Measuring inbreeding depression in the wild: the old ways are the best

Measuring inbreeding depression in normally outbreeding natural populations is an uphill task, because it requires inbreeding coefficients that are calculated from pedigrees. Instead of calculating inbreeding coefficients directly, several studies have reported the use of microsatellite-derived metrics, such as heterozygosity, to infer relative inbreeding among individuals. In two new papers, Slate et al. and Balloux et al. show that these molecular metrics are often only weakly correlated with inbreeding coefficients, and that correlations between heterozygosity and fitness require a new interpretation.     

Estimation of individual level of inbreeding using relatedness measures in haplodiploids

Although male haploidy in haplodiploid species aids purging of deleterious alleles, haplodiploid animals may nevertheless suffer significant negative effects of inbreeding. The effects may even be stronger in social Hymenoptera because the negative fitness consequences may be expressed at two levels: the individual level (inbred queens) and colony level (inbred workers). Surprisingly, in natural populations the impact of inbreeding on fitness has been studied in very few insects, and even fewer haplodiploid ones. Hence there is currently little understanding of the potential effects of inbreeding. One reason may be the difficulties in estimating inbreeding especially at the individual level, apart from the additional problems posed by haplodiploidy. In order to study the impact of inbreeding, its individual level must be estimated as precisely as possible. When the population pedigree is unknown, relatedness-based estimates of the individual inbreeding coefficient can be used to estimate inbreeding. Here we examine the relationship between inbreeding coefficients and relatedness in diploid and haplodiploid organisms, and provide guidelines for estimating inbreeding both at the individual and the colony level. Received 7 March 2005; revised 18 April 2005, accepted 20 April 2005. An erratum to this article is available at .     

Two are better than one: combining landscape genomics and common gardens for detecting local adaptation in forest trees

Predicting likely species responses to an alteration of their local environment is key to decision‐making in resource management, ecosystem restoration and biodiversity conservation practice in the face of global human‐induced habitat disturbance. This is especially true for forest trees which are a dominant life form on Earth and play a central role in supporting diverse communities and structuring a wide range of ecosystems. In Europe, it is expected that most forest tree species will not be able to migrate North fast enough to follow the estimated temperature isocline shift given current predictions for rapid climate warming. In this context, a topical question for forest genetics research is to quantify the ability for tree species to adapt locally to strongly altered environmental conditions (Kremer et al. 2012 ). Identifying environmental factors driving local adaptation is, however, a major challenge for evolutionary biology and ecology in general but is particularly difficult in trees given their large individual and population size and long generation time. Empirical evaluation of local adaptation in trees has traditionally relied on fastidious long‐term common garden experiments (provenance trials) now supplemented by reference genome sequence analysis for a handful of economically valuable species. However, such resources have been lacking for most tree species despite their ecological importance in supporting whole ecosystems. In this issue of Molecular Ecology, De Kort et al. ( 2014 ) provide original and convincing empirical evidence of local adaptation to temperature in black alder, Alnus glutinosa L. Gaertn, a surprisingly understudied keystone species supporting riparian ecosystems. Here, De Kort et al. ( 2014 ) use an innovative empirical approach complementing state‐of‐the‐art landscape genomics analysis of A. glutinosa populations sampled in natura across a regional climate gradient with phenotypic trait assessment in a common garden experiment (Fig. 1 ). By combining the two methods, De Kort et al. ( 2014 ) were able to detect unequivocal association between temperature and phenotypic traits such as leaf size as well as with genetic loci putatively under divergent selection for temperature. The research by De Kort et al. ( 2014 ) provides valuable insight into adaptive response to temperature variation for an ecologically important species and demonstrates the usefulness of an integrated approach for empirical evaluation of local adaptation in nonmodel species (Sork et al. 2013 ).     

Estimating the prevalence of inbreeding from incomplete pedigrees

A previous review of inbreeding in natural populations suggested that close inbreeding (inbreeding coefficient f = 0.25) is generally rare in wild birds and mammals. However, the review did not assess rates of moderate inbreeding (f = 0.125), which may make a rather larger contribution to overall inbreeding in a population. Furthermore, previous studies may have underestimated the prevalence of inbreeding in wild populations with incomplete pedigrees. By categorizing inbreeding events by the relationship of the parental pair, we suggest a simple method for estimating rates of close and moderate inbreeding from incomplete pedigree data. We applied this method to three wild populations of ruminants: red deer on Rum, Scotland, Soay sheep on Hirta, Scotland and reintroduced Arabian oryx on the Jiddat-al-Harasis, Oman. Although paternal half-sib pairs were the most common category of inbreeding in all three populations, there was considerable variation among populations in the frequencies of the various categories of inbreeding. This variation may be largely explained by differences in population size and dynamics, in maternal and paternal sibship size and in the overlap of reproductive lifespan of consecutive generations. Close and moderate inbreeding appear to be a routine part of breeding behaviour in these ruminant populations.     

