Geographical variation and population structure in the White-rumped Sandpiper Calidris fuscicollis as shown by morphology, mitochondrial DNA and carbon isotope ratios

We studied the population structure of a high arctic breeding wader bird species, the White-rumped Sandpiper Calidris fuscicollis. Breeding adults, chicks and juveniles were sampled at seven localities throughout the species' breeding range in arctic Canada in 1999. The mitochondrial control region was analysed by DNA sequencing, feathers were analysed for carbon isotope ratios (C13/C12) by isotope ratio mass spectrometry, and morphological measurements were analysed using principal component analyses, taking the effect of sex into account (identified by molecular genetic methods). In general, our results support the notion that the White-rumped Sandpiper is a monotypic species with no subspecies, and most of the morphological and genetic variation occurs within sites. Nevertheless, some differences between sites were found. Birds from the two northernmost sites (Ellesmere and Devon Islands) had relatively longer bill and wing and shorter tarsus than birds sampled further south, possibly reflecting genetic differences between populations. The carbon isotope ratios were higher at the easternmost site (Baffin Island), revealing differences in the isotope content of the food. The mtDNA sequences showed no significant differentiation between sites and no pattern of isolation-by-distance was found. Based on the mtDNA variation, the species was estimated to have a long-term effective population size of approximately 9,000 females. The species shows no clear evidence of any population expansion or decline. Our results indicate that carbon isotope ratios, and possibly also certain mtDNA haplotypes, may be useful as tools for identifying the breeding origin of White-rumped Sandpipers on migration and wintering sites.

Use of expert knowledge to elicit population trends for the koala (Phascolarctos cinereus)

Aim: The koala is a widely distributed Australian marsupial with regional populations that are in rapid decline, are stable or have increased in size. This study examined whether it is possible to use expert elicitation to estimate abundance and trends of populations of this species. Diverse opinions exist about estimates of abundance and, consequently, the status of populations. Location: Eastern and south-eastern Australia Methods: Using a structured, four-step question format, a panel of 15 experts estimated population sizes of koalas and changes in those sizes for bioregions within four states. They provided their lowest plausible estimate, highest plausible estimate, best estimate and their degree of confidence that the true values were contained within these upper and lower estimates. We derived estimates of the mean population size of koalas and associated uncertainties for each bioregion and state. Results: On the basis of estimates of mean population sizes for each bioregion and state, we estimated that the total number of koalas for Australia is 329,000 (range 144,000-605,000) with an estimated average decline of 24% over the past three generations and the next three generations. Estimated percentage of loss in Queensland, New South Wales, Victoria and South Australia was 53%, 26%, 14% and 3%, respectively. Main conclusions: It was not necessary to achieve high levels of certainty or consensus among experts before making informed estimates. A quantitative, scientific method for deriving estimates of koala populations and trends was possible, in the absence of empirical data on abundances.

Population structure and effects of inbreeding on milk yield and quality of Murrah buffaloes

To provide data for conservation, selection, and expansion programs of buffalo herds, this study evaluated the history of a population of Murrah buffaloes based on population structure and the effect of inbreeding on accumulated 305-d milk yield (MY), fat yield (FY), protein yield (PY), mozzarella production (MProd), and somatic cell score (SCS). The usefulness of including the individual inbreeding coefficient (F) or individual increase in inbreeding coefficient (Delta F) in the model to describe inbreeding depression was evaluated. Pedigree information from 8,054 animals born between 1976 and 2008 and 4,497 lactation records obtained from 12 herds were used. The realized effective population size was 40.10 +/- 1.27, and the mean F of the entire population was 2.14%. The ratio between the number of founders and ancestors demonstrated the existence of a bottleneck in the pedigree of this population, which may contribute to a reduction of genetic diversity. The effect of F on MY, FY, PY, MProd, and SCS was -1.005 kg, -0.299 kg, -0.246 kg, -1.201 kg, and -0.002 units, and the effect of Delta F transformed to equivalent F (%) for a mean of 2.57 equivalent generations was -4.287 kg, -0.581 kg, -0.383 kg, -2.001 kg, and -0.007 units, respectively. The inbreeding depression observed may have important economic repercussions for production systems. The Delta F can be considered the better of the two indicators of inbreeding depression due to its properties that prevent underestimation of this effect. A designed mating system to avoid inbreeding may be applied to this population to maintain genetic diversity.

