Traditionally, broadcast spawning and planktonic larvae have been considered the plesiomorphic ‘ground plan’ for the Polychaeta and other metazoan groups. To assess whether this reproductive mode is in fact ‘primitive’, the study of monophyletic groups with various reproductive modes should be informative. A large range of body sizes would allow testing the ideas that aspects of reproductive mode may be functionally constrained. The family Sabellidac is one such group, with sexual reproductive modes ranging from broadcast spawning to intratubular brooding to ovovivi‐parity, and a body size range over more than five orders of magnitude. Sabellids have previously been the subject of detailed cladistic analyses (Fitzhugh 1989, 1991); here we introduce several new characters based on morphology of reproductive structures. Larval development in four brooding sabellid species is also described with the aim of introducing new characters for future systematic analyses. Our cladistic analysis of sabellid genera suggests that gonochorism and brooding of direct‐developing larvae are plesiomorphic in the Sabellidae, with external fertilization and swimming larvae limited to apomorphie clades in the subfamily Sabellinae. The presence of sperm with elongate heads may be correlated with the presence of intratubular brooding, though an adequate causal explanation for this relationship can not yet be presented. The concept that ‘modified’ sperm must be derived from ‘primitive’ sperm is shown to be false, with ‘modified’ sperm being plesiomorphic for the Sabellidae, from which ‘primitive’ sperm is derived in apomorphic Sabellinae. All sabellids have lecithotrophic development and appear to be phylogenetically constrained in this regard. Data gathered on body size and reproductive variables in the Sabellidac suggests the following (when phylogenetic effects are not controlled): (1) egg number and total egg volume are significantly correlated with body size, with small animals having fewer, larger eggs than large animals; (2) individual egg volume is not correlated with body size; (3) reproductive mode is significantly correlated with body size; intratubular brooders tend to be small‐bodied, whereas broadcast spawners are large. However when the effect of body size is controlled for, then (4) egg number, egg volume and total egg volume all vary significantly with reproductive mode. Broadcast spawners expel a large number of small eggs for a high total egg volurne. Intratubular brooders have a few relatively large eggs for a small total egg volume. When statistics arc performed using phylogenetically independent contrasts there is a significant correlation between total egg volume and body size but not for egg number and body size. The effect of non‐independence (due to phylogeny) of our data needs to be more fully controlled in future analyses but methods of incorporating continuous data into cladistic analyses should also be investigated. We show that some predictions can be made about reproductive mode based on body size but ad ho...

A comprehensive phylogenetic analysis of the Terebellidae and related families was undertaken. Type material of all genera of Terebellinae was examined, together with representatives of nearly all genera of remaining Terebellidae subfamilies, and representatives of the families that have been traditionally regarded as being closely related, comprising the Terebelliformia. In total, 85 species were coded using 118 subjects (‘characters’) and 286 subject–predicate relations (‘states’). The results indicate: (1) the paraphyly of Terebellidae by the placements of Trichobranchidae, Ampharetidae, Alvinellidae and Pectinariidae within that clade; (2) the occurrences of Thelepodinae as separate clades, consistent with groups ‘A’ and ‘B’ recognised by Nogueira et al. (2010a); and (3) the monophyly of Polycirrinae and Terebellinae. The previously considered subfamilies of Terebellidae are raised to familial level and a new family is described. Revised definitions are provided for: Terebelliformia, Polycirridae, stat. nov., Telothelepodidae, fam. nov., Terebellidae emend., and Thelepodidae, stat. nov., along with a discussion of character evolution in the Terebellidae.

