Evidence of an Absence of Inbreeding Depression in a Wild Population of Weddell Seals (Leptonychotes weddellii).

Inbreeding depression can reduce the viability of wild populations. Detecting inbreeding depression in the wild is difficult; developing accurate estimates of inbreeding can be time and labor intensive. In this study, we used a two-step modeling procedure to incorporate uncertainty inherent in estimating individual inbreeding coefficients from multilocus genotypes into estimates of inbreeding depression in a population of Weddell seals (Leptonychotes weddellii). The two-step modeling procedure presented in this paper provides a method for estimating the magnitude of a known source of error, which is assumed absent in classic regression models, and incorporating this error into inferences about inbreeding depression. The method is essentially an errors-in-variables regression with non-normal errors in both the dependent and independent variables. These models, therefore, allow for a better evaluation of the uncertainty surrounding the biological importance of inbreeding depression in non-pedigreed wild populations. For this study we genotyped 154 adult female seals from the population in Erebus Bay, Antarctica, at 29 microsatellite loci, 12 of which are novel. We used a statistical evidence approach to inference rather than hypothesis testing because the discovery of both low and high levels of inbreeding are of scientific interest. We found evidence for an absence of inbreeding depression in lifetime reproductive success, adult survival, age at maturity, and the reproductive interval of female seals in this population.

Genetic connectivity for two bear species at wildlife crossing structures in Banff National Park.

Roads can fragment and isolate wildlife populations, which will eventually decrease genetic diversity within populations. Wildlife crossing structures may counteract these impacts, but most crossings are relatively new, and there is little evidence that they facilitate gene flow. We conducted a three-year research project in Banff National Park, Alberta, to evaluate the effectiveness of wildlife crossings to provide genetic connectivity. Our main objective was to determine how the Trans-Canada Highway and crossing structures along it affect gene flow in grizzly (Ursus arctos) and black bears (Ursus americanus). We compared genetic data generated from wildlife crossings with data collected from greater bear populations. We detected a genetic discontinuity at the highway in grizzly bears but not in black bears. We assigned grizzly bears that used crossings to populations north and south of the highway, providing evidence of bidirectional gene flow and genetic admixture. Parentage tests showed that 47% of black bears and 27% of grizzly bears that used crossings successfully bred, including multiple males and females of both species. Differentiating between dispersal and gene flow is difficult, but we documented gene flow by showing migration, reproduction and genetic admixture. We conclude that wildlife crossings allow sufficient gene flow to prevent genetic isolation.

Demographic connectivity for ursid populations at wildlife crossing structures in Banff National Park.

Wildlife crossing structures are one solution to mitigating the fragmentation of wildlife populations caused by roads, but their effectiveness in providing connectivity has only been superficially evaluated. Hundreds of grizzly (Ursus arctos) and black bear (Ursus americanus) passages through under and overpasses have been recorded in Banff National Park, Alberta, Canada. However, the ability of crossing structures to allow individual and population-level movements across road networks remains unknown. In April 2006, we initiated a 3-year investigation into whether crossing structures provide demographic connectivity for grizzly and black bears in Banff National Park. We collected hair with multiple noninvasive methods to obtain genetic samples from grizzly and black bears around the Bow Valley. Our objectives were to determine the number of male and female grizzly and black bears that use crossing structures; examine spatial and temporal patterns of crossings; and estimate the proportions of grizzly and black bear populations in the Bow Valley that use crossing structures. Fifteen grizzly (7 female, 8 male) and 17 black bears (8 female, 9 male) used wildlife crossing structures. The number of individuals detected at wildlife crossing structures was highly correlated with the number of passages in space and time. Grizzly bears used open crossing structures (e.g., overpasses) more often than constricted crossings (e.g., culverts). Peak use of crossing structures for both bear species occurred in July, when high rates of foraging activity coincide with mating season. We compared the number of bears that used crossings with estimates of population abundance from a related study and determined that substantial percentages of grizzly (15.0% in 2006, 19.8% in 2008) and black bear (17.6% in 2006, 11.0% in 2008) populations used crossing structures. On the basis of our results, we concluded wildlife crossing structures provide demographic connectivity for bear populations in Banff National Park.

