The impact of molecular systematics on hypotheses for the evolution of root nodule symbioses and implications for expanding symbioses to new host plant genera

Current taxonomic schemes place plants that can participate in root nodule symbioses among disparate groups of angiosperms. According to the classification scheme of Cronquist (1981) which is based primarily on the analysis of morphological characters, host plants of rhizobial symbionts are placed in subclasses Rosidae and Hamamelidae, and those of Frankia are distributed among subclasses Rosidae, Hamamelidae, Magnoliidae and Dilleniidae. This broad phylogenetic distribution of nodulated plants has engendered the notion that nitrogen fixing endosymbionts, particularly those of actinorhizal plants, can interact with a very broad range of unrelated host plant genotypes. New angiosperm phylogenies based on DNA sequence comparisons reveal a markedly different relationship among nodulated plants and indicate that they form a more coherent group than has previously been thought (Chase et al., 1993; Swensen et al., 1994; Soltis et al., 1995). Molecular data support a single origin of the predisposition for root nodule symbiosis (Soltis et al., 1995) and at the same time support the occurrence of multiple origins of symbiosis within this group (Doyle, 1994; Swensen, 1996; Swensen and Mullin, In Press).     

The Evolution of the Linnaean Hierarchy

The Linnaean system of classification is a threefold system of theoretical assumptions, sorting rules, and rules of nomenclature. Over time, that system has lost its theoretical assumptions as well as its sorting rules. Cladistic revisions have left it less and less Linnaean. And what remains of the system is flawed on pragmatic grounds. Taking all of this into account, it is time to consider alternative systems of classification.     

The use of karyotyping in the systematics of yeasts

The use of electrophoretic karyotyping in systematics of yeasts is discussed. New data are provided on the karyotypes of the medically important fungiHortaea werneckii, Filobasidiella (=Cryptococcus)neoformans, andMalassezia species.Hortaea werneckii has twelve to eighteen bands of chromosomal DNA, ranging in size between 500 and 2300 kb. The karyotypes ofFilobasidiella neoformans consist of seven to fourteen bands of chromosomal DNA. The varietiesneoformans andbacillispora cannot be separated by their karyotypes, and no obvious correlation was found with serotypes, geography or habitat. All strains ofMalassezia pachydermatis studied have similar karyotypes consisting of five bands, whereas inM. furfur, four different karyotypes are prevalent. However, each of these karyotypes is stable.     

Phylogenetic relationships among actinorhizal plants. The impact of molecular systematics and implications for the evolution of actinorhizal symbioses

A review of recent molecular systematic studies of actinorhizal plants and their Frankia endosymbionts is presented. For comparative purposes, a discussion of recent studies pertaining to the evolution of nodulation in the legume-rhizobium system is included. Molecular systematic studies have revealed that actinorhizal plants are more closely related than current taxonomic schemes imply. Broad-based analyses of the chloroplast gene rbcL indicate that all symbiotic root-nodulating higher plants belong to a single large clade. More focused molecular analyses of both legume and actinorhizal hosts within this large clade indicate that symbioses have probably arisen more than once. By comparing host phylogenies and recently published bacterial phylogenies, we consider the coevolution of bacterial symbionts with their actinorhizal hosts.     

分子系统学原理及其在林木上的应用

综述了林木分子系统学的是新研究进展,分析了现代分子生物学方法的不断改进给林木系统学研究带来的革命性进展,阐述了RAPD,cpDNA,rDNA等在林木分子系统学研究中的应用及取得的成果,评述了各种不同分子标记的适用范围以及对相关基因进化规律的认识,同时提出了这些分子标记在分子系统学研究中应注意的一些问题。     

