict function using both orthologs and paralogs. Both datasets show that paralogs are often a much better predictor of function than are orthologs, even at lower sequence identities. Among paralogs, those found within the same species are consistently more functionally similar than those found in a different species. We also find that paralogous pairs residing on the same chromosome are more functionally similar than those on different chromosomes, perhaps due to higher levels of interlocus gene conversion between these pairs. In addition to offering implications for the computational prediction of protein function, our results shed light on the relationship between sequence divergence and functional divergence. We conclude that the most important factor in the evolution of function is not amino acid sequence, but rather the cellular context in which proteins act.     

A quantitative assessment of bone area increase due to ornamentation in the Crocodylia

Bone ornamentation, in the form of highly repetitive motives created by pits and ridges, is a frequent feature on vertebrate skull roofs and osteoderms. The functional significance of this character remains a matter of controversy and speculation. The many diverging hypotheses proposed to explain it all share a common logical prerequisite: bone ornamentation should increase significantly the surface area of the bones that bear it. In order to test this assumption in the Crocodylia, we developed a method for quantifying the gain in area due to ornamentation using a three‐dimensional‐surface scanner. On crocodylian osteoderms, the gain in area can be up to 40%, and on the cranial table, it ranges between 10 and 32% in adult specimens (in both cases, it shows substantial differences between the adults of the various species included in the sample). Area gain on the snout is lesser (0–20% in adults), and more variable between species. In general, bone ornamentation is less pronounced, and results in fewer area gains in juvenile specimens. The main morphometric results yielded by this study are discussed in reference to the few comparative data available hitherto, and to the functional interpretations proposed by previous authors. J. Morphol. 276:1183–1192, 2015. © 2015 Wiley Periodicals, Inc.     

猕猴属种间颅骨差异的探讨

为了研究狒猴属的颅骨差异性,从面探讨种间在形态、功能和系统分化方面联系,测定了１１１个猕猴种类的７７个颅骨变量,用于主成分分析和判别分析。应用巢式分析方法,分析过程包括３个步骤。所有变量根据功能和部位的不同首先分为７个单位：下颌、下颌齿、上颌齿、上面颅、下面颅,、面颅后部和颅腔。第２步根据它们所揭示的相似性（具有相同的种间及种内差异性类型）合并为３个解剖区域：咀嚼器官（下颌、下颌齿、上颌齿）,面颅     

Virtual anthropology meets biomechanics

A meeting in Vienna in October 2010 brought together researchers using Virtual Anthropology (VA) and Finite Element Analysis (FEA) in order to explore the benefits and problems facing a collaboration between the two fields. FEA is used to test mechanical hypotheses in functional anatomy and VA complements and augments this process by virtue of its tools for acquiring data, for segmenting and preparing virtual specimens, and for generating reconstructions and artificial forms. This represents a critical methodological advance because geometry is one of the crucial inputs of FEA and is often the variable of interest in functional anatomy. However, we currently lack tools that quantitatively relate differences in geometry to differences in stress and strain, or that evaluate the impact on FEA of variation within and between biological samples. Thus, when comparing models of different geometry, we do not currently obtain sufficiently informative answers to questions such as “How different are these models, and in what manner are they different? Are they different in some anatomical regions but not others?" New methodologies must be developed in order to maximize the potential of FEA to address questions in comparative and evolutionary biology. In this paper we review these and other important issues that were raised during our Vienna meeting.     

长白山阔叶树种木质部环孔和散孔结构特征的分化导致其水力学性状的显著差异

木质部的解剖结构特征对树木水分传输功能有重要的影响,阔叶树种木质部环孔和散孔结构特征的分化,很可能导致两个功能类群在水力学结构上存在显著差异,但是有关两个功能类群间细致的水力学性状的对比研究还较少,二者整枝水平的导水率及纹孔水平的细致结构差异尚未见报道.本试验以长白山阔叶红松林常见的3个环孔材和4个散孔材乔木树种为研究对象,对比了两个功能类群树种的整枝导水率(k_shoot)、枝条木质部栓塞脆弱性(p_50)等重要水力学相关生理功能特征,并分析了两个功能类群间的木质部组织水平和纹孔水平上的解剖结构特征差异.结果表明:与茎段导水率差异一致,环孔材树种的整枝导水率也显著高于散孔材,但枝条木质部气穴化抵抗力显著弱于散孔材,二者的差异反映了整枝水平上木质部导水效率和安全性之间的权衡关系,与两个功能类群的水力学生理特征存在显著差异一致,二者在最大导管长度、导管直径、纹孔开口面积、纹孔开口比例等光学和扫描电镜观测解剖结构特征上都存在显著差异;木质部解剖特征(组织水平、纹孔水平)和k_shoot、p_50等生理特征间,以及木质部不同解剖特征之间存在显著的相关,且两个功能类群遵循相同的规律,反映了木质部结构对水分传输功能的重要影响,而导水率和气穴化抵抗力对木质部对立的结构要求,体现了树木水分传输系统构建的生物物理局限性.     

