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.     

Adolf Remane (1898–1976) and his views on systematics, homology and the Modern Synthesis

Adolf Remane was primarily a morphologist and systematist. In 1952, he published an influential book on the foundations of systematics and phylogenetics in which he advocated homology as the central concept of morphology and the basis of the natural system and discussed criteria serving to discriminate homology from homoplasy in great detail. During the decades when the Modern Synthesis of evolution was created, he repeatedly commented on and criticised the synthetic theory of evolution, which he never fully accepted. Remane disapproved of idealistic morphology and was strongly opposed to Lamarckian, saltationist and orthogenetic theories of evolution. Yet, while appreciating the synthetic theory's validity in the realm of speciation and microevolution, he rejected the claim that the current genetic knowledge was sufficient to explain complex morphological transformations on the basis of random mutations and selection. Instead, he seems to have favoured mutation pressure as the most important factor in macroevolution. Nevertheless, the sometimes vicious disputes between Remane and the adherents of the Modern Synthesis may at least partly have been brought about by personal factors rather than by scientific differences.     

Morphological integration and the evolution of knuckle-walking

The evolution of knuckle-walking has profound implications for our understanding of the emergence of bipedalism. The modern debate surrounding its evolution is concerned with whether or not it is homologous in chimpanzees and gorillas. Here, this problem is approached using the methods of morphological integration to test hypotheses of patterns and magnitudes of integration in the third manual ray and capitate. If knuckle-walking morphologies are highly integrated and evolve in a correlated bundle (i.e., comprising a functional complex), it seems reasonable that they could have been recruited independently relatively easily in gorillas and chimpanzees, thus increasing the likelihood of homoplasy. If, however, there is no evidence for a knuckle-walking complex, then it seems less likely that chimpanzees and gorillas would have evolved knuckle-walking independently. Results indicate that chimpanzees and gorillas are not characterized by high magnitudes of integration or unique patterns of integration that distinguish them from non-knuckle-walking taxa. This does not support the hypothesis of a knuckle-walking complex, nor does it support the contention that knuckle-walking could have been easily evolved independently in chimpanzees and gorillas. Implications for trait analysis and the evolution of bipedalism are discussed, as are recent analyses supporting the independent origins of knuckle-walking.     

Homoplasy in the ear region of Tethytheria and the systematic position of Embrithopoda (Mammalia,Afrotheria)

The ear region of mammals has long been considered as morphologically very conservative and accordingly, phylogenetically useful. In this study, the anatomy of the petrosal and bony labyrinth (osseous inner ear) of Numidotherium (Proboscidea) and Arsinoitherium (Embrithopoda) are investigated and compared in order to assess the evolution of ear region characters in proboscideans and embrithopods. Using a cladistic analysis across Paenungulata based on ear region characters only, we found that Arsinoitherium is surprisingly best placed as a crown proboscideans to the exclusion of Numidotherium and Phosphatherium, which results in the paraphyly of proboscidean. The clade Proboscidea is actually well supported by dental and post-cranial characters, and we propose that this result underlines the great amount of morphological convergences in the ear region of Embrithopoda and Proboscidea, possibly due to convergent evolution of capabilities toward infrasonic hearing.     

鸟类形态特征的同质性比较

鸟类作为脊椎动物中的主要类群之一,其内部演化关系一直是动物学研究的重点。形态特征及分子特征在推断鸟类内部类群间的系统发育关系时被广泛应用,但长久以来受制于同质性的影响,不同形态特征难以得到一致的系统发育关系。随着基因组测序技术及分析方法的快速发展,基于大量DNA序列数据所建的物种树成为领域内普遍认可的鸟类系统发育关系。在此基础之上,重新挖掘形态特征的研究价值成为可能。本研究基于Prum发表于2015年的鸟类科级水平系统发育树,比较了不同形态特征同质性水平的差异,讨论了形态特征对于提高分子特征系统发育信号及分子树支持率的作用。研究发现,不同种类形态特征的同质性水平存在显著的差异,以一致性指数为标准,杂项特征(包括神经、肌腱及肠道的特征)的得分显著高于骨学特征和肌学特征(P < 0.01),颅骨特征的得分显著高于非颅骨、躯干及腿部特征的得分(P < 0.05);加入形态特征能够显著提高分子特征的系统发育信号(P < 0.05),也提高了分子树的支持率。综上所述,不同的形态特征在同质性水平的得分上具有显著差异,在分子特征上加入形态特征既能够提高分子特征的系统发育信号,也能够提高分子树的支持率。     

The evolution of the reptilian hindfoot and the homology of the hooked fifth metatarsal

