‘Total evidence’ in phylogenetic systematics

Taking its clues from Popperian philosophy of science, cladistics adopted a number of assumptions of the empiricist tradition. These include the identification of a dichotomy between observation reports and theoretical statements and its subsequent abandonment on the basis of the insight that all observation reports are theory-laden. The neglect of the ‘context of discovery’, which is the step of theory (hypothesis) generation. The emphasis on coherentism in the ‘context of justification’, which is the step of evaluation of the relative merits of alternative theories. The appeal to a total evidence approach in phylogenetic inference. And finally, a silence about causation, which results in an instrumentalist approach to phylogeny reconstruction. This paper explores how these empiricist assumptions are embedded in phylogenetic systematics, and why these assumptions are problematic for cladists (or any taxonomists).     

The language of systematics,and the philosophy of ‘total evidence’

This contribution analyses the primacy of classification over generalization, and the philosophy of total evidence that emerges from the relation of homology to character statements. Primary conjectures of homology are basic character statements, i.e. statements that predicate properties of organisms, properties that are instantiated by those organisms and/or their parts. Secondary conjectures of homology are embedded in a second‐level (metalinguistic) discourse that turns on the coherence or incoherence of those basic character statements relative to a hierarchy. The coherence or incoherence of character statements is a logical relation between statements, not a causal (historical) relation between organisms. The choice of the hypothesis of relationships that is supported by the largest set of coherent basic character statements is based on the empirical presupposition that the properties referred to by the set of coherent character statements are grounded in causally efficacious relations of inheritance and ontogeny, and co‐instantiated because they are inherited through common ancestry (Hennig's auxiliary principle). Unless that empirical presupposition is causally grounded, phylogeny reconstruction is of an inherently probabilistic nature, whether under parsimony or other models of analysis. The causal grounding of a coherent set of character statements typically seeks a link between character statements and causally efficacious generative mechanisms for morphological characters (as is defeasibly indicated by topology and connectivity), or secondary structure information for molecular characters.     

The ‘requirement of total evidence’ and its role in phylogenetic systematics

The question of whether or not to partition data for the purposes of inferring phylogenetic hypotheses remains controversial. Opinions have been especially divided since Kluge's (1989, Systematic Zoology 38, 7–25) claim that data partitioning violates the requirement of total evidence (RTE). Unfortunately, advocacy for or against the RTE has not been based on accurate portrayals of the requirement. The RTE is a basic maxim for non-deductive inference, stipulating that evidence must be considered if it has relevance to an inference. Evidence is relevant if it has a positive or negative effect on a given conclusion. In the case of ℈partitioned’ phylogenetic inferences, the RTE is violated, and the basis for rational belief in any conclusion is compromised, unless it is shown that the partitions are evidentially irrelevant to one another. The goal of phylogenetic systematics is to hypothesize past causal conditions to account for observed shared similarities among two or more species. Such inferences are non-deductive, necessitating consideration of the RTE. Some phylogeneticists claim the parsimony criterion as justification for the RTE. There is no relation between the two – parsimony is a relation between a hypothesis and causal question(s). Parsimony does not dictate the content of premises prior to an inference. ℈Taxonomic congruence,’ ℈supertrees,’ and ℈conditional combination’ methods violate the RTE. Taxonomic congruence and supertree methods also fail to achieve the intended goal of phylogenetic inference, such that ℈consensus trees’ and ℈supertrees’ lack an empirical basis. ℈Conditional combination’ is problematic because hypotheses derived from partitioned data cannot be compared – a causal hypothesis inferred to account for a set of effects only has relevance to those effects, not any comparative relevance to other causal hypotheses. A similar problem arises in the comparisons of hypotheses derived from different causal theories.     

‘Ins’ and ‘outs’ of triple therapy

Chronic oral anticoagulant treatment is obligatory in patients (class I) with mechanical heart valves and in patients with atrial fibrillation with CHADS2 score >1. When these patients undergo percutaneous coronary intervention with placement of a stent, there is also an indication for treatment with aspirin and clopidogrel. Unfortunately, triple therapy is known to increase the bleeding risk. For this group of patients, the bottom line is to find the ideal therapy in patients with indications for both chronic anticoagulation therapy and percutaneous intervention to prevent thromboembolic complications such as stent thrombosis without increasing the risk of bleeding. (Neth Heart J 2010;18:444-50.)     

