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.     

Convergence and parallelism: is a new life ahead of old concepts?

In comparative biology, character observations initially separate similar and dissimilar characters. Only similar characters are considered for phylogeny reconstruction; their homology is attested in a two‐step process, firstly a priori of phylogeny reconstruction by accurate similarity statements, and secondly a posteriori of phylogeny analysis by congruence with other characters. Any pattern of non‐homology is then a homoplasy, commonly, but vaguely, associated with “convergence”. In this logical scheme, there is no way to analyze characters which look similar, but cannot meet usual criteria for homology statements, i.e., false similarity detected a priori of phylogenetic analysis, even though such characters may represent evolutionarily significant patterns of character transformations. Because phylogenies are not only patterns of taxa relationships but also references for evolutionary studies, we propose to redefine the traditional concepts of parallelism and convergence to associate patterns of non‐homology with explicit theoretical contexts: homoplasy is restricted to non‐similarity detected a posteriori of phylogeny analysis and related to parallelism; non‐similarity detected a priori of phylogenetic analysis and necessarily described by different characters would then correspond to a convergence event s. str. We propose to characterize these characters as heterologous (heterology). Heterology and homoplasy correspond to different non‐similarity patterns and processes; they are also associated with different patterns of taxa relationships: homoplasy can occur only in non‐sister group taxa; no such limit exists for heterology. The usefulness of these terms and concepts is illustrated with patterns of acoustic evolution in ensiferan insects. © The Willi Hennig Society 2005.     

On necessary and sufficient conditions for group selection efficacy

The statement “group selection predominates over individual selection” is formulated within a class of patch-structured models. Conditions involving both “selfish” and “altruistic” predator characteristics are then shown to be necessary and sufficient for group selection predominance in this class of models. Maynard Smith's criterion M < 1 (Group selection, Quart. Rev. Biol., June 1976, pp. 277–283) is shown to be sufficient but not necessary for group selection predominance.     

Homology of Hox Genes and the Zootype Concept in Early Metazoan Evolution

The correct identification of homologous Hox genes within and between diplo- and triploblastic animals is of crucial importance for recent hypotheses on the anagenetic evolution of animal bauplans. While the homology discussion in general has reached new heights, we apply traditional homology criteria to assign homology to Hox genes from diploblastic animals. Comparison of theTrox-2gene from the presumably most basal metazoan animal, the placozoanTrichoplax adhaerens,to other Hox genes suggests the presence of unambiguous homologs in Hydrozoa and Scyphozoa and the absence of any specific homolog in triploblasts. Furthermore, the comparisons provide support for the idea that Hox genes—at least in diploblastic animals—are composed of functional subunits (modules), which to some degree have undergone independent evolution. The findings are not readily compatible with the existence of the “zootype” in diploblastic animals.     

Praon Haliday (Hymenoptera: Braconidae: Aphidiinae) of Southeastern Europe: key, host range and phylogenetic relationships

A review of species in the genus Praon Haliday, 1833 is presented. Twenty described species are keyed and illustrated with scanning electron micrographs and line drawings. The Praon species presented in this work have been identified from 67 aphid taxa occurring on 120 plant taxa. Furthermore, 87 original parasitoid–aphid–plant associations of the species mentioned in the key are presented. Phylogenetic relationships among Praon species are reconstructed using parsimony and cladistic distance methods. Praon abjectum is the sister taxon to the remaining Praon species. We recognized three species group: “Parapraon”, “dorsale-yomenae” and “rosaecola”. Monophyly is suggested for “Parapraon” species group and paraphyly for “dorsale-yomenae” group. Finally, by phylogenetic reconstruction, a close phylogenetic relationship between “Parapraon” and “dorsale-yomenae” species group was found.     

