WorldWideScience

Sample records for structured tuna population

  1. Population genetic structure of skipjack tuna Katsuwonus pelamis from the Indian coast using sequence analysis of the mitochondrial DNA D-loop region

    Digital Repository Service at National Institute of Oceanography (India)

    Menezes, M.R.; Kumar, G.; Kunal, S.P.

    Biology (2012) 80, 2198–2212 doi:10.1111/j.1095-8649.2012.03270.x, available online at wileyonlinelibrary.com Population genetic structure of skipjack tuna Katsuwonus pelamis from the Indian coast using sequence analysis of the mitochondrial DNA D...-loop region M. R. Menezes*, G. Kumar and S. P. Kunal Biological Oceanography Division, National Institute of Oceanography (CSIR), Dona Paula, Goa 403 004, India (Received 26 May 2011, Accepted 14 February 2012) Genetic structure of skipjack tuna Katsuwonus...

  2. A spatial ecosystem and populations dynamics model (SEAPODYM) Modeling of tuna and tuna-like populations

    Science.gov (United States)

    Lehodey, Patrick; Senina, Inna; Murtugudde, Raghu

    2008-09-01

    An enhanced version of the spatial ecosystem and population dynamics model SEAPODYM is presented to describe spatial dynamics of tuna and tuna-like species in the Pacific Ocean at monthly resolution over 1° grid-boxes. The simulations are driven by a bio-physical environment predicted from a coupled ocean physical-biogeochemical model. This new version of SEAPODYM includes expanded definitions of habitat indices, movements, and natural mortality based on empirical evidences. A thermal habitat of tuna species is derived from an individual heat budget model. The feeding habitat is computed according to the accessibility of tuna predator cohorts to different vertically migrating and non-migrating micronekton (mid-trophic) functional groups. The spawning habitat is based on temperature and the coincidence of spawning fish with presence or absence of predators and food for larvae. The successful larval recruitment is linked to spawning stock biomass. Larvae drift with currents, while immature and adult tuna can move of their own volition, in addition to being advected by currents. A food requirement index is computed to adjust locally the natural mortality of cohorts based on food demand and accessibility to available forage components. Together these mechanisms induce bottom-up and top-down effects, and intra- (i.e. between cohorts) and inter-species interactions. The model is now fully operational for running multi-species, multi-fisheries simulations, and the structure of the model allows a validation from multiple data sources. An application with two tuna species showing different biological characteristics, skipjack ( Katsuwonus pelamis) and bigeye ( Thunnus obesus), is presented to illustrate the capacity of the model to capture many important features of spatial dynamics of these two different tuna species in the Pacific Ocean. The actual validation is presented in a companion paper describing the approach to have a rigorous mathematical parameter optimization

  3. Genomic differentiation and demographic histories of Atlantic and Indo-Pacific yellowfin tuna (Thunnus albacares) populations.

    Science.gov (United States)

    Barth, J M I; Damerau, M; Matschiner, M; Jentoft, S; Hanel, R

    2017-04-13

    Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population structure of the yellowfin tuna, and to investigate its demographic history. We detect significant differentiation of Atlantic and Indo-Pacific yellowfin tuna populations as well as the possibility of a third diverged yellowfin tuna group in the Arabian Sea. We further observe evidence for past population expansion as well as asymmetric gene flow from the Indo-Pacific to the Atlantic. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  4. Preliminary forecasts of Pacific bigeye tuna population trends under the A2 IPCC scenario

    Science.gov (United States)

    Lehodey, P.; Senina, I.; Sibert, J.; Bopp, L.; Calmettes, B.; Hampton, J.; Murtugudde, R.

    2010-07-01

    An improved version of the spatial ecosystem and population dynamics model SEAPODYM was used to investigate the potential impacts of global warming on tuna populations. The model included an enhanced definition of habitat indices, movements, and accessibility of tuna predators to different vertically migrant and non-migrant micronekton functional groups. The simulations covered the Pacific basin (model domain) at a 2° × 2° geographic resolution. The structure of the model allows an evaluation from multiple data sources, and parameterization can be optimized by adjoint techniques and maximum likelihood using fishing data. A first such optimized parameterization was obtained for bigeye tuna ( Thunnus obesus) in the Pacific Ocean using historical catch data for the last 50 years and a hindcast from a coupled physical-biogeochemical model driven by the NCEP atmospheric reanalysis. The parameterization provided very plausible biological parameter values and a good fit to fishing data from the different fisheries, both within and outside the time period used for optimization. We then employed this model to forecast the future of bigeye tuna populations in the Pacific Ocean. The simulation was driven by the physical-biogeochemical fields predicted from a global marine biogeochemistry - climate simulation. This global simulation was performed with the IPSL climate model version 4 (IPSL-CM4) coupled to the oceanic biogeochemical model PISCES and forced by atmospheric CO 2, from historical records over 1860-2000, and under the SRES A2 IPCC scenario for the 21st century (i.e. atmospheric CO 2 concentration reaching 850 ppm in the year 2100). Potential future changes in distribution and abundance under the IPCC scenario are presented but without taking into account any fishing effort. The simulation showed an improvement in bigeye tuna spawning habitat both in subtropical latitudes and in the eastern tropical Pacific (ETP) where the surface temperature becomes optimal for

  5. Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839)

    OpenAIRE

    Gonzalez, Elena G; Beerli, Peter; Zardoya, Rafael

    2008-01-01

    Abstract Background Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour) and physical (e.g. present-day ocean currents, past changes in sea temperature and levels) factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitoc...

  6. Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839

    Directory of Open Access Journals (Sweden)

    Beerli Peter

    2008-09-01

    Full Text Available Abstract Background Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour and physical (e.g. present-day ocean currents, past changes in sea temperature and levels factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitochondrial clades (Clades I and II, which are assumed to have been originated during the last Pleistocene glacial maxima. We assess genetic structure patterns of Atlantic bigeye tuna at the nuclear level, and compare them with mitochondrial evidence. Results We examined allele size variation of nine microsatellite loci in 380 individuals from the Gulf of Guinea, Canary, Azores, Canada, Indian Ocean, and Pacific Ocean. To investigate temporal stability of genetic structure, three Atlantic Ocean sites were re-sampled a second year. Hierarchical AMOVA tests, RST pairwise comparisons, isolation by distance (Mantel tests, Bayesian clustering analyses, and coalescence-based migration rate inferences supported unrestricted gene flow within the Atlantic Ocean at the nuclear level, and therefore interbreeding between individuals belonging to both mitochondrial clades. Moreover, departures from HWE in several loci were inferred for the samples of Guinea, and attributed to a Wahlund effect supporting the role of this region as a spawning and nursery area. Our microsatellite data supported a single worldwide panmictic unit for bigeye tunas. Despite the strong Agulhas Current, immigration rates seem to be higher from the Atlantic Ocean into the Indo-Pacific Ocean, but the actual number of individuals moving per generation is relatively low compared to the large population sizes inhabiting each ocean basin. Conclusion Lack of congruence between mt and nuclear evidences, which

  7. Genetic structuring and migration patterns of Atlantic bigeye tuna, Thunnus obesus (Lowe, 1839).

    Science.gov (United States)

    Gonzalez, Elena G; Beerli, Peter; Zardoya, Rafael

    2008-09-17

    Large pelagic fishes are generally thought to have little population genetic structuring based on their cosmopolitan distribution, large population sizes and high dispersal capacities. However, gene flow can be influenced by ecological (e.g. homing behaviour) and physical (e.g. present-day ocean currents, past changes in sea temperature and levels) factors. In this regard, Atlantic bigeye tuna shows an interesting genetic structuring pattern with two highly divergent mitochondrial clades (Clades I and II), which are assumed to have been originated during the last Pleistocene glacial maxima. We assess genetic structure patterns of Atlantic bigeye tuna at the nuclear level, and compare them with mitochondrial evidence. We examined allele size variation of nine microsatellite loci in 380 individuals from the Gulf of Guinea, Canary, Azores, Canada, Indian Ocean, and Pacific Ocean. To investigate temporal stability of genetic structure, three Atlantic Ocean sites were re-sampled a second year. Hierarchical AMOVA tests, RST pairwise comparisons, isolation by distance (Mantel) tests, Bayesian clustering analyses, and coalescence-based migration rate inferences supported unrestricted gene flow within the Atlantic Ocean at the nuclear level, and therefore interbreeding between individuals belonging to both mitochondrial clades. Moreover, departures from HWE in several loci were inferred for the samples of Guinea, and attributed to a Wahlund effect supporting the role of this region as a spawning and nursery area. Our microsatellite data supported a single worldwide panmictic unit for bigeye tunas. Despite the strong Agulhas Current, immigration rates seem to be higher from the Atlantic Ocean into the Indo-Pacific Ocean, but the actual number of individuals moving per generation is relatively low compared to the large population sizes inhabiting each ocean basin. Lack of congruence between mt and nuclear evidences, which is also found in other species, most likely reflects

  8. Genetic Structure of Bluefin Tuna in the Mediterranean Sea Correlates with Environmental Variables

    Science.gov (United States)

    Riccioni, Giulia; Stagioni, Marco; Landi, Monica; Ferrara, Giorgia; Barbujani, Guido; Tinti, Fausto

    2013-01-01

    Background Atlantic Bluefin Tuna (ABFT) shows complex demography and ecological variation in the Mediterranean Sea. Genetic surveys have detected significant, although weak, signals of population structuring; catch series analyses and tagging programs identified complex ABFT spatial dynamics and migration patterns. Here, we tested the hypothesis that the genetic structure of the ABFT in the Mediterranean is correlated with mean surface temperature and salinity. Methodology We used six samples collected from Western and Central Mediterranean integrated with a new sample collected from the recently identified easternmost reproductive area of Levantine Sea. To assess population structure in the Mediterranean we used a multidisciplinary framework combining classical population genetics, spatial and Bayesian clustering methods and a multivariate approach based on factor analysis. Conclusions FST analysis and Bayesian clustering methods detected several subpopulations in the Mediterranean, a result also supported by multivariate analyses. In addition, we identified significant correlations of genetic diversity with mean salinity and surface temperature values revealing that ABFT is genetically structured along two environmental gradients. These results suggest that a preference for some spawning habitat conditions could contribute to shape ABFT genetic structuring in the Mediterranean. However, further studies should be performed to assess to what extent ABFT spawning behaviour in the Mediterranean Sea can be affected by environmental variation. PMID:24260341

  9. Spawning of bluefin tuna in the black sea: historical evidence, environmental constraints and population plasticity

    DEFF Research Database (Denmark)

    Mackenzie, Brian R; Mariani, Patrizio

    2012-01-01

    The lucrative and highly migratory Atlantic bluefin tuna, Thunnus thynnus (Linnaeus 1758; Scombridae), used to be distributed widely throughout the north Atlantic Ocean, Mediterranean Sea and Black Sea. Its migrations have supported sustainable fisheries and impacted local cultures since antiquity...