Estimation of inbreeding by random walks in pedigrees

Summary Wright and McPhee (1925) suggested a method of estimating the inbreeding coefficient of an individual based on the probability that a pair of lineages traced randomly, one through the maternal line and one through the paternal line, both contain a common ancestor. (One-half of this probability is an unbiased estimate of the inbreeding coefficient). In their procedure, maternal and paternal lines are chosen in pairs, and comparisons are made only between the lines in a pair. A more efficient procedure is to compare every maternal line with every paternal line, a procedure used by Robertson and Mason (1954). In this paper we provide estimates of the sampling variance of the inbreeding coefficient as estimated by the multiple comparison method, and we examine the relative efficiency of this method and the Wright-McPhee procedure. Formulae are also provided for ascertaining the optimal sampling method for estimating the average inbreeding coefficient of a group or herd.Work supported by NSF grant GB43209, NIH grant GM21732 and by Research Career Award GM0002301.     

Bird communication: two voices are better than one

How do emperor penguins find their mates on a featureless ice flow, packed at densities of ten animals per square meter? A recent study has revealed how use of their 'two-voice' calls enables emperor penguins to locate their mates and chicks under some of nature's most extreme conditions.     

Protein transport: two translocons are better than one

The translocon is the gateway to the endoplasmic reticulum (ER). In yeast this is the Sec61p complex. However, new evidence suggests that a second translocon containing the Sec61p homolog Ssh1p provides important flexibility to the ER translocation machinery.     

Pharmacological chaperoning: two 'hits' are better than one

Protein folding disorders comprise a rapidly growing group of diseases that involve virtually every organ system and affect individuals of all ages. Their principal pathology is the inability of a protein to acquire or maintain its physiological three-dimensional structure. In cells, this generally results in one of three outcomes: accumulation of misfolded protein aggregates, cell death, or recognition by cellular quality control machinery and rapid degradation. Large-scale screening efforts to identify and design small molecules that either repair the folding defect or enable the protein to escape degradation have been encouraging. However, most compounds identified to date restore only a small fraction of molecules to the normal folding pathway, and hence are relatively poor therapeutic candidates. Results published by Wang et al. in this issue of the Biochemical Journal show that, for mutant forms of two ABC (ATP-Binding-Cassette) transporters, P-glycoprotein and CFTR (cystic fibrosis transmembrane conductance regulator), modest correction of trafficking by single agents can be additive when multiple compounds are used in combination. These findings raise the intriguing possibility that corrector molecules acting at different steps along the folding pathway might provide a multidrug approach to human protein folding disorders.     

Dynein motility: four heads are better than two

Cytoplasmic dynein is a microtubule-based motor protein that transports membranes in cells. The movement driven by a single dynein molecule in vitro is not as robust as dynein-driven movements in cells. A new study suggests that transport by multiple dyneins is more similar to cellular motions.     

Vital imaging: Two photons are better than one

The recently developed technique of two-photon fluorescence microscopy causes much less photodamage than conventional confocal microscopy, expanding the possibilities for imaging living specimens.     

Circadian clockwork: two loops are better than one

The spectacularly successful race over the past three years to place our understanding of the circadian clockwork of mammals into a molecular framework is beginning to yield the cardinal example of the molecular-genetic control of behaviour. This perspective describes recent evidence for the conservation of a double-loop, autoregulatory feedback mechanism across the best understood eukaryotic circadian systems, and discusses how these findings may illuminate some long-standing puzzles concerning our subliminal sense of circadian time.     

The relevance of pedigrees in the conservation genomics era

Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long-standing tools available to manage genetics—the pedigree—has been widely used to characterize diversity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome-wide functional diversity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well-informed sampling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.     

Cargo transport: two motors are sometimes better than one

Molecular motor proteins are crucial for the proper distribution of organelles and vesicles in cells. Much of our current understanding of how motors function stems from studies of single motors moving cargos in vitro. More recently, however, there has been mounting evidence that the cooperation of multiple motors in moving cargos and the regulation of motor-filament affinity could be key mechanisms that cells utilize to regulate cargo transport. Here, we review these recent advances and present a picture of how the different mechanisms of regulating the number of motors moving a cargo could facilitate cellular functions.     

Odor recognition memory: two encoding trials are better than one

The primary purpose of this study was to determine the effect of one versus two encoding trials in the classical yes/no recognition memory paradigm using olfactory stimuli. A group of 24 young adults rated 18 standard microencapsulated odorant targets for familiarity (first encoding block) or pleasantness (second encoding block). Once-encoded targets were in only one block and twice-encoded targets were in both, with items counterbalanced across participants. Participants performed a 20-min nonverbal distractor task followed by a yes/no recognition test incorporating 18 additional odors as foils. Memory performance for twice-encoded targets was superior to that for once-encoded targets. For once-encoded targets, performance did not differ between those rated for familiarity versus those rated for pleasantness. Less pleasant odors produced overall better recognition, with a tendency for less familiar odors to produce overall better recognition. There was a tendency for the second encoding trial to have a larger effect for less pleasant or familiar odors than for more pleasant or familiar odors. The main conclusion is that recognition memory for odors is better for items encoded two times than for items encoded only once. Implications of these findings and suggestions for future research are discussed.