The homology of the fifth metatarsal in turtles and in diapsid reptiles is reassessed in the light of new phylogenetic studies. The two nearest outgroups to turtles — pareiasaurs and procolophonoids — both lack a fifth distal tarsal but retain a normal fifth metatarsal. The fifth distal tarsal was therefore lost at the base of the clade that contains turtles. Thus, the hooked fifth metatarsal in turtles must consist entirely of a modified fifth metatarsal: it does not include contributions from the fifth distal tarsal, as commonly supposed. In diapsids, loss of the fifth distal tarsal appears to have occurred at the base of crown-clade diapsids, hooking of the fifth metatarsal subsequently occurring within lepidosauromorphs, and in archosauromorphs. If so, the hooked fifth metatarsal in archosauromorphs, and some lepidosauromorphs, consists entirely of a modified fifth metatarsal. In both turtles and diapsids, integration of the elements distal to the mesotarsal joint precedes evolution of the hooked fifth metatarsal, supporting the view that the latter element evolved to perform a lever function (analogous to the “heel bone” of mammals).     

Invertibility of the TKF model of sequence evolution

We consider character sequences evolving on a phylogenetic tree under the TKF91 model. We show that as the sequence lengths tend to infinity the topology of the phylogenetic tree and the edge lengths are determined by any one of (a) the alignment of sequences (b) the collection of sequence lengths. We also show that the probability of any homology structure on a collection of sequences related by a TKF91 process on a tree is independent of the root location.     

Homoplasy and the evolution of ontogeny in papionin primates

Recent advances in developmental biology reveal that patterns of morphological development, even during early phases, may be highly susceptible to evolutionary change. Consequently, developmental data may be uninformative with regard to distinguishing homology and homoplasy. The present analysis evaluates postnatal ontogeny in papionin primates to test hypotheses about homology and homoplasy during later periods of development. Specifically, the analysis studies the allometric bases of craniometric resemblances among four papionin genera to test the hypothesis that homoplasy in adult cranial form, particularly of baboons (Papio) and mandrills (Mandrillus), is underwritten by divergent patterns of development. Bivariate and multivariate allometric analyses demonstrate that the developmental patterns in Papio baboons diverge markedly from ontogenetic allometric trajectories in other papionin species. The resemblances between Papio and Mandrillus (assuming that patterns of development in smaller papionins are ancestral) are largely consequences of perinatal increases in relative brain size in juvenile Papio. Postnatal growth to large size and strong negative allometry of neurocranial form results in shape similarities because developmental pathways for large papionin genera intersect. Analyses show that allometric data may not be particularly informative in revealing homoplasy. However, placed into proper phylogenetic context, such data illustrate derived patterns of development that may reflect critically important life-history or ontogenetic adaptations.     

What's in a name: the taxonomic status of human head and body lice

Human head lice (Anoplura: Pediculidae: Pediculus) are pandemic, parasitizing countless school children worldwide due to the evolution of insecticide resistance, and human body (clothing) lice are responsible for the deaths of millions as a result of vectoring several deadly bacterial pathogens. Despite the obvious impact these lice have had on their human hosts, it is unclear whether head and body lice represent two morphological forms of a single species or two distinct species. To assess the taxonomic status of head and body lice, we provide a synthesis of publicly available molecular data in GenBank, and we compare phylogenetic and population genetic methods using the most diverse geographic and molecular sampling presently available. Our analyses find reticulated networks, gene flow, and a lack of reciprocal monophyly, all of which indicate that head and body lice do not represent genetically distinct evolutionary units. Based on these findings, as well as inconsistencies of morphological, behavioral, and ecological variability between head and body lice, we contend that no known species concept would recognize these louse morphotypes as separate species. We recommend recognizing head and body lice as morphotypes of a single species, Pediculus humanus, until compelling new data and analyses (preferably analyses of fast evolving nuclear markers in a coalescent framework) indicate otherwise.     

Behavior reuse and virtual sensors in the evolution of complex behavior architectures

Summary In this paper we discuss some of the new work we have been carrying out with the objective of making evolutionarily obtained behavior based architectures and modules for autonomous robots more standardized and interchangeable. The architectures contemplated here are based on a multiple behavior structure where all of the modules, as well as their interconnections, are automatically obtained through evolutionary processes. The main objective of this line of research is to obtain procedures that permit producing behavior based controllers that work on real robots operating in real environments as independently of the platform as possible. In this particular paper we will concentrate on different aspects regarding the inclusion of virtual sensors as a way to make improved use of the capabilities of the different platforms and on the reuse of behavior modules. This reuse will be contemplated within the same behavioral architecture and from the point of view of transferring behavior modules from one platform to a different one.     