The nature and affinities of the “robust” Australopithecines: a review

The fossil evidence of the “robust” australopithecines is reviewed with an emphasis on the taxonomic divisions and evolutionary relationships among this group of hominids. The hypodigms of A. robustus, A. crassidens and A. boisei are described, and the significance of morphological variation within and between these species is assessed. Phylogenetic relationships among the “robust” australopithecines are examined using maximum parsimony analysis, and evolutionary scenarios are evaluated in the light of recent discoveries in East Africa.     

Congruence,non‐homology,and the phylogeny of basal turtles

Joyce, W.G. and Sterli J. 2010. Congruence, non‐homology, and the phylogeny of basal turtles.–Acta Zoologica (Stockholm) Modern cladistic analysis is characterized by the assembly of increasingly larger data sets coupled with the use of congruence as the final test of homology. Some critics of this development have recently called for a return to more detailed primary homology analysis while questioning the utility of congruence. This discussion appears to be central to the debate regarding the phylogenetic relationships of basal turtles, as the large data sets developed by us have been criticized recently for utilizing poorly constructed characters and including too many homoplasy‐prone characters. Our analysis of this critique reveals that (1) new information regarding poorly understood taxa has a greater impact on the outcome of turtle phylogenies than the characters under dispute; (2) most current turtle phylogenies differ in taxon sampling, not character sampling, and so it appears illogical to condemn a particular analysis for its character sampling; (3) even evolutionary taxonomists should agree that key characters utilized to resolve basal turtle relationships cannot be thought to be ‘infallible’; (4) whereas various criteria provide positive evidence for homology, only congruence provides positive evidence for non‐homology; and (5) a stalemate between conflicting camps within a congruence frame work is preferable to the ad hoc dismissal of data sets, because authoritative statements are untestable.     

Kinetoplast DNA in the insect trypanosomes Crithidia luciliae and Crithidia fasciculata: III. Heteroduplex analysis of the C. luciliae minicircles

We have investigated the nature of the sequence heterogeneity of the minicircles of Crithidia luciliae kinetoplast DNA by EM heteroduplex analysis of minicircles cleaved with endonuclease HindIII. Approximately 40% of the minicircles showed—after denaturation and reannealing—structures indicative of sequence rearrangements: the majority contained heteroduplex “eyes” interpreted as due to inversions; about 10% of the heteroduplexes yielded structures interpreted as due to translocations and a similar fraction showed insertions and deletions. The category of “eyed” molecules was analyzed in detail: four minicircle segments were found that displayed a high incidence of such eyes indicating that the rearrangements were not scattered at random over the minicircles. Moreover, since also “eyes” were found overlapping two or three of the four regions, we postulate that these segments are capable of recombining with each other. We conclude that specific segmental rearrangements form the main basis of the minicircle sequence heterogeneity in Crithidia.     

Some connections between physiognomic traits and intelligence

A sample of 84 female subjects (students) was taken and split up on the basis of the IST-ratings (“Intelligence Structure Test” by Amthauer) into two extreme groups of “more intelligent” (N = 14) and “less intelligent” (N = 11) subjects with an aim to testing Kozeny's findings. Using his photographic-statistical method, Kozeny had observed that “more intelligent” people have a more open eye, a smaller and straighter mouth, a stronger chin, and—above all in its side dimensions—a better developed forehead. These physiognomic indicators of differences in intelligence were confirmed to a large extent by the measurements taken from the portraits of the subjects.     

Historical biogeography and speciation in the Neotropical highlands: Molecular phylogenetics of the jay genus Cyanolyca

Phylogenetic relationships were studied in the genus Cyanolyca, an assemblage of jays distributed from Mexico south to Bolivia. Given its fragmented distribution along the humid forests of the Neotropics, the genus Cyanolyca is a model group for exploring hypotheses on biogeography and speciation. Phylogenetic analyses were based on two mitochondrial and three nuclear loci; taxon sampling includes all species in the genus and most subspecies. Maximum parsimony, maximum likelihood, and Bayesian analyses produced trees that were congruent and highly robust at both terminal and deep nodes of the phylogeny. Cyanolyca comprises two major clades: one contains the Mesoamerican “dwarf” jays, and the other consists of two main groups—C. cucullata + C. pulchra and the “core” South American species. Prior hypotheses of relationships were explored statistically using Maximum Likelihood and Bayesian approaches. Dispersal-Vicariance analysis revealed the importance of the Northern Andes as a major center for biological diversification, and the effects of dispersal across the Panamanian Land Bridge in the composition of South American and Mesoamerican avifaunas. Phylogenetic patterns are highly congruent with an allopatric mode of speciation. Implications of these results are discussed in the context of the biogeography of Neotropical montane forests.     

