DNA hybridization,cladistics, and the phylogeny of phalangerid marsupials

Summary Single-copy DNA/DNA hybridization experiments and numerical cladistic analyses of anatomical characters were used to investigate relationships among nine phalangerid (Marsupialia) species from four different genera. Both rate-dependent and rate-independent analyses of molecular data indicate that species ofTrichosurus form one clade and thatStrigocuscus, Phalanger, andSpilocuscus form a second. Within the latter group,Spilocuscus is excluded from aStrigocuscus-Phalanger calde, which, in turn, is not fully resolved on a jackknife strict consensus tree. Minimum-length Dollo, Wagner, and Camin-Sokal parsimony trees based on 35 anatomical characters, in contrast, suggest placement ofStrigocuscus withTrichosurus rather than withSpilocuscus andPhalanger. However, there are two derived characters that support the alternative arrange ofStrigocuscus withSpilocuscus andPhalanger and one character that further unitesStrigocuscus andPhalanger. Thus, DNA hybridization results are not inconsistent with the distribution of derived character states among anatomical characters, only with minimum-length trees based on character data.     

Paleobotany in cladistics and cladistics in paleobotany: enlightenment and uncertainty

Data on fossil taxa can, and should, be incorporated into cladistic analyses. Potential problems with such analyses include large amounts of missing data, and uncertainty about homology of parts that are present. Ambiguity of character data may also occur with extant taxa, but rarely to the extent that it occurs in fossil data. Such ambiguity reduces the strength of the test of character congruence among taxa, in effect relaxing the criterion of parsimony. In order to minimize such effects, composite fossil taxa should be avoided when possible, and polymorphisms reduced by breaking terminals into monomorphic subunits. When results including fossils differ radically from those that exclude fossils, such differences should be approached with caution, keeping in mind the reduced strength of the parsimony analysis when large numbers of cells in a matrix are scored as ambiguous. At this point, there is no simple way to compare the “strength” of parsimony between two data sets that have different numbers of characters and/or taxa in relation to missing data. However, methods under development may provide ways to incorporate the effect of missing values into relative measures of group support such as Bremer support, character removal, and the bootstrap.     

Cytogenetics and cladistics

Chromosomal data have been underutilized in phylogenetic investigations despite the obvious potential that cytogenetic studies have to reveal both structural and functional homologies among taxa. In large part this is associated with difficulties in scoring conventional and molecular cytogenetic information for phylogenetic analysis. The manner in which chromosomal data have been used by most authors in the past was often conceptionally flawed in terms of the methods and principles underpinning modern cladistics. We present herein a review of the different methods employed, examine their relative strengths, and then outline a simple approach that considers the chromosomal change as the character, and its presence or absence the character state. We test this using one simulated and several empirical data sets. Features that are unique to cytogenetic investigations, including B-chromosomes, heterochromatic additions/deletions, and the location and number of nucleolar organizer regions (NORs), as well as the weighting of chromosomal characters, are critically discussed with regard to their suitability for phylogenetic reconstruction. We conclude that each of these classes of data have inherent problems that limit their usefulness in phylogenetic analyses and in most of these instances, inclusion should be subject to rigorous appraisal that addresses the criterion of unequivocal homology.     

The place of genetics in ageing research

Rapidly increasing numbers of older people present many countries with growing social and economic challenges. Yet despite the far-reaching implications of ageing, its biological basis remains a topic of much debate. Recent advances in genomics have spurred research on ageing and lifespan in human populations, adding to extensive genetic studies being carried out in model organisms. But how far is ageing controlled by our genes? In this Viewpoint, six experts present their opinions and comment on future directions in ageing research.     

The Body Plan Concept and Its Centrality in Evo-Devo

A body plan is a suite of characters shared by a group of phylogenetically related animals at some point during their development. The concept of bauplane, or body plans, has played and continues to play a central role in the study of evolutionary developmental biology (evo-devo). Despite the importance of the body plan concept in evo-devo, many researchers may not be familiar with the progression of ideas that have led to our current understanding of body plans, and/or current research on the origin and maintenance of body plans. This lack of familiarity, as well as former ties between the body plan concept and metaphysical ideology is likely responsible for our underappreciation of the body plan concept in its own right, as well as its role in evo-devo. My aim in this review is to outline how we have arrived at our modern definition of body plan, the controversies associated with the concept, its role in evo-devo, and how current research is informing us on body plans. To this end, I integrate concepts such as the nature of phyla, the Cambrian explosion, constraint, evolvability, and results from recent research on gene regulatory networks with the much older concept of the body plan.     