Diversity and cell type specificity of local excitatory connections to neurons in layer 3B of monkey primary visual cortex

In the primary visual cortex of macaque monkeys, laminar and columnar axonal specificity are correlated with functional differences between locations. We describe evidence that embedded within this anatomical framework is finer specificity of functional connections. Photostimulation-based mapping of functional input to 31 layer 3B neurons revealed that input sources to individual cells were highly diverse. Although some input differences were correlated with neuronal anatomy, no 2 neurons received excitatory input from the same cortical layers. Thus, input diversity reveals far more cell types than does anatomical diversity. This implies relatively little functional redundancy; despite trends related to laminar or columnar position, pools of neurons contributing uniquely to visual processing are likely relatively small. These results also imply that similarities in the anatomy of circuits in different cortical areas or species may not indicate similar functional connectivity.     

Sexual dimorphism of facial width-to-height ratio in human skulls and faces: A meta-analytical approach

Facial width-to-height ratio (FWHR), defined as the width of the face divided by the upper facial height, is a cue to behaviour. Explanations for this link often involve the idea that FWHR is sexually dimorphic, resulting from intersexual selection pressures. However, few studies have considered sexual dimorphism in skulls since the original paper on this topic, and it is possible that different explanations may be required if faces show sex differences but skulls do not. Here, meta-analyses of skulls found that men did have larger FWHR than women, although this effect was small. However, after categorising samples by ethnicity and geographical origin, meta-analyses only found evidence of sex differences in East Asians, and again, this effect was small. A re-analysis of previous studies after excluding skull samples found little evidence of sexual dimorphism in faces. Again, considering ethnicities separately, I found no differences for White samples but a medium-sized effect with East Asians, although this was not statistically significant with only three samples. Taken together, I found no reason to consider FWHR as a sexually dimorphic measure in skulls or faces, at least not universally, and so accounts based upon this assumption need rethinking if researchers are to explain the relationship between FWHR and behaviour.     

An evolutionary space-time model with varying among-site dependencies

It is now widely accepted that sites in a protein do not undergo independent evolutionary processes. The underlying assumption is that proteins are composed of conserved and variable linear domains, and thus rates at neighboring sites are correlated. In this paper, we comprehensively examine the performance of an autocorrelation model of evolutionary rates in protein sequences. We further develop a model in which the level of correlation between rates at adjacent sites is not equal at all sites of the protein. High correlation is expected, for example, in linear functional domains. On the other hand, when we consider nonlinear functional regions (e.g., active sites), low correlation is expected because the interaction between distant sites imposes independence of rates in the linear sequence. Our model is based on a hidden Markov model, which accounts for autocorrelation at certain regions of the protein and rate independence at others. We study the differences between the novel model and models which assume either independence or a fixed level of dependence throughout the protein. Using a diverse set of protein data sets we show that the novel model better fits most data sets. We further analyze the potassium-channel protein family and illustrate the relationship between the dependence of rates at adjacent sites and the tertiary structure of the protein.     

Identification and Functional Analysis of the S-Layer Protein SplA of Paenibacillus larvae, the Causative Agent of American Foulbrood of Honey Bees

The Gram-positive, spore-forming bacterium Paenibacillus larvae is the etiological agent of American Foulbrood (AFB), a globally occurring, deathly epizootic of honey bee brood. AFB outbreaks are predominantly caused by two genotypes of P. larvae, ERIC I and ERIC II, with P. larvae ERIC II being the more virulent genotype on larval level. Recently, comparative proteome analyses have revealed that P. larvae ERIC II but not ERIC I might harbour a functional S-layer protein, named SplA. We here determine the genomic sequence of splA in both genotypes and demonstrate by in vitro self-assembly studies of recombinant and purified SplA protein in combination with electron-microscopy that SplA is a true S-layer protein self-assembling into a square 2D lattice. The existence of a functional S-layer protein is novel for this bacterial species. For elucidating the biological function of P. larvae SplA, a genetic system for disruption of gene expression in this important honey bee pathogen was developed. Subsequent analyses of in vivo biological functions of SplA were based on comparing a wild-type strain of P. larvae ERIC II with the newly constructed splA-knockout mutant of this strain. Differences in cell and colony morphology suggest that SplA is a shape-determining factor. Marked differences between P. larvae ERIC II wild-type and mutant cells with regard to (i) adhesion to primary pupal midgut cells and (ii) larval mortality as measured in exposure bioassays corroborate the assumption that the S-layer of P. larvae ERIC II is an important virulence factor. Since SplA is the first functionally proven virulence factor for this species, our data extend the knowledge of the molecular differences between these two genotypes of P. larvae and contribute to explaining the observed differences in virulence. These results present an immense advancement in our understanding of P. larvae pathogenesis.     

Reconstruction of behavior-relevant individual brain activity: an individualized fMRI study

Different patterns of brain activity are observed in various subjects across a wide functional domain.However,these individual differences,which are often neglected through the group average,are not yet completely understood.Based on the fundamental assumption that human behavior is rooted in the underlying brain function,we speculated that the individual differences in brain activity are reflected in the individual differences in behavior.Adopting 98 behavioral measures and assessing the brain activity induced at seven task functional magnetic resonance imaging states,we demonstrated that the individual differences in brain activity can be used to predict behavioral measures of individual subjects with high accuracy using the partial least square regression model.In addition,we revealed that behavior-relevant individual differences in brain activity transferred between different task states and can be used to reconstruct individual brain activity.Reconstructed individual brain activity retained certain individual differences which were lost in the group average and could serve as an individual functional localizer.Therefore,our results suggest that the individual differences in brain activity contain behavior-relevant information and should be included in group averaging.Moreover,reconstructed individual brain activity shows a potential use in precise and personalized medicine.