Landscape influences on genetic differentiation among bull trout populations in a stream-lake network.

This study examined the influence of landscape heterogeneity on genetic differentiation between migratory bull trout (Salvelinus confluentus) populations in Glacier National Park, Montana. An information-theoretic approach was used to compare different conceptual models of dispersal associated with barriers, different models of isolation by distance, and the combined effects of barriers, waterway distance, patch size, and intra- and inter-drainage distribution of populations on genetic differentiation between bull trout populations. The effect of distance between populations on genetic differentiation was best explained by partitioning the effects of mainstem and tributary stream sections. Models that categorized barriers as having a one-way effect (i.e. allowed downstream dispersal) or a two-way effect were best supported. Additionally, patch size and the distribution of populations among drainages influenced genetic differentiation. Genetic differentiation between bull trout populations in Glacier National Park is linked to landscape features that restrict dispersal. However, this analysis illustrates that modelling variability within landscape features, such as dispersal corridors, will benefit landscape genetic analyses. Additionally, the framework used for evaluating the effects of barriers must consider not just barrier presence, but also potential asymmetries in barrier effects with respect to the organism under investigation.

A Graphical Method for Displaying the Model Fit of Item Response Theory Trace Lines.

Item response theory (IRT) is a statistical paradigm for developing educational tests and assessing students. IRT, however, currently lacks an established graphical method for examining model fit for the three-parameter logistic model, the most flexible and popular IRT model in educational testing. A method is presented here to do this. The graph, which is referred to herein as a "bin plot," is the IRT equivalent of a scatterplot for linear regression. Bin plots display a conventional IRT trace line (with ability on the horizontal axis and probability correct on the vertical axis). Students are binned according to how well they performed on the entire test, and the proportion of students in each bin who answered the focal question correctly is displayed on the graph as points above or below the trace line. With this arrangement, the difference between each point and the trace line is the residual for the bin. Confidence intervals can be added to the observed proportions in order to display uncertainty. Computer simulations were used to test four alternative ways for binning students. These simulations showed that binning students according to number of questions they answered correctly on the entire test works best. Simulations also showed confidence intervals for bin plots had coverage probabilities close to nominal values for common testing scenarios, but that there are scenarios in which confidence intervals had inflated error rates.

Sex-biased natal dispersal and inbreeding avoidance in American black bears as revealed by spatial genetic analyses.

We tested the hypothesis that sex-biased natal dispersal reduces close inbreeding in American black bears, a solitary species that exhibits nearly complete male dispersal and female philopatry. Using microsatellite DNA and spatial data from reproductively mature bears (>or= 4 years old), we examined the spatial genetic structure of two distinct populations in New Mexico from 1993 to 2000. As predicted, relatedness (r) and the frequency of close relationships (parent-offspring or full siblings) decreased with distance among female dyads, but little change was observed among male or opposite-sex dyads. Neighbouring females were more closely related than neighbouring males. The potential for inbreeding was low. Most opposite-sex pairs that lived sufficiently close to facilitate mating were unrelated, and few were close relatives. We found no evidence that bears actively avoided inbreeding in their selection of mates from this nearby pool, as mean r and relationship frequencies did not differ between potential and actual mating pairs (determined by parentage analysis). These basic patterns were apparent in both study areas despite a nearly two-fold difference in density. However, the sex bias in dispersal was less pronounced in the lower-density area, based on proportions of bears with male and female relatives residing nearby. This result suggests that male bears may respond to reduced competition by decreasing their rate or distance of dispersal. Evidence supports the hypothesis that inbreeding avoidance is achieved by means of male-biased dispersal but also indicates that competition (for mates or resources) modifies dispersal patterns.

How are humans related to other primates? A guided inquiry laboratory for undergraduate students.

