Mapping responsible conduct in the uncharted field of research-creation: A scoping review.

This scoping review addresses the issues of responsible conduct of research (RCR) that can arise in the practice of research-creation (RC), an emergent, interdisciplinary, and heterogeneous field at the interface of academic research and creative activities. Little is yet known about the nature and scope of RCR issues in RC, so our study examined three questions: (1) What are the specific issues in RC in relation to RCR? (2) How does the specificity of RC influence the understanding and practice of RCR? (3) What recommendations could help address the issues highlighted in the literature? To answer these questions, we conducted a scoping review of the academic literature (n = 181 texts) dealing with RCR in RC. We found that researcher-creators faced some very different RCR challenges in comparison with their colleagues in the rest of academia. Addressing these issues is important for both the RCR and RC communities in order to ensure that the rapid development of this field occurs in line with the norms of RCR which, nonetheless, should be adapted to respect the particularities of RC and allow its contributions to the academic world.

Peromyscus populations and their Cuterebra parasites display congruent phylogeographical structure.

The relationships between populations of the Deer Mouse (Peromyscus maniculatus) and the White-footed Mouse (P. leucopus) and their respective Cuterebra parasites were examined. Population genetic structure of hosts and parasites was inferred using cytochrome oxidase mitochondrial sequences of specimens from 7 populations. Genetic analyses revealed that isolation-by-distance applies for P. maniculatus and its associated parasite (C. grisea). A significant correlation was also observed between the genetic distances of these host and parasite species. Furthermore, populations of P. maniculatus and C. grisea from the North and South shores of the St Lawrence River were found to be significantly different. This structure may be explained by the St Lawrence River being a dispersal barrier for both species. A robust analysis of the other species pair (P. leucopus and C. fontinella) could not be performed because of limited sample sizes.

Molecular identification of two species of myiasis-causing Cuterebra by multiplex PCR and RFLP.

The myiasis-causing flies Cuterebra grisea (Coquillet) and Cuterebra fontinella (Clark) (Diptera: Oestridae) are normally parasites of mice, predominantly of the genus Peromyscus. The morphological similarities of these species and the existence of intermediate morphotypes bearing characters of both species make the identification of adults problematic; furthermore the identification of larvae is apparently not possible. This study presents two molecular approaches to discriminate between these species using specific band patterns: (i) species-specific primers designed in the cytochrome oxidase II (COII) region used in multiplex polymerase chain reaction (PCR) and (ii) restriction fragment length polymorphism (RFLP) on amplified segments of cytochrome oxidase I (COI) gene. Both methods were tested on Cuterebra larvae and on adult museum specimens. The two techniques showed a clear difference between C. grisea and C. fontinella, although species-specific primers were more successful than RFLP for degraded DNA. No intraspecific variation in RFLP and species-specific amplifications were detected for the two species of Cuterebra. The results exhibit discrepancies between molecular and morphological identification, suggesting that some of the adults were misidentified.

War and peace in phylogenetics: a rejoinder on total evidence and consensus.

For more than 10 years, systematists have been debating the superiority of character or taxonomic congruence in phylogenetic analysis. In this paper, we demonstrate that the competing approaches can converge to the same solution when a consensus method that accounts for branch lengths is selected. Thus, we propose to use both methods in combination, as a way to corroborate the results of combined and separate analyses. This so-called "global congruence" approach is tested with a wide variety of examples sampled from the literature, and the results are compared with those obtained by standard consensus methods. Our analyses show that when the total evidence and consensus trees differ topologically, collapsing weakly supported nodes with low bootstrap support usually improves "global congruence".

Total evidence, consensus, and bat phylogeny: A distance-based approach.