  10. [Otolith microchemistry of tuna species: research progress].

    Science.gov (United States)

    Zhu, Guo-ping

    2011-08-01

    Microchemistry analysis of trace elements and isotopes in fishes' calcified substances is an emerging approach to analyze the population structure, life history, and migration environmental history of fishes. With the increasing improvement of the researches and applications of otolith microchemistry, this approach has been a good tool for studying the ecology of tuna species. Currently, the research contents of tuna species' otolith microchemistry mainly include trace elements and isotopes, and the former is the emphasis and hotspot in applied research, playing a vital role in the researches of population partitioning, natal origin, migration environmental history, and life history of tuna species, especially bluefin tuna. However, most of the researches are focusing on the variation of otolith's Sr/Ca ratio, and there is no final conclusion on the relationships between the fractionation of isotopes C and O in otolith and the temperature. For the sake of exploiting the huge value of otolith microchemistry, it would be necessary to strengthen the researches on the deposition mechanisms of trace elements in otolith, and to analyze the spatio-temporal variations of various trace elements in otolith by comprehensive research methods.

  11. Distinct Yellowfin Tuna (Thunnus albacares Stocks Detected in Western and Central Pacific Ocean (WCPO Using DNA Microsatellites.

    Directory of Open Access Journals (Sweden)

    Roselyn D Aguila

    Full Text Available The yellowfin tuna, Thunnus albacares (Bonnaterre, 1788, covers majority of the Philippines' tuna catch, one of the major fisheries commodities in the country. Due to its high economic importance sustainable management of these tunas has become an imperative measure to prevent stock depletion. Currently, the Philippine yellowfin tuna is believed to be part of a single stock of the greater WCPO though some reports suggest otherwise. This study therefore aims to establish the genetic stock structure of the said species in the Philippines as compared to Bismarck Sea, Papua New Guinea using nine (9 DNA microsatellite markers. DNA microsatellite data revealed significant genetic differentiation between the Philippine and Bismarck Sea, Papua New Guinea yellowfin tuna samples. (FST = 0.034, P = 0.016, which is further supported by multilocus distance matrix testing (PCoA and model-based clustering (STRUCTURE 2.2.With these findings, this study posits that the yellowfin tuna population in the Philippines is a separate stock from the Bismarck Sea population. These findings add evidence to the alternative hypothesis of having at least 2 subpopulations of yellowfin tuna in the WCPO and calls for additional scientific studies using other parameters to investigate this. Accurate population information is necessary in formulating a more appropriate management strategy for the sustainability of the yellowfin tuna not only in the Philippines but also in the WCPO.

  12. Value Chain Model Development of Tuna and Tuna Alike In Indonesia

    Directory of Open Access Journals (Sweden)

    Ateng Supriatna

    2014-11-01

    Full Text Available Sustainability of tuna and tuna alike fisheries depend on chain value system formed by stakeholders ranging from product fishing, processing/diversification, distribution, and marketing. The objective of this research was to create chain value system model of tuna and tuna alike fisheries, to predict the interaction pattern of stakeholders and to formulate the precise strategy to minimize the synergy resistance of chain value system development strategy of tuna and tuna alike fisheries. Structural Equation Modelling (SEM was applied to analyze the chain value model. The stakeholders/the players of tuna and tuna alike fisheries basically have positive interaction (CE>0.The negative interaction occured on retailers and consumers. Interaction of retailers with consumers is significant (p<0.05 0.01. Interaction pattern of fishermen, retailers, collectors, and exporters affected significantlly by pricing and the level of role played by the stakeholders. The strategy to minimize the sinergy resistance of chain value system development are respectivelly the strategy of involving the group of fishermen on products pricing (CE= 1,176 and P= 0,000, the strategy of involving the seller groups on products pricing (CE-PE=1,08, CE-PB= 0,766, CE EKS= 2,028 AND P= 0,000, and the strategy on guaranteeing flexible interaction between retailer and consumers (CE= 0,179 and p = 0,01.Keywords: tuna and tuna alike, interaction, tuna and tuna alike stakeholders, and value chain

  13. Baja visión en la población pediátrica de Las Tunas Low vision of the pediatric population in Las Tunas province

    Directory of Open Access Journals (Sweden)

    Yunia Herbania Labrada Rodríguez

    2006-12-01

    Full Text Available Se presentan los resultados de un estudio descriptivo en 35 pacientes ciegos y débiles visuales matriculados en la Escuela de Ciegos de la provincia Las Tunas. Los pacientes fueron agrupados según categoría visual, sexo, y etiología de baja visión. El sexo masculino fue el más afectado, el mayor número de pacientes eran débiles visuales y las etiologías más frecuentes de baja visión fueron la catarata congénita y la retinopatía de la prematuridadThe results of a descriptive study of 35 blind and impaired vision patients, who study at the School for Blind People in Las Tunas province were presented in this paper. The patients were grouped according to their visual category, sex and etiology of low vision. Males were the most affected, the highest number of patients had impaired vision and the most common causes of low vision were congenital cataract and prematurity retinopathy

  14. Mapping Risks of Indonesian Tuna Supply Chain

    Science.gov (United States)

    Karningsih, P. D.; Anggrahini, D.; Kurniati, N.; Suef, M.; Fachrur, A. R.; Syahroni, N.

    2018-04-01

    Due to its high economic value and is produced by many countries, Tuna is considered as one of the world’s popular fish. Demand for Tuna species are very high and it usually sells in three form: fresh, frozen or canned. Competition in Tuna trading is challengin with the potential risk of price and supply fluctuations. With recent focus of Indonesia government that see the future of Indonesia civilization depend on the oceans and as the three biggest Tuna producing country, Ministry of Marine Affairs and Fisheries should ensure sustainability and competitiveness of Indonesian tuna. Therefore, there is a great need to develop a proper and effective strategy to manage potential risks in Indonesian Tuna supply chain. This paper is aimed at identifying and mapping potential Tuna supply chain risks and its interrelationships that would assist government in determining proper strategies to manage Indonesian Tuna. A framework for identifying Tuna supply chain risks is proposed. Generic risk structure of Supply Chain Risk Identification System is adopted and modified to match with particular object, which is Indonesian Tuna. The proposed model consists of hierarchical and causal structure that encompass potential risks of Tuna supply chain operations from fishing, trading, processing and distribution. The causal structure consist of risk events and its risk agents which is the cause of risk events. To ensure the root cause of risk events are identified properly, five why’s analysis is utilized to obtain risk agents. This proposed model also captures risk interrelationship between internal and external environment of Tuna supply chain. Preliminary result of this study identifies 15 risk events and 13 risk factors on fishing and trading operations and maps their interrelationships.

  15. Otolith chemistry discriminates natal signatures of yellowfin tuna (Thunnus albacares) in the Atlantic Ocean

    Science.gov (United States)

    Kitchens, L. L.; Rooker, J. R.

    2016-02-01

    In this study, the otolith chemistry of young-of-the-year (YOY) yellowfin tuna (Thunnus albacares) was examined to determine whether chemical signatures are distinct across different putative spawning areas in the Atlantic Ocean. Yellowfin tuna is a highly migratory species that is currently managed as a single panmictic stock in the Atlantic Ocean; however, uncertainty remains regarding the population structure of yellowfin in this region, particularly concerning the degree of mixing between spawning populations. Analysis of naturally occurring chemical tracers in otoliths provides a valuable means to reconstruct a fish's environmental history and is thus a promising approach for delineating stock structure of Atlantic yellowfin tuna. YOY yellowfin tuna otoliths were collected from 5 locations in the Atlantic Ocean (Gulf of Mexico, SE Caribbean, Brazil, Cape Verde, and Gulf of Guinea) from 2013-2015 and trace element (Li, Mg, Mn, Co, Cu, Sr, Zn, and Ba) and stable isotope (δ13C and δ18O) analyses were conducted to investigate regional variation in otolith chemical composition. Results show significant differences among nursery areas in both trace element (MANOVA, p<0.001) and δ13C and δ18O signatures (ANOVA, p=0.017 and p=0.001, respectively). Particularly high spatial separation was observed based on eastern Atlantic (Gulf of Guinea + Cape Verde) and western Atlantic (Gulf of Mexico + Brazil + Martinique) nursery areas, indicating the approach has promise for distinguishing migrants displaying trans-ocean movement. These chemical signatures will be used to assign adult yellowfin tuna to their nursery of origin, ultimately providing an improved understanding of the stock structure and movement of yellowfin tuna in the Atlantic Ocean.