Hallucal grasping behavior in Caluromys (Didelphimorphia: Didelphidae): Implications for primate pedal grasping

A key feature in primate evolution is a foot with a divergent opposable hallucal metatarsal bearing a large peroneal process. Extant primates are characterized by a powerful hallucal grasp—an either “euprimate” or “plesiadapoid-euprimate” ancestor acquisition—that facilitates the exploitation of fine branches, an ability that increased the fitness of ancestral euprimates. In this context, the didelphid marsupial Caluromys has been used as the extant analog to this primate morphotype stage due to some morphological, ecological, and behavioral features. However, the extent to which and the positional and support contexts in which Caluromys uses powerful hallucal grasping are not known. This renders analogies to any mode of “euprimate” or “stem primate” grasping poorly substantiated. The present paper quantifies locomotor and postural behavior, support use, and associated frequencies of hallucal grasping in captive Caluromys philander via analysis of video recordings. During locomotion, Caluromys primarily used diagonal sequence walk, clamber, and climb, whereas stand, foot-hang, and bipedal stand were the dominant postures. Small, fine, horizontal, and moderately inclined branches were frequently used. Overall rates of “apparently powerful hallucal grasps” were high, but were exceptionally high during clamber, climb, foot-hang, and bipedal stand. Additionally, an “apparently powerful hallucal grasp” was very common upon fine, small, steep, and vertical branches. The extensive use of such powerful hallucal grasping provided stability and safety that enabled Caluromys to proficiently utilize fine branches of various orientations. The ability to negotiate such unstable supports, further reflected in foot anatomy, provides evidence that the morphobehavioral complex of Caluromys can serve as an extant analog to the plesiadapoid-euprimate ancestor, represented as a terminal branch feeder with effective hallucal grasping.     

On the interaction between stabilizing social factors and destabilizing trophic factors in small rodent populations

Mathematical models are developed in order to analyze whether or not social factors, such as, for example, the “social fence” (J. B. Hestbeck, 1982, Oikos 39, 157–163) will stabilize population density: the dynamic interaction between social factors and (dynamic) trophic factors is analyzed. It is concluded that social factors such as the “social fence” tend to stabilize population density; hence, if density cycles (as, e.g., seen in many microtine rodents) are observed in nature, it seems reasonable to conclude that density cycles are driven by, for example, trophic interactions and not by social factors. It is suggested that the “social fence” may explain why so many populations including several microtine populations have fairly stable densities despite the ever-existing destabilizing trophic interactions. Contrary to what is implied by J. B. Hestbeck (1983, “A Mathematical Model of Population Regulation in Cyclic Mammals,” Lecture notes in biomathematics, Vol. 52, Springer-Verlag, Berlin/New York), the analysis presented in this paper demonstrates that seasonal environmental changes are not essential for the generation of regular density cycles. Seasonal changes may, however, be necessary for generating a microtine-like density cycle. Empirical information on microtine rodents relating to the “social fence hypothesis” is discussed.     

