THE ORIGIN OF MORPHOLOGICAL CHARACTERS AND THE BIOLOGICAL BASIS OF HOMOLOGY

A homolog is a part of the phenotype that is homologous to equivalent parts in other species. A biological homology concept is expected to explain three properties of homologs: 1) the conservation of those features that are used to define a homolog, 2) the individualization of the homolog with regard to the rest of the body, and 3) the uniqueness of homologs, i.e., their specificity for monophyletic groups. The main obstacle to describing a mechanistic basis for homology is the variability of the developmental pathways of undoubtedly homologous characters. However, not all aspects of the developmental pathway are of equal importance. The only organizational features of the developmental system that matter are those that have been historically acquired and cause developmental constraints on the further evolutionary modification of the characters. Two main factors contribute to historically acquired developmental constraints: generative rules of pattern formation and ontogenetic networks. In particular, hierarchical and cyclical inductive networks have the required properties to explain homology. How common such networks are is an open empirical question. The development and variation of pectoral fin hooks in blenniid fishes is presented as a model for the study of a simple ontogenetic network.     

双歧杆菌的数值分类及代表性菌株同源性的分析

对不同来源的55株双歧杆菌进行了数值分类研究。这些菌包括13株参照菌株和42株新分离物。在这些菌株中19株来源于人体,25株来自动物源,11株分离自污水。有的菌株是从未曾报道过的动物来源分离到的。通过数值分析比较了75项性状（形态、生理生化和对抗生素敏感性等）,以不加权平均链锁聚类的方式进行族群归类。在70％Sm水平上划分成5个聚类群和12个亚群。对这些聚类群菌株间的关系进行了分析。在数值分类树状图谱的簇群归类中,人和动物来源的菌株基本上彼此分开,而分离自污水的菌株穿插在人或动物来源的聚类群中。在数值分类的基础上对各聚类群中的一些菌株的DNA中G＋Cmol％进行了测定。依据16SrRNA可变区序列的分析,以PCR方法合成的生物素标记探针,对某些代表性菌株的DNA片段同源性进行了分析．同种的菌株间与不同种菌株间的同源性显示有差别。     

HOMOLOGY OF THE PALLIAL AND PULMONARY CAVITY OF GASTROPODS

The development and morphology of the pallial and pulmonarycavities of various gastropods has been investigated using epoxy-resinserial sections. In the veliger larvae of Cellana sandwicensis(Patellogastro-poda), Gibbula adansonii (Vetigastropoda), Modulustectum (Caenogastropoda) and Ovatella myosotis (Pulmonata) theformation of the pallial cavity is nearly identical. After shellformation a shallow dorsal pallial groove develops beneath themantle edge. During the late veliger stage, the ectoderm formsa deep invagination along the bottom of the pallial groove onthe right side of the larva, giving rise to the pallial cavity.In the ellobiid O. myosotis the pallial cavity becomes the lung(=pulmonary cavity), without any major post-metamorphic modification.Thus, the lung of this species is clearly homologous with thepallial cavity of prosobranchs. The lung of pulmonates withveliger development, as well as of fresh water basommatophoransand stylommatophorans, can be shown to be homologous by comparisonof adult morphology. In contrast to previous views, the pulmonatelung should be regarded as truly homologous with the pallialcavity of prosobranchs and opisthobranchs. In the onchidiidpulmonate Onchidium cf. branchiferum, the larval pallial cavityshifts posteriorly after metamorphosis, where it gives riseto a lung and a cloaca. Contrary to previous interpretations,it can be shown that the onchidiid lung is homologous with atleast part of the pallial cavity. Smeagol climoi has only asmall pallial cavity and no separate lung. The previously described‘lung’ is shown to be a gland. The re-evaluationof the development and morphology of the pulmonate lung hasimportant systematic implications: (1) The pulmonary cavitydoes not represent a synapomorphic character of pulmonates.(2) The gymnomorphs cannot be separated from the remaining pulmonatesbased on lung development. (3) The lack of a lung in the smeagolidsmight give reason to reconsider this group's systematic placementwithin the pulmonates.     

