Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences

Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (~800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.

Tracking the fin trade: Genetic stock identification in western Atlantic scalloped hammerhead sharks Sphyrna lewini

Location or stock-specific landing data are necessary to improve management of shark stocks, especially those imperiled by overexploitation as a result of the international shark fin trade. In the current absence of catch monitoring directly at extraction sites, genetic stock identification of fins collected from major market supply chain endpoints offers an overlooked but potentially useful approach for tracing the fins back to their geographical, or stock of, origin. To demonstrate the feasibility of this approach, we used mitochondrial control region (mtCR) sequences to trace the broad geographical origin of 62 Hong Kong market-derived Sphyrna lewini fins. Of these fins 21% were derived from the western Atlantic, where this species is listed as 'Endangered' by the International Union for the Conservation of Nature (IUCN). We also show that S. lewini mtCR sequences are geographically segregated in the western Atlantic (overall ΦST = 0.74, n = 177 sharks), indicating that breeding females either remain close to, or home back to, their natal region for parturition. Mixed stock analysis simulations showed that it is possible to estimate the relative contributions of these mitochondrial stocks to fin mixtures in globally sourced trade hubs. These findings underscore the feasibility of using genetic stock identification to source market-derived shark fins to obtain essential and otherwise unavailable data on exploitation levels, and thus to productively inform stock assessment and management of S. lewini and potentially also of other fished shark species. © Inter-Research 2009.

Report of the Stock Identification Methods Working Group (SIMWG) 2016

The Stock Identification Methods Working Group (SIMWG) worked by correspondence in 2016. The working group was chaired by Lisa Kerr (USA). The work plan for SIMWG in 2016 comprised four Terms of Reference (ToR), some of which are continuing goals for SIMWG: a ) Review recent advances in stock identification methods; b ) Build a reference database with updated information on known biological stocks for species of ICES interest; c ) Provide technical reviews and expert opinions on matters of stock identifica-tion, as requested by specific Working Groups and SCICOM; d ) Review and report on advances in mixed stock analysis, and assess their po-tential role in improving precision of stock assessment. ToR a) is an ongoing task of SIMWG in which we provide a comprehensive update on recent applications of stock identification techniques to ICES species of interest, summa-rize new approaches in stock identification, and novel combinations of existing applica-tions. ToR b) is a multi-annual ToR in which SIMWG has taking steps to build a reference data-base consisting of SIMWG reviews of issues of stock identity for ICES species. ToR c) is a key ongoing task by SIMWG in which we addresses specific requests by ICES working groups for technical advice on issues of stock identity. This year we provided advice on mackerel in the Northeast Atlantic as requested by WGWIDE. ToR d) is a multi-annual ToR that is focused on tracking developments in the application of mixed stock analysis and the integration of this information into assessment and management.