Comparison of selective genotyping strategies for prediction of breeding values in a population undergoing selection

Genomewide marker information can improve the reliability of breeding value predictions for young selection candidates in genomic selection. However, the cost of genotyping limits its use to elite animals, and how such selective genotyping affects predictive ability of genomic selection models is an open question. We performed a simulation study to evaluate the quality of breeding value predictions for selection candidates based on different selective genotyping strategies in a population undergoing selection. The genome consisted of 10 chromosomes of 100 cM each. After 5,000 generations of random mating with a population size of 100 (50 males and 50 females), generation G(0) (reference population) was produced via a full factorial mating between the 50 males and 50 females from generation 5,000. Different levels of selection intensities (animals with the largest yield deviation value) in G(0) or random sampling (no selection) were used to produce offspring of G(0) generation (G(1)). Five genotyping strategies were used to choose 500 animals in G(0) to be genotyped: 1) Random: randomly selected animals, 2) Top: animals with largest yield deviation values, 3) Bottom: animals with lowest yield deviations values, 4) Extreme: animals with the 250 largest and the 250 lowest yield deviations values, and 5) Less Related: less genetically related animals. The number of individuals in G(0) and G(1) was fixed at 2,500 each, and different levels of heritability were considered (0.10, 0.25, and 0.50). Additionally, all 5 selective genotyping strategies (Random, Top, Bottom, Extreme, and Less Related) were applied to an indicator trait in generation G(0), and the results were evaluated for the target trait in generation G(1), with the genetic correlation between the 2 traits set to 0.50. The 5 genotyping strategies applied to individuals in G(0) (reference population) were compared in terms of their ability to predict the genetic values of the animals in G(1) (selection candidates). Lower correlations between genomic-based estimates of breeding values (GEBV) and true breeding values (TBV) were obtained when using the Bottom strategy. For Random, Extreme, and Less Related strategies, the correlation between GEBV and TBV became slightly larger as selection intensity decreased and was largest when no selection occurred. These 3 strategies were better than the Top approach. In addition, the Extreme, Random, and Less Related strategies had smaller predictive mean squared errors (PMSE) followed by the Top and Bottom methods. Overall, the Extreme genotyping strategy led to the best predictive ability of breeding values, indicating that animals with extreme yield deviations values in a reference population are the most informative when training genomic selection models.

Geographic Distribution and Population Estimate of Leaf-cutting Ants of the Genus Acromyrmex (Hymenoptera: Formicidae) in Southwestern Bahia

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Seasonal population dynamics and the genetic structure of the mosquito vector Aedes aegypti in São Paulo, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Spatio-temporal dynamics and transition from asymptotic equilibrium to bounded oscillations in Chrysomya albiceps (Diptera, Calliphoridae)

The sensitivity of parameters that govern the stability of population size in Chrysomya albiceps and describe its spatial dynamics was evaluated in this study. The dynamics was modeled using a density-dependent model of population growth. Our simulations show that variation in fecundity and mainly in survival has marked effect on the dynamics and indicates the possibility of transitions from one-point equilibrium to bounded oscillations. C. albiceps exhibits a two-point limit cycle, but the introduction of diffusive dispersal induces an evident qualitative shift from two-point limit cycle to a one fixed-point dynamics. Population dynamics of C. albiceps is here compared to dynamics of Cochliomyia macellaria, C. megacephala and C. putoria.

Fermi acceleration with memory-dependent excitation

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estimation of population profiles of two strains of the fly Megaselia scalaris (Diptera: Phoridae) by bootstrap simulation

A partir de perfis populacionais experimentais de linhagens do díptero forídeo Megaselia scalaris, foi determinado o número mínimo de perfis amostrais que devem ser repetidos, via processo de simulação bootstrap, para se ter uma estimativa confiável do perfil médio populacional e apresentar estimativas do erro-padrão como medida da precisão das simulações realizadas. Os dados originais são provenientes de populações experimentais fundadas com as linhagens SR e R4, com três réplicas cada, e que foram mantidas por 33 semanas pela técnica da transferência seriada em câmara de temperatura constante (25 ± 1,0ºC). A variável usada foi tamanho populacional e o modelo adotado para cada perfíl foi o de um processo estocástico estacionário. Por meio das simulações, os perfis de três populações experimentais foram amplificados, determinando-se, dessa forma, o tamanho mínimo de amostra. Fixado o tamanho de amostra, simulações bootstrap foram realizadas para construção de intervalos de confiança e comparação dos perfis médios populacionais das duas linhagens. Os resultados mostram que com o tamanho de amostra igual a 50 inicia-se o processo de estabilização dos valores médios.