PARSIMONY,MOLECULAR EVOLUTION,AND BIOGEOGRAPHY: THE CASE OF THE NORTH AMERICAN GIANT SALAMANDER

To draw biogeographic conclusions about the Central Highlands region of the United States, we reconstructed the phylogeny of hellbender (Cryptobranchus alleganiensis) populations from restriction-site variation in mtDNA. We were unable to root the phylogeny using an outgroup and therefore could not weight restriction-site gains more heavily than site losses. As a result, maximum parsimony results in low phylogenetic resolution because of high levels of homoplasy in the data set. Use of a recently published algorithm based on an explicit model of molecular evolution yielded much greater resolution of the mtDNA relationships. This phylogeny indicates the two subspecies of hellbenders are paraphyletic with respect to one another. Hellbenders found in the southern Ozarks (C. a. bishopi) are either most closely related to populations of C. a. alleganiensis inhabiting the Tennessee River drainage or are so divergent that phylogenetic affinities are undetectable. Extremely low levels of divergence among mtDNA haplotypes found in populations from Pennsylvania, Indiana, Illinois, and the northern Missouri Ozarks suggest a recent, probably post-Pleistocene, invasion of this region from a refugium in one of these areas. Biogeographic hypotheses of the causes and timing of hellbender distributions differ significantly from those postulated from analyses of fish species relationships. Possible reasons for the discrepancy are discussed.     

棉铃虫蛹和成虫形态特征的数值分析

通过对棉铃虫Helicoverpa armigera(Hubner)及其近缘种的蛹和成虫进行了形态特征变异的数值分析,结果表明：棉铃虫种群内个体变异较大,但种群间相对分化较小,无明显的地理分化,也没有发现棉铃虫种群有稳定变异的地理特征;但发现雄性抱器冠的长、宽、抱器瓣长宽比及抱器瓣长与冠宽比4个特征与纬度有一定的相关性,其相关系数分别为：-0.612,-0.699,0.693和0.691。尽管如此,棉铃虫还是相对比较单一的一个种,而近缘种在阳茎刺和抱器瓣的形态及阳茎端囊上的大刺数等方面有明显而稳定的差异和间断。     

CONCEPTS AND TESTS OF HOMOLOGY IN THE CLADISTIC PARADIGM

Abstract— Logical equivalence between the notions of homology and synapomorphy is reviewed and supported. So-called transformational homology embodies two distinct logical components, one related to comparisons among different organisms and the other restricted to comparisons within the same organism. The former is essentially hierarchical in nature, thus being in fact a less obvious form of taxic homology. The latter is logically equivalent to so-called serial homology in a broad sense (including homonomy, mass homology or iterative homology). Of three tests of homology proposed to date (similarity, conjunction and congruence) only congruence serves as a test in the strict sense. Similarity stands at a basic level in homology propositions, being the source of the homology conjecture in the first place. Conjunction is unquestionably an indicator of non-homology, but it is not specific about the pairwise comparison where non-homology is present, and depends on a specific scheme of relationship in order to refute a hypothesis of homology. The congruence test has been previously seen as an application of compatibility analysis. However, congruence is more appropriately seen as an expression of strict parsimony analysis. A general theoretical solution is proposed to determine evolution of characters with ambiguous distributions, based on the notion of maximization of homology propositions. According to that notion, ambiguous character-state distributions should be resolved by an optimization that maximizes reversals relative to parallelisms. Notions of homology in morphology and molecular biology are essentially the same. The present tendency to adopt different terminologies for the two sources of data should be avoided, in order not to obscure the fundamental uniformity of the concept of homology in comparative biology. “A similar hierarchy is found both in ‘structures’ and in ‘functions’. In the last resort, structure (i.e. order of parts) and function (order of processes) may be the very same thing […].” L. von Bertalanlfy “[…] it is the fact that certain criteria enable us to match parts of things consistently which suggests that mechanisms of certain kinds must have been involved in their origin.” N. Jardine and C. Jardine     