The use of indicator taxa as representatives of communities in bioassessment

1. Sampling and processing of benthic macroinvertebrate samples is time consuming and expensive. Although a number of cost‐cutting options exist, a frequently asked question is how representative a subset of data is of the whole community, in particular in areas where habitat diversity is high (like Dutch surface water habitats). 2. Weighted averaging was used to reassign 650 samples to a typology of 40 community types, testing the representativeness of different subsets of data: (i) four different types of data (presence/absence, raw, ²log‐ and ln‐transformed abundance), (ii) three subsets of ‘indicator’ taxa (taxa with indicator weights 4–12, 7–12, and 10–12) and (iii) single taxonomic groups (n = 14) by determining the classification error. 3. ²log‐ and ln‐transformed abundances resulted in the lowest classification error, whilst the use of qualitative data resulted in a reduction of 10% of the samples assigned to their original community type compared to the use of ln‐transformed abundance data. 4. Samples from community types with a high number of unique indicator taxa had the lowest classification error, and classification error increased as similarity among community types increased. Using a subset of indicator taxa resulted in a maximum increase of the classification error of 15% when only taxa with an indicator weight 10–12 were included (error = 49.1%). 5. Use of single taxonomic groups resulted in high classification error, the lowest classification error was found using Trichoptera (68%), and was related to the frequency of the taxonomic group among samples and the indicator weights of the taxa. 6. Our findings that the use of qualitative data, subsets of indicator taxa or single taxonomic groups resulted in high classification error implies low taxonomic redundancy, and supports the use of all taxa in characterising a macroinvertebrate community, in particular in areas where habitat diversity is high.     

On the information content of characters in comparative morphology and molecular systematics

A review of the fundamental difference between single molecular-sequence positions, or numerical characters, and complex morphological characters is the subject of this study. It has been found that transformation series of single complex structures contain enough information to allow a priori determination of character order and that rooting of a dendrogram is possible without out-group comparison, while trees based on less-informative characters can usually only be rooted with out-group comparison. Furthermore, the quality of total information used is decisive in discriminating between hypotheses of relationships. Numerical methods for the inference of phylogenies have been found to be useful for high numbers of characters that have only a low information content, while the Hennigian procedure seems to be preferable for complex characters.

Zusammenfassung

Ein fundamentaler Unterschied zwischen der einzelnen Sequenzposition oder auch numerischen Merkmalen und komplexen morphologischen Merkmalen ist ihr Informationsgehalt. Merkmalsreihen komplexer Strukturen enthalten meist genügend Information, um a priori die Bestimmung der Lesrichtung zu ermöglichen. Die Feststellung des Ursprunges eines Dendrogramms ist somit ohne kladistischen Außengruppenvergleich möglich, während Bäume (Topologien), die auf wenig informativen Merkmalen beruhen, allgemein nur mit dem kladistischen Außengruppenvergleich 'gewurzelt' werden können. Die Qualität der insgesamt verwendeten Information ist entscheidend für die Wahl zwischen alternativen Verwandtschaftshypothesen. Numerische Methoden der Rekonstruktion der Phylogenese sind nützlich bei Verwendung einer gro β en Zahl informationsarmer Merkmale; das Hennigsche Verfahren ist für komplexe Merkmale vorzuziehen.     

On the information content of characters in comparative morphology and molecular systematics

A review of the fundamental difference between single molecular-sequence positions, or numerical characters, and complex morphological characters is the subject of this study. It has been found that transformation series of single complex structures contain enough information to allow a priori determination of character order and that rooting of a dendrogram is possible without out-group comparison, while trees based on less-informative characters can usually only be rooted with out-group comparison. Furthermore, the quality of total information used is decisive in discriminating between hypotheses of relationships. Numerical methods for the inference of phylogenies have been found to be useful for high numbers of characters that have only a low information content, while the Hennigian procedure seems to be preferable for complex characters.     