cDNA cloning, expression pattern, genomic structure and chromosomal location of RAB6KIFL, a human kinesin-like gene

Purple acid phosphatases (PAPs) comprise a family of binuclear metal-containing hydrolases, members of which have been isolated from plants, mammals and fungi. Polypeptide chains differ in size (animal 35 kDa, plant 55 kDa) and exhibit low sequence homology between kingdoms but all residues involved in co-ordination of the metal ions are invariant. A search of genomic databases was undertaken using a sequence pattern which includes the conserved residues. Several novel potential PAP sequences were detected, including the first known examples from bacterial sources. Ten plant ESTs were also identified which, although possessing the conserved sequence pattern, were not homologous throughout their sequences to previously known plant PAPs. Based on these EST sequences, novel cDNAs from sweet potato, soybean, red kidney bean and Arabidopsis thaliana were cloned and sequenced. These sequences are more closely related to mammalian PAP than to previously characterized plant enzymes. Their predicted secondary structure is similar to that of the mammalian enzyme. A model of the sweet potato enzyme was generated based on the coordinates of pig PAP. These observations strongly suggest that the cloned cDNA sequences represent a second group of plant PAPs with properties more similar to the mammalian enzymes than to the high molecular weight plant enzymes.     

Mutational analysis and homology modelling of SyrC, the aminoacyltransferase in the biosynthesis of syringomycin

SyrC, a component of the multienzyme system of syringomycin biosynthesis, has been shown to shuttle Thr/4-Cl-Thr between the thiolation domains SyrB1-T1 and SyrE-T8,9 by transiently linking it to Cys224 in the enzyme active site. We present data on the structure-function relationship in vivo of this protein and an in silico model of its three-dimensional structure. The biosynthetic activity of SyrC was not influenced when either Asp348 or His376 that together with Cys224 form a putative catalytic triad, were replaced with Ala, but it was abolished by the exchange Cys224 with Ser. The presence of the FLAG peptide on either the N- or C-terminus of the protein did not affect activity, whereas the deletion of the first 16 amino acids at the N-terminus or the insertion of Maltose Binding Protein abolished the production of syringomycin. We present the model of the three-dimensional structure of SyrC suggesting a homodimeric structure for the protein and biochemical data that are supportive of this model.     

Nonuniformity of nucleotide substitution rates in molecular evolution: Computer simulation and analysis of 5S ribosomal RNA sequences

Summary The effects of temporal (among different branches of a phylogeny) and spatial (among different nucleotide sites within a gene) nonuniformities of nucleotide substitution rates on the construction of phylogenetic trees from nucleotide sequences are addressed. Spatial nonuniformity may be estimated by using Shannon's (1948) entropy formula to measure the Relative Nucleotide Variability (RNV) at each nucleotide site in an aligned set of sequences; this is demonstrated by a comparative analysis of 5S rRNAs. New methods of constructing phylogenetic trees are proposed that augment the Unweighted Pair-Group Using Arithmetic Averages (UPGMA) algorithm by estimating and compensating for both spatial and temporal nonuniformity in substitution rates. These methods are evaluated by computer simulations of 5S rRNA evolution that include both kinds of nonuniformities. It was found that the proposed Reference Ratio Method improved both the ability to reconstruct the correct topology of a tree and also the estimation of branch lengths as compared to UPGMA. A previous method (Farris et al. 1970; Klotz et al. 1979; Li 1981) was found to be less successful in reconstructing topologies when there is high probability of multiple mutations at some sites. Phylogenetic analyses of 5S rRNA sequences support the endosymbiotic origins of both chloroplasts and mitochondria, even though the latter exhibit an accelerated rate of nucleotide substitution. Phylogenetic trees also reveal an adaptive radiation within the eubacteria and another within the eukaryotes for the origins of most major phyla within each group during the Precambrian era.     

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。     

The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species

The incredible development of comparative genomics during the last decade has required a correct use of the concept of homology that was previously utilized only by evolutionary biologists. Unhappily, this concept has been often misunderstood and thus misused when exploited outside its evolutionary context. This review brings back to the correct definition of homology and explains how this definition has been progressively refined in order to adapt it to the various new kinds of analysis of gene properties and of their products that appear with the progress of comparative genomics. Then, we illustrate the power and the proficiency of such a concept when using the available genomics data in order to study the evolution of individual genes, of entire genomes and of species, respectively. After explaining how we detect homologues by an exhaustive comparison of a hundred of complete proteomes, we describe three main lines of research we have developed in the recent years. The first one exploits synteny and gene context data to better understand the mechanisms of genome evolution in prokaryotes. The second one is based on phylogenomics approaches to reconstruct the tree of life. The last one is devoted to reminding that protein homology is often limited to structural segments (SOH=segment of homology or module). Detecting and numbering modules allows tracing back protein history by identifying the events of gene duplication and gene fusion. We insist that one of the main present difficulties in such studies is a lack of a reliable method to identify genuine orthologues. Finally, we show how these homology studies are helpful to annotate genes and genomes and to study the complexity of the relationships between sequence and function of a gene.     