  16. Spatially explicit estimates of stock sizes, structure and biomass of herring and blue whiting, and catch data of bluefin tuna

    DEFF Research Database (Denmark)

    Huse, G.; MacKenzie, B. R.; Trenkel, V.

    2015-01-01

    The North Atlantic is a productive marine region which has supported important commercial fisheries for centuries. Many of these fisheries have exploited the pelagic species, including herring, blue whiting and tuna. Here we present data on the distribution of herring and blue whiting based on th...

  17. Exploring future scenarios for the global supply chain of tuna

    Science.gov (United States)

    Mullon, C.; Guillotreau, P.; Galbraith, E. D.; Fortilus, J.; Chaboud, C.; Bopp, L.; Aumont, O.; Kaplan, D.

    2017-06-01

    The abundance of tuna, an important top predator that ranges throughout tropical and subtropical oceans, is now largely determined by fishing activity. Fishing activity, in turn, is determined by the interaction of fish availability, fishing capacity, fishing costs and global markets for tuna products. In the face of overfishing, the continued sustainable supply of tuna is likely to require improved global governance, that would benefit from modeling frameworks capable of integrating market forces with the availability of fish in order to consider alternative future projections. Here we describe such a modeling framework, in which we develop several simple, contrasting scenarios for the development of the tuna supply chain in order to illustrate the utility of the approach for global evaluation of management strategies for tuna and other complex, stock-structured fisheries. The model includes multiple national and multi-national fishing fleets, canneries and fresh/frozen markets, and connects these to global consumers using a network of flows. The model is calibrated using recent data on fish catch, cannery and fresh/frozen production, and consumption. Scenarios explore the control on future outcomes in the global tuna fishery by representing, in a simple way, the effects of (1) climate change, (2) changes in the global demand for tuna, and (3) changes in the access to fishing grounds (marine reserves). The results emphasize the potential importance of increasing demand in provoking a global collapse, and suggest that controlling tuna production by limiting technical efficiency is a potential countermeasure. Finally we discuss the outcomes in terms of potential extensions of the scenario approach allowed by this global network model of the tuna supply chain.

  18. Genetic stock structure of frigate tuna (Auxis thazard) along Indian coast based on PCR-RFLP analyses of mtDNA D-Loop region

    Digital Repository Service at National Institute of Oceanography (India)

    GirishKumar; Kunal, S.P.; Menezes, M.R.

    : 547-572. Pillai, N.G.K. and Mallia, J.V. 2007. Bibliography on Tunas. CMFRI Special Publication No. 92: 325 pp Pillai, P.P. and Gopakumar, G. 2003. In: M. Mohan Joseph, A.A. Jayaprakash, (Eds.), Status of exploited marine fishery resources...

  19. Population structure in Argentina.

    Directory of Open Access Journals (Sweden)

    Marina Muzzio

    Full Text Available We analyzed 391 samples from 12 Argentinian populations from the Center-West, East and North-West regions with the Illumina Human Exome Beadchip v1.0 (HumanExome-12v1-A. We did Principal Components analysis to infer patterns of populational divergence and migrations. We identified proportions and patterns of European, African and Native American ancestry and found a correlation between distance to Buenos Aires and proportion of Native American ancestry, where the highest proportion corresponds to the Northernmost populations, which is also the furthest from the Argentinian capital. Most of the European sources are from a South European origin, matching historical records, and we see two different Native American components, one that spreads all over Argentina and another specifically Andean. The highest percentages of African ancestry were in the Center West of Argentina, where the old trade routes took the slaves from Buenos Aires to Chile and Peru. Subcontinentaly, sources of this African component are represented by both West Africa and groups influenced by the Bantu expansion, the second slightly higher than the first, unlike North America and the Caribbean, where the main source is West Africa. This is reasonable, considering that a large proportion of the ships arriving at the Southern Hemisphere came from Mozambique, Loango and Angola.

  20. Governance innovation networks for sustainable tuna

    NARCIS (Netherlands)

    Miller, A.M.M.

    2014-01-01

    Governance Innovation Networks for Sustainable Tuna

    Alice M.M. Miller

    Tuna fisheries are among the most highly capitalised and valuable fisheries in the world and their exploitation will continue for the foreseeable future. This means the sustainability of tuna

  1. U-Pb age constraints for the La Tuna Granite and Montevideo Formation (Paleoproterozoic, Uruguay): Unravelling the structure of the Río de la Plata Craton

    Science.gov (United States)

    Pamoukaghlián, Karina; Gaucher, Claudio; Frei, Robert; Poiré, Daniel G.; Chemale, Farid; Frei, Dirk; Will, Thomas M.

    2017-11-01

    The Río de la Plata Craton is a continental block that crops out in Uruguay, eastern Argentina, southernmost Brazil and Paraguay. It comprises in Uruguay the Piedra Alta, Tandilia and Nico Pérez terranes, separated by the Colonia and the Sarandí del Yí megashears. The La Tuna Granite, which intrudes the Araminda metasandstones in the Tandilia Terrane, was considered Cambrian in age and the intruded sandstones were assigned to the Neoproterozoic Piedras de Afilar Formation. We show that the granite is Paleoproterozoic in age and that the host metasandstones do not belong to the Piedras de Afilar Formation, but to the Paleoproterozoic Montevideo Formation. U-Pb LA ICP-MS of zircon ages for the La Tuna Granite yielded a concordant crystallization age of 2156 ± 26 Ma. Furthermore a metamorphic event at 2010 ± 9 Ma is revealed by Pb stepwise leaching dating of monazites. U-Pb detrital zircon ages of the host Araminda metasandstone yield an upper intercept discordia age of 2152 ± 29 Ma, which marks the intrusion of the La Tuna pluton, and which is in accordance with the zircon U-Pb LA ICP MS constraints. A concordant U-Pb detrital zircon age of 2465 ± 40 Ma provides a maximum depositional age constraint for the metapsammites. Comparing quartz arenites of the Ediacaran Piedras de Afilar Formation with the Araminda metaquartzites, we conclude that they are very similar regarding petrology but they differ in age and metamorphic overprint. Detrital zircons in quartz arenites of the Piedras de Afilar Formation show youngest ages of 1.0 Ga. On the other hand, detrital zircons recovered from the Araminda metasandstones and the age of the intruding granite allow interpreting a depositional age between 2465 and 2150 Ma. Nd model ages show crustal residence times in average more than 200 myr older for the Tandilia Terrane both in Uruguay and Argentina, with a significant Neoarchean component, which is lacking in the Piedra Alta Terrane. Whereas the Piedra Alta Terrane was

  2. Thawing of Frozen Tuna Meat

    Science.gov (United States)

    Tanaka, Takeo; Nishiwaki, Kôji; Kakuda, Kitonari; Tomimatsu, Takao

    Frozen southern bluefin tuna meat discolors easily and sometimes contracts when thawed caused by thaw rigor. These phenomenon often become problematic in the transaction or handling of this kind of frozen tuna. Frozen meat blocks of southern Bluefin tuna were thawed separately by air thawing, running water thawing and microwave thawing. Changes occurring during thawing were checked for meat color by met-myoglobin ratio determination and for contract by microscopic observation. Results are as follows : (1) Discoloration scarcely occurred in the process of running water thawing (at 10°C for 50 min, or at 0°C for 6 hr). (2) No contraction was observed during thawing with running water described above and air thawing (at 18-20°C for 6 hr). (3) Discoloration and contraction seemed to be minimized, as to latently contractile blocks, when meat temperature passed through rapidly between -10°C and -5°C, and slowly (for 5-6 hr) between -5°C and -1°C. When the block was originally not contractile, discloration was minimized by rising meat temperature rapidly from -10°C to -l°C.

  3. Modelling retention and dispersion mechanisms of bluefin tuna eggs and larvae in the Northwest Mediterranean Sea

    DEFF Research Database (Denmark)

    Mariani, Patrizio; MacKenzie, Brian; Iudicone, D.

    2010-01-01

    Knowledge of early life history of most fish species in the Mediterranean Sea is sparse and processes affecting their recruitment are poorly understood. This is particularly true for bluefin tuna, Thunnus thynnus, even though this species is one of the world's most valued fish species. Here we...... develop, apply and validate an individually based coupled biological-physical oceanographic model of fish early life history in the Mediterranean Sea. We first validate the general structure of the coupled model with a 12-day Lagrangian drift study of anchovy (Engraulis encrasicolus) larvae in the Catalan...... mesoscale processes in the Balearic area and thus potentially affect bluefin tuna larvae. These modelling approaches can increase understanding of bluefin tuna recruitment processes and eventually contribute to management of bluefin tuna fisheries....