Understanding that phylogenies depict the evolutionary history of species is a critical concept for undergraduate biology students. We present an inquiry-based laboratory exercise exploring this concept in the context of the human phylogeny. This activity reinforces several important biological concepts and skills. Bolstered concepts include that evolution is descent with modification, that evolution is a genetic process, and that humans are closely related to apes. In terms of thinking skills, the lab gives students practice with hypothetical-deductive thinking, quantifying patterns from complex data, and evaluating evidence.

Can random mutation mimic design?: a guided inquiry laboratory for undergraduate students.

Complex biological structures, such as the human eye, have been interpreted as evidence for a creator for over three centuries. This raises the question of whether random mutation can create such adaptations. In this article, we present an inquiry-based laboratory experiment that explores this question using paper airplanes as a model organism. The main task for students in this investigation is to figure out how to simulate paper airplane evolution (including reproduction, inheritance, mutation, and selection). In addition, the lab requires students to practice analytic thinking and to carefully delineate the implications of their results.

Evaluating prey switching in wolf-ungulate systems.

Wolf restoration has become a widely accepted conservation and management practice throughout North America and Europe, though the ecosystem effects of returning top carnivores remain both scientific and societal controversies. Mathematical models predicting and describing wolf-ungulate interactions are typically limited to the wolves' primary prey, with the potential for prey switching in wolf-multiple-ungulate systems only suggested or assumed by a number of investigators. We used insights gained from experiments on small taxa and field data from ongoing wolf-ungulate studies to construct a model of predator diet composition for a wolf-elk-bison system in Yellowstone National Park, Wyoming, USA. The model explicitly incorporates differential vulnerability of the ungulate prey types to predation, predator preference, differences in prey biomass, and the possibility of prey switching. Our model demonstrates wolf diet shifts with changes in relative abundance of the two prey, with the dynamics of this shift dependent on the combined influences of preference, differential vulnerability, relative abundances of prey, and whether or not switching occurs. Differences in vulnerability between elk and bison, and strong wolf preference for elk, result in an abrupt dietary shift occurring only when elk are very rare relative to bison, whereas incorporating switching initiates the dietary shift more gradually and at higher bison-elk ratios. We demonstrate how researchers can apply these equations in newly restored wolf-two-prey systems to empirically evaluate whether prey switching is occurring. Each coefficient in the model has a biological interpretation, and most can be directly estimated from empirical data collected from field studies. Given the potential for switching to dramatically influence predator-prey dynamics and the wide range of expected prey types and abundances in some systems where wolves are present and/or being restored, we suggest that this is an important and productive line of research that should be pursued by ecologists working in wolf-ungulate systems.

Development and Validation of the Conceptual Assessment of Natural Selection (CANS).

We developed and validated the Conceptual Assessment of Natural Selection (CANS), a multiple-choice test designed to assess how well college students understand the central principles of natural selection. The expert panel that reviewed the CANS concluded its questions were relevant to natural selection and generally did a good job sampling the specific concepts they were intended to assess. Student interviews confirmed questions on the CANS provided accurate reflections of how students think about natural selection. And, finally, statistical analysis of student responses using item response theory showed that the CANS did a very good job of estimating how well students understood natural selection. The empirical reliability of the CANS was substantially higher than the Force Concept Inventory, a highly regarded test in physics that has a similar purpose.

Relationship of Effective to Census Size in Fluctuating Populations.

The effective size of a population ( Ne  ) rather than the census size ( N) determines its rate of genetic drift. Knowing the ratio of effective to census size, Ne / N, is useful for estimating the effective size of a population from census data and for examining how different ecological factors influence effective size. Two different multigenerational ratios have been used in the literature based on either the arithmetic mean or the harmonic mean in the denominator. We clarify the interpretation and meaning of these ratios. The arithmetic mean Ne / N ratio compares the total number of real individuals to the long-term effective size of the population. The harmonic mean Ne / N ratio summarizes variation in the Ne / N ratio for each generation. In addition, we show that the ratio of the harmonic mean population size to the arithmetic mean population size provides a useful measure of how much fluctuation in size reduced the effective size of a population. We discuss applications of these ratios and emphasize how to use the harmonic mean Ne / N ratio to estimate the effective size of a population over a period of time for which census counts have been collected.