Genetic variation along time in a brazilian population of Aedes aegypti (Diptera : Culicidae), detected by changes in the esterase patterns

Aedes aegypti from the Brazilian cities of Sao Jose do Rio Preto (SJ) and Goiania (GO) were analyzed as to their esterase patterns and the results were compared with data obtained about 5 years before for SJ population. Esterase bands not detected in the previous study were now observed in mosquitoes from both SJ and GO populations, being the last considered a population resistant to insecticides. Other similarities between SJ and GO populations in this study, and some differences in comparison with the previous data on SJ were observed, involving, in addition to changes in band type, changes in frequency of mosquitoes expressing them and differential gene activation during development. As it is generally true for genetic features, changes in the esterase patterns are expected to be the result of factors such as selection by environmental conditions and genetic drift. In the present case, continuous use of insecticides aiming mosquito population size control in SJ by sanitary authorities could be involved in the observed changes. Changed esterases were classified as carboxylesterases and cholinesterases, which are enzymes already shown to take part in the development of resistance in several organisms. In addition, data obtained in the elapsed time by authorities responsible for the mosquito control has shown increasing insecticide resistance of SJ population mosquitoes parallel to increase in the total amount of esterases, reinforcing the mentioned possibility.

The spatial dynamics of native and introduced blowflies (Dipt., Calliphoridae)

The spatial dynamics of three blowfly species was investigated using a spatially extended model of density-dependent population growth and the results indicate an overall stabilizing effect. Introduction of diffusive dispersal induced a quantitative effect of damping variation in population size on the route to a one-fixed point equilibrium in the native species, Cochliomyia macellaria. On the other hand, diffusive dispersal caused qualitative shifts in the dynamics of two invading species, Chrysomya megacephala and Chrysomya putoria. In both species diffusive dispersal can produce a qualitative shift from a two-point limit cycle to a one fixed-point dynamics. Quantitatively, dispersal also has the effect of damping oscillations in population size in the invading species.

Solving the Levins' paradox in the logistic model to the population growth

We introduce a new method to improve Markov maps by means of a Bayesian approach. The method starts from an initial map model, wherefrom a likelihood function is defined which is regulated by a temperature-like parameter. Then, the new constraints are added by the use of Bayes rule in the prior distribution. We applied the method to the logistic map of population growth of a single species. We show that the population size is limited for all ranges of parameters, allowing thus to overcome difficulties in interpretation of the concept of carrying capacity known as the Levins paradox. © Published under licence by IOP Publishing Ltd.

Population, social equity and changing production patterns

Includes bibliography

Distribution of Brazilian dermatologists according to geographic location, population and HDI of municipalities: an ecological study

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm

Population genetics theory predicts loss in genetic variability because of drift and inbreeding in isolated plant populations; however, it has been argued that long-distance pollination and seed dispersal may be able to maintain gene flow, even in highly fragmented landscapes. We tested how historical effective population size, historical migration and contemporary landscape structure, such as forest cover, patch isolation and matrix resistance, affect genetic variability and differentiation of seedlings in a tropical palm (Euterpe edulis) in a human-modified rainforest. We sampled 16 sites within five landscapes in the Brazilian Atlantic forest and assessed genetic variability and differentiation using eight microsatellite loci. Using a model selection approach, none of the covariates explained the variation observed in inbreeding coefficients among populations. The variation in genetic diversity among sites was best explained by historical effective population size. Allelic richness was best explained by historical effective population size and matrix resistance, whereas genetic differentiation was explained by matrix resistance. Coalescence analysis revealed high historical migration between sites within landscapes and constant historical population sizes, showing that the genetic differentiation is most likely due to recent changes caused by habitat loss and fragmentation. Overall, recent landscape changes have a greater influence on among-population genetic variation than historical gene flow process. As immediate restoration actions in landscapes with low forest amount, the development of more permeable matrices to allow the movement of pollinators and seed dispersers may be an effective strategy to maintain microevolutionary processes.