  4. Pseudomonas aeruginosa Population Structure Revisited

    Science.gov (United States)

    Pirnay, Jean-Paul; Bilocq, Florence; Pot, Bruno; Cornelis, Pierre; Zizi, Martin; Van Eldere, Johan; Deschaght, Pieter; Vaneechoutte, Mario; Jennes, Serge; Pitt, Tyrone; De Vos, Daniel

    2009-01-01

    At present there are strong indications that Pseudomonas aeruginosa exhibits an epidemic population structure; clinical isolates are indistinguishable from environmental isolates, and they do not exhibit a specific (disease) habitat selection. However, some important issues, such as the worldwide emergence of highly transmissible P. aeruginosa clones among cystic fibrosis (CF) patients and the spread and persistence of multidrug resistant (MDR) strains in hospital wards with high antibiotic pressure, remain contentious. To further investigate the population structure of P. aeruginosa, eight parameters were analyzed and combined for 328 unrelated isolates, collected over the last 125 years from 69 localities in 30 countries on five continents, from diverse clinical (human and animal) and environmental habitats. The analysed parameters were: i) O serotype, ii) Fluorescent Amplified-Fragment Length Polymorphism (FALFP) pattern, nucleotide sequences of outer membrane protein genes, iii) oprI, iv) oprL, v) oprD, vi) pyoverdine receptor gene profile (fpvA type and fpvB prevalence), and prevalence of vii) exoenzyme genes exoS and exoU and viii) group I pilin glycosyltransferase gene tfpO. These traits were combined and analysed using biological data analysis software and visualized in the form of a minimum spanning tree (MST). We revealed a network of relationships between all analyzed parameters and non-congruence between experiments. At the same time we observed several conserved clones, characterized by an almost identical data set. These observations confirm the nonclonal epidemic population structure of P. aeruginosa, a superficially clonal structure with frequent recombinations, in which occasionally highly successful epidemic clones arise. One of these clones is the renown and widespread MDR serotype O12 clone. On the other hand, we found no evidence for a widespread CF transmissible clone. All but one of the 43 analysed CF strains belonged to a ubiquitous P

  5. Direct reciprocity in structured populations.

    Science.gov (United States)

    van Veelen, Matthijs; García, Julián; Rand, David G; Nowak, Martin A

    2012-06-19

    Reciprocity and repeated games have been at the center of attention when studying the evolution of human cooperation. Direct reciprocity is considered to be a powerful mechanism for the evolution of cooperation, and it is generally assumed that it can lead to high levels of cooperation. Here we explore an open-ended, infinite strategy space, where every strategy that can be encoded by a finite state automaton is a possible mutant. Surprisingly, we find that direct reciprocity alone does not lead to high levels of cooperation. Instead we observe perpetual oscillations between cooperation and defection, with defection being substantially more frequent than cooperation. The reason for this is that "indirect invasions" remove equilibrium strategies: every strategy has neutral mutants, which in turn can be invaded by other strategies. However, reciprocity is not the only way to promote cooperation. Another mechanism for the evolution of cooperation, which has received as much attention, is assortment because of population structure. Here we develop a theory that allows us to study the synergistic interaction between direct reciprocity and assortment. This framework is particularly well suited for understanding human interactions, which are typically repeated and occur in relatively fluid but not unstructured populations. We show that if repeated games are combined with only a small amount of assortment, then natural selection favors the behavior typically observed among humans: high levels of cooperation implemented using conditional strategies.

  6. Modelling retention and dispersion mechanisms of bluefin tuna eggs and larvae in the northwest Mediterranean Sea

    Science.gov (United States)

    Mariani, Patrizio; MacKenzie, Brian R.; Iudicone, Daniele; Bozec, Alexandra

    2010-07-01

    Knowledge of early life history of most fish species in the Mediterranean Sea is sparse and processes affecting their recruitment are poorly understood. This is particularly true for bluefin tuna, Thunnus thynnus, even though this species is one of the world’s most valued fish species. Here we develop, apply and validate an individually based coupled biological-physical oceanographic model of fish early life history in the Mediterranean Sea. We first validate the general structure of the coupled model with a 12-day Lagrangian drift study of anchovy ( Engraulis encrasicolus) larvae in the Catalan Sea. The model reproduced the drift and growth of anchovy larvae as they drifted along the Catalan coast and yielded similar patterns as those observed in the field. We then applied the model to investigate transport and retention processes affecting the spatial distribution of bluefin tuna eggs and larvae during 1999-2003, and we compared modelled distributions with available field data collected in 2001 and 2003. Modelled and field distributions generally coincided and were patchy at mesoscales (10s-100s km); larvae were most abundant in eddies and along frontal zones. We also identified probable locations of spawning bluefin tuna using hydrographic backtracking procedures; these locations were situated in a major salinity frontal zone and coincided with distributions of an electronically tagged bluefin tuna and commercial bluefin tuna fishing vessels. Moreover, we hypothesized that mesoscale processes are responsible for the aggregation and dispersion mechanisms in the area and showed that these processes were significantly correlated to atmospheric forcing processes over the NW Mediterranean Sea. Interannual variations in average summer air temperature can reduce the intensity of ocean mesoscale processes in the Balearic area and thus potentially affect bluefin tuna larvae. These modelling approaches can increase understanding of bluefin tuna recruitment processes and

  7. Mercury in fish products: what's the best for consumers between bluefin tuna and yellowfin tuna?

    Science.gov (United States)

    Cammilleri, Gaetano; Vazzana, Mirella; Arizza, Vincenzo; Giunta, Francesca; Vella, Antonio; Lo Dico, Gianluigi; Giaccone, Vita; Giofrè, Salvatore V; Giangrosso, Giuseppe; Cicero, Nicola; Ferrantelli, Vincenzo

    2018-02-01

    A total of 205 bluefin and yellowfin tuna samples were examined for mercury detection in order to verify possible differences and have a detailed risk assessment of the two tuna species. The results showed significant higher mercury concentration in muscle tissue of bluefin tuna respect yellowfin tuna (p < 0.001) with mean concentration of 0.84 mg/kg and maximum value of 1.94 mg/kg. These differences can be due the different biological and ecological aspects of the two tuna species and to different oceanographic aspects between Atlantic Ocean and Mediterranean sea. The results obtained in this study suggest an advisable containment of the sources of pollution and further studies on the closed-loop farming of bluefin tuna, in order to ensure the product safety.

  8. Global habitat preferences of commercially valuable tuna

    KAUST Repository

    Arrizabalaga, Haritz; Dufour, Florence; Kell, Laurence T.; Merino, Gorka; Ibaibarriaga, Leire; Chust, Guillem; Irigoien, Xabier; Santiago, Josu; Murua, Hilario; Fraile, Igaratza; Chifflet, Marina; Goikoetxea, Nerea; Sagarminaga, Yolanda; Aumont, Olivier; Bopp, Laurent; Herrera, Miguel Angel; Marc Fromentin, Jean; Bonhomeau, Sylvain

    2015-01-01

    In spite of its pivotal role in future implementations of the Ecosystem Approach to Fisheries Management, current knowledge about tuna habitat preferences remains fragmented and heterogeneous, because it relies mainly on regional or local studies that have used a variety of approaches making them difficult to combine. Therefore in this study we analyse data from six tuna species in the Pacific, Atlantic and Indian Oceans in order to provide a global, comparative perspective of habitat preferences. These data are longline catch per unit effort from 1958 to 2007 for albacore, Atlantic bluefin, southern bluefin, bigeye, yellowfin and skipjack tunas. Both quotient analysis and Generalised Additive Models were used to determine habitat preference with respect to eight biotic and abiotic variables. Results confirmed that, compared to temperate tunas, tropical tunas prefer warm, anoxic, stratified waters. Atlantic and southern bluefin tuna prefer higher concentrations of chlorophyll than the rest. The two species also tolerate most extreme sea surface height anomalies and highest mixed layer depths. In general, Atlantic bluefin tuna tolerates the widest range of environmental conditions. An assessment of the most important variables determining fish habitat is also provided. © 2014 Elsevier Ltd.

  9. Global habitat preferences of commercially valuable tuna

    KAUST Repository

    Arrizabalaga, Haritz

    2015-03-01

    In spite of its pivotal role in future implementations of the Ecosystem Approach to Fisheries Management, current knowledge about tuna habitat preferences remains fragmented and heterogeneous, because it relies mainly on regional or local studies that have used a variety of approaches making them difficult to combine. Therefore in this study we analyse data from six tuna species in the Pacific, Atlantic and Indian Oceans in order to provide a global, comparative perspective of habitat preferences. These data are longline catch per unit effort from 1958 to 2007 for albacore, Atlantic bluefin, southern bluefin, bigeye, yellowfin and skipjack tunas. Both quotient analysis and Generalised Additive Models were used to determine habitat preference with respect to eight biotic and abiotic variables. Results confirmed that, compared to temperate tunas, tropical tunas prefer warm, anoxic, stratified waters. Atlantic and southern bluefin tuna prefer higher concentrations of chlorophyll than the rest. The two species also tolerate most extreme sea surface height anomalies and highest mixed layer depths. In general, Atlantic bluefin tuna tolerates the widest range of environmental conditions. An assessment of the most important variables determining fish habitat is also provided. © 2014 Elsevier Ltd.

  10. Keterpaduan Pasar Tuna Segar Benoa/Bali, Indonesia Dan Pasar Sentral Tuna Tokyo, Jepang

    OpenAIRE

    SITORUS, EDYANTO

    2007-01-01

    Tuna fish is which forming life and horde in tropical territorial water until subtropics. Tuna type which important in commerce is Yellowfin, Bigeye, Poor Southern Bluefin, Northern Bluefin, Albacore and of Skipjack (Cakalang). Objective of this research is analyze integrity of market that happened between local market (Market of Benoa, Bali) with reference market (Tuna Central Market of Tokyo, Japan), It is seen from the research that in Benoa there are 3 system of selling fresh tu...

  11. Dominance and population structure of freshwater crabs ...

    African Journals Online (AJOL)

    To understand how this would affect wild populations we also investigated the population structure (sex ratio, size distribution, density and population growth) of a wild population. Using Landau's index of linearity (h) we found three captive groups of P. perlatus to show moderate linearity, i.e. h = 0.9; 0.81 and 0.83.