The threefold parallelism of Agassiz and Haeckel,and polarity determination in phylogenetic systematics

A parallel exists between the threefold parallelism of Agassiz and Haeckel and the three valid methods of polarity determination in phylogenetic systematics. The structural gradation among taxa within a linear hierarchy, ontogenetic recapitulation, and geological succession of the threefold parallelism resemble outgroup comparison, the ontogenetic method, and the paleontological method, respectively, which are methods of polarity determination in phylogenetic systematics. The parallel involves expected congruence among similar components of the distribution of character states among organisms. The threefold parallelism is a manifestation of a world view based on linear hierarchies, whereas polarity determination is part of the methodology of phylogenetic systematics which assumes that organisms are grouped into a nested hierarchy. The threefold parallelism facilitated the ranking of previously established taxa into linear hierarchies consisting mostly of paraphyletic groups. In contrast, methods of polarity determination identify apomorphies that determine and diagnose monophyletic taxa (clades) in the nested genealogical hierarchy. Taxa in linear hierarchies are defined by sets of character states, whereas clades are defined by common ancestry. Although the threefold parallelism was ostensibly abandoned with the rejection of Haeckel's biogenetic law, some of its components continue to facilitate the progressive scenarios that are common in evolutionary thought. Although a general view of progression in organismal history may be invalid, the progressive or directional sequence of character state changes that results in the characterization of a particular clade has considerable heuristic value. Agassiz's ostensibly nested hierarchy and other pre-Darwinian classifications do not provide support for the view that the natural system can be discovered without recourse to the principle of common descent.     

The paradox of enrichment in an adaptive world

Paradoxically, enrichment can destabilize a predator-prey food web. While adaptive dynamics can greatly influence the stability of interaction systems, few theoretical studies have examined the effect of the adaptive dynamics of interaction-related traits on the possibility of resolution of the paradox of enrichment. We consider the evolution of attack and defence traits of a predator and two prey species in a one predator-two prey system in which the predator practises optimal diet use. The results showed that optimal foraging alone cannot eliminate a pattern of destabilization with enrichment, but trait evolution of the predator or prey can change the pattern to one of stabilization, implying a possible resolution of the paradox of enrichment. Furthermore, trait evolution in all species can broaden the parameter range of stabilization. Importantly, rapid evolution can stabilize this system, but weaken its stability in the face of enrichment.     

鼓翅蝇科(双翅目:沼蝇总科)的分类研究进展

对双翅目鼓翅蝇科分类沿革,分类地位,分类系统,系统发育的研究进展作了详细的介绍,同时提出了在该科昆虫研究中存在的一些主要问题。     

The screening of selected microorganisms for use as models of mammalian drug metabolism

Summary Fifty fungi and two Streptomyces species were screened for their ability to metabolise the probe substrates aminopyrine, diazepam, testosterone, theophylline and warfarin. The metabolism of the ¹⁴C-labelled substrates by whole growing cells was compared with that by rat liver microsomes using TLC-autoradiography. Testosterone, warfarin and diazepam were readily metabolised by most microorganisms, and aminopyrine and theophylline were only metabolised by a few. A relationship between substrate lipophilicity and number of microorganisms able to biotransform the substrate was observed, lipophilic substrates being favoured for metabolism, analogous to mammalian cytochrome P-450. A wide variety of metabolites were produced by the screened cultures, with a significant number co-chromatographing with mammalian metabolites. Most microorganisms appeared to exhibit cytochrome P-450-type oxidative reactions such as hydroxylation and N-demethylation, similar to mammalian hepatic microsomal cytochrome P-450 systems.Offprint requests to: D. A. Griffiths     

The role of parsimony,outgroup analysis,and theory of evolution in phylogenetic systematics