东北虎促卵泡激素和促黄体激素基因的克隆及其序列分析

本研究首次从东北虎（Panthea tigris altaica)脑垂体提取总RNA,利用RT－PCR技术扩增出东北虎垂体促性腺激素α亚基,促卵泡激素（FSH）β亚基和促黄体激素（LH）β亚基的编码区序列,并进行克隆,测序和比较分析。结果表明,其α亚基,FSHβ亚基,LHβ亚基基因的开放阅读框分别为363bp,390bp和420bp,分别编码120,129和142氨基酸的前体蛋白。与已发表的人,牛,绵羊,猪,大鼠,小鼠等物种相应序列比较,无论在核苷酸水平,还是在氨基酸水平都显示出较高的同源性（64．7％－96．6％）,其中与猪的同源性最高（86％－96．6％）。东北虎的基因序列还具有其明显的特异性,首次发现LHβ亚基cDNA编码的前体蛋白在信号肽部分比其它物种相应序列多一个亮氨酸残基（Leu)。     

PHYLOGENY OF THE EUGLENOPHYTES: ANALYSIS USING SSU RDNA AND ULTRASTRUCTURAL CHARACTERS

The use of both molecular and morphological data to determine relationships among the euglenoids is vital for a complete understanding of their phylogeny, and the development of an accurate taxonomy. Analyses of the SSU (18S) rDNA from 12 euglenoid genera have resulted in tree topologies that are in agreement with many defining morphological characters. The euglenoid lineage is formed by phagotrophic euglenoids at its base, followed by the divergence of phototrophs that in-turn gave rise to osmotrophs. The photosynthetic lineage is anchored by euglenoids with two emergent flagella, Eutreptia and Eutreptiella , while the remainder of the lineage is composed of euglenoids with a single emergent flagellum. Among the photosynthetic euglenoids with a single emergent flagellum those that secrete mucilaginous stalks, Colacium , or form a lorica, Trachelomonas and Strombomonas , are closely associated. The remaining photosynthetic genera Euglena , Phacus , and Lepocinclis are intermixed with each other and the osmotrophic genera Astasia , and Khawkinea. Hence, they are not monophyletic, sensu Hennig. To reinforce molecular phylogenies, a robust morphological character database is necessary. For taxa with complex internal structures complete serial reconstruction is required. Serial reconstruction of the flagellar and feeding apparatuses in Ploeotia costata illustrate this necessity. Originally described as having both an MTR (Type I) and a Type II feeding apparatus, reconstruction has shown P. costata to have a single, Type II, feeding apparatus. Moreover, the Type II now appears to be an autapomorphy for Ploeotia species, while euglenoid feeding apparatuses, in toto, appear to form a continuum of structural types.     

PARSIMONY ANALYSIS OF THE PHYLOGENY OF SOME OLIGOCHAETA (ANNELIDA) USING SPERMATOZOAL ULTRASTRUCTURE

Abstract— Quantitative and qualitative ultrastructural data from the spermatozoa of 11 oligochaete species, representing all orders (Tubificida, Lumbriculida, and Haplotaxida, yielded a single most parsimonious tree, using the Wagner-tree (PAUP) method of Swofford (1984). The Haplotaxida ( Haplotaxis through Megascolecidae) form a discrete monophyletic group, with inclusion, however, of the reproductively exceptional tubificidan Phreodrilus. Bythonomus , representing the Lumbriculidae, the phylogenetic position of which has been so controversial, forms the plesiomorphic sister group of the Haplotaxida, a position which is supported from other evidence. The Tubificida, represented by two tubificids ( Rhizodrilus and Limnodriloides ) and by the enchytraeid Lumbricillus , are plesiomorphic relative to the lumbriculid+haplotaxid assemblage and lie at the base of the tree, but all three appear mutually paraphyletic. Monophyly of the Tubificida cannot, however, be considered conclusively refuted from the small sample used. Lumbricillus appears to have the most plesiomorphic sperm in the investigated oligochaetes. The Megascolecidae ( Amynthas and Fletcherodrilus ) form the highest affinity and most apomor-phic group. The implications of relative apomorphy of the Lumbriculida ( Bythonomus ) are profound. Branchiobdellids and leeches are generally regarded as sharing a common ancestry with lumbriculids and would, because of the revised position of the latter, cladistically constitute part of the Oligochaeta sensu lato .     