  12. Polychlorinated biphenyls and organochlorine pesticides as intrinsic tracer tags of foraging grounds of bluefin tuna in the northwest Atlantic Ocean

    International Nuclear Information System (INIS)

    Deshpande, Ashok D.; Dickhut, Rebecca M.; Dockum, Bruce W.; Brill, Richard W.; Farrington, Cameron

    2016-01-01

    from offshore Virginia, Gulf of Maine, and Nova Scotia could have had extended residences and foraging within the areas of capture to be able to sustain the stable signatures of PCB congeners. The DFA cluster results supported the concept of metapopulation theory of spatial ecology comprising discrete aggregates of local populations of bluefin tuna where the desired prey species are likely to be abundant. Despite their highly migratory trait and endothermic advantage of foraging in broader and colder habitats, the movements and mixing across the aggregation ranges related to feeding did not appear to be extensive. Advancement in the understanding of bluefin tuna population dynamics beyond the coarse concept of trans-Atlantic migrations to the metapopulation hypothesis provides a novel exploratory tool in the stock assessment and resource management. As the chemical tracer tags are fortified naturally and document the time- and space-integrated foraging history, they promise to serve as the low-cost alternatives to the high-cost electronic data recording tags employed for addressing the migratory movements of bluefin tuna. Between the different potential chemical tracer tags, a distinct advantage of PCB/pesticide analysis over the otolith micro-constituent analysis is that the muscle tissue of a given individual bluefin tuna can be sampled repeatedly for PCB/pesticide analysis over different spatial and temporal scales in a non-lethal manner. - Highlights: •Unique PCB and pesticide tags in bluefin tuna provided a low-cost method for studying migration, mixing, and feeding. •t-nonachlor/PCB 153 ratios suggested that one juvenile and one large bluefin tuna made east to west Atlantic migrations. •Discriminant function analysis of PCB signatures suggested extended residence of bluefin tuna on a given foraging ground. •PCB congener based groupings suggested metapopulation behavior of bluefin tuna with limited inter-population exchange. •A possibility of muscle

  13. Mercury in canned tuna marketed in Cartagena, Colombia, and estimation of human exposure.

    Science.gov (United States)

    Alcala-Orozco, Maria; Morillo-Garcia, Yenifer; Caballero-Gallardo, Karina; Olivero-Verbel, Jesus

    2017-12-01

    The presence of mercury in tuna is ubiquitous, so national authorities should guarantee food safety of canned tuna available on the market, according to legal regulations. The objective of this survey was to assess total mercury (T-Hg) levels in brands of canned tuna marketed in Cartagena, Colombia, and determine fish consumption-based risks after ingestion. For that purpose, 252 cans of tuna were collected, representing 6 brands (A-F), in 2 mediums (water and oil). Mean T-Hg levels were 0.66 ± 0.05 and 0.61 ± 0.05 µg g -1 wet weight, for water and oil, respectively. High T-Hg concentrations were measured in brands B and D. Only brands E and F guaranteed low risk for Hg-related health problems. According to Colombia's legislation, 15.5% of the samples exceeded the maximum level of 1.0 µg g -1 for mercury and 18.3% was higher than limits as recommended by Food and Agriculture Organization/World Health Organisation (0.5 µg g -1 ). It was concluded that consumption of canned tuna could represent a high risk for the Colombian population, particularly to vulnerable groups.

  14. Effects of frozen storage on survival of Staphylococcus aureus and enterotoxin production in precooked tuna meat.

    Science.gov (United States)

    Wu, Xulei; Su, Yi-Cheng

    2014-08-01

    This study investigated the survival of Staphylococcus aureus in precooked tuna meat for producing canned products during frozen storage (-20 ± 2 °C) as well as its growth and enterotoxin production at 35 to 37 °C after the storage. Samples (50 ± 5 g) of precooked albacore (loin, chunk, and flake) and skipjack (chunk and flake) tuna were inoculated with 5 enterotoxin-producing strains of S. aureus at a level of approximately 3.5 log CFU/g and individually packed in a vacuum bag after 3 h incubation at 35 to 37 °C. Vacuum-packed samples were stored in a freezer (-20 ± 2 °C) for 4 wk. The frozen samples were then thawed in 37 °C circulating water for 2 h and incubated at 35 to 37 °C for 22 h. Populations of S. aureus in all precooked tuna samples decreased slightly (canned tuna within 6 to 8 h of thawing to avoid product spoilage and potential enterotoxin production by S. aureus in contaminated precooked tuna meat. © 2014 Institute of Food Technologists®

  15. Population Structure of West Greenland Narwhals

    DEFF Research Database (Denmark)

    Riget, F.; Dietz, R.; Møller, P.

    The hypothesis that different populations of narwhals in the West Greenland area exist has been tested by different biomarkers (metal and organochlorine concentrations, stable isotopes and DNA). Samples of muscle, liver, kidney, blubber and skin tissues of narwhals from West Greenland have been...... isotopes could not support the population structure with two West Greenland populations suggested by the genetic study....

  16. Global integration of European tuna markets

    Science.gov (United States)

    Jiménez-Toribio, Ramòn; Guillotreau, Patrice; Mongruel, Rémi

    2010-07-01

    This paper evaluates the degree of integration between the world market and the major European marketplaces of frozen and canned tuna through both vertical and horizontal price relationships. Spatial linkages are investigated horizontally in order to estimate the connection between the European market and the world-wide market on the primary stage of the value chain. One of the key results is the high level of market integration at the ex-vessel stage, and the price leadership of yellowfin tuna over skipjack tuna. The same approach is applied at the ex-factory level. Basically, the European market for final goods appears to be segmented between the Northern countries consuming low-priced canned skipjack tuna imported from Asia (mainly Thailand) and the Southern countries (Italy, Spain) processing and importing yellowfin-based products sold at higher prices. France appears to be an intermediate market where both products are consumed. The former market is found to be well integrated to the world market and can be considered to be competitive, but there is a suspicion of market power being exercised on the latter. Price relationships are therefore tested vertically between the price of frozen tuna paid by the canneries and the price of canned fish in both Italy and France. The two species show an opposite pattern in prices transmission along the value chain: price changes along the chain are far better transmitted for the “global” skipjack tuna than for the more “European” yellowfin tuna. The results are discussed, along with their implications for the fishing industry.

  17. Symbolic trephinations and population structure

    Directory of Open Access Journals (Sweden)

    László Szathmáry

    2006-12-01

    Full Text Available The sample examined consists of 19 skulls with symbolic trephinations and 86 skulls without trepanations dated from the X century. Skulls were all excavated in the Great Hungarian Plain in the Carpathian Basin, which was occupied by the Hungarian conquerors at the end of the IX century. The variations of 12 cranial dimensions of the trephined skulls were investigated and compared to the skulls without trepanations after performing a discriminant analysis. The classification results evince that the variability of non-trephined skulls shows a more homogeneous and a more characteristic picture of their own group than the trephined samples, which corresponds to the notion, formed by archaeological evidence and written historical sources, of a both ethnically and socially differing population of the Hungarian conquerors. According to historical research, a part of the population was of Finno-Ugric origin, while the military leading layer of society can be brought into connection with Turkic ethnic groups. All the same, individuals dug up with rich grave furniture and supposed to belong to this upper stratum of society are primarily characterized by the custom of symbolic trephination, and, as our results demonstrate, craniologically they seem to be more heterogeneous.

  18. Population structure and adaptation in fishes

    DEFF Research Database (Denmark)

    Limborg, Morten

    Marine fishes represent a valuable resource for the global economy and food consumption. Accordingly, many species experience high levels of exploitation necessitating effective management plans. However, long term sustainability may be jeopardized from insufficient knowledge about intra-specific......Marine fishes represent a valuable resource for the global economy and food consumption. Accordingly, many species experience high levels of exploitation necessitating effective management plans. However, long term sustainability may be jeopardized from insufficient knowledge about intra......-specific population structure and adaptive divergence. The large population sizes and high migration rates common to most marine fishes impede the differentiating effect of genetic drift, having led to expectations of no population structure and that the occurrence of local adaptation should be rare in these species....... Comprehensive genetic analyses on the small pelagic fish European sprat (Sprattus sprattus) revealed significant population structure throughout its distribution with an overall pattern of reduced connectivity across environmental transition zones. Population structure reflected both historical separations over...

  19. [Genetic structure of natural populations

    International Nuclear Information System (INIS)

    1988-01-01

    Our efforts in the first eight months were concentrated in obtaining a genomic clone of the copper-zinc superoxide dismutase (SOD) in Drosophila melanogaster and other Drosophila species. This we have now successfully accomplished. We seek to understand the role of SOD in radioresistance; how genetic variation in this enzyme is maintained in populations; and relevant aspects of its evolution that may contribute to these goals as well as to an understanding of molecular evolution in general. To accomplish these goals we are undertaking the following experiments: cloning and sequencing of (at least) one F allele, one S allele, and the null allele for SOD; cloning and sequencing SOD from species related to D. melanogaster; and cloning and sequencing the SOD gene from several independently sampled S and F alleles in D. melanogaster. We are also preparing to test the radioprotective effects of SOD. 67 refs

  20. Structured population models in biology and epidemiology

    CERN Document Server

    Ruan, Shigui

    2008-01-01

    This book consists of six chapters written by leading researchers in mathematical biology. These chapters present recent and important developments in the study of structured population models in biology and epidemiology. Topics include population models structured by age, size, and spatial position; size-structured models for metapopulations, macroparasitc diseases, and prion proliferation; models for transmission of microparasites between host populations living on non-coincident spatial domains; spatiotemporal patterns of disease spread; method of aggregation of variables in population dynamics; and biofilm models. It is suitable as a textbook for a mathematical biology course or a summer school at the advanced undergraduate and graduate level. It can also serve as a reference book for researchers looking for either interesting and specific problems to work on or useful techniques and discussions of some particular problems.