It is argued that both the principle of parsimony and the theory of evolution, especially that of natural selection, are essential analytical tools in phylogenetic systematics, whereas the widely used outgroup analysis is completely useless and may even be misleading. In any systematic analysis, two types of patterns of characters and character states must be discriminated which are referred to as completely and incompletely resolved. In the former, all known species are presented in which the characters and their states studied occur, whereas in the latter this is not the case. Dependent on its structure, a pattern of characters and their states may be explained by either a unique or by various conflicting, equally most parsimonious hypotheses of relationships. The so-called permutation method is introduced which facilitates finding the conflicting, equally most parsimonious hypotheses of relationships. The utility of the principle of parsimony is limited by the uncertainty as to whether its application in systematics must refer to the minimum number of steps needed to explain a pattern of characterts and their states most parsimoniously or to the minimum number of evolutionary events assumed to have caused these steps. Although these numbers may differ, the former is usually preferred for simplicity. The types of outgroup analysis are shown to exist which are termed parsimony analysis based on test samples and cladistic type of outgroup analysis. Essentially, the former is used for analysing incompletely resolved patterns of characters and their states, the latter for analysing completely resolved ones. Both types are shown to be completely useless for rejecting even one of various conflicting, equally most parsimonious hypotheses of relationships. According to contemporary knowledge, this task can be accomplished only by employing the theory of evolution (including the theory of natural selection). But even then, many phylogenetic-systematic problems will remain unsolved. In such cases, arbitrary algorithms like those offered by phenetics can at best offer pseudosolutions to open problems. Despite its limitations, phylogenetic systematics is superior to any kind of aphylogenetic systematics (transformed cladistics included) in approaching a (not: the) “general reference system” of organisms.     

The use of amino acid sequence analysis in assessing evolution

The thirteen year history of assessing evolution by amino acid sequence analysis has made apparent the limitations imposed upon this system by the finite nature of the characters. This finiteness exists on several levels and ultimately expresses itself as parallelism, back mutation and the retention of primitive characters in the sequences of proteins from present day species and the putative ancestral protein chains. Sequence analysis shares these problems with other molecular approaches, but because it is concerned both with the nucleotide substitutions in the genome and with the functional roles of proteins, it has unique advantages. For example, the large fluctuation in the rate of fixation of mutations in a protein's evolution can be detected and used to point out the unreliability of any molecular clock for estimating divergence dates. Moreover, when consideration is given to studies which assign functional significance to specific amino acid sites in a protein, changes in function during the descent of a protein can be appreciated and their significance correlated with organismal evolution.     

A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain

Although spliceosomal introns are present in all characterized eukaryotes, intron numbers vary dramatically, from only a handful in the entire genomes of some species to nearly 10 introns per gene on average in vertebrates. For all previously studied intron-rich species, significant fractions of intron positions are shared with other widely diverged eukaryotes, indicating that 1) large numbers of the introns date to much earlier stages of eukaryotic evolution and 2) these lineages have not passed through a very intron-poor stage since early eukaryotic evolution. By the same token, among species that have lost nearly all of their ancestral introns, no species is known to harbor large numbers of more recently gained introns. These observations are consistent with the notion that intron-dense genomes have arisen only once over the course of eukaryotic evolution. Here, we report an exception to this pattern, in the intron-rich diatom Thalassiosira pseudonana. Only 8.1% of studied T. pseudonana intron positions are conserved with any of a variety of divergent eukaryotic species. This implies that T. pseudonana has both 1) lost nearly all of the numerous introns present in the diatom-apicomplexan ancestor and 2) gained a large number of new introns since that time. In addition, that so few apparently inserted T. pseudonana introns match the positions of introns in other species implies that insertion of multiple introns into homologous genic sites in eukaryotic evolution is less common than previously estimated. These results suggest the possibility that intron-rich genomes may have arisen multiple times in evolution. These results also provide evidence that multiple intron insertion into the same site is rare, further supporting the notion that early eukaryotic ancestors were very intron rich.     

