A statistical test to show negligible trend: Reply

Camp et al. (2008) extend the ideas discussed in Dixon and Pechmann (2005). Our paper used equivalence regions to test for negligible trends (null hypothesis that trends are not negligible). Their paper suggests also using equivalence regions to test an alternative hypothesis of “ecologically meaningful” trends (null hypothesis that trends are negligible but not zero)

A statistical test to show negligible trend

The usual statistical tests of trend are inappropriate for demonstrating the absence of trend. This is because failure to reject the null hypothesis of no trend does not prove that null hypothesis. The appropriate statistical method is based on an equivalence test. The null hypothesis is that the trend is not zero, i.e., outside an a priori specified equivalence region defining trends that are considered to be negligible. This null hypothesis can be tested with two one-sided tests. A proposed equivalence region for trends in population size is a log-linear regression slope of (−0.0346, 0.0346). This corresponds to a half-life or doubling time of 20 years for population size. A less conservative region is (−0.0693, 0.0693), which corresponds to a halving or doubling time of 10 years. The approach is illustrated with data on four amphibian populations; one provides significant evidence of no trend

Relative size underlies alternative morph development in a salamander

Size thresholds commonly underlie the induction of alternative morphological states. However, the respective importance of absolute and relative size to such thresholds remains uncertain. If absolute size governs expression, morph frequency should differ among environments that influence absolute sizes (e.g. resources, competition), and individuals of the same morph should have similar average sizes across environments. If relative size determines expression, the frequency of each morph may not differ among environments, but morphs within each environment should differ in size relative to one another. We tested these predictions in a salamander (Ambystoma talpoideum) that develops into either a terrestrial metamorph or an aquatic paedomorph. To generate size variation within and among environments, we reared individuals in mesocosm ponds across three conspecific densities. We found that morph frequency did not differ among density treatments, and the morphs were not similarly sized within each density treatment. Instead, within each environment, relatively larger individuals became metamorphs and relatively smaller individuals became paedomorphs. Relative size therefore determined morph development, highlighting the importance of an individual’s social context to size-dependent morph induction

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins

Cotranslational protein folding can facilitate rapid formation of functional structures. However, it might also cause premature assembly of protein complexes, if two interacting nascent chains are in close proximity. By analyzing known protein structures, we show that homomeric protein contacts are enriched towards the C-termini of polypeptide chains across diverse proteomes. We hypothesize that this is the result of evolutionary constraints for folding to occur prior to assembly. Using high-throughput imaging of protein homomers in vivo in E. coli and engineered protein constructs with N- and C-terminal oligomerization domains, we show that, indeed, proteins with C-terminal homomeric interface residues consistently assemble more efficiently than those with N-terminal interface residues. Using in vivo, in vitro and in silico experiments, we identify features that govern successful assembly of homomers, which have implications for protein design and expression optimization

Supplement 1. SAS program code to estimate regression slopes and then test equivalence, and Ambystoma data.

<h2>File List</h2><blockquote> <p><a href="EquivSlope.sas">EquivSlope.sas</a> -- EquivSlope.sas: SAS (SAS 1999) program code to estimate regression slopes, assuming ar(1) errors, then test equivalence.</p> <p><a href="Ambystoma.txt">Ambystoma.txt</a> -- Ambystoma data set.</p> <p> </p></blockquote><h2>Description</h2><blockquote> <p>The file "EquivSlope.sas" is SAS (SAS 1999) program code to estimate regression slopes, assuming ar(1) errors, then test equivalence.  The code was written for SAS version 8.2.  It produces identical results in SAS version 9.0.  Comments are the text surrounded by /* and */.  The first data step (data trend;) reads the raw data and produces a SAS data set with one observation per species and year.  The proc mixed step estimates the regression slope for a log-linear model with ar(1), i.e., autocorrelated at lag 1, errors.  Parameter estimates are stored in the data set named parms.  The slopes are identified as effect = ‘year’.  The second data step (data tests;) does the equivalence test calculations for the slope, using an equivalence interval of (-0.0346, 0.0346).  LT is the <i>t</i> statistic for testing H0a (slope less than lower boundary).  UT is the t statistic for testing H0b (slope greater than upper boundary).  LP and UP are the corresponding <i>P</i> values.  This information is saved in a text file (ests.txt) and a SAS data set.  The final proc print step prints the equivalence test results.</p> <p> The file "Ambystoma.txt" is an <i>Ambystoma</i> data set.  The first line is a header line with variable names.  Subsequent lines contain the species (<i>A.</i> <i>talpoideum</i> or <i>A</i>. <i>tigrinum</i>), the year, and the count of breeding females.</p> </blockquote