RESUMEN: El tamaño efectivo de una población ( Ne  ) y no el tamaño censal ( N) determina su tasa de deriva génica. Conocer la proporción del tamaño efectivo con el censal, Ne / N, es de utilidad para estimar el tamaño efectivo de una población a partir de datos censales y para examinar como influyen en el tamaño efectivo diferentes factores ecológicos. Se han utilizado dos diferentes proporciones Ne / N en la literatura basados en la media aritmética o en la media armónica en el denominador. Aclaramos la interpretación y significado de esas proporciones. La media aritmética en la relación Ne / N compara el total de individuos reales con el tamaño efectivo de la población a largo plazo. La relación Ne / N con base en la media armónica sintetiza la variación en la proporción Ne / N para cada generación. Adicionalmente, mostramos que la proporción de la media armónica del tamaño poblacional con la media aritmética del tamaño poblacional es una medida útil de como la fluctuación en tamaño reduce el tamaño efectivo de una población. Discutimos las aplicaciones de estas proporciones y enfatizamos como utilizar la proporción Ne / N basada en la media armónica para estimar el tamaño efectivo de una población en un período de tiempo en el cual se han colectado datos censales.

Misconceptions Yesterday, Today, and Tomorrow.

A recent essay in CBE-Life Sciences Education criticized biology education researchers' use of the term misconceptions and recommended that, in order to be up-to-date with education research, biology education researchers should use alternative terms for students' incorrect ideas in science. We counter that criticism by reviewing the continued use and the meaning of misconceptions in education research today, and describe two key debates that account for the controversy surrounding the term. We then identify and describe two areas of research that have real implications for tomorrow's biology education research and biology instruction: 1) hypotheses about the structure of student knowledge (coherent vs. fragmented) that gives rise to misconceptions; and 2) the "warming trend" that considers the effects of students' motivation, beliefs about the nature of knowledge and learning (their epistemic beliefs), and learning strategies (their cognitive and metacognitive skills) on their ability to change their misconceptions in science. We conclude with a description of proposed future work in biology education research related to misconceptions.

Six classroom exercises to teach natural selection to undergraduate biology students.

Students in introductory biology courses frequently have misconceptions regarding natural selection. In this paper, we describe six activities that biology instructors can use to teach undergraduate students in introductory biology courses how natural selection causes evolution. These activities begin with a lesson introducing students to natural selection and also include discussions on sexual selection, molecular evolution, evolution of complex traits, and the evolution of behavior. The set of six topics gives students the opportunity to see how natural selection operates in a variety of contexts. Pre- and postinstruction testing showed students' understanding of natural selection increased substantially after completing this series of learning activities. Testing throughout this unit showed steadily increasing student understanding, and surveys indicated students enjoyed the activities.

Are Africans, Europeans, and Asians different "races"? A guided-inquiry lab for introducing undergraduate students to genetic diversity and preparing them to study natural selection.

Many students do not recognize that individual organisms within populations vary, and this may make it difficult for them to recognize the essential role variation plays in natural selection. Also, many students have weak scientific reasoning skills, and this makes it difficult for them to recognize misconceptions they might have. This paper describes a 2-h laboratory for college students that introduces them to genetic diversity and gives them practice using hypothetico-deductive reasoning. In brief, the lab presents students with DNA sequences from Africans, Europeans, and Asians, and asks students to determine whether people from each continent qualify as distinct "races." Comparison of the DNA sequences shows that people on each continent are not more similar to one another than to people on other continents, and therefore do not qualify as distinct races. Ninety-four percent of our students reported that the laboratory was interesting, and 79% reported that it was a valuable learning experience. We developed and used a survey to measure the extent to which students recognized variation and its significance within populations and showed that the lab increased student awareness of variation. We also showed that the lab improved the ability of students to construct hypothetico-deductive arguments.