Recombination During In Vitro Evolution

Recombination, the swapping of large portions of genetic information between and among parental genotypes, can be applied to in vitro evolution experiments on functional nucleic acids. Both homologous and heterologous recombination can be achieved using standard laboratory techniques. In many cases, recombination can allow for the discovery of a ribozyme or DNAzyme phenotype that would not likely be encountered by reliance on point mutations alone. In addition, recombination can often aid in the discovery of global optima in sequence space and/or lessen the number of generations it would take to reach optima. Recombination is most efficiently used in combination with point mutations and applied after the first couple of rounds of selection but before high-fitness genotypes dominate the selection. The “recombination zone” describes that region of sequence space—defined by the residues that will ultimately participate in the function of the winning nucleic acid(s)—where recombination is expected to be the most beneficial in the search for high-fitness genotypes.[Reviewing Editor: Martin Kreitman]Author order determined by a single Bernoulli trial as implemented by RPS.     

Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis

Ciona intestinalis is a useful model organism to analyze chordate development and genetics. However, unlike vertebrates, it shares a unique mechanism called trans-splicing with lower eukaryotes. In the computational analysis of trans-splicing in C. intestinalis we report here, we discovered that although the amount of non-trans-spliced and trans-spliced genes is usually equivalent, the expression ratio between the two groups varies significantly with tissues and developmental stages. Among the seven tissues studied, the observed ratios ranged from 2.53 in “gonad” to 19.53 in “endostyle”, and during development they increased from 1.68 at the “egg” stage to 7.55 at the “juvenile” stage. We further hypothesize that this enrichment in trans-spliced mRNAs in early developmental stages might be related to the abundance of trans-spliced mRNAs in “gonad”. Our analysis indicates that in C. intestinalis, although there may not exist strong fundamental requirements for genes to be trans-spliced, the populations of non-trans-spliced and trans-spliced genes are likely to be spatially and temporally regulated differently.     

Testing German shepherd puppies to assess their chances of certification

Behavioral activity of 7-week-old German shepherd puppies was tested and the activities analyzed if they could be used for predicting police efficiency of the individual. In total 206 individuals sired by 42 sires and 44 dams were used. The activities were divided into 10 tasks in which reactions and behavior of pups were scored from 0 to 5 points. All pups were tested separately from other conspecifics. Probability that the puppy will pass the certification was tested by a logistic regression. Of the 206 puppies, 148 passed the certification while 58 failed. Some tested behavioral variables were moderately to highly correlated with one another. Therefore we applied a factor analysis. Three factors were retained accounting for 100% of the shared variance. After inspection of the rotated factor pattern matrix and its confidence intervals, it appeared that variables “Independent movement and interactions with the tester”, “Negotiating obstacles”, “Entering a room”, “Behavior toward a person”, and “Behavior in new environments” loaded on Factor 1 (“Factor for movement”), while variables “Response to distracting stimuli caused by a shovel”, “Response to a distracting noise while left alone in a room”, and “Response to loud distracting stimuli” on Factor 2 (“Factor for responding to noise”) and variables “Retrieval” and “Tug of war” on Factor 3 (“Factor for attitude to predation”). In the final logistic regression model, the probability that the puppy will pass the certification depended on the higher weight at the time of testing (, P = 0.0005), on the “Factor for attitude to predation” (, P = 0.0007), on the “Factor for responding to noise”, where the higher the score, the weaker was the response (, P = 0.0232), and on the “Factor for movement” showing an increasing probability with decreasing score (, P = 0.0219). The tests in our study seem to be a good base which might enable selection for suitable dogs as early as 7 weeks of age. The puppies having high probability to pass certification in adulthood were heavy individuals willing to chase, catch, and fetch a tennis ball, and follow a rag drawn away from them, while weakly responding to a distracting noise in various situations and showing low activity while negotiating obstacles and moving and interacting with the tester. To conclude, contrary to skeptical assumptions expressed by various authors, the specific puppy tests for police dogs provide a reliable tool for predicting future service ability of a puppy. Differences in methodology are likely to contribute to a lack of consensus among various studies.     