Ecological Studies Related to Construction of the Defense Waste Processing Facility on the Savannah River Site

The Defense Waste Processing Facility (DWPF) was built on the Savannah River Site (SRS) during the mid-1980's. The Savannah River Ecology Laboratory (SREL) has completed 12 years of ecological studies related to the construction of the DWPF complex. Prior to construction, the 600-acre site (S-Area) contained a Carolina bay and the headwaters of a stream. Research conducted by the SREL has focused primarily on four questions related to these wetlands: (1) Prior to construction, what fauna and flora were present at the DWPF site and at similar, yet undisturbed, alternative sites (2) By comparing the Carolina bay at the DWPF site (Sun Bay) with an undisturbed control Carolina bay (Rainbow Bay), what effect is construction having on the organisms that inhabited the DWPF site (3) By comparing control streams with streams on the periphery of the DWPF site, what effect is construction having on the peripheral streams (4) How effective have efforts been to lessen the impacts of construction, both with respect to erosion control measures and the construction of refuge ponds'' as alternative breeding sites for amphibians that formerly bred at Sun Bay Through the long-term census-taking of biota at the DWPF site and Rainbow Bay, SREL has begun to evaluate the impact of construction on the biota and the effectiveness of mitigation efforts. Similarly, the effects of erosion from the DWPF site on the water quality of S-Area peripheral streams are being assessed. This research provides supporting data relevant to the National Environmental Policy Act (NEPA) of 1969, the Endangered Species Act of 1973, Executive Orders 11988 (Floodplain Management) and 11990 (Protection of Wetlands), and United States Department of Energy (DOE) Guidelines for Compliance with Floodplain/Wetland Environmental Review Requirements (10CFR1022)

Global amphibian population declines

The decline and disappearance of relatively undisturbed populations of amphibians in several high-altitude regions since the 1970s suggests that they may have suffered a global decline, perhaps with a common cause or causes¹⁻³. Houlahan et al.⁴ examined means of trends for 936 amphibian populations and concluded that global declines began in the late 1950s, peaked in the 1960s, and have continued at a reduced rate since. Here we re-analyse their data using a method that accounts for the sampling of different populations over different time periods, and find evidence of a mean global decline in monitored populations only in the 1990s. However it is calculated, the global mean not only masks substantial spatial and temporal variation in population trends and sampling effort, but also fails to distinguish between a global decline with global causes and the cumulative effects of local declines with local causes

Perceptions of species abundance, distribution, and diversity: Lessons from four decades of sampling on a government-managed reserve

We examined data relative to species abundance, distribution, and diversity patterns of reptiles and amphibians to determine how perceptions change over time and with level of sampling effort. Location data were compiled on more than one million individual captures or observations of 98 species during a 44-year study period on the US Department of Energy's (DOE) Savannah River Site Natichal Environmental Research Park (SRS-NERP) in South Carolina. We suggest that perceptions of herpetofaunal species diversity are strongly dependent on level of effort and that land management decisions based on short-term data bases for some faunal groups could result in serious errors in environmental management. We provide evidence that acquiring information on biodiversity distribution patterns is compatible with multiyear spatially extensive research programs and also provide a perspective of what might be achieved if long-term, coordinated research efforts were instituted nationwide. To conduct biotic surveys on government- managed lands, we recommend revisions in the methods used by government agencies to acquire and report biodiversity data. We suggest that government and industry employees engaged in biodiversity survey efforts develop proficiency in field identification for one or more major taxonomic groups and be encouraged to measure the status of populations quantitatively with consistent and reliable methodologies. We also suggest that widespread academic cooperation in the dissemination of information on regional patterns of biodiversity could result by establishment of a peer-reviewed, scientifically rigorous journal concerned with status and trends of the biota of the United States