Conservation Genetics of Exploited Finnish Salmonid Fishes

Genetic diversity is one of the levels of biodiversity that the World Conservation Union (IUCN) has recognized as being important to preserve. This is because genetic diversity is fundamental to the future evolution and to the adaptive flexibility of a species to respond to the inherently dynamic nature of the natural world. Therefore, the key to maintaining biodiversity and healthy ecosystems is to identify, monitor and maintain locally-adapted populations, along with their unique gene pools, upon which future adaptation depends. Thus, conservation genetics deals with the genetic factors that affect extinction risk and the genetic management regimes required to minimize the risk. The conservation of exploited species, such as salmonid fishes, is particularly challenging due to the conflicts between different interest groups. In this thesis, I conduct a series of conservation genetic studies on primarily Finnish populations of two salmonid fish species (European grayling, Thymallus thymallus, and lake-run brown trout, Salmo trutta) which are popular recreational game fishes in Finland. The general aim of these studies was to apply and develop population genetic approaches to assist conservation and sustainable harvest of these populations. The approaches applied included: i) the characterization of population genetic structure at national and local scales; ii) the identification of management units and the prioritization of populations for conservation based on evolutionary forces shaping indigenous gene pools; iii) the detection of population declines and the testing of the assumptions underlying these tests; and iv) the evaluation of the contribution of natural populations to a mixed stock fishery. Based on microsatellite analyses, clear genetic structuring of exploited Finnish grayling and brown trout populations was detected at both national and local scales. Finnish grayling were clustered into three genetically distinct groups, corresponding to northern, Baltic and south-eastern geographic areas of Finland. The genetic differentiation among and within population groups of grayling ranged from moderate to high levels. Such strong genetic structuring combined with low genetic diversity strongly indicates that genetic drift plays a major role in the evolution of grayling populations. Further analyses of European grayling covering the majority of the species’ distribution range indicated a strong global footprint of population decline. Using a coalescent approach the beginning of population reduction was dated back to 1 000-10 000 years ago (ca. 200-2 000 generations). Forward simulations demonstrated that the bottleneck footprints measured using the M ratio can persist within small populations much longer than previously anticipated in the face of low levels of gene flow. In contrast to the M ratio, two alternative methods for genetic bottleneck detection identified recent bottlenecks in six grayling populations that warrant future monitoring. Consistent with the predominant role of random genetic drift, the effective population size (N_e) estimates of all grayling populations were very low with the majority of N_e estimates below 50. Taken together, highly structured local populations, limited gene flow and the small N_e of grayling populations indicates that grayling populations are vulnerable to overexploitation and, hence, monitoring and careful management using the precautionary principles is required not only in Finland but throughout Europe. Population genetic analyses of lake-run brown trout populations in the Inari basin (northernmost Finland) revealed hierarchical population structure where individual populations were clustered into three population groups largely corresponding to different geographic regions of the basin. Similar to my earlier work with European grayling, the genetic differentiation among and within population groups of lake-run brown trout was relatively high. Such strong differentiation indicated that the power to determine the relative contribution of populations in mixed fisheries should be relatively high. Consistent with these expectations, high accuracy and precision in mixed stock analysis (MSA) simulations were observed. Application of MSA to indigenous fish caught in the Inari basin identified altogether twelve populations that contributed significantly to mixed stock fisheries with the Ivalojoki river system being the major contributor (70%) to the total catch. When the contribution of wild trout populations to the fisheries was evaluated regionally, geographically nearby populations were the main contributors to the local catches. MSA also revealed a clear separation between the lower and upper reaches of Ivalojoki river system – in contrast to lower reaches of the Ivalojoki river that contributed considerably to the catch, populations from the upper reaches of the Ivalojoki river system (>140 km from the river mouth) did not contribute significantly to the fishery. This could be related to the available habitat size but also associated with a resident type life history and increased cost of migration. The studies in my thesis highlight the importance of dense sampling and wide population coverage at the scale being studied and also demonstrate the importance of critical evaluation of the underlying assumptions of the population genetic models and methods used. These results have important implications for conservation and sustainable fisheries management of Finnish populations of European grayling and brown trout in the Inari basin.

Genetic patterns in recovered specimens of Caretta caretta from the Adriatic Sea

The Adriatic Sea is considered a feeding and developmental area for Mediterranean loggerhead turtles, but this area is severely threatened by human impacts. In the Adriatic Sea loggerhead turtles are often found stranded or floating, but they are also recovered as by-catch from fishing activities. Nevertheless, information about population structuring and origin of individuals found in the Adriatic Sea are still limited. Cooperation with fishermen and a good network of voluntary collaborators are essential for understanding their distribution, ecology and for developing conservation strategies in the Adriatic Sea. In this study, a comparative analysis of biometric data and DNA sequence polymorphism of the long fragment of the mitochondrial control region was carried out on ninety-three loggerheads recovered from three feeding areas in the Adriatic Sea: North-western, North-eastern and South Adriatic. Differences in turtles body sizes (e.g. Straight Carapace Length) among the three recovery areas and relationship between SCL and the type of recovery were investigated. The origin of turtles from Mediterranean rookeries and the use of the Adriatic feeding habitats by loggerheads in different life-stages were assessed to understand the migratory pathway of the species. The analysis of biometric data revealed a significant difference in turtle sizes between the Southern and the Northern Adriatic. Moreover, size of captured turtles resulted significantly different from the size of stranded and floating individuals. Actually, neritic sub-adults and adults are more affected by incidental captures than juveniles because of their feeding behavior. The Bayesian mixed-stock analysis showed a strong genetic relationship between the Adriatic aggregates and Mediterranean rookeries, while a low pro¬portion of individuals of Atlantic origin were detected in the Adriatic feeding grounds. The presence of migratory pathways towards the Adriatic Sea due to the surface current system was reinforced by the finding of individuals bearing haplotypes endemic to the nesting populations of Libya, Greece and Israel. A relatively high contribution from Turkey and Cyprus to the Northwest and South Adriatic populations was identified when the three sampled areas were analyzed independently. These results have to be taken in account in a conservative perspective, since coastal hazards, affecting the population of turtles feeding in the Adriatic Sea may also affect the nesting populations of the Eastern Mediterranean with a unique genetic pattern.