  1. Coexistence of competing stage-structured populations.

    KAUST Repository

    Fujiwara, Masami

    2011-10-05

    This paper analyzes the stability of a coexistence equilibrium point of a model for competition between two stage-structured populations. In this model, for each population, competition for resources may affect any one of the following population parameters: reproduction, juvenile survival, maturation rate, or adult survival. The results show that the competitive strength of a population is affected by (1) the ratio of the population parameter influenced by competition under no resource limitation (maximum compensatory capacity) over the same parameter under a resource limitation due to competition (equilibrium rate) and (2) the ratio of interspecific competition over intraspecific competition; this ratio was previously shown to depend on resource-use overlap. The former ratio, which we define as fitness, can be equalized by adjusting organisms\\' life history strategies, thereby promoting coexistence. We conclude that in addition to niche differentiation among populations, the life history strategies of organisms play an important role in coexistence.

  2. Predicting the Distribution of Yellowfin Tuna in Philippine Waters

    Science.gov (United States)

    Perez, G. J. P.; Leonardo, E. M.

    2015-12-01

    The Philippines is considered as a major tuna producer in the Western and Central Pacific Ocean, both for domestic consumption and on industrial scale. However, with the ever-increasing demand of growing population, it has always been a challenge to achieve sustainable fishing. The creation of satellite-derived potential fishing zone maps is a technology that has been adopted by advanced countries for almost three decades already and has led to reduction in search times by up to 40%. In this study, a Generalized Additive Model (GAM) is developed to predict the distribution of the Yellowfin tuna species in seas surrounding the Philippines based on the Catch-Per-Unit-Effort (CPUE) index. Level 3 gridded chlorophyll-a and sea surface temperature from the Moderate Resolution Imaging Spectroradiometer (MODIS) aboard the Aqua satellite of the National Aeronautics and Space Administration (NASA) are the main input parameters of the model. Chlorophyll-a is linked with the presence of phytoplankton, which indicates primary productivity and suggests potential regions of fish aggregation. Fish also prefers to stay in regions where the temperature is stable, thus the sea surface temperature fronts serve as a guide to locate concentrations of fish school. Historical monthly tuna catch data from Western and Central Pacific Commissions (WCPFC) is used to train the model. The resulting predictions are converted to potential fishing zone maps and are evaluated within and beyond the historical time range of the training data used. Diagnostic tests involving adjusted R2 value, GAM residual plots and root mean square error value are used to assess the accuracy of the model. The generated maps were able to confirm locations of known tuna fishing grounds in Mindanao and other parts of the country, as well us detect their seasonality and interannual variability. To improve the performance of the model, ancillary data such as surface winds reanalysis from National Centers for

  3. Population structure of the Classic period Maya.

    Science.gov (United States)

    Scherer, Andrew K

    2007-03-01

    This study examines the population structure of Classic period (A.D. 250-900) Maya populations through analysis of odontometric variation of 827 skeletons from 12 archaeological sites in Mexico, Guatemala, Belize, and Honduras. The hypothesis that isolation by distance characterized Classic period Maya population structure is tested using Relethford and Blangero's (Hum Biol 62 (1990) 5-25) approach to R matrix analysis for quantitative traits. These results provide important biological data for understanding ancient Maya population history, particularly the effects of the competing Tikal and Calakmul hegemonies on patterns of lowland Maya site interaction. An overall F(ST) of 0.018 is found for the Maya area, indicating little among-group variation for the Classic Maya sites tested. Principal coordinates plots derived from the R matrix analysis show little regional patterning in the data, though the geographic outliers of Kaminaljuyu and a pooled Pacific Coast sample did not cluster with the lowland Maya sites. Mantel tests comparing the biological distance matrix to a geographic distance matrix found no association between genetic and geographic distance. In the Relethford-Blangero analysis, most sites possess negative or near-zero residuals, indicating minimal extraregional gene flow. The exceptions were Barton Ramie, Kaminaljuyu, and Seibal. A scaled R matrix analysis clarifies that genetic drift is a consideration for understanding Classic Maya population structure. All results indicate that isolation by distance does not describe Classic period Maya population structure. (c) 2006 Wiley-Liss, Inc.

  4. 21 CFR 161.190 - Canned tuna.

    Science.gov (United States)

    2010-04-01

    .... (a) Identity. (1) Canned tuna is the food consisting of processed flesh of fish of the species... deemed to be safe if it is not a food additive as defined in section 201(s) of the Federal Food, Drug, and Cosmetic Act (the act), or if it is a food additive as so defined, it is used in conformity with...

  5. Calculating evolutionary dynamics in structured populations.

    Directory of Open Access Journals (Sweden)

    Charles G Nathanson

    2009-12-01

    Full Text Available Evolution is shaping the world around us. At the core of every evolutionary process is a population of reproducing individuals. The outcome of an evolutionary process depends on population structure. Here we provide a general formula for calculating evolutionary dynamics in a wide class of structured populations. This class includes the recently introduced "games in phenotype space" and "evolutionary set theory." There can be local interactions for determining the relative fitness of individuals, but we require global updating, which means all individuals compete uniformly for reproduction. We study the competition of two strategies in the context of an evolutionary game and determine which strategy is favored in the limit of weak selection. We derive an intuitive formula for the structure coefficient, sigma, and provide a method for efficient numerical calculation.

  6. Development of a qPCR Method for the Identification and Quantification of Two Closely Related Tuna Species, Bigeye Tuna (Thunnus obesus) and Yellowfin Tuna (Thunnus albacares), in Canned Tuna.

    Science.gov (United States)

    Bojolly, Daline; Doyen, Périne; Le Fur, Bruno; Christaki, Urania; Verrez-Bagnis, Véronique; Grard, Thierry

    2017-02-01

    Bigeye tuna (Thunnus obesus) and yellowfin tuna (Thunnus albacares) are among the most widely used tuna species for canning purposes. Not only substitution but also mixing of tuna species is prohibited by the European regulation for canned tuna products. However, as juveniles of bigeye and yellowfin tunas are very difficult to distinguish, unintentional substitutions may occur during the canning process. In this study, two mitochondrial markers from NADH dehydrogenase subunit 2 and cytochrome c oxidase subunit II genes were used to identify bigeye tuna and yellowfin tuna, respectively, utilizing TaqMan qPCR methodology. Two different qPCR-based methods were developed to quantify the percentage of flesh of each species used for can processing. The first one was based on absolute quantification using standard curves realized with these two markers; the second one was founded on relative quantification with the universal 12S rRNA gene as the endogenous gene. On the basis of our results, we conclude that our methodology could be applied to authenticate these two closely related tuna species when used in a binary mix in tuna cans.

  7. Structural stability of nonlinear population dynamics.

    Science.gov (United States)

    Cenci, Simone; Saavedra, Serguei

    2018-01-01

    In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

  8. Structural stability of nonlinear population dynamics

    Science.gov (United States)

    Cenci, Simone; Saavedra, Serguei

    2018-01-01

    In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

  9. Visualizing the Food-Web Effects of Fishing for Tunas in the Pacific Ocean

    Directory of Open Access Journals (Sweden)

    Jefferson T. Hinke

    2004-06-01

    Full Text Available We use food-web models to develop visualizations to compare and evaluate the interactions of tuna fisheries with their supporting food webs in the eastern tropical Pacific (ETP and the central north Pacific (CNP Oceans. In the ETP and CNP models, individual fisheries use slightly different food webs that are defined by the assemblage of targeted tuna species. Distinct energy pathways are required to support different tuna species and, consequently, the specific fisheries that target different tuna assemblages. These simulations suggest that catches of tunas, sharks, and billfishes have lowered the biomass of the upper trophic levels in both systems, whereas increases in intermediate and lower trophic level animals have accompanied the decline of top predators. Trade-offs between fishing and predation mortality rates that occur when multiple fisheries interact with their respective food webs may lead to smaller changes in biomass than if only the effect of a single fishery is considered. Historical simulations and hypothetical management scenarios further demonstrate that the effects of longline and purse seine fisheries have been strongest in upper trophic levels, but that lower trophic levels may respond more strongly to purse-seine fisheries. The apex predator guild has responded most strongly to longlining. Simulations of alternative management strategies that attempt to rebuild shark and billfish populations in each ecosystem reveal that (1 changes in longlining more effectively recover top predator populations than do changes in purse seining and (2 restrictions on both shallow-set longline gear and shark finning may do more to recover top predators than do simple reductions in fishing effort.

  10. Population structure of Staphylococcus aureus in China

    NARCIS (Netherlands)

    Yan, Xiaomei

    2015-01-01

    The present PhD research was aimed at analysing the population structure of Staphylococcus aureus in China. Between 2000 and 2005 we found that patients from a single Chinese hospital showed increasing trends in antimicrobial resistance. Among methicillin-resistant S. aureus (MRSA), resistance

  11. Social structural consequences of population growth.

    Science.gov (United States)

    Adams, R E

    1981-01-01

    Estimates from archaeological data of the numbers in the elite classes, nonelite occupational specialists, density of population, city size, and size of political units in the ancient Maya civilization suggest that there was a quantum shift in rate of development in the Early Classic period, associated with intensification of agriculture, and that the social structure approximated to a generalized feudal pattern.