Cytophotometric evidence for cell ‘transdifferentiation’ in planarian regeneration

Summary The role and fate of male germ cells in planarian regeneration was studied in a population ofDugesia lugubris s.1. which provided a suitable karyological marker to distinguish diploid male germ cells from triploid embryonic and somatic cells. The nuclear Feulgen-DNA content in non-replicating triploid muscle cells of the pharynx and in non-replicating male gonia of testes from intact animals were measured by the cytophotometric technique. The pharynx was then removed by transection and each anterior regenerant was allowed to completely regenerate this organ. Measurements of the Feulgen-DNA content in muscle cells of the regenerated pharynx showed that most of these cells (95%) have a DNA content typical of triploid cells; however, some muscle cells (5%) with a nuclear DNA content typical of male gonia alone were observed.These results were interpreted in the following way. After transection, young male germ cells move from the testes to the wound where they participate in blastema formation along with reserve and/or somatic dedifferentiated cells. During regeneration some of these cells of male origin differentiate into pharyngeal muscle cells. Our findings are discussed in relation to the occurrence of mataplasia in planarians.     

‘For her protection and benefit’: the regulation of marriage-related migration to the UK

This paper argues that a two-tier system has evolved dividing intra-UK/EU marriages from extra-UK/EU marriages. For the former, marriage is a contract between two individuals overseen by a facilitating state. For the latter, marriage has become more of a legal status defined and controlled by an intrusive and obstructive state. I argue that this divergence in legislating regulation is steeped in an ethnicized imagining of ‘Britishness’ whereby the more noticeably ‘other’ migrants (by skin colour or religion) are perceived as a threat to the national character. The conceptualization of women as legally ‘disabled’ citizens (1870 Naturalisation Act) for whom a state must act as responsible patriarch, is a fundamental part of this imagining of the nation. The paper therefore examines the social (gendered and ethnicized) assumptions and political aims embedded within the legislation.     

Structural and Narrative Reconstruction of Rural Residents’ Representations of ‘Nature’, ‘Wildlife’, and ‘Landscape’

The objective of this paper is the structural and narrative reconstruction of representations of ‘nature’, ‘wildlife’ and ‘landscape’, held by rural residents of the Dadia Forest Reserve. Data collection involved in-depth interviews. Employing a social representations’ approach, we recovered representational elements that are expected in the case of rural belief systems, such as negative dispositions towards wolves and foxes, as well as elements of an urban adherence, such as nature’s independence. Representational elements refer to visual aspects of the countryside, which seem compatible with the figurative nucleus of the rural idyll. Concerning ‘wildlife’, residents focused on vultures, which comprise the main tourist attraction of the reserve. Scientific knowledge adds to the complexity of the narrative schema, which corresponds to the representation of ‘wildlife’. Interviewees perceived the rural landscape as an interface between the natural and the human-conditioned environment. Our study shows that interviewees make no reference to environmental conservation or quality of life issues, as it could be expected according to relatively wide definitions of the term ‘environmentalism’. Environmental messages reinforced by ecotourism development seem to be recalled primarily in terms of their compatibility with the perceived economic benefit of local people. Despite ecotourism development, representational elements that diverge from a tourist version of ‘nature’, ‘wildlife’ and ‘landscape’ were not pronounced within rural belief-systems. Further interventions within the study area are needed, in order to address a variety of topics under the environmental conservation discourse and raise the environmental awareness of rural residents.     

Special Issue on‘‘Metagenomics of Marine Environments’’

<正>We are pleased to announce a special issue on‘‘Metagenomics of Marine Environments’’of the journal Genomics,ProteomicsBioinformatics(GPB),aiming to provide a platform for high-quality papers focusing on the topic and we invite submissions for this special issue(to be published in the fall of 2015).With most microbes being difficult or impossible to culture     

Scanning and transmission electron microscopy evidence of the cytological effect of pyrrolnitrin on ‘Microsporon audouinii’ Gruby CBS 313-54 ‘in vitro’

Scanning and transmission electron microscopy showed that a ceiling quantity (1.56 mcg) of antifungal antibiotic Pyrrolnitrin caused heavy damage to dermathophyteMicrosporon audouinii Gruby CBS 313-54in vitro. Suitable preparation technique made it clear that the changes involved consisted of hyphal collapse on the edge of the culture, with loss of euplasmic organelles identity and cell autolysis. The cell wall, however, was apparently undamaged. These findings fit in with the suggestion that the mode of action of the antibiotic leads to generalised lipoproteic membranes damage. They must, however, be considered as representing the result of the terminal phase of cell distress.     

