Search

This registration is for meta-analysis based on a systematized review that seeks to examine publication bias in ecology and evolution by examining effect sizes and other factors related to citation performance.

Additional file 3. Accession numbers and names of species included in Fig. 1. The names of undefended species of poison frogs (Dendrobatidae) are in black and those of defended species are in blue.

Additional file 7. Antibody verification. Oocytes were injected with cRNA encoding Epipedobates anthonyi α4β2 nAChRs (ratio 1:1, 4 ng each). A) Currents induced by 1 mM ACh 7 days after injection (n = 21); uninjected oocytes were assumed to have no response to ACh based on previous experiments. B) Raw counts obtained with an iodinated antibody directed against the β2 subunit (125I-mAb 295) in each group (n = 3 experiments with 7 pooled oocytes per experiment). C) Correlation between the maximal ACh-induced current and the specific binding observed for each of the pooled oocytes expressing Epipedobates nAChRs tested for this study (R2= 0.83). β2(LC) represents L106 and C108 in the β2 subunit. When used for residues, the bold font indicates substitutions in the wild type background.Uninjected oocytes were used as blanks, and their counts subtracted from the values of injected oocytes for each experiment.

Additional file 2. Effects of reciprocal substitutions on ACh concentration-response curves (CRC) in the β2 subunit of human and dendrobatid frog, Epipedobates anthonyi. Data redrawn from Tarvin et al. [13], presented as mean ± SD. (A) A high ratio of β2 to α4 (1α:3β) of cRNA of the wild type human receptor subunits produces a monophasic CRC with a single EC50 indicating only high sensitivity (HS) binding sites (black curve: β2(FS) represents F106 and S108 in β2 subunit; n = 7). Introduction of the S108C substitution adds a low sensitivity (LS) binding site so that the CRC is now best fit with a biphasic curve reflecting both HS and LS sites (green curve: β2(FC), amino acid in bold indicates a substitution; n = 6). Further addition of F106L to S108C eliminates the LS sites, thus compensating for the effect of S108C [orange curve: β2(LC); n = 6]. (B) A low ratio of β2 to α4 (3α:1β) of the wild type human receptor subunits produces an ACh CRC shifted rightward and best fit with a monophasic curve with a shallow slope [black curve: β2(FS); n = 13]. Introduction of the S108C substitution shifted the curve further right (green curve: β2(FC); n = 6]. Addition of F106L to S108C partially compensates for the effect of S108C alone [orange curve: β2(LC); n = 5]. (C) When the ratio of injected human β subunit cRNA/α subunit cRNA is high, the nAChR stoichiometry is 2α:3β. However, with paucity of β subunits the stoichiometry shifts to 3α:2β. (D,E) Even with more extreme ratios of α and β subunits (1:7 and 7:1) and the introduction of the ancestral amino acids (FS, FC), there was no change in the CRC of Epipedobates anthonyi (n = 5-13). (F) The stoichiometry of frog nAChR receptors is unknown but we conjectured it is 2α:3β because they show a single kind of binding site (HS). This conjecture is noted by the question mark over the grey arrow.

Additional file 5. Representative tracings from ACh CRC from α4β2 nAChR of two species of non-dendrobatids Tracings from Xenopus tropicalis α4β2 nAChR with an α:β ratio of (A) 1:3 and (B) 7:1, and from Nanorana parkeri α4β2 nAChR with an α:β ratio of (C) 1:3 and (D) 7:1. ACh concentration is indicated above each peak, in μM.

Additional file 1. Subunit arrangements and structure of α4β2 nAChRs in different stoichiometries. (A and B). Diagrams of nAChRs in different stoichiometries, seen from the extracellular side. (A) nAChR formed by two α4 and three β2 subunits (2α:3β) that possesses high sensitivity (HS) binding sites for ACh located at α4(+):β2(-) interfaces. (B) nAChR formed by three α4 and two β2 subunits (3α:2β). In addition to the HS binding sites, it possesses a low sensitivity (LS) binding site for ACh located at the interface between two adjacent α subunits, α(+):α(-). + and – signs indicate the principal and complementary components of the subunit interfaces. (C-E). Structure of human α4β2 nAChRs determined by cryo-electron microscopy [33] with bound ligand and antibody fragments. (C) Stoichiometry 2:3β (Protein Data Bank, PDB: 6CNJ), viewed from the extracellular side. (D and E) Stoichiometry 3α:2β (PDB: 6CNK), viewed from the membrane side (D) and the extracellular side (E). Molecular graphics performed with UCSF Chimera [51]. Alpha subunit in salmon, β subunit in grey, Fragment antigen-binding (Fab) from monoclonal antibodies in cyan. The arrows indicate the interfaces where nicotine (black, present in the structure) and acetylcholine bind. Red arrows indicate HS binding sites and blue arrows indicate LS binding site.