The Skull of Stephanomys and a Review of Malpaisomys Relationships (Rodentia: Muridae): Taxonomic Incongruence in Murids

The cranial morphology of the extinct murid genus Stephanomys, previously known only by dental remains, is described here on the basis of partial skulls of three species of Pliocene age. Important cranial characters of the genus are a robust rostrum, a high zygoma, a wide zygomatic arch, a narrow interorbit, a large orbit, and an optic foramen in the backward position. In addition to some dental characters, Stephanomys shares most of these cranial traits with the extinct Malpaisomys from the Canary Islands. Some of these traits may be linked to the development of large eyes and life in a rocky environment. The peculiar dental pattern of Stephanomys (stephanodonty) is also present in some recent murids (Oenomys and Thamnomys) having a different skull morphology. A comparison with nine other extant genera of murids verified the relationship among Malpaisomys, Stephanomys, and Acomys, supporting our previous conclusion. Phenetic and cladistic analyses of 17 cranial and 23 dental characters show that skull morphology is phylogenetically informative but highly convergent and incongruent with other partial evidence based on dental and biochemical characters. The combined analyses of skull and teeth illustrate a case of mosaic evolution in murids.     

Evolution of cultural traits occurs at similar relative rates in different world regions

A fundamental issue in understanding human diversity is whether or not there are regular patterns and processes involved in cultural change. Theoretical and mathematical models of cultural evolution have been developed and are increasingly being used and assessed in empirical analyses. Here, we test the hypothesis that the rates of change of features of human socio-cultural organization are governed by general rules. One prediction of this hypothesis is that different cultural traits will tend to evolve at similar relative rates in different world regions, despite the unique historical backgrounds of groups inhabiting these regions. We used phylogenetic comparative methods and systematic cross-cultural data to assess how different socio-cultural traits changed in (i) island southeast Asia and the Pacific, and (ii) sub-Saharan Africa. The relative rates of change in these two regions are significantly correlated. Furthermore, cultural traits that are more directly related to external environmental conditions evolve more slowly than traits related to social structures. This is consistent with the idea that a form of purifying selection is acting with greater strength on these more environmentally linked traits. These results suggest that despite contingent historical events and the role of humans as active agents in the historical process, culture does indeed evolve in ways that can be predicted from general principles     

The use of ruminant models in biomedical perinatal research

Animal models are of critical importance in biomedical research. Although rodents and lagomorphs are the most commonly used species, larger species are required, especially when surgical approaches or new medical devices have to be evaluated. In particular, in the field of perinatal medicine, they are critical for the evaluation of new pharmacologic treatments and the development of new invasive procedures in fetuses. In some areas, such as developmental genetics, reproductive biotechnologies and metabolic programming, the contribution of ruminants is essential. The current report focuses on some of the most outstanding examples of great biomedical advances carried out with ruminant models in the field of perinatal research. Experiments recently carried in our research unit using ruminants are also briefly described.     

The morphology and systematics of Mammalodon colliveri (Cetacea: Mysticeti), a toothed mysticete from the Oligocene of Australia

Mammalodon colliveri is an unusual toothed archaic mysticete (Cetacea) from the Upper Oligocene Jan Juc Formation of south‐east Australia. The morphology of the holotype skull and postcrania are described in detail. Superimposed on the generally plesiomorphic archaeocete‐like morphology of Mammalodon are subtle mysticete synapomorphies. Derived features of Mammalodon include a short and bluntly rounded rostrum, reduced premaxillae, and anterodorsally directed orbits. Within Mysticeti, this suite of features is unique. The aberrant rostral morphology of Mammalodon suggests specialization for suction feeding. Janjucetus hunderi is placed in an expanded family Mammalodontidae. Phylogenetic analysis corroborates the monophyly of Basilosauridae, Neoceti, Odontoceti, and Mysticeti, and yields a novel hypothesis of toothed mysticete relationships: a basal clade of undescribed toothed mysticetes from South Carolina, a Llanocetidae + Mammalodontidae clade, and monophyletic Aetiocetidae are posited as successive sister taxa to edentulous baleen whales (Chaeomysticeti). Toothed archaic mysticetes clearly employed diverse prey capture strategies, with exaptations for filter feeding evolving sequentially in stem group Mysticeti. A stratigraphically calibrated phylogeny implies that the initial diversification of Mysticeti occurred during the Late Eocene. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 367–476.