The adequacy of aging techniques in vertebrates for rapid estimation of population mortality rates from age distributions

As a key parameter in population dynamics, mortality rates are frequently estimated using mark–recapture data, which requires extensive, long‐term data sets. As a potential rapid alternative, we can measure variables correlated to age, allowing the compilation of population age distributions, from which mortality rates can be derived. However, most studies employing such techniques have ignored their inherent inaccuracy and have thereby failed to provide reliable mortality estimates. In this study, we present a general statistical model linking birth rate, mortality rate, and population age distributions. We next assessed the reliability and data needs (i.e., sample size) for estimating mortality rate of eight different aging techniques. The results revealed that for half of the aging techniques, correlations with age varied considerably, translating into highly variable accuracies when used to estimate mortality rate from age distributions. Telomere length is generally not sufficiently correlated to age to provide reliable mortality rate estimates. DNA methylation, signal‐joint T‐cell recombination excision circle (sjTREC), and racemization are generally more promising techniques to ultimately estimate mortality rate, if a sufficiently high sample size is available. Otolith ring counts, otolithometry, and age‐length keys in fish, and skeletochronology in reptiles, mammals, and amphibians, outperformed all other aging techniques and generated relatively accurate mortality rate estimation with a sample size that can be feasibly obtained. Provided the method chosen is minimizing and estimating the error in age estimation, it is possible to accurately estimate mortality rates from age distributions. The method therewith has the potential to estimate a critical, population dynamic parameter to inform conservation efforts within a limited time frame as opposed to mark–recapture analyses.     

Loss of periodicity in breeding success of waders links to changes in lemming cycles in Arctic ecosystems

Lemming population cycles in the Arctic have an important impact on the Arctic food web, indirectly also affecting breeding success in Arctic‐nesting birds through shared predators. Over the last two decades lemming cycles have changed in amplitude and even disappeared in parts of the Arctic. To examine the large scale effect of these recent changes we re‐analysed published data from the East Atlantic Flyway (EAF), where a relationship between lemming cycles and wader breeding success was earlier found, and new data on breeding success of waders in the East Asian–Australasian Flyway (EAAF). We found that 1) any long‐term periodicities in wader breeding success existed only until the year 2000 in the EAAF and until the 1980s in the EAF; 2) studying these patterns at a smaller spatial scale, where the Siberian–Alaskan breeding grounds were divided into five geographical units largely based on landscape features, breeding success of waders from the EAAF was not correlated to an index of predation pressure, but positively correlated to Arctic summer temperatures in some species. We argue that fading out of lemming cycles in some parts of the Arctic is responsible for faltering periodicity in wader breeding success along both flyways. These changed conditions have not yet resulted in any marked changing trends in breeding success across years, and declining numbers of waders along the EAAF are therefore more likely a result of changing conditions at stop‐over and wintering sites.     

The exception to the rule: retreating ice front makes Bewick's swans Cygnus columbianus bewickii migrate slower in spring than in autumn

In the vast majority of migratory bird species studied so far, spring migration has been found to proceed faster than autumn migration. In spring, selection pressures for rapid migration are purportedly higher, and migratory conditions such as food supply, daylength, and/or wind support may be better than in autumn. In swans, however, spring migration appears to be slower than autumn migration. Based on a comparison of tundra swan Cygnus columbianus tracking data with long‐term temperature data from wheather stations, it has previously been suggested that this was due to a capital breeding strategy (gathering resources for breeding during spring migration) and/or to ice cover constraining spring but not autumn migration. Here we directly test the hypothesis that Bewick's swans Cygnus columbianus bewickii follow the ice front in spring, but not in autumn, by comparing three years of GPS tracking data from individual swans with concurrent ice cover data at five important migratory stop‐over sites. In general, ice constrained the swans in the middle part of spring migration, but not in the first (no ice cover was present in the first part) nor in the last part. In autumn, the swans migrated far ahead of ice formation, possibly in order to prevent being trapped by an early onset of winter. We conclude that spring migration in swans is slower than autumn migration because spring migration speed is constrained by ice cover. This restriction to spring migration speed may be more common in northerly migrating birds that rely on freshwater resources.     

Genomic prediction of genetic merit using LD-based haplotypes in the Nordic Holstein population

Background

A haplotype approach to genomic prediction using high density data in dairy cattle as an alternative to single-marker methods is presented. With the assumption that haplotypes are in stronger linkage disequilibrium (LD) with quantitative trait loci (QTL) than single markers, this study focuses on the use of haplotype blocks (haploblocks) as explanatory variables for genomic prediction. Haploblocks were built based on the LD between markers, which allowed variable reduction. The haploblocks were then used to predict three economically important traits (milk protein, fertility and mastitis) in the Nordic Holstein population.