LIKELIHOOD AND PARSIMONY: COMPARISON OF CRITERIA AND SOLUTIONS

Abstract— The merits of alternative approaches to the inference of evolutionary trees have been much discussed, but there have been few attempts to compare inferences systematically or to pinpoint the source of differences. The two major classes of approach are via likelihood inference under an evolutionary model and estimates based upon parsimony methods. Within the general class of likelihood approaches, there are differences depending upon the particular class of models considered. This paper makes comparisons of the characteristics of inferences for the case of quantitative variation (of allele frequencies, for example), concentrating on the case of very small numbers of populations where explicit solutions are possible, but also upon features which apply as well to inferences for larger groups of populations. The parsimony method of "minimum evolution" was proposed by Edwards and Cavalli-Sforza (1964) to provide an approximation to the likelihood solution for an intractable model. In fact, its estimated phylogenies are closest to those of a more recent model of Felsenstein (1981) which, like parsimony, produces a fundamentally unrooted tree. Likelihood estimates based upon models involving an implicit or explicit root are radically different. These differ also from each other, depending upon whether or not the root is explicitly estimated, and upon whether or not a model for the fissioning of populations is included. Some general features of the comparisons can be summarized.     

我国23个群体体质的聚类分析与主成分分析

作者选取13项指标（头长、头宽、额最小宽、面宽、形态面高、鼻宽、鼻高、口裂宽、两眼内宽、身高、坐高、肩宽、骨盆宽）对我国23个群体体质特征进行了聚类分析与主成分分析。研究结果显示：23个群体可分为南方组、北方组（含两个小组）和中间类群组。南方组与北方组的体质区别主要为体部的长度、宽度的差异。北方组各群体之间头面部指标值差异较大,南方组各群体之间头面部指标值则较为接近。     

IN SEARCH OF A METHOD FOR CLADISTIC BIOGEOGRAPHY: AN EMPIRICAL COMPARISON OF COMPONENT ANALYSIS, BROOKS PARSIMONY ANALYSIS, AND THREE-AREA STATEMENTS

Abstract— Three quantitative cladistic biogeographic methods, namely, component analysis, Brooks parsimony analysis (BPA), and three-area statements (TAS) have been proposed for obtaining general area cladograms from taxon-area cladograms. Available programs implementing these methods include COMPONENT versions 1.5 and 2.0 for component analysis, TAS for three-area statements, and Hennig86 for analysing matrices for both three-area statements and BPA. Ten different data sets were analysed with these programs and items of error were used to evaluate the general area cladograms obtained. None of the computer implementations of the methods compared proved to be more effective than the others.
"…all methodologies, even the most obvious ones, have their limits…"
Feyerabend (1993:231)     

小麦品质和农艺性状的配合力分析

依据田间试验和室内生化分析数据,按ｐｘｑ交配模式,对１０个冬小麦亲本２５个杂交组合Ｆ１的蛋白质含量,赖氨酸含量,穗粒重和千粒重的一般配合力和特殊配合力效应进行了分析。结果表明,除蛋白质含量的ｓｃａ外,其余性状的ｇｃａ和ｓｃａ效应均达极显著水平,表明在本研究中,基因的加性效应和非加性效应均起重要作用。由于一般配合力差δ＾２ｓｃａ大,表明基因的加性效应更加重要。根据ｇｃａ,ｓｃａ和δ＾２ｓｃａ估值,分     

METHODS FOR FASTER PARSIMONY ANALYSIS

Abstract — Several algorithms to speed up branch swapping searches for most parsimonious trees are described. The method for indirect tree length calculation when moving a clipped clade, based on final states for the divided tree, is expanded to take into account polymorphic characters, and to include the possibility of rejecting several locations as suboptimal by checking just one node. Three different algorithms for faster estimation of final state assignments for the divided tree based on calculations for the whole tree are presented. The first of these is approximate; it uses information from the final state sets for the whole tree. The second is exact, but it is slower than the first, and requires more memory; it is based on the union of the state sets of the descendants for each node. The third is also exact; it requires more memory and programming effort than the other two but it is faster, it is based on final and preliminary state sets for the whole tree ("incremental two-pass optimization"). Efficient ways to derive state assignments for collapsing trees, based on final states for the divided tree, are described. The recently proposed method of "incremental optimization" is discussed. It is likely that searches using that method will be no faster than searches using indirect calculation as originally described, and will be quite slower than the modified indirect calculation described here. Searches using that method will probably be significantly slowed down when zero-length branches are to be collapsed, since shortcuts for faster collapsing are not directly applicable.     