Simulation of ‘hitch-hiking’ genealogies

An ancestral influence graph is derived, an analogue of the coalescent and a composite of Griffiths' (1991) two-locus ancestral graph and Krone and Neuhauser's (1997) ancestral selection graph. This generalizes their use of branching-coalescing random graphs so as to incorporate both selection and recombination into gene genealogies. Qualitative understanding of a ‘hitch-hiking’ effect on genealogies is pursued via diagrammatic representation of the genealogical process in a two-locus, two-allele haploid model. Extending the simulation technique of Griffiths and Tavaré (1996), computational estimation of expected times to the most recent common ancestor of samples of n genes under recombination and selection in two-locus, two-allele haploid and diploid models are presented. Such times are conditional on sample configuration. Monte Carlo simulations show that ‘hitch-hiking’ is a subtle effect that alters the conditional expected depth of the genealogy at the linked neutral locus depending on a mutation-selection-recombination balance. Received: 21 July 2000 / Published online: 5 December 2000     

No evidence for an ‘evolution of increased competitive ability’ for the invasive Lepidium draba

The ‘evolution of increased competitive ability’ (EICA) hypothesis states that reduced herbivory in the introduced range causes an evolutionary shift in resource allocation from herbivore defense to growth. Therefore, according to EICA, introduced genotypes are expected to grow more vigorously than conspecific native genotypes when cultivated under common standardized conditions. The EICA hypothesis also assumes that herbivores will perform better on introduced genotypes compared to native genotypes, because they are less well defended. However, selection for either defense or growth will depend on the type of defense (quantitative or qualitative) employed by the plant, and whether the plant is released from generalist or specialist herbivores. The predictions of the EICA hypothesis might be reversed if a plant experiences increased generalist herbivore pressure in the introduced range, and therefore invests more in qualitative defense. We examined this idea with the invasive perennial mustard, Lepidium draba. We grew a total of 16 populations of L. draba from both its native European and introduced western US ranges under common conditions in a greenhouse. We also tested for differences in plant resistance to the specialist herbivore, Psylliodes wrasei, by conducting a leaf disc feeding bioassay with native and introduced L. draba genotypes. Furthermore, we quantified the generalist herbivore load on L. draba in both ranges in order to assess the selection pressure for increased qualitative defense. Contrary to the original EICA prediction, all plant traits (biomass, number of shoots, length and diameter of longest leaf) tended to be greater for the native, rather than introduced L. draba genotypes. There was no significant difference in the proportion of leaf area consumed by the specialist herbivore between native and introduced genotypes. The generalist herbivore load on L. draba was significantly greater in the introduced range. Our data suggest that the EICA hypothesis does not explain the invasion success of L. draba in the US. Instead, we propose that the reduced vigor of introduced genotypes may be due to selection for increased defense against generalist herbivores in the introduced range.     

‘The realm of hard evidence’: novelty,persuasion and collaboration in botanical cladistics

In 1998 a new classification of flowering plants generated headlines in the non-specialist press in Britain. By interviewing those involved with, or critical of, the new classification, this essay examines the participants' motives and strategies for creating and maintaining a research group. It argues that the classification was produced by an informal alliance whose members collaborated despite their disagreements. This collaboration was possible because standardised methods and common theoretical assumptions served as ‘boundary objects’. The group also created a novel form of collective publication that helped to unite them. Both the collaboration and the publishing strategy were partly motivated by the need to give taxonomy a degree of ‘big science’ credibility that it had previously lacked: creating an international team allowed more comprehensive results; and collective publication served to emphasise both the novelty of the work and its claims to objectivity. Creating a group identity also served to exclude practitioners of alternative forms of taxonomy. Finally, the need to obtain funding for continuing work both created the need to collaborate and influenced the way the classification was presented to the public.     