Parallel alterations in the timing of ovarian Ecdysone Receptor and Ultraspiracle expression characterize the independent evolution of larval reproduction in two species of gall midges (Diptera: Cecidomyiidae)

Although most insects reproduce in the adult stage, facultative larval or pupal reproduction (paedogenesis) has evolved at least six times indepently in insects, twice in gall midges of the family Cecidomyiidae (Diptera). Paedogenesis in gall midges involves the precocious growth and differentiation of the ovary in an otherwise larval form. We have previously shown that the timing of expression of the Ecdysone Receptor (EcR) and Ultraspiracle (USP), the two proteins that constitute the functional receptor for the steroid hormone 20-hydroxyecdysone, regulates the timing and progression of ovarian differentiation in Drosophila melanogaster (Diptera: Drosophilidae). Here we test the hypothesis that precocious activation of EcR and USP in the ovaries of paedogenetic gall midges allows for precocious ovarian differentiation. Using monoclonal antibodies directed against insect EcR and USP proteins, we first show that when these gall midges are reared under conditions that promote typical, metamorphic development, up- regulation of EcR and USP occurs in the final larval stage. By contrast, in the paedogenetic life cycle, EcR and USP are up-regulated early in the first larval stage. A similar pattern is seen for two independently-evolved paedogenetic gall midges, Heteropeza pygmaea and Mycophila speyeri. We discuss our results in the context of developmental constraints on the evolution of paedogenesis in dipteran insects. Received: 30 July 1999 / Accepted: 23 Feburary 2000     

中国动物行为学研究现状的文献计量学分析

采用文献计量学的方法,在《中国学术期刊网络出版总库》和《Science Citation Index》数据库中,以“动物行为”、“animal behavior”、“ethology”作为检索词,检索了中国学者在国内外期刊上发表的中英文文献,并对中国动物行为学领域发文的年代、期刊、研究单位、作者、被引频次、国际合作、基金项目、研究对象和领域等内容进行了定量分析。结果表明：中国动物行为学研究起步较晚,近三十多年来相关动物行为学文献在波动中增长,并在近几年有从中文向英文转移的趋势;平均每篇文献被引2.81次;作者和研究单位虽然分散,但已经形成了专门从事动物行为研究的核心作者群、研究机构群;国内外均存在动物行为学文献的主要期刊分布区,但国内迫切需要一种动物行为学的专业期刊;动物行为研究的基金来源广泛,其中国家自然科学基金占重要地位;有国外作者参与的英文文献比例远大于中文文献,主要合作国家是美国;中国动物行为研究对象主要为哺乳动物,鸟类是中文文献第二位研究对象而昆虫是英文文献的第二位研究对象;繁殖行为是中国动物行为主要研究领域,中文文献在行为观察记录和行为谱、活动节律和时间分配方面的比例远远大于英文文献。总体上看,中国动物行为学文献发展符合科学文献逻辑增长曲线;整体研究水平偏低,国际影响力有待提高;中国动物行为学已步入新的发展阶段。     

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.     

Phylogenetics, species boundaries and timing of resource tracking in a highly specialized group of seed beetles (Coleoptera: Chrysomelidae: Bruchinae)

Though for a long time it was hypothesized that the extraordinary diversity of phytophagous insects was better explained by a synchronous pattern of co-diversification with plants, the results of recent studies have led to question this theory, suggesting that the diversification of insects occurred well after that of their hosts. In this study we address this issue by investigating the timing of diversification of a highly specialized group of seed beetles, which mostly feeds on legume plants from the tribe Indigofereae. To that purpose, a total of 130 specimens were sequenced for six genes and analyzed under a Bayesian phylogenetic framework. Based on the resulting trees we performed several analyses that allowed a better definition of the group boundaries and to investigate the status of several taxa through the use of molecular species delimitation analyses in combination with morphological evidences. In addition the evolution of host plant use was reconstructed and different molecular-dating approaches were carried out in order to assess the ages of several clades of interest. The resulting framework suggests a more ancient than previously thought origin for seed beetles, and a pattern of rapid host plant colonization. These findings call for further similar studies in other highly specialized groups of phytophagous insects.