形态和分子进化研究中的同源概念

在比较生物学中,同源是一个中心概念,是系统学的心脏,同源最基本的意义就是共同祖先。然而,这只是对同源的解释而非告诉我们怎样去发现它。同源又可被看成是特别类群间的联系。形态进化研究中同源比较的对象是生物的结构,而分子进化研究中的同源比较对象是DNA中的核着酸序列,现对这两种层次的同源概念及其相互间的关系进行讨论。       

CLADISTIC ANALYSIS OF THE OCTOPODS BASED ON ANATOMICAL CHARACTERS

Parsimony analysis of 29 finned and finless octopod taxa considered66 anatomical and morphological characters to discover synapomorphiesthat unite monophyletic groups. The resultant cladogram (177equally parsimonious trees at 191 steps, CI 0.429) resolvedall relationships except those among the 16 exemplars of theOctopodidae included and those among Tremoctopus, Ocythoe andArgonauta. Bootstrap values of over 90% support the monophylyof the finned and finless octopods, relationships among thefinned octopods, the bolitaenids and the monophyly of Haliphron,Tremoctopus, Ocythoe and Argonauta; bootstrap values for othernodes range from 57 to 79%. Among finned octopods, specimensrepresenting Grimpoteuthis are basal, as Voss (1988a) suggested.Specimens of Opisthoteuthis represent a distinct lineage, andare sister taxon, in this analysis, of Cirroteuthis (althoughspecimens of Stauroteuthis could not be included). New definitionsof the genera Opisthoteuthis and Grimpoteuthis are providedto reflect their separate evolutionary histories rather thantheir overt morphological similarity. Among finless octopods,bolitaenids are basal. The monophyletic Octopodidae is the sistertaxon to the clade containing the sister taxa Vitreledonellaand Amphitretus, and Haliphron, Tremoctopus, Ocythoe and Argonauta.The Ctenoglossa and Heteroglossa, families grouped by sharedradular dentition, are diphyletic and paraphyletic, respectively.The cladistic relationships demonstrate that both the Vitrele-donellidaeand Idioctopodidae are junior synonyms of the Amphitretidae;despite conspicuous morphological differences separating thesetaxa, they share a recent evolutionary history.     

THE COADAPTATION OF PARENTAL AND OFFSPRING CHARACTERS

Parents often have important influences on their offspring's traits and/or fitness (i.e., maternal or paternal effects). When offspring fitness is determined by the joint influences of offspring and parental traits, selection may favor particular combinations that generate high offspring fitness. We show that this epistasis for fitness between the parental and offspring genotypes can result in the evolution of their joint distribution, generating genetic correlations between the parental and offspring characters. This phenomenon can be viewed as a coadaptive process in which offspring genotypes evolve to function with the parentally provided environment and, in turn, the genes for this environment become associated with specific offspring genes adapted to it. To illustrate this point, we present two scenarios in which selection on offspring alone alters the correlation between a maternal and an offspring character. We use a quantitative genetic maternal effect model combined with a simple quadratic model of fitness to examine changes in the linkage disequilibrium between the maternal and offspring genotypes. In the first scenario, stabilizing selection on a maternally affected offspring character results in a genetic correlation that is opposite in sign to the maternal effect. In the second scenario, directional selection on an offspring trait that shows a nonadditive maternal effect can result in selection for positive covariances between the traits. This form of selection also results in increased genetic variation in maternal and offspring characters, and may, in the extreme case, promote host-race formation or speciation. This model provides a possible evolutionary explanation for the ubiquity of large genetic correlations between maternal and offspring traits, and suggests that this pattern of coinheritance may reflect functional relationships between these characters (i.e., functional integration).