Estimating grizzly and black bear population abundance and trend in Banff National Park using noninvasive genetic sampling.

We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos) and black bear (U. americanus) populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears (N= 73.5, 95% CI = 64-94 in 2006; N= 50.4, 95% CI = 49-59 in 2008) and black bears (N= 62.6, 95% CI = 51-89 in 2006; N= 81.8, 95% CI = 72-102 in 2008) in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males (λ= 0.93, 95% CI = 0.74-1.17) and females (λ= 0.90, 95% CI = 0.67-1.20) using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains.

Permanent genetic resources added to Molecular Ecology Resources Database 1 August 2010-30 September 2010.

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis × Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

Nothing in evolution makes sense except in the light of DNA.

Natural selection is one of the most important concepts for biology students to understand, but students frequently have misconceptions regarding how natural selection operates. Many of these misconceptions, such as a belief in "Lamarckian" evolution, are based on a misunderstanding of inheritance. In this essay, we argue that evolution instructors should clarify the genetic basis of natural selection by discussing examples of DNA sequences that affect fitness. Such examples are useful for showing how natural selection works, for establishing connections between genetics and evolution, and for creating cognitive conflict within students having misconceptions. We describe several examples of genes that instructors might use during lectures, and present preliminary evidence from our classroom that an evolution curriculum rich in DNA sequences is effective at reducing student misconceptions of natural selection.

Twelve microsatellite loci for lake trout (Salvelinus namaycush).

We describe 12 microsatellite loci isolated from lake trout (Salvelinus namaycush). The number of alleles at these loci ranged from two to 11 with an average of 5.3 alleles per locus. The expected heterozygosity ranged from 0.29 to 0.76, with an average of 0.68. Accidental (or illegal) introductions of lake trout into watersheds are decimating native trout populations in the northern Rocky Mountains, and these loci will be useful for identifying the source of these introductions and for estimating the number of founding individuals.

Hybridization rapidly reduces fitness of a native trout in the wild.

Human-mediated hybridization is a leading cause of biodiversity loss worldwide. How hybridization affects fitness and what level of hybridization is permissible pose difficult conservation questions with little empirical information to guide policy and management decisions. This is particularly true for salmonids, where widespread introgression among non-native and native taxa has often created hybrid swarms over extensive geographical areas resulting in genomic extinction. Here, we used parentage analysis with multilocus microsatellite markers to measure how varying levels of genetic introgression with non-native rainbow trout (Oncorhynchus mykiss) affect reproductive success (number of offspring per adult) of native westslope cutthroat trout (Oncorhynchus clarkii lewisi) in the wild. Small amounts of hybridization markedly reduced fitness of male and female trout, with reproductive success sharply declining by approximately 50 per cent, with only 20 per cent admixture. Despite apparent fitness costs, our data suggest that hybridization may spread due to relatively high reproductive success of first-generation hybrids and high reproductive success of a few males with high levels of admixture. This outbreeding depression suggests that even low levels of admixture may have negative effects on fitness in the wild and that policies protecting hybridized populations may need reconsideration.

Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment.

Genotypes are frequently used to identify parentage. Such analysis is notoriously vulnerable to genotyping error, and there is ongoing debate regarding how to solve this problem. Many scientists have used the computer program CERVUS to estimate parentage, and have taken advantage of its option to allow for genotyping error. In this study, we show that the likelihood equations used by versions 1.0 and 2.0 of CERVUS to accommodate genotyping error miscalculate the probability of observing an erroneous genotype. Computer simulation and reanalysis of paternity in Rum red deer show that correcting this error increases success in paternity assignment, and that there is a clear benefit to accommodating genotyping errors when errors are present. A new version of CERVUS (3.0) implementing the corrected likelihood equations is available at http://www.fieldgenetics.com.