Naming taxa from cladograms: a cautionary tale

The recent publication of a new hypothesis of cladistic relationships among American frogs referred to the genus Rana, accompanied by a new taxonomy and a new nomenclature of this group [Hillis D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Molecular Phylogenetics and Evolution 34, 299-314], draws attention to the problems posed by the use of a "double nomenclature", following both the rules of the International Code of Zoological Nomenclature (designated here as "onomatophore-based nomenclature") and the rules of the draft Phylocode (designated here as "definition-based nomenclature"). These two nomenclatural systems, which rely upon widely different theoretical bases, are incompatible, and the latter cannot be viewed as a "modification" of the former. Accordingly, scientific names (nomina) following both systems should be clearly distinguished in scientific publications. Onomatophore-based nomina should continue to be written as they have been for about 250 years, whereas definition-based nomina should be written in a specific way, e.g., Lithobates. The combined use of both nomenclatural systems for the same taxonomy in the same paper requires good knowledge and careful respect of the rules of the Code regarding availability, allocation and validity of nomina. As shown by this example, not doing so may result in various problems, in particular in publishing nomina nuda or in using nomenclatural ranks invalid under the current Code. Attention is drawn to the fact that new nomina published without diagnostic characters are not available under the Code, and that the latter currently forbids the use of more than two ranks (subgenus and "aggregate of species") between the ranks genus and species.     

HLA and AIDS: a cautionary tale

The human major histocompatibility complex HLA has been implicated repeatedly as a regulator of the outcome of HIV exposure and infection. A new study of long-term survivors who naturally depress HIV-1 replication and avoid the signs of AIDS for years after infection suggests that homozygosity for a group of HLA-B locus alleles termed Bw4 confers resistance, ostensibly by regulating natural killer cell-ligand interactions. However, close inspection of the accumulated evidence raises some questions and urges validation of the potential Bw4 effects in additional studies.     

Elevational gradient analyses and the use of historical museum specimens: a cautionary tale

Aim The value of biodiversity informatics rests upon the capacity to assess data quality. Yet as these methods have developed, investigating the quality of the underlying specimen data has largely been neglected. Using an exceptionally large, densely sampled specimen data set for non‐flying small mammals of Utah, I evaluate measures of uncertainty associated with georeferenced localities and illustrate the implications of uncritical incorporation of data in the analysis of patterns of species richness and species range overlap along elevational gradients. Location Utah, USA, with emphasis on the Uinta Mountains. Methods Employing georeferenced specimen data from the Mammal Networked Information System (MaNIS), I converted estimates of areal uncertainty into elevational uncertainty using a geographic information system (GIS). Examining patterns in both areal and elevational uncertainty measures, I develop criteria for including localities in analyses along elevational gradients. Using the Uinta Mountains as a test case, I then examine patterns in species richness and species range overlap along an elevational gradient, with and without accounting for data quality. Results Using a GIS, I provide a framework for post‐hoc 3‐dimensional georeferencing and demonstrate collector‐recorded elevations as a valuable technique for detecting potential errors in georeferencing. The criteria established for evaluating data quality when analysing patterns of species richness and species range overlap in the Uinta Mountains test case reduced the number of localities by 44% and the number of associated specimens by 22%. Decreasing the sample size in this manner resulted in the subsequent removal of one species from the analysis. With and without accounting for data quality, the pattern of species richness along the elevational gradient was hump‐shaped with a peak in richness at about mid‐elevation, between 2300 and 2600 m. In contrast, the frequencies of different pair‐wise patterns of elevational range overlap among species differed significantly when data quality was and was not accounted for. Main conclusions These results indicate that failing to assess spatial error in data quality did not alter the shape of the observed pattern in species richness along the elevational gradient nor the pattern of species’ first and last elevational occurrences. However, it did yield misleading estimates of species richness and community composition within a given elevational interval, as well as patterns of elevational range overlap among species. Patterns of range overlap among species are often used to infer processes underlying species distributions, suggesting that failure to account for data quality may alter interpretations of process as well as perceived patterns of distribution. These results illustrate that evaluating the quality of the underlying specimen data is a necessary component of analyses incorporating biodiversity informatics.     

