Which statistics should tropical biologists learn?

Tropical biologists study the richest and most endangered biodiversity in the planet, and in these times of climate change and mega-extinctions, the need for efficient, good quality research is more pressing than in the past. However, the statistical component in research published by tropical authors sometimes suffers from poor quality in data collection; mediocre or bad experimental design and a rigid and outdated view of data analysis. To suggest improvements in their statistical education, we listed all the statistical tests and other quantitative analyses used in two leading tropical journals, the Revista de Biología Tropical and Biotropica, during a year. The 12 most frequent tests in the articles were: Analysis of Variance (ANOVA), Chi-Square Test, Student's T Test, Linear Regression, Pearson's Correlation Coefficient, Mann-Whitney U Test, Kruskal-Wallis Test, Shannon's Diversity Index, Tukey's Test, Cluster Analysis, Spearman's Rank Correlation Test and Principal Component Analysis. We conclude that statistical education for tropical biologists must abandon the old syllabus based on the mathematical side of statistics and concentrate on the correct selection of these and other procedures and tests, on their biological interpretation and on the use of reliable and friendly freeware. We think that their time will be better spent understanding and protecting tropical ecosystems than trying to learn the mathematical foundations of statistics: in most cases, a well designed one-semester course should be enough for their basic requirements.     

Ventilation inhomogeneity during controlled ventilation. Which index should be used?

Six indexes for diagnosing uneven ventilation by tracer gas washout were studied. The indexes were lung clearance index, mixing ratio, Becklake index, multiple-breath alveolar mixing inefficiency, moment ratio, and pulmonary clearance delay, all of which increase with impaired pulmonary gas mixing. In model lung tests, indexes that compared the actual washout curve with a calculated ideal curve (mixing ratio, multiple-breath alveolar mixing inefficiency, and pulmonary clearance delay) were unaffected by changes in tidal volume and series dead space, whereas the others varied markedly. In both spontaneously breathing and mechanically ventilated patients all indexes showed a significant difference between smokers and nonsmokers (P less than 0.002), but the indexes were somewhat different in their assessment of different ventilatory patterns. However, the mean value for all indexes, with the exception of mixing ratio, was smallest with a fast insufflation followed by an end-inspiratory pause. Any of the indexes may be useful if its limitations are recognized, but mixing ratio, multiple-breath alveolar mixing inefficiency, and pulmonary clearance delay seem preferable, because they are not affected by changes in tidal volume and dead space fraction.     

Which fields under a coverslip should one assess to estimate sperm motility?

Under field conditions the motility of bull semen often has to be estimated under a coverslip on a microscope slide. This study was aimed at determining which combination of fields under coverslips provides measurements of sperm motility that best represent the motility in semen specimens as measured in a specially designed chamber for use in a computer-assisted sperm analyzer (CASA). We measured the motility (percentages motile, progressively motile, and aberrantly motile spermatozoa) in each of four straws of frozen-thawed semen from each of 10 bulls five times, ranging from 5 to 120 minutes after thawing with each bull by straw by time combination yielding one semen specimen. Motility was measured in duplicate in a Hamilton, Thorne IVOS CASA; once in each of 12 fields equally spaced along the equatorial radius of a coverslip (Field 0 at the edge and Field 11 at the center) and once in each of eight equally spaced fields along the equator of a Leja 4 chamber designed for use in a CASA. We used the weighted average motility of all fields in a chamber as gold standard and compared it to the average motility of each the following combinations of fields under the coverslip: all 12 fields, Fields 2 to 4, Fields 2 and four, Field 3 and the center three fields. The concordance correlation coefficient (CCC) was determined between the motility in each combination of fields under coverslips and the chambers as a reproducibility index, which evaluates the agreement between the readings under the coverslips and the gold standard readings in the chambers (n = 187 for each CCC). We performed pairwise comparisons of the CCCs (P < 0.005 for each comparison) and established that the average motility under all 12 fields better reproduced the motility in the chamber than the center three fields or Field 3. The averages of Fields 2 to 4 and Fields 2 and 4 reproduced chamber motility as well as the average of all 12 fields, except for the percentage motile sperm, where the average of all 12 fields was better. Using the average motility of Fields 2 and 4, 50% of estimates fell within 6%, 4% and 3% above or below the percentages motile, progressively motile and aberrantly motile spermatozoa in the Leja 4 chamber, 80% of estimates fell within 12%, 8% and 7% thereof and 95% fell within 23%, 13% and 12% thereof. In conclusion, for the method of spreading semen under a coverslip and the range in motility values used, this study shows that the average of the motility over the 12 fields along the equatorial radius under a coverslip provides the best estimate of the motility of a semen specimen, while the average of Fields 2 and 4 is also suitable for the subjective estimation of motility under field conditions, although the estimated motility is expected to fall within 6% above or below the motility of the specimen in only 50% of semen specimens.     

Science policies: How should science funding be allocated? An evolutionary biologists’ perspective

In an ideal world, funding agencies could identify the best scientists and projects and provide them with the resources to undertake these projects. Most scientists would agree that in practice, how funding for scientific research is allocated is far from ideal and likely compromises research quality. We, nine evolutionary biologists from different countries and career stages, provide a comparative summary of our impressions on funding strategies for evolutionary biology across eleven different funding agencies. We also assess whether and how funding effectiveness might be improved. We focused this assessment on 14 elements within four broad categories: (a) topical shaping of science, (b) distribution of funds, (c) application and review procedures, and (d) incentives for mobility and diversity. These comparisons revealed striking among‐country variation in those elements, including wide variation in funding rates, the effort and burden required for grant applications, and the extent of emphasis on societal relevance and individual mobility. We use these observations to provide constructive suggestions for the future and urge the need to further gather informed considerations from scientists on the effects of funding policies on science across countries and research fields.     

Do high-tannin leaves require more roots?

The well-known deceleration of nitrogen (N) cycling in the soil resulting from addition of large amounts of foliar condensed tannins may require increased fine-root growth in order to meet plant demands for N. We examined correlations between fine-root production, plant genetics, and leaf secondary compounds in Populus angustifolia, P. fremontii, and their hybrids. We measured fine-root (<2mm) production and leaf chemistry along an experimental genetic gradient where leaf litter tannin concentrations are genetically based and exert strong control on net N mineralization in the soil. Fine-root production was highly correlated with leaf tannins and individual tree genetic composition based upon genetic marker estimates, suggesting potential genetic control of compensatory root growth in response to accumulation of foliar secondary compounds in soils. We suggest, based on previous studies in our system and the current study, that genes for tannin production could link foliar chemistry and root growth, which may provide a powerful setting for external feedbacks between above- and belowground processes.