Formulating Mixed Models for Experiments, Including Longitudinal Experiments

Mixed models have become important in analyzing the results of experiments, particularly those that require more complicated models (e.g., those that involve longitudinal data). This article describes a method for deriving the terms in a mixed model. Our approach extends an earlier method by Brien and Bailey to explicitly identify terms for which autocorrelation and smooth trend arising from longitudinal observations need to be incorporated in the model. At the same time we retain the principle that the model used should include, at least, all the terms that are justified by the randomization. This is done by dividing the factors into sets, called tiers, based on the randomization and determining the crossing and nesting relationships between factors. The method is applied to formulate mixed models for a wide range of examples. We also describe the mixed model analysis of data from a three-phase experiment to investigate the effect of time of refinement on Eucalyptus pulp from four different sources. Cubic smoothing splines are used to describe differences in the trend over time and unstructured covariance matrices between times are found to be necessary.

A methodology for analysis of sugarcane productivity trends - I. Analysis across districts

Historically, few articles have addressed the use of district level mill production data for analysing the effect of varietal change on sugarcane productivity trends. This appears to be due to lack of compiled district data sets and appropriate methods by which to analyse these data. Recently, varietal data on tonnes of sugarcane per hectare (TCH), sugar content (CCS), and their product, tonnes of sugar content per hectare (TSH) on a district basis, have been compiled. This study was conducted to develop a methodology for regular analysis of such data from mill districts to assess productivity trends over time, accounting for variety and variety x environment interaction effects for 3 mill districts (Mulgrave, Babinda, and Tully) from 1958 to 1995. Restricted maximum likelihood methodology was used to analyse the district level data and best linear unbiased predictors for random effects, and best linear unbiased estimates for fixed effects were computed in a mixed model analysis. In the combined analysis over districts, Q124 was the top ranking variety for TCH, and Q120 was top ranking for both CCS and TSH. Overall production for TCH increased over the 38-year period investigated. Some of this increase can be attributed to varietal improvement, although the predictors for TCH have shown little progress since the introduction of Q99 in 1976. Although smaller gains have been made in varietal improvement for CCS, overall production for CCS decreased over the 38 years due to non-varietal factors. Varietal improvement in TSH appears to have peaked in the mid-1980s. Overall production for TSH remained stable over time due to the varietal increase in TCH and the non-varietal decrease in CCS.

Analysis of multi-scale systemic risk in Brazil's financial market

This work analyzes whether the relationship between risk and returns predicted by the Capital Asset Pricing Model (CAPM) is valid in the Brazilian stock market. The analysis is based on discrete wavelet decomposition on different time scales. This technique allows to analyze the relationship between different time horizons, since the short-term ones (2 to 4 days) up to the long-term ones (64 to 128 days). The results indicate that there is a negative or null relationship between systemic risk and returns for Brazil from 2004 to 2007. As the average excess return of a market portfolio in relation to a risk-free asset during that period was positive, it would be expected this relationship to be positive. That is, higher systematic risk should result in higher excess returns, which did not occur. Therefore, during that period, appropriate compensation for systemic risk was not observed in the Brazilian market. The scales that proved to be most significant to the risk-return relation were the first three, which corresponded to short-term time horizons. When treating differently, year-by-year, and consequently separating positive and negative premiums, some relevance is found, during some years, in the risk/return relation predicted by the CAPM. However, this pattern did not persist throughout the years. Therefore, there is not any evidence strong enough confirming that the asset pricing follows the model.

Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology

Genome-wide association studies (GWAS) have been widely used in genetic dissection of complex traits. However, common methods are all based on a fixed-SNP-effect mixed linear model (MLM) and single marker analysis, such as efficient mixed model analysis (EMMA). These methods require Bonferroni correction for multiple tests, which often is too conservative when the number of markers is extremely large. To address this concern, we proposed a random-SNP-effect MLM (RMLM) and a multi-locus RMLM (MRMLM) for GWAS. The RMLM simply treats the SNP-effect as random, but it allows a modified Bonferroni correction to be used to calculate the threshold p value for significance tests. The MRMLM is a multi-locus model including markers selected from the RMLM method with a less stringent selection criterion. Due to the multi-locus nature, no multiple test correction is needed. Simulation studies show that the MRMLM is more powerful in QTN detection and more accurate in QTN effect estimation than the RMLM, which in turn is more powerful and accurate than the EMMA. To demonstrate the new methods, we analyzed six flowering time related traits in Arabidopsis thaliana and detected more genes than previous reported using the EMMA. Therefore, the MRMLM provides an alternative for multi-locus GWAS.

Recursive hierarchic segmentation analysis of bone mineral density changes on digital panoramic images

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

La convivialità urbana nei quartieri di Milano, Bologna e Roma. Un'analisi mixed-methods sulle Social Streets

Le Social Street sono gruppi di vicini di casa che vogliono ricreare legami di convivialità avendo notato un indebolimento delle relazioni sociali nei loro quartieri. Nascono come gruppi online, tramite la piattaforma Facebook, per materializzarsi in incontri offline andando a costruire legami conviviali grazie pratiche di socialità, inclusività e gratuità. Questa Tesi ha come obiettivo l’analisi dei profili socio-demografici degli Streeter e dei quartieri coinvolti per comprendere come sia possibile creare convivialità e come la variabile urbana intervenga in questi processi. Inoltre, si vuole comprendere le dinamiche di attaccamento al quartiere, gli interessi portati avanti dagli Streeter, il loro profilo civico e il posizionamento di quest’esperienza rispetto all’associazionismo tradizionale. Per perseguire l’obiettivo della ricerca, sono state studiate le tre città che vedono la maggiore presenza di Social Street: Milano, Bologna, Roma. La ricerca ha previsto sia un’analisi degli Streeter grazie a un questionario online replicato in tutti i contesti. Inoltre, sono state realizzate 131 interviste ad amministratori e fondatori di Social Street e condotte osservazioni etnografiche e netnografiche. I risultati mostrano come gli Streeter siano appartenenti alle classi medio-alte, tra trenta e cinquanta anni, che hanno sperimentato la mobilità tra un quartiere e l’altro o tra diversi contesi nazionali ed internazionali e trovano nelle Social Street un modo per creare legami di vicinato che hanno perso nei loro trasferimenti. Gli stessi quartieri dove si diffondono le Social Street sono agiati e vi è una buona corrispondenza tra Streeter e modello della centralità sociale elaborato da Milbrath (1965) per cui anche la partecipazione civica è molto sentita tra gli aderenti alle Social Street. Il contributo di questa Tesi al dibattito sociologico risiede nell’aver offerto un’analisi empirica di un’azione collettiva a livello urbano, quella delle Social Street, mostrando come vi sia circolarità tra azione e contesto grazie all’azione mutualistica conviviale.