Similarity

Recent debates concerning conflicting hypotheses of higher-level phylogeny such as the sister-group relationships of tetrapods, turtles, birds and snakes, serve as examples in the analysis of the nature of morphological evidence as it is currently used in phylogeny reconstruction. We note a recent shift of emphasis towards ever-larger data matrices, which may come at the cost of detailed character analysis and argumentation. Because the assessment of morphological characters necessarily entails a conceptual element of abstraction, there is also a threat that preconceived notions of phylogeny influence character analysis. Because the test of congruence does not address character analysis in itself, we argue that character hypotheses, i.e. primary conjectures of homology, need to be testable, and potentially refutable, in their own right. We demonstrate the use of classical criteria of homology (topological relations and/or connectivity, in conjunction with the subsidiary criteria of special similarity and intermediate forms) in the test, and refutation, of morphological characters. Rejection of the classical criteria of homology in the test of morphological character hypotheses requires the formulation of alternative methods of test and potential falsification of morphological characters that have so far not been proposed. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 75 , 59–82.     

A note on the effectiveness of behavioural rehabilitation for reducing inter-dog aggression in shelter dogs

The effectiveness of a rehabilitation program for reducing inter-dog aggression was evaluated at the municipal animal shelter. Sixteen dogs (of 60 examined) met the study criteria of medium inter-dog aggression as determined by an inter-dog aggression test. These dogs received a 10-day treatment of daily rehabilitation for 30 min (rehabilitation group, n = 9) or daily release into an outdoor enclosure for 30 min (control group, n = 7). Rehabilitation consisted of desensitising and counter-conditioning dogs to the approach of other “stimulus” dogs. Most dogs in the rehabilitation group showed a decline in aggression scores when re-tested after the last treatment (day 11), and differed significantly from the control dogs which showed either an increase or no change in aggression scores (U = 8.5, P < 0.01). Rehabilitation dogs also showed lower frequencies of aggressive body postures (“facing the stimulus dog”, P < 0.05, and “stiff posture”, P < 0.10) and higher frequencies of less assertive postures (“ears back”, P < 0.05, and “lowered neck”, P < 0.10) on day 11. The differences between groups were no longer significant when a reduced sample of dogs was tested 1 week after rehabilitation ended (day 18). The study shows short-term reduction of inter-dog aggression through rehabilitation, but further work is needed on effective ways of maintaining the behavioural change.     

PARSIMONY, HOMOLOGY AND THE ANALYSIS OF MULTISTATE CHARACTERS

Abstract— The order of states in a transformation series describes an internested set of synapomorphies. States adjacent to each other in the transformation series thus share a degree of homology not found in the other states. Whether the level of homology is relatively apomorphic is determined by rooting the order with outgroup comparison. The analysis of state order is a homology problem and is solved with a two-step process using similarity and congruence with other characters as criteria. Other methods that have been proposed (e.g. transformation series analysis, non-additive analysis, morphocline analysis, ontogenetic analysis) fail to apply both similarity and congruence, and thus cannot be used independently for determining character state order.     

Anatomy of a cladistic analysis

The sequential stages culminating in the publication of a morphological cladistic analysis of weevils in the Exophthalmus genus complex (Coleoptera: Curculionidae: Entiminae) are reviewed, with an emphasis on how early‐stage homology assessments were gradually evaluated and refined in light of intermittent phylogenetic insights. In all, 60 incremental versions of the evolving character matrix were congealed and analysed, starting with an assembly of 52 taxa and ten traditionally deployed diagnostic characters, and ending with 90 taxa and 143 characters that reflect significantly more narrow assessments of phylogenetic similarity and scope. Standard matrix properties and analytical tree statistics were traced throughout the analytical process, and series of incongruence length indifference tests were used to identify critical points of topology change among succeeding matrix versions. This kind of parsimony‐contingent rescoping is generally representative of the inferential process of character individuation within individual and across multiple cladistic analyses. The expected long‐term outcome is a maturing observational terminology in which precise inferences of homology are parsimony‐contingent, and the notions of homology and parsimony are inextricably linked. This contingent view of cladistic character individuation is contrasted with current approaches to developing phenotype ontologies based on homology‐neutral structural equivalence expressions. Recommendations are made to transparently embrace the parsimony‐contingent nature of cladistic homology.