  12. Depressed resilience of bluefin tuna in the western atlantic and age truncation.

    Science.gov (United States)

    Secor, D H; Rooker, J R; Gahagan, B I; Siskey, M R; Wingate, R W

    2015-04-01

    Following intense overfishing in the 1970s, the western stock of Atlantic bluefin tuna (Thunnus thynnus) experienced a long period of depressed abundance, which has been attributed to failure of the population to periodically produce large numbers of juveniles, the western stock mixing with the more highly exploited eastern stock (fisheries in the Northeast Atlantic Ocean and Mediterranean Sea), and regime shift in the population's ecosystem resulting in lower replacement rates. To evaluate the presence of relatively strong years of juvenile production, we analyzed age structure from a recent sample of otoliths (ear stones) collected from the western stock (2011-2013, North Carolina, U.S.A., winter fishery). Mixing levels for the recent sample were analyzed using otolith stable isotopes to test whether age structure might be biased through immigration of eastern stock bluefin tuna. Age structure from historical samples collected from United States and Canadian fisheries (1975-1981) was compared with more recent samples (1996-2007) to examine whether demographic changes had occurred to the western stock that might have disrupted juvenile production. Relatively high juvenile production occurred in 2003, 2005, and 2006. Otolith stable isotope analysis showed that these recruitments were mostly of western stock origin. However, these high recruitments were >2-fold less than historical recruitment. We found substantial age truncation in the sampled fisheries. Half the historical sample was >20 years old (mean age = 20.1 [SD 3.7]; skewness = -0.3), whereas 20 years old (mean age = 13.4 [SD 3.8]; skewness = 1.3). Loss of age structure is consistent with changes in fishing selectivity and trends in the stock assessment used for management. We propose that fishing, as a forcing variable, brought about a threshold shift in the western stock toward lower biomass and production, a shift that emulates the regime shift hypothesis. An abbreviated reproductive life span

  13. Familial identification: population structure and relationship distinguishability.

    Science.gov (United States)

    Rohlfs, Rori V; Fullerton, Stephanie Malia; Weir, Bruce S

    2012-02-01

    With the expansion of offender/arrestee DNA profile databases, genetic forensic identification has become commonplace in the United States criminal justice system. Implementation of familial searching has been proposed to extend forensic identification to family members of individuals with profiles in offender/arrestee DNA databases. In familial searching, a partial genetic profile match between a database entrant and a crime scene sample is used to implicate genetic relatives of the database entrant as potential sources of the crime scene sample. In addition to concerns regarding civil liberties, familial searching poses unanswered statistical questions. In this study, we define confidence intervals on estimated likelihood ratios for familial identification. Using these confidence intervals, we consider familial searching in a structured population. We show that relatives and unrelated individuals from population samples with lower gene diversity over the loci considered are less distinguishable. We also consider cases where the most appropriate population sample for individuals considered is unknown. We find that as a less appropriate population sample, and thus allele frequency distribution, is assumed, relatives and unrelated individuals become more difficult to distinguish. In addition, we show that relationship distinguishability increases with the number of markers considered, but decreases for more distant genetic familial relationships. All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States.

  14. Phytophthora infestans population structure: A worldwide scale

    International Nuclear Information System (INIS)

    Cardenas, Martha; Danies, Giovanna; Tabima, Javier; Bernal, Adriana; Restrepo, Silvia

    2012-01-01

    Phytophthora infestans, the causal agent of late blight disease in potato and other members of the Solanaceae family, is responsible for causing the Irish potato famine and, even today, it causes enormous economic losses all over the world. For the establishment of an adequate pest management strategy, the determination of the pathogen's population structure is required. To characterize P. infestans populations worldwide two allozymes, Gpi (Glucose-6-phospate isomerase) and Pep (Pep tidase), the RG57 DNA RFLP fingerprinting probe, as well as resistance to the fungicide metalaxyl and mating type, have been used as markers. P. infestans populations in Mexico have been one of the main focuses of research in the population biology of this pathogen because this country has been considered as one of the possible centers of origin of this oomycete. In this review we present the population structure of P. infestans in Mexico, Europe, Africa, Asia, North America, and South America, expanding it on the present situation of P. infestans in Colombia. Finally, we will discuss different lines of research that are being carried out today with respect to P. infestans in Colombia, which have shown the importance of continuing the study of this devastating plant pathogen in our country.

  15. Phytophthora infestans population structure: a worldwide scale

    Directory of Open Access Journals (Sweden)

    Martha Cárdenas Toquica

    2012-05-01

    Full Text Available Phytophthora infestans, the causal agent of late blight disease in potato and other members of the Solanaceae family, is responsible for causing the Irish potato famine and, even today, it causes enormous economic losses all over the world. For the establishment of an adequate pest management strategy, the determination of population structure is required. To characterize P. infestans populations worldwide two allozymes, Gpi (Glucose-6-phospate isomerase and Pep (Peptidase, the RG57 DNA RFLP fingerprinting probe, as well as resistance to the fungicide metalaxyl and the mating type, have been used as markers. P. infestans populations in Mexico have been one of the main focuses of research in the population biology of this pathogen because this country has been considered as one of the possible centers of origin of this oomycete. In this review we present the population structure of P. infestans in Mexico, Europe, Africa, Asia, North America, and South America expanding on the present situation of P. infestans in Colombia. Finally, we will discuss different lines of research that are being carried out today with respect to P. infestans in Colombia, which have shown the importance of continuing the study of this devastating plant pathogen in our country.

  16. Familial identification: population structure and relationship distinguishability.

    Directory of Open Access Journals (Sweden)

    Rori V Rohlfs

    2012-02-01

    Full Text Available With the expansion of offender/arrestee DNA profile databases, genetic forensic identification has become commonplace in the United States criminal justice system. Implementation of familial searching has been proposed to extend forensic identification to family members of individuals with profiles in offender/arrestee DNA databases. In familial searching, a partial genetic profile match between a database entrant and a crime scene sample is used to implicate genetic relatives of the database entrant as potential sources of the crime scene sample. In addition to concerns regarding civil liberties, familial searching poses unanswered statistical questions. In this study, we define confidence intervals on estimated likelihood ratios for familial identification. Using these confidence intervals, we consider familial searching in a structured population. We show that relatives and unrelated individuals from population samples with lower gene diversity over the loci considered are less distinguishable. We also consider cases where the most appropriate population sample for individuals considered is unknown. We find that as a less appropriate population sample, and thus allele frequency distribution, is assumed, relatives and unrelated individuals become more difficult to distinguish. In addition, we show that relationship distinguishability increases with the number of markers considered, but decreases for more distant genetic familial relationships. All of these results indicate that caution is warranted in the application of familial searching in structured populations, such as in the United States.

  17. Structured population dynamics: continuous size and discontinuous stage structures.

    Science.gov (United States)

    Buffoni, Giuseppe; Pasquali, Sara

    2007-04-01

    A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

  18. Trading Stages: Life Expectancies in Structured Populations

    Science.gov (United States)

    Tuljapurkar, Shripad; Coulson, Tim; Horvitz, Carol

    2012-01-01

    Interest in stage-and age structured models has recently increased because they can describe quantitative traits such as size that are left out of age-only demography. Available methods for the analysis of effects of vital rates on lifespan in stage-structured models have not been widely applied because they are hard to use and interpret, and tools for age and stage structured populations are missing. We present easily interpretable expressions for the sensitivities and elasticities of life expectancy to vital rates in age-stage models, and illustrate their application with two biological examples. Much of our approach relies on trading of time and mortality risk in one stage for time and risk in others. Our approach contributes to the new framework of the study of age- and stage-structured biodemography. PMID:22664576

  19. Ecological role of bluefin tuna (Thunnus thynnus) fish farms for associated wild fish assemblages in the Mediterranean Sea.

    Science.gov (United States)

    Stagličić, Nika; Šegvić-Bubić, Tanja; Ugarković, Pero; Talijančić, Igor; Žužul, Iva; Tičina, Vjekoslav; Grubišić, Leon

    2017-12-01

    The ecological effects of tuna fish farms are largely undocumented. This study confirmed their high capacity to attract surrounding wild fish. The aggregation effect persisted year round, without detectable seasonal differences. Farm impact was restricted to close proximity of the sea cages, and was more prominent over the bottom than in the water column strata. Tuna fish farms proved to be high energy trophic resources, as indicated by the enhanced fitness status of two focal species, bogue and seabream. Under abundant food supply, seabream appear to allocate the majority of energy reserves to gonad development. Farm associated bogue had greater parasite loads, with no detrimental effect on fitness status. Overall, tuna fish farms can be regarded as population sources for aggregated wild fish, and under the no fishing conditions within the leasehold areas, can serve as functional marine protected areas. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Fairness and Trust in Structured Populations

    Directory of Open Access Journals (Sweden)

    Corina E. Tarnita

    2015-07-01

    Full Text Available Classical economic theory assumes that people are rational and selfish, but behavioral experiments often point to inconsistent behavior, typically attributed to “other regarding preferences.” The Ultimatum Game, used to study fairness, and the Trust Game, used to study trust and trustworthiness, have been two of the most influential and well-studied examples of inconsistent behavior. Recently, evolutionary biologists have attempted to explain the evolution of such preferences using evolutionary game theoretic models. While deterministic evolutionary game theoretic models agree with the classical economics predictions, recent stochastic approaches that include uncertainty and the possibility of mistakes have been successful in accounting for both the evolution of fairness and the evolution of trust. Here I explore the role of population structure by generalizing and expanding these existing results to the case of non-random interactions. This is a natural extension since such interactions do not occur randomly in the daily lives of individuals. I find that, in the limit of weak selection, population structure increases the space of fair strategies that are selected for but it has little-to-no effect on the optimum strategy played in the Ultimatum Game. In the Trust Game, in the limit of weak selection, I find that some amount of trust and trustworthiness can evolve even in a well-mixed population; however, the optimal strategy, although trusting if the return on investment is sufficiently high, is never trustworthy. Population structure biases selection towards strategies that are both trusting and trustworthy trustworthy and reduces the critical return threshold, but, much like in the case of fairness, it does not affect the winning strategy. Further considering the effects of reputation and structure, I find that they act synergistically to promote the evolution of trustworthiness.