Laboratory-dependent bacterial ecology: a cautionary tale

Although laboratory dependence is an acknowledged problem in microbiology, it is seldom intensively studied or discussed. We demonstrate that laboratory dependence is real and quantifiable even in the popular model Escherichia coli. Here laboratory effects alter the equilibrium composition of a simple community composed of two strains of E. coli. Our data rule out changes in the bacterial strains, chemical batches, and human handling but implicate differences in growth medium, especially the water component.     

FURIN and placental syncytialisation: a cautionary tale

FURIN is a pro-protein convertase previously shown to be important for placental syncytialisation (Zhou et al. [1]), a process of cell fusion whereby placental cytotrophoblast cells fuse to form a multinucleated syncytium. This finding has been broadly accepted however, we have evidence suggesting the contrary. Spontaneously syncytialising term primary human trophoblast cells and BeWo choriocarcinoma cells were treated with either FURIN siRNA or negative control siRNA or the protease inhibitor, DEC-RVKR-CMK, or vehicle. Cells were then left to either spontaneously syncytialise (primary trophoblasts) or were induced to syncytialise with forskolin (BeWo). Effects on syncytialisation were measured by determining human chorionic gonadotrophin secretion and E-cadherin protein levels. We showed that FURIN is not important for syncytialisation in either cell type. However, in primary trophoblasts another protease also inhibited by DEC-RVKR-CMK, may be involved. Our results directly contrast with those published by Zhou et al. Zhou et al. however, used first trimester villous explants to study syncytialisation, and we used term primary trophoblasts. Therefore, we suggest that FURIN may be involved in syncytialisation of first trimester trophoblasts, but not term trophoblasts. What is more concerning is that our results using BeWo cells do not agree with their results, even though for the most part, we used the same experimental design. It is unclear why these experiments yielded different results, however we wanted to draw attention to simple differences in measuring syncytialisation or flaws in method reporting (including omission of cell line source and passage numbers, siRNA concentration and protein molecular weights) and choice of immunoblot loading controls, that could impact on experimental outcomes. Our study shows that careful reporting of methods by authors and thorough scrutiny by referees are vital. Furthermore, a universal benchmark for measuring syncytialisation is required so that various studies of syncytialisation can be validated.Subject terms: Proteases, Differentiation     

Characterization of the Drosophila gene-switch system in aging studies: a cautionary tale

Genetic studies have shown that in many model organisms, single gene mutations can dramatically influence aging. Systems that allow researchers to control a gene's temporal and spatial expression pattern, known as inducible gene-expression systems, are a valuable asset for the study of the influence of single genes on aging. One inducible gene-expression system reported to allow temporal and tissue-specific control of gene expression in Drosophila is the Gene-Switch system. However, this system has not been extensively characterized in the context of aging research. This report uses six Gene-Switch strains to examine the tissue localization and amount of expression achievable in the major tissue types of the fly. The quantitative analysis of adult flies fed with inducer through life reveals that the levels of expression are influenced by both the inducer concentration and the age of the animal in a strain-specific manner. Furthermore, the relationship between inducer concentration and expression level is unique to each strain and, in some cases, to each gender. The analysis of the spatial expression patterns in several strains revealed expression in more tissue types than previously assumed. Finally, most Gene-Switch strains display expression in the absence of inducer during development and/or during adulthood. These findings have important implications that may reconcile contradictions reported in studies investigating the effects of dFOXO on longevity. This study is an important guide to the design and interpretation of aging studies based on the Gene-Switch system.     