Comparação entre o dano muscular de flexores do cotovelo e extensores do joelho em idosos= : Muscle damage comparison between elbow flexors and knee extensors in older adults

Universidade Estadual de Campinas . Faculdade de Educação Física

Effect of eccentric contraction velocity on muscle damage in repeated bouts of elbow flexor exercise

Eccentric exercise induces muscle damage, but controversy exists concerning the effect of contraction velocity on the magnitude of muscle damage, and little is known about the effect of contraction velocity on the repeated-bout effect. This study examined slow (60 degrees.s(-1)) and fast (180 degrees.s(-1)) velocity eccentric exercises for changes in indirect markers of muscle damage following 3 exercise bouts that were performed every 2 weeks. Fifteen young men were divided into 2 groups based on the velocity of eccentric exercise: 7 in the Ecc60 (60 degrees.s(-1)) group, and 8 in the Ecc180 (180 degrees.s(-1)) group. The exercise consisted of 30 maximal eccentric contractions of the elbow flexors at each velocity, in which the elbow joint was forcibly extended from 60 degrees to 180 degrees (full extension) on an isokinetic dynamometer. Changes in maximal voluntary isometric contraction strength, range of motion, muscle soreness, and plasma creatine kinase activity before and for 4 days after the exercise were compared in the 2 groups using a mixed-model analysis (group x bout x time). No significant differences between groups were evident for changes in any variables following exercise bouts; however, the changes were significantly smaller (p < 0.05) after the second and third bouts than after the first bout. These results indicate that the contraction velocity does not influence muscle damage or the repeated-bout effect.

Cyclic deformation of bidisperse two-dimensional foams

In-plane deformation of foams was studied experimentally by subjecting bidisperse foams to cycles of traction and compression at a prescribed rate. Each foam contained bubbles of two sizes with given area ratio and one of three initial arrangements: sorted perpendicular to the axis of deformation (iso-strain), sorted parallel to the axis of deformation (iso-stress), or randomly mixed. Image analysis was used to measure the characteristics of the foams, including the number of edges separating small from large bubbles N-sl, the perimeter (surface energy), the distribution of the number of sides of the bubbles, and the topological disorder mu(2)(N). Foams that were initially mixed were found to remain mixed after the deformation. The response of sorted foams, however, depended on the initial geometry, including the area fraction of small bubbles and the total number of bubbles. For a given experiment we found that (i) the perimeter of a sorted foam varied little; (ii) each foam tended towards a mixed state, measured through the saturation of N-sl; and (iii) the topological disorder mu(2)(N) increased up to an "equilibrium" value. The results of different experiments showed that (i) the change in disorder, Delta mu(2)(N), decreased with the area fraction of small bubbles under iso-strain, but was independent of it under iso-stress; and (ii) Delta mu(2)(N) increased with Delta N-sl under iso-strain, but was again independent of it under iso-stress. We offer explanations for these effects in terms of elementary topological processes induced by the deformations that occur at the bubble scale.

Swiss Interdisciplinary Management Programme for Heart Failure (SWIM-HF): a randomised controlled trial study of an outpatient inter-professional management programme for heart failure patients in Switzerland.

PRINCIPLES: International guidelines for heart failure (HF) care recommend the implementation of inter-professional disease management programmes. To date, no such programme has been tested in Switzerland. The aim of this randomised controlled trial (RCT) was to test the effect on hospitalisation, mortality and quality of life of an adult ambulatory disease management programme for patients with HF in Switzerland.METHODS: Consecutive patients admitted to internal medicine in a Swiss university hospital were screened for decompensated HF. A total of 42 eligible patients were randomised to an intervention (n = 22) or usual care group (n = 20). Medical treatment was optimised and lifestyle recommendations were given to all patients. Intervention patients additionally received a home visit by a HF-nurse, followed by 17 telephone calls of decreasing frequency over 12 months, focusing on self-care. Calls from the HF nurse to primary care physicians communicated health concerns and identified goals of care. Data were collected at baseline, 3, 6, 9 and 12 months. Mixed regression analysis (quality of life) was used. Outcome assessment was conducted by researchers blinded to group assignment.RESULTS: After 12 months, 22 (52%) patients had an all-cause re-admission or died. Only 3 patients were hospitalised with HF decompensation. No significant effect of the intervention was found on HF related to quality of life.CONCLUSIONS: An inter-professional disease management programme is possible in the Swiss healthcare setting but effects on outcomes need to be confirmed in larger studies.