Results

The haploblock approach improved prediction accuracy compared with the commonly used individual single nucleotide polymorphism (SNP) approach. Furthermore, using an average LD threshold to define the haploblocks (LD≥0.45 between any two markers) increased the prediction accuracies for all three traits, although the improvement was most significant for milk protein (up to 3.1 % improvement in prediction accuracy, compared with the individual SNP approach). Hotelling’s t-tests were performed, confirming the improvement in prediction accuracy for milk protein. Because the phenotypic values were in the form of de-regressed proofs, the improved accuracy for milk protein may be due to higher reliability of the data for this trait compared with the reliability of the mastitis and fertility data. Comparisons between best linear unbiased prediction (BLUP) and Bayesian mixture models also indicated that the Bayesian model produced the most accurate predictions in every scenario for the milk protein trait, and in some scenarios for fertility.

Conclusions

The haploblock approach to genomic prediction is a promising method for genomic selection in animal breeding. Building haploblocks based on LD reduced the number of variables without the loss of information. This method may play an important role in the future genomic prediction involving while genome sequences.     

Triazole fungicides can induce cross-resistance to medical triazoles in Aspergillus fumigatus

Background

Azoles play an important role in the management of Aspergillus diseases. Azole resistance is an emerging global problem in Aspergillus fumigatus, and may develop through patient therapy. In addition, an environmental route of resistance development has been suggested through exposure to 14α-demethylase inhibitors (DMIs). The main resistance mechanism associated with this putative fungicide-driven route is a combination of alterations in the Cyp51A-gene (TR₃₄/L98H). We investigated if TR₃₄/L98H could have developed through exposure to DMIs.

Methods and Findings

Thirty-one compounds that have been authorized for use as fungicides, herbicides, herbicide safeners and plant growth regulators in the Netherlands between 1970 and 2005, were investigated for cross-resistance to medical triazoles. Furthermore, CYP51-protein homology modeling and molecule alignment studies were performed to identify similarity in molecule structure and docking modes. Five triazole DMIs, propiconazole, bromuconazole, tebuconazole, epoxiconazole and difenoconazole, showed very similar molecule structures to the medical triazoles and adopted similar poses while docking the protein. These DMIs also showed the greatest cross-resistance and, importantly, were authorized for use between 1990 and 1996, directly preceding the recovery of the first clinical TR₃₄/L98H isolate in 1998. Through microsatellite genotyping of TR₃₄/L98H isolates we were able to calculate that the first isolate would have arisen in 1997, confirming the results of the abovementioned experiments. Finally, we performed induction experiments to investigate if TR₃₄/L98H could be induced under laboratory conditions. One isolate evolved from two copies of the tandem repeat to three, indicating that fungicide pressure can indeed result in these genomic changes.

Conclusions

Our findings support a fungicide-driven route of TR₃₄/L98H development in A. fumigatus. Similar molecule structure characteristics of five triazole DMIs and the three medical triazoles appear the underlying mechanism of cross resistance development. Our findings have major implications for the assessment of health risks associated with the use of triazole DMIs.     

Time and energy constraints in demanding phases of the annual cycle: an example of time limitation in refuelling migratory swans

The daily metabolizable energy intake of an animal is potentially limited by either the available feeding time or by its capacity to process energy. Animals are generally considered not to be time-limited but rather to be energy-processing-limited. This is concluded from the common observation that an animal's feeding time per day increases with a decrease in food density. We argue that such changes in feeding time are in theory also expected when no constraints are operating. Thus, a study of the constraints on energy intakes of free-living animals should be performed during demanding phases of the year. As an example, we collected data on time and energy budgets of Bewick's swan ( Cygnus columbianus bewickii ) refuelling during migration on fennel pondweed ( Potamogeton pectinatus ) tubers in two years differing two-fold in tuber biomass density. As predicted by time limitation, the feeding time (defined as the time with the head submerged) did not change in response to a change in food biomass density, both within and between years (averaging 12.2 h d⁻¹). Contrary to energy-processing limitation, and again in line with time limitation, the daily metabolizable energy intake varied, being greater in the year with high than in the year with low food densities. We conclude that more studies are needed of animals operating under demanding conditions before it can be assessed whether free-living animals are generally energy-processing- or time-limited.