Numerical cladistics of the phylogeny of the genus Leishmania Ross, 1903 (Kinetoplastida-Trypanosomatidae). Use of enzyme characteristics

Numerical cladistics is applied to the phyletic analysis of the genus Leishmania Ross, 1903. 128 Old World stocks are characterized by means of electrophoretic techniques using 13 enzymes. The 68 electromorphs detected allow to group the stocks into 17 zymodemes. Data are treated with the Farris' method (1970). The resultant cladogram appears to be coherent. It recognizes classical systematics entities. It sets off two sister groups: major-gerbilli on one hand, donovani-tropica-aethiopica on the other. It confirms L. aethiopica and L. gerbilli as archaic groups and points out a certain divergence between L. infantum and L. donovani s. st.     

Evo-Devo: the long and winding road

Evolutionary developmental biology (Evo-Devo) aims to unveil how developmental processes and mechanisms become modified during evolution and how from these changes the past and present biodiversity arose. The first wave of Evo-Devo identified a conserved set of toolkits common to most metazoans. The present second wave has changed gear and aims to identify how genes and modules were used differently through evolution to build the past and present morphological diversity. The burgeoning third wave is introducing experimental testing of predictions drawn from the first and second waves. Here we review some of the hottest topics, contributions and insights of present Evo-Devo related to basic concepts and paradigms of evolutionary research. Future directions of Evo-Devo are also highlighted; in other words, Quo Vadis, Evo-Devo?     

Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition

Embryonic development is defined by the hierarchical dynamical process that translates genetic information (genotype) into a spatial gene expression pattern (phenotype) providing the positional information for the correct unfolding of the organism. The nature and evolutionary implications of genotype–phenotype mapping still remain key topics in evolutionary developmental biology (evo-devo). We have explored here issues of neutrality, robustness, and diversity in evo-devo by means of a simple model of gene regulatory networks. The small size of the system allowed an exhaustive analysis of the entire fitness landscape and the extent of its neutrality. This analysis shows that evolution leads to a class of robust genetic networks with an expression pattern characteristic of lateral inhibition. This class is a repertoire of distinct implementations of this key developmental process, the diversity of which provides valuable clues about its underlying causal principles.     

LisBeth: New cladistics for phylogenetics and biogeography

Within phylogenetics, two methods are known to implement cladistics: parsimony or maximum parsimony (MP) and three-item analysis (3ia). Despite the lack of suitable software, 3ia is occasionally used in systematic, and more regularly, in historical biogeography. Here, we present LisBeth, the first and only phylogenetic/biogeographic program freely available that uses the 3ia approach and offer some insights into its theoretical propositions. LisBeth does not rely on the conventional taxon/character matrix. Instead, characters are represented as rooted trees. LisBeth performs 3ia analyses based on maximum congruence of three-item statements and calculates the intersection tree (which differs from usual consensus). In biogeography, it applies the transparent method to handle widespread taxa and implements paralogy-free subtree analysis to remove redundant distributions. For the sake of interoperability, LisBeth may import/export characters from/to matrix in NEXUS format, allowing comparison with other cladistic programs. LisBeth also imports phylogenetic characters from Xper² knowledge bases.     

介形类动物系统发育的研究现状及其趋势

近年来,世界各国的研究者越来越多地关注节肢动物系统进化问题,作为节肢动物一员的介形类,其系统进化问题也相应地引起了研究者的注意,这主要涉及介形类动物系统学定位问题,单系性问题,以及介形类动物各类群间的系统学关系等。就目前这几个问题的研究现状进行简单的介绍,同时对介形类动物系统学研究的趋势作了分析。     

Punctuationism,cladistics and the legacy of medieval neoplatonism

The current dominant orthoxy in paleoanthropology has adopted the stance of cladistics and/or punctuationism and abandonned any concern for the mechanics by which selection has operated to control the course of human evolution. Rather than being a «new» intellectual development, this is simply the most recent manifestation of a tradition of thinking that goes back via Linnaeus to medieval scholasticism where reality was assumed to consist of discrete entities that can be dealt with solely by the exercis of deductive logic. While the construction of cladograms serves the useful function of proposing testable hypotheses, the promotion of cladistic logic as the only valid approach represents a great leap backwards into medieval intellectual stagnation. If an inductive component is not restored to paleoanthropology, it will cease to maintain its credibility as a productive science.     