Dangerous weapons: a cautionary tale of CRISPR defence

The Cas/CRISPR system of prokaryotes is a recently recognized defence system that protects cells from invasion by foreign nucleic acids, such as plasmids or bacteriophages. Using the archaeon Sulfolobus, Gudbergsdottir et al. have demonstrated that when foreign DNA is both a target of the CRISPR system and also carries a gene that is essential for cell growth, surviving cells display mutations in the CRISPR system that eliminate the target directed spacer. This simulates natural scenarios where the invading DNA cannot be readily destroyed, such as a temperate bacteriophage that manages to evade CRISPR attack and integrate into the genome, so becoming ‘self’. CRISPR deletions ranged from precise removal of a single spacer up to elimination of an entire CRISPR array but the mechanism involved is not understood. Another surprising feature was that from one to two base mutations in the same target protospacer did not affect recognition by the Sulfolobus CRISPR system, something unexpected from studies in bacteria where spacer and target protospacer must match exactly. This study shows that even though the CRISPR system is a powerful weapon it can also be a dangerous one for the cell that carries it.     

Dating archaeobotanical remains: a cautionary tale from Port au Choix,Newfoundland

In this paper we report on the first ¹⁴C dated archaeological seeds from the island of Newfoundland, Canada. Ninety-three archaeobotanical specimens were recovered from a midden deposit adjacent to a small dwelling at Point Riche (EeBi-20), a large Dorset Palaeoeskimo site near Port au Choix, northwestern Newfoundland. These remains were collected from a seemingly secure context within the midden, but AMS ¹⁴C testing of a sample of specimens produced modern ¹⁴C dates, indicating that the remains are intrusive to the Dorset occupation. While the majority of Newfoundland-based research assumes antiquity of archaeobotanical remains, we recommend using AMS ¹⁴C dating and other proxy data in future archaeobotanical studies to confirm antiquity prior to making interpretations regarding human–plant interactions.     

Bateman gradients in field and laboratory studies: a cautionary tale

Since tools of molecular genetics became readily available,our understanding of bird mating systems has undergone a revolution.The majority of passerine species investigated are sociallymonogamous, but have been shown to be genetically polygamous.Data sets from natural populations of juncos suggest that multiplemating by females results in a sexual selection gradient assteep for females as for males (a result that does not supportBateman's predictions). However, in males, fitness is enhanceddirectly through fertilization success with multiple matings;in females fitness benefits may be enhanced immediately throughdirect access to food, protection against predators, or otherresources received from males, or they may be delayed throughimprovement in offspring quality (e.g., through good genes,or greater genetic compatibility between the female and theextra-pair male). But a steep sexual selection gradient forfemales can be difficult to interpret. If all females copulatewith multiple partners that are equally likely to fertilizeeggs, then females that produce larger clutch sizes, for anyreason, will appear to have copulated with more males. Thatis, multiple sires have a higher probability of detection inlarger clutches than in smaller ones, giving the impressionthat females that mate with multiple males increase their reproductivesuccess. Yet, in most studies in which there is a correlationbetween number of offspring produced by females and number ofextra-pair males, causation has not been clearly establishedand other factors may explain the results. Additional complicationsin understanding male and female reproductive strategies are:(1) Molecular studies cannot detect extra-pair copulations thatdid not result in fertilizations; yet if a female acquires foodor other resources from extra-pair males, such extra-pair matingsmay have significant effects on female fitness. Thus, molecularstudies provide only a conservative estimate of the number ofextra-pair copulations or "mates" that a female has. (2) Clutchsize affects the probability that any given male will be successfulin fertilizing a female's eggs. Specifically, at any given point,a male's chances of fertilizing at least one egg in the female'sclutch will be greater as clutch size increases. We predictthat in avian species with small clutch sizes, males may beselected to be choosy and avoid extra-pair copulations, whilefemales should be selected to be less discriminating. Moreover,if extra-pair males provide resources that increase female fitness,the females should seek extra-pair copulations, whether or notthe males are likely to fertilize any of her eggs. Laboratory studies with insects have yielded clearer evidenceof the causal relationship between multiple mating and increasedfemale fitness. We review studies on a tenebrionid beetle inwhich female fecundity increases directly with number of mates.In these experiments, the nutritive value of the spermatophoresdoes not fully explain the increase in female reproductive success.     

Behavioral phenotyping of transgenic and knockout animals: a cautionary tale

Knockout and transgenic mice are extremely useful for behavioral research, especially for linking specific genes with behaviors. The authors present caveats to be aware of when using such mice in research situations.