The formal structure of the inference of a phylogenetic hypothesis is analyzed in the context of the different classes of reasoning applied in all fields of science. Rather than making the traditional distinction between deductive and inductive reasoning, it is shown that phylogenetic hypotheses are derived from a form of non-deductive inference commonly known as abduction. In making distinctions between abductive, deductive, and inductive inferences, the relationships between the origins of hypotheses and their testing become apparent. Abduction serves to provide explanatory hypotheses as tentative answers to specifiable causal questions. It is by way of deduction that specific potential test consequences are determined, whereas induction sensu stricto characterizes the act of carrying out a particular test. The formal structure of phylogenetic inference as a form of abduction is presented. Significant implications arise in recognizing that phylogenetic hypotheses are the products of abductive inference. The most apparent of these are that the distinctions between parsimony and likelihood as methodological criteria are unfounded. Parsimony refers to the relation between a causal question(s) and the hypothesis that serves as an answer for that question(s), whereas likelihood refers to the relation between the evidence as premises and the hypothesis allowed by those premises. The consequence is that parsimony has logical priority over likelihood in abduction, such that the likelihood of any hypothesis is maximized in the event that a causal theory of descent with modification is applied as fully as possible to observed shared similarities. In contrast, the application of rate-dependent theories, under the guise of maximum likelihood, are at odds with observations of shared similarities among two or more species and the causal questions regarding such observations; any rate-dependent theory only pertains to effects that are only tokogenetic in scope, not phylogenetic (sensu Hennig 1966). In recognizing phylogenetic hypotheses as answers to causal questions, the popular conception of testing such hypotheses by the introduction of new characters is incorrect. New character distributions cannot be deduced from a cladogram since such a structure only has causal relevance to the characters for which the hypothesis was inferred. The proper testing of a phylogenetic hypothesis requires the deduction of specific consequences as closely related as possible to the specified causal events of character origins and fixation, and subsequent speciation events. Such consequences must be effects that are independent of the class of effects the hypothesis was intended to explain, i.e., character data. As a result, effects that stand as legitimate potential test evidence are those effects that best support the different sets of causal events presented in the hypothesis. Problems with the popular applications of support indices, as offered by the bootstrap, jackknife, and permutation tests, are discussed. The main problem with these techniques is that they are only useful for testing statistical hypotheses, not explanatory hypotheses. Similarly, Bremer support analysis cannot provide indications of clade support because it is empirically meaningless to compare cladograms of different length, as each hypothesis only has relevance to the respective observations it explains.

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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.

Cladistic relationships of the sabellid subfamilies Fabriciinae and Sabellinae are examined in light of recent revisions of fabriciin taxa. The potential placement of Caobangia in the Sabellinae is suggested from an initial analysis of selected fabriciin species and genera. Subsequent cladistic analyses at the family level produced over 1800 cladograms, among which Caobangia is the most plesiomorphic taxon of either the Fabriciinae or Sabellinae. Successive approximations weighting reduced this ambiguity, consistently placing Caobangia in the Sabellinae. Subfamilies are emended on the basis of these results. Cladistic relationships of fabriciin taxa, exclusive of Caobangia, display topological instability among some genera and species. Genera are, however, monophyletic in all topologies. Incorporating ontogenetic data for branching ventral filamentous appendages in Augeneriella reduces ambiguity among genera and suggests alternative transformation series for ventral filamentous appendages.

261 Fitzhugh, K. (2006). The philosophical basis of character coding for the inference of phylogenetic hypotheses. -Zoologica Scripta , 35 , 261-286. The coding of observations of organisms into a data matrix for the inference of phylogenetic hypotheses has suffered from a variety of problems that have precluded development of a uniform approach to the issue. Probably the most notable consequence is that the philosophical basis for coding has been prominently ignored in lieu of emphasis placed on specific coding strategies. From an epistemic standpoint, part of the problem lies with the distinction of 'characters' and 'character states', which does not accurately convey perceptual beliefs or observation statements. The ability to perceive objects is by the nature of the properties of those objects. One's sense perceptions are of characters, not states; or more appropriately, one observes objects by way of the properties perceived of those objects. The proper distinction is therefore not one of character/state, but one of object/character, as communicated by subject-predicate relations. With observation statements referring to shared similarities among organisms distributed among two or more species, and phylogenetic hypotheses in the form of cladograms serving as at least tentative explanations for those effects, then what dictates the coding of observations is not adherence to a particular coding strategy, but the need to accurately convey the causal questions that address those observations. A phylogenetic data matrix is therefore not composed of columns as 'characters' and cells as 'states'. Rather, column headings indicate the observed subjects that instantiate various characters; columns represent specifiable causal questions based on observations, and cells present the subject-predicate relations of observation statements. Since data matrices must represent one's causal questions, the inclusion of outgroup taxa is justified as components of those questions. With these criteria, the coding strategies summarized by Pleijel (1995) are critiqued. It is shown that advocacy of any one of those approaches is not possible, and that strategies that incorrectly apply the notion of 'absence' are especially prone to misrepresent observations.

ProblemThe subject of how biologists should define the term 'species' remains unsettled.