Modularity in Development and Why It Matters to Evo-Devo

The concept of modularity is fundamental to research in bothevolutionary and developmental biology, though workers in eachfield use the idea in different ways. Although readily and intuitivelyrecognized, modularity is difficult to define precisely. Mostdefinitions of modularity are operational and implicit, particularlyin developmental biology. Examination of several proposed definitionspoints to some general characteristics of developmental modules,for example their internal integration, and suggests the importanceof devising a definition applicable at different levels of thebiological hierarchy. Modules, like homologs, must be definedwith respect to a specified level of the hierarchy, and a generaldefinition should support both analyses of the evolving causalrelationships between levels, and studies of the interconnectionsbetween modules of the same type. The designation of a developmentalstructure, process, or function as a "module" is a testablehypothesis; this hypothesis is confirmed in the case of thedorsal marginal zone of the amphibian gastrula, which acts asa morphogenetic module. Discussions of developmental modularitycan provide a meeting place for developmental and evolutionarybiologists by helping us articulate key questions at the intersectionof the two fields, and design experiments to begin answeringthem.     

A strategy for sequence phylogeny research.

Minimal mutation trees, and almost minimal trees, are constructed from two data sets, one of phenylalanine tRNA sequences, and the other of 5S RNA sequences, from a diverse range of organisms. The two sets of results are mutually consistent. Trees representing previous evolutionary hypotheses are compared using a total weighted mutational distance criterion. The importance of sequence data from relatively little-studed phylogenetic lines is stressed. A procedure is illustrated which circumvents the computational difficulty of evaluating the astronomically large number of possible trees, without resorting to suboptimal methods.     

Wnt信号通路与后口动物体轴的进化发育

动物体轴极性的建立和最初胚轴的形成涉及到一系列信号通路的调控,Wnt信号通路是其中一条十分保守的信号通路,并且Wnt/β-catenin信号通路中的关键成员早在海绵动物中就有发现,暗示这一信号通路相对于其他信号路径来说可能是最早参与原始后生动物体轴发育的信号通路之一,并且在体轴后端和腹部的发育及命运分化方面发挥着重要作用。近年来,随着体外功能实验体系的建立,人们发现Wnt信号通路中很多基因都不同程度地影响了早期胚轴的形成,例如wnt基因、母源性基因β-catenin以及一系列转录因子等。文章首先对参与后生动物体轴发育的wnt基因家族的起源与进化关系做一简要分析,并进一步就经典的Wnt/β-catenin通路与后口动物的海胆、文昌鱼、斑马鱼、爪蟾和小鼠等类群体轴极性的建立乃至整个体轴形成方面的研究进展做一综述。     

The cladistics and higher classification of the Pimpliformes (Hymenoptera: Ichneumonidae)

The monophyly of the ichneumonid clade Pimpliformes is established and the phylogenetic relationships of the eight component subfamilies are resolved. The clade (Acaenitinae + (Diacritinae + (Cylloceriinae + (Diplazontinae + Orthocentrinae)))) is the sister-lineage to the clade (Pimplinae + (Rhyssinae + Poemeniinae)). The Nearctic genus Cressonia Dasch is transferred to the Diacritinae from the Orthocentrinae. Tribes are not recognized in the Acaenitinae as the Coleocentrini (sensu Townes, 1971) is paraphyletic with respect to the Acaenitini. The Cylloceriinae is recognized as comprising three genera, Cylloceria Schiødte, Allomacrus Förster and Sweaterella gen.n. The Orthocentrinae, including the Helictinae of authors, is shown to be monophyletic, but the latter is clearly shown to be paraphyletic if the Orthocentrus genus-group is excluded. The Pimplinae comprises four monophyletic tribes: the Delomeristini, consisting of Delomerista Förster and Atractogaster Kriechbaumer; the Perithoini trib.n., which includes only Perithous Holmgren (= Hybomischos Baltazar syn.n.); the Pimplini, which includes the Theronia genus-group as well as the Pimpla genus-group; and the Ephialtini, which includes the Polysphinctini syn.n., a monophyletic group that previously rendered the restricted Ephialtini paraphyletic. The tribe Delomeristini is the sister-group to the clade (Ephialtini + (Perithoini + Pimplini)). The subfamily Poemeniinae is recognized as comprising three tribes: the Pseudorhyssini (trib.n.) which includes the single Holarctic genus Pseudorhyssa Merrill; the Rodrigamini (trib.n.) which includes only the Costa Rican genus Rodrigama Gauld; and the Poemeniini. The tribe Pseudorhyssini is the sister-group to the clade (Rodrigamini + Poemeniini). The phylogenetic inter-relationships of the genera of Poemeniini are resolved. A new genus from South Africa, Guptella (gen.n.) is described, and Achorocephalus Kriechbaumer is shown to be a synonym of Eugalta Cameron (syn.n.). The evolution of biological traits within the Pimpliformes is discussed with reference to the elucidated phylogeny, and zoogeographic patterns are outlined.