No evidence of a generalized potential ‘cost’ of apical dominance for species that have strong apical dominance

尚无证据表明顶端优势强的物种存在广义顶端优势潜在“成本”     

Making sense of ‘mixture’: states and the classification of ‘mixed’ people

Caribbean diaspora intellectuals have contributed significantly to African-American political struggles over the years, despite arguments by some African-American intellectuals about what they discern as West Indian negativism, extremism, and divisiveness in American political life. This essay examines the legacy of a representative sample of diasporic Caribbean intellectuals since the time of the Harlem Renaissance in the 1920s and culminating in the 1970s, notably, Garvey, members of the African Blood Brotherhood [ABB], C.L.R. James, and Walter Rodney, to demonstrate the phenomenal ideological vision, organizational capability, and political activism they have brought into fostering solidarity with African Americans in the struggle for fundamental change. The focus here is on their respective contributions to the debate on the relationship between class and race in America and the black diaspora generally, which has helped to shape the form, and orient the direction of African-American and Caribbean diasporic struggles for the better part of the twentieth century.     

Lichen moths do not benefit from ‘element imitation’ masquerade in the absence of a matching background

Evolutionary Ecology - Predation places significant selection pressures on prey species and many have evolved incredible and diverse colour patterns in response. A fascinating example of such...     

Polarization microscopic evidence for an oriented cytoplasmic structure in the ‘dark’ variants of adrenalin-storing cells

Summary A diffuse cytoplasmic birefringence confined to dark adrenalinstoring cells has been described. The main optical characteristics of the birefringence factor include: regular orientation of birefringence relative to the base-apex axis of cells; additive anisotropic staining with methods based on the principle of topo-optical staining reactions; dependence of birefringence on labile morphologic properties. On the basis of the capacity of the macromolecular matrix of chromaffin granules to form lamellar liposomal structures in vitro it has been proposed that a reorientation of molecular organization in the matrix of chromaffin cells is responsible for the observed optical phenomenon. The direction of birefringence was explained by a preferential direction of contractile forces acting during dark cell formation.     

The ‘curse’ of Westermarck 1

This article consists of a critical application of recent theory of nationalism to the unusual case of Mauritius. It is a poly‐ethnic and poly‐religious society whose inhabitants neither share a mythical distant past nor consider themselves culturally identical, but where nation‐building has nevertheless been moderately successful since the late 1960s. Through an examination of the processes of institutional and cultural nation‐building in the island, it is argued that the current Eurocentric view of the nation (notably as a culturally homogeneous imagined community) must be modified to fit cases like this one. Thus, the value of nationalism and nationhood as comparative concepts is questioned.     

No evidence for ‘skewed’ inactivation of the X-chromosome as cause of Leber's hereditary optic neuropathy in female carriers

Leber’s hereditary optic neuropathy (LHON) is a maternally inherited disorder of the optic nerves. It has been proposed that the specific mutations in the mitochondrial DNA (mtDNA) that are associated with LHON require and X-chromosomally encoded permissive factor in order to become expressed. This would explain both the preponderance of male patients and the fact that most carriers of specific mtDNA mutations remain unaffected. Although linkage studies have been negative so far, the existence of such a factor has not been ruled out. We investigated the genealogical data of 24 large LHON pedigrees and concluded that the presumed X-linked factor would be recessively inherited and that at least 57% of the affected females would be heterozygous. Therefore, these females must be the victim of nonrandom X-chromosomal inactivation (skewed lyonization). However, analysis of X-chromosomal methylation patterns in 16 LHON-affected females revealed substantial skewing in only 15%–20% of cases, which is not significantly different from the patterns in 49 controls. Moreover, we found the frequency of LHON in daughters of affected heterozygous females to be twice to three times as high as in daughters of unaffected heterozygous females, which cannot be explained by an X-chromosomally inherited factor. We conclude that the results of our investigations do not support the hypothesis that LHON is a digenic disease with an X-linked factor being the main cause of loss of vision in the presence of relevant mtDNA mutations. Received: 1 June 1995 / Revised: 20 September 1995