Resolution of the total evidence (i.e., character congruence) versus consensus (i.e., taxonomic congruence) debate has been impeded by (1) a failure to employ validation methods consistently across both tree-building and consensus analyses, (2) the incomparability of methods for constructing as opposed to those for combining trees, and (3) indifference to aspects of trees other than their topologies. We demonstrate a uniform, distance-based approach which allows for comparability among the results of character- and taxonomic-congruence studies, whether or not an identical suite of taxa has been included in all contributing data sets. Our results indicate that total-evidence and consensus trees differ little in topology if branch lengths are taken into account when combining two or more trees. In addition, when character-state data are converted to distances, our method permits their combination with information produced by techniques which generate distances directly. Moreover, treating all data sets or trees as distance matrices avoids the problem that different numbers of characters in contributing studies may confound the conclusions of a total-evidence or consensus analysis. Our protocol is illustrated with an example involving bats, in which the three component studies based on serology, DNA hybridization, and anatomy imply distinct phylogenies. However, the total-evidence and consensus trees support a fourth, somewhat different, topology resolved at all but one node and which conforms closely to the currently accepted higher category classification of Chiroptera.

Rhythmic melatonin secretion in different teleost species: an in vitro study.

The rhythmic production of melatonin is governed by intrapineal oscillators in all fish species so far investigated except the rainbow trout. To determine whether the latter represents an exception among fish, we measured in vitro melatonin secretion in pineal organs of nine wild freshwater and six marine teleost species cultured at constant temperature and under different photic conditions. The results demonstrate that pineal organs of all species maintain a rhythmic secretion of melatonin under light:dark cycles and complete darkness, and strongly suggest that most fish possess endogenous intrapineal oscillators driving the rhythm of melatonin production, with the exception of the rainbow trout.

Matching behavioral evolution to brain morphology.

A method is presented to test the relationship between a phylogenetic tree derived from brain morphology, and different hypotheses describing the evolution of a behavioral trait. This is a question of interest for evolutionary psychologists and behavioral biologists. The paper first discusses how hypotheses for behavioral evolution should be coded for such a comparison, then a triple-per-mutation test, originally proposed to compare independently obtained evolutionary trees, is used for the statistical assessment of each hypothesis. Non-parametric correlation coefficients computed between brain components and appropriately coded behavioral states can then be used to suggest what brain components are responsible for the development of the various states of the behavioral trait of interest. The procedure is illustrated with three different applications relating brain evolution to habitat selection in marsupials, locomotory specialization in primates, and trophic adaptation in bats.

DNA-DNA hybridization-based phylogeny for "higher" nonpasserines: reevaluating a key portion of the avian family tree.

A matrix of delta T mode values for 10 birds, including 9 nonpasserines and a suboscine passerine flycatcher, was generated by DNA-DNA hybridization. Within the most derived lineages, all bootstrapped and jackknifed FITCH trees lend strong support to sister-groupings of the two swift families, of hummingbirds to swifts, and of these to a clade containing both owls and night-hawks. The outgroup duck roots the tree between the woodpecker (Piciformes) and the remaining taxa, indicating that Piciformes are among the earliest branches within nonpasserines. However, the succeeding branches to kingfisher, mousebird, and suboscine passerine flycatcher are based on short internodes that are poorly supported by bootstrapping and that give inconsistent results in jackknifing. Although these 3 orders may have arisen through rapid or near-simultaneous divergence, placement of the "advanced" Passeriformes deep within a more "primitive" radiation indicates that nonpasserines are paraphyletic, echoing the same distinction for reptiles with respect to their advanced descendants. Despite significant rate variation among different taxa, these results largely concur with those obtained with the same technique by Sibley and Ahlquist, who used the delta T50H measure and UPGMA analysis. This agreement lends credence to some of their more controversial claims.

Jackknifing of weighted trees: validation of phylogenies reconstructed from distance matrices.

The jackknife strict consensus has been used to detect topological incompatibilities in phylogenetic trees derived from distance data. We here extend this approach to account for branch lengths, as well as topological relationships, when comparing jackknife pseudoreplicates. The average consensus procedure is used to derive a tree reflecting the agreement among the jackknife phylogenies. Combining the average tree with a minimum and a maximum consensus provides information about jackknife tree variability; the range consensus between the minimum and the maximum represents the topological agreement among them. We also demonstrate the effect of the number of pseudoreplicates on the resulting consensus trees by considering single and multiple deletions. The jackknife extensions that we propose are applied to both hypothetical and DNA-DNA hybridization distance data. Consideration of branch lengths reveals greater stability of the jackknife phylogeny than would be demonstrated by a strict consensus based on topology alone.