Count data in biology-Data transformation or model reformation?

Statistical analyses are an integral component of scientific research, and for decades, biologists have applied transformations to data to meet the normal error assumptions for F and t tests. Over the years, there has been a movement from data transformation toward model reformation-the use of non-normal error structures within the framework of the generalized linear model (GLM). The principal advantage of model reformation is that parameters are estimated on the original, rather than the transformed scale. However, data transformation has been shown to give better control over type I error, for simulated data with known error structures. We conducted a literature review of statistical textbooks directed toward biologists and of journal articles published in the primary literature to determine temporal trends in both the text recommendations and the practice in the refereed literature over the past 35 years. In this review, a trend of increasing use of reformation in the primary literature was evident, moving from no use of reformation before 1996 to >50% of the articles reviewed applying GLM after 2006. However, no such trend was observed in the recommendations in statistical textbooks. We then undertook 12 analyses based on published datasets in which we compared the type I error estimates, residual plot diagnostics, and coefficients yielded by analyses using square root transformations, log transformations, and the GLM. All analyses yielded acceptable residual versus fit plots and had similar p-values within each analysis, but as expected, the coefficient estimates differed substantially. Furthermore, no consensus could be found in the literature regarding a procedure to back-transform the coefficient estimates obtained from linear models performed on transformed datasets. This lack of consistency among coefficient estimates constitutes a major argument for model reformation over data transformation in biology.

Increasing phenological asynchrony between spring green-up and arrival of migratory birds.

Consistent with a warming climate, birds are shifting the timing of their migrations, but it remains unclear to what extent these shifts have kept pace with the changing environment. Because bird migration is primarily cued by annually consistent physiological responses to photoperiod, but conditions at their breeding grounds depend on annually variable climate, bird arrival and climate-driven spring events would diverge. We combined satellite and citizen science data to estimate rates of change in phenological interval between spring green-up and migratory arrival for 48 breeding passerine species across North America. Both arrival and green-up changed over time, usually in the same direction (earlier or later). Although birds adjusted their arrival dates, 9 of 48 species did not keep pace with rapidly changing green-up and across all species the interval between arrival and green-up increased by over half a day per year. As green-up became earlier in the east, arrival of eastern breeding species increasingly lagged behind green-up, whereas in the west-where green-up typically became later-birds arrived increasingly earlier relative to green-up. Our results highlight that phenologies of species and trophic levels can shift at different rates, potentially leading to phenological mismatches with negative fitness consequences.

Effects of local point source polychlorinated biphenyl (PCB) contamination on bone mineral density in deer mice (Peromyscus maniculatus).

A former local source of PCBs has contaminated soil and the terrestrial food web at Saglek, Labrador. The relationship between PCB exposure and bone mineral density as an osteoporosis biomarker in deer mice (Peromyscus maniculatus) was investigated at two sites at Saglek: a contaminated Beach and a reference area. Bone mineral density was measured on the femur of twenty-six deer mice using dual-energy X-ray absorptiometry (DXA) technology. Bone mineral density was significantly lower in deer mice from the high exposure site (average whole body summation operatorPCB=5769 ng/g wet weight, n=20) than at the reference site (average whole body summation operatorPCB=79.8 ng/g wet weight, n=7). We used T-scores from the World Health Organization to determine the degree of decreased bone mineral density in exposed mice. Assuming the same biomechanical forces apply as for humans, and using a conservative factor of 1.5 (fracture risk increases 1.5 to 3 fold for every standard deviation decrease in bone mineral density), mice from the contaminated Beach are up to five folds more susceptible to fracture risk than mice from the reference area. Therefore, the PCB concentrations found locally at contaminated military sites such as Saglek are high enough to affect local wildlife.

Comparing an estimate of seabirds at risk to a mortality estimate from the November 2004 Terra Nova FPSO oil spill.

On 21 November 2004, about 1000 barrels of crude oil were accidentally released from the Terra Nova FPSO (floating production, storage and offloading) onto the Grand Banks, approximately 340 km east-southeast of St. John's, Newfoundland. We estimated the number of vulnerable seabirds (murres (Uria spp.) and dovekies (Alle alle)) at risk from this incident by multiplying observed densities of seabirds with the total area covered by the slick, estimated at 793 km(2). A mean density of 3.46 murres/km(2) and 1.07 dovekies/km(2) on the sea surface was recorded during vessel-based surveys on 28 and 29 November 2004, with a mean density of 6.90 murres/km(2) and 13.43 dovekies/km(2) combining those on the sea and in flight. We calculated a mean of 9858 murres and dovekies were at risk of being oiled, with estimates ranging from 3593 to 16,122 depending on what portion of birds in flight were assumed to be at risk. A mortality model based on spill volume was derived independently of the risk model, and estimated that 4688 (CI 95%: 1905-12,480) birds were killed during this incident. A low mortality estimate based strictly on spill volume would be expected for this incident, which occurred in an area of relatively high seabird densities. Given that the risk and mortality estimates are statistically indistinguishable, we estimate that on the order of 10,000 birds were killed by the Terra Nova spill.

Are natural microcosms useful model systems for ecology?

Several recent, high-impact ecological studies feature natural microcosms as tools for testing effects of fragmentation, metacommunity theory or links between biodiversity and ecosystem processes. These studies combine the microcosm advantages of small size, short generation times, contained structure and hierarchical spatial arrangement with advantages of field studies: natural environmental variance, 'openness' and realistic species combinations with shared evolutionary histories. This enables tests of theory pertaining to spatial and temporal dynamics, for example, the effects of neighboring communities on local diversity, or the effects of biodiversity on ecosystem function. Using examples, we comment on the position of natural microcosms in the roster of ecological research strategies and tools. We conclude that natural microcosms are as versatile as artificial microcosms, but as complex and biologically realistic as other natural systems. Research to date combined with inherent attributes of natural microcosms make them strong candidate model systems for ecology.