Additional file 6. Maximal currents from α4β2 nAChR of two species of non-dendrobatids (A) Xenopus tropicalis (n = 10-39) (B) Nanorana parkeri (n = 9-20). The number over each bar indicates the total amount of cRNA (ng) injected per oocyte, while maintaining the α:β RNA ratio indicated. β2(FS) represents F106 and S108 in the β2 subunit. β2(FC) and β2(LC) indicates the residues present in position 106 and 108 in the β2 subunit, with the bold font indicating substitutions in the wild type background. The different amounts of cRNA injected precluded a complete statistical analysis of each data set, but we performed a two-way ANOVA on the Nanorana parkeri data set, followed by a Holm-Šídák analysis to correct for multiple comparisons (all conditions against all conditions). We only show the significant differences within each RNA ratio, as those oocytes were injected with the same total amount of cRNA. **p < 0.01, ****p < 0.0001.

The cardiovascular system is critical for delivering O2 to tissues. Here, we examined the cardiovascular responses to progressive hypoxia in four high-altitude Andean duck species compared with four related low-altitude populations in North America, tested at their native altitude. Ducks were exposed to stepwise decreases in inspired partial pressure of O2 while we monitored heart rate, O2 consumption rate, blood O2 saturation, haematocrit (Hct) and blood haemoglobin (Hb) concentration. We calculated O2 pulse (the product of stroke volume and the arterial–venous O2 content difference), blood O2 concentration and heart rate variability. Regardless of altitude, all eight populations maintained O2 consumption rate with minimal change in heart rate or O2 pulse, indicating that O2 consumption was maintained by either a constant arterial–venous O2 content difference (an increase in the relative O2 extracted from arterial blood) or by a combination of changes in stroke volume and the arterial–venous O2 content difference. Three high-altitude taxa (yellow-billed pintails, cinnamon teal and speckled teal) had higher Hct and Hb concentration, increasing the O2 content of arterial blood, and potentially providing a greater reserve for enhancing O2 delivery during hypoxia. Hct and Hb concentration between low- and high-altitude populations of ruddy duck were similar, representing a potential adaptation to diving life. Heart rate variability was generally lower in high-altitude ducks, concurrent with similar or lower heart rates than low-altitude ducks, suggesting a reduction in vagal and sympathetic tone. These unique features of the Andean ducks differ from previous observations in both Andean geese and bar-headed geese, neither of which exhibit significant elevations in Hct or Hb concentration compared with their low-altitude relatives, revealing yet another avian strategy for coping with high altitude.

Manuscript Purpose/Abstract Statistics on representation in graduate programs show that, while academia is moving forward in terms of generating diverse cohorts of students and faculty, representation still has not reached parity. These discrepancies in representation are seen at the graduate student level and intensify as academic rank increases. While there have been strides to improve representation through more thoughtful recruitment, a new discussion is emerging around inclusion and retention of under-represented minorities. Inclusive programs are that which center and prioritize support for diverse experiences, identities, career goals, and perspectives actively and continuously from recruitment through graduation. An emerging area of focus for inclusion efforts is graduate student programs. Graduate education programs provide significant opportunities for inclusive programming, and conversely, a program that does not take efforts to improve both diversity and inclusion can often contribute to further disparity in representation. While there are many efforts across programs to address inclusion, there is room for improvement on developing cohesive and effective programming that targets the many areas of needed change in order to improve institutional inclusivity. Here, we argue that graduate education programs should utilize a systems change framework to evaluate areas of progress and need in their program as it relates to inclusion. A systems-change approach emphasizes three levels of changes: explicit change (e.g. policies), semi-explicit change (e.g. power dynamics), and implicit change (e.g. biases). We use the Ecology, Evolution, and Behavior (EEB) PhD Program at the University of Texas at Austin in an exercise to (1) identify areas of concern regarding inclusive programming voiced by graduate students and (2) categorize efforts to address these concerns about inclusive programming into a systems change frame, and finish by (3) integrating and evaluating which areas of the systems change framework show the greatest progress and greatest need for the UT EEB graduate program. We acknowledge that the specific examples here are of particular relevance to other EEB programs, as they may see similar patterns in graduate student needs and efforts to address them. But, the exercise itself is certainly not limited to EEB programs. We encourage any graduate program, as well as any departments or even larger institution, to consider undergoing this exercise in order to more effectively address inequity in their own domains.