  1. Population structure of Staphylococcus aureus in China

    OpenAIRE

    Yan, Xiaomei

    2015-01-01

    The present PhD research was aimed at analysing the population structure of Staphylococcus aureus in China. Between 2000 and 2005 we found that patients from a single Chinese hospital showed increasing trends in antimicrobial resistance. Among methicillin-resistant S. aureus (MRSA), resistance against rifampicin doubled to 68%. Staphylococcal food poisoning (SFP) is frequent in China. Two predominant S. aureus lineages, ST6 and ST943, were identified causing outbreaks of SFP in Southern China...

  2. Addition of different tuna meal levels to pizza dough

    Directory of Open Access Journals (Sweden)

    Daniel Abreu Vasconcelos Campelo

    Full Text Available Abstract The aim of this study was to develop pizza dough with different levels of tuna meal (Tunnus spp.. In order to produce tuna meal, tuna torsos without fins were used, cooked for 1 hour, pressed, milled and dehydrated for 24 hours at 60 °C. Pizza dough was produced without (0% or with the addition of 5, 10, 15 and 20% of tuna meal, calculated based on the quantity of wheat flour. The tuna meal and different pizza pastries were analyzed for moisture content, crude protein, total lipids, ash, carbohydrates, caloric value and fatty acid profiles. Microbiological and sensory analyses were also carried out on the pizza pastries. The increasing addition of tuna meal resulted in gains in the crude protein (10.89 to 18.94%, total lipid (4.63 to 5.89% and ash (2.54 to 3.54% contents of the pizza pastries, not influencing the moisture content or caloric value. The inclusion of tuna meal linearly increased the quantity of n-3 series fatty acids in the pizza pastry, from 1.56 to 5.93 g/kg with the addition of 20% tuna meal. The ratio between the polyunsaturated and saturated fatty acids in the tuna meal and pizza pastries varied from 1.21 to 1.85. The microbiological analyses showed that the pizza pastries were produced under proper hygiene conditions. It was also observed that the addition of 5 to 20% of tuna meal to the pizza pastry did not significantly (p>0.05 alter the parameters of aroma, flavor, overall impression and purchase intention. It was therefore concluded that the addition of 5 to 20% tuna meal is effective in improving the nutritional value and fatty acid profile of pizza pastry.

  3. KEBIJAKAN PENGELOLAAN HASIL TANGKAPAN SAMPINGAN TUNA LONGLINE DI SAMUDERA HINDIA

    Directory of Open Access Journals (Sweden)

    Budi Nugraha

    2013-11-01

    Full Text Available Tuna longline atau rawai tuna merupakan salah satu alat tangkap yang sangat efektif untuk menangkap tuna. Selain efektif alat tangkap ini juga merupakan alat tangkap yang selektif terhadap hasil tangkapannya. Namun demikian, alat tangkap ini masih menimbulkan suatu masalah dimana ikan hasil tangkapan yang diperoleh tidak semuanya merupakan hasil tangkapan utama (target species, ada sebagian yang merupakan hasil tangkapan sampingan (by-catch. Sebagian besar hasil tangkapan sampingan tuna longline memiliki nilai ekonomis, hanya jenis pari lumpur dan ikan naga yang tidak memiliki nilai ekonomis. Namun demikian, justru yang tidak memiliki nilai ekonomis mendominasi hasil tangkapan sampingan pada perikanan tuna longline. Oleh karena itu perlu adanya tindak lanjut dengan menyusun peraturan atau regulasi yang terkait dengan pengelolaan ikan hasil tangkapan sampingan dan pengelolaan yang benar terhadap hasil tangkapan tersebut beserta habitatnya agar terjaga kelestarian sumberdayanya dan juga tetap menjadi sumber pendapatan masyarakat.Tulisan ini membahas secara ringkas tentang isu hasil tangkapan sampingan pada perikanan tuna longline, komposisi jenisnya, pemanfaatannya dan kebijakannya. Tuna longline is one of the most effective fishing gears to catch tuna. In addition, this fishing gear is selective to catch tuna. However, this gear is still causing a problem where some species other than their target species were caught as by-catch. Most of by-catch species from the tuna longliners have an economic value, except pelagic stingrays and lancetfish. In fact, these by-catch species (non economical-valued species dominated the longline catch. Therefore, it is needed to develop rules or regulations related to the management of the fish by-products, and properly manage the fishing activities on these by-catch species and habitat preservation to preserve its resources and also remain as a source of income. This paper briefly discusses the issue of by

  4. Polychlorinated biphenyls and organochlorine pesticides as intrinsic tracer tags of foraging grounds of bluefin tuna in the northwest Atlantic Ocean.

    Science.gov (United States)

    Deshpande, Ashok D; Dickhut, Rebecca M; Dockum, Bruce W; Brill, Richard W; Farrington, Cameron

    2016-04-15

    from offshore Virginia, Gulf of Maine, and Nova Scotia could have had extended residences and foraging within the areas of capture to be able to sustain the stable signatures of PCB congeners. The DFA cluster results supported the concept of metapopulation theory of spatial ecology comprising discrete aggregates of local populations of bluefin tuna where the desired prey species are likely to be abundant. Despite their highly migratory trait and endothermic advantage of foraging in broader and colder habitats, the movements and mixing across the aggregation ranges related to feeding did not appear to be extensive. Advancement in the understanding of bluefin tuna population dynamics beyond the coarse concept of trans-Atlantic migrations to the metapopulation hypothesis provides a novel exploratory tool in the stock assessment and resource management. As the chemical tracer tags are fortified naturally and document the time- and space-integrated foraging history, they promise to serve as the low-cost alternatives to the high-cost electronic data recording tags employed for addressing the migratory movements of bluefin tuna. Between the different potential chemical tracer tags, a distinct advantage of PCB/pesticide analysis over the otolith micro-constituent analysis is that the muscle tissue of a given individual bluefin tuna can be sampled repeatedly for PCB/pesticide analysis over different spatial and temporal scales in a non-lethal manner. Published by Elsevier Ltd.

  5. Mercury in canned tuna: white versus light and temporal variation

    International Nuclear Information System (INIS)

    Burger, Joanna; Gochfeld, Michael

    2004-01-01

    There are abundant data and advisories for mercury levels in wild fish, but far fewer for commercial fish that compose a large majority of the fish most people eat. Until recently, relatively little attention has been devoted to examining mercury in canned tuna, despite its great importance in human diets. There is substantial media coverage of the benefits and risk from fish consumption, but few peer-reviewed data on canned tuna, the most commonly consumed fish in the United States. In this paper, we examine the levels of total mercury in canned tuna obtained from a New Jersey grocery store from 1998 to 2003, looking for temporal consistency within this data set and particularly for comparison with the Food and Drug Administration's 1991 study. We analyzed 168 cans individually for total mercury. All values are reported as parts per million (=μg/g) on a wet weight basis. In a subset of samples analyzed for total and inorganic mercury, the inorganic mercury was below detection levels; hence at least 89% of the mercury can be considered methylmercury. We found that white-style tuna had significantly more total mercury (mean 0.407 ppm) than light-style tuna (mean 0.118 ppm), presumably reflecting that 'white' tuna is albacore, a species relatively larger than the skipjack tuna, which is commonly available as 'light' or 'chunk light'. The maximum mercury in a can was 0.997 ppm, but 25% of white tuna samples exceeded 0.5 ppm. Data suggest a slight increase in levels since 1991, and mercury levels were significantly higher in 2001 than in other years. The mean level of mercury in white tuna (mean 0.407 ppm) was significantly higher than the mean value of 0.17 ppm currently used by the U.S. Food and Drug Administration (FDA) in its risk assessment and public information. There were no significant differences in mercury levels in tuna packed in oil compared to water. Draining contents had no effect on mercury levels, and the fluid, both oil and water, contained little

  6. 76 FR 13583 - Atlantic Highly Migratory Species; Atlantic Bluefin Tuna Quotas and Atlantic Tuna Fisheries...

    Science.gov (United States)

    2011-03-14

    ... address concerns raised in a recent decision by a NOAA Administrative Law Judge (see Atlantic Tunas Transfer at Sea section for case reference). NMFS has prepared a draft Environmental Assessment (EA... subtraction of these allocations directly from the TAC, the recommendation allocates the remainder to the UK...

  7. Relative growth pattern and hard tissue of vertebral centra by microradiography of bluefin tuna

    International Nuclear Information System (INIS)

    Kubo, Y.; Asano, H.

    1989-01-01

    To clarify the growth feature and the structure of hard tissue, we studied the vertebral centrum of three species, bluefin tuna Thunnus thynnus, bigeye tuna T. obesus and skipjack Katsuwonus pelamis (BL: 44.2, 39.5 and 40.0cm respectively). We examined the ratio of cetrum length to diameter in each vertebral centrum and obtained the value of 0.9-1.3 in most centra among three species. This indicates that the examined species belong to the equivalent type of the relative growth pattern of vertebral centra. The hard tissue was observed by microradiography, with the longitudinal and cross sections (about 100 μm) cut through the center of notochordal pore. The major centra of the vertebral column were composed of characteristic simple structure like a cross, when seen in the microradiographs of cross sections. Microradiographs indicated that the bone has complicated canals with minute spaces like the bone cavities

  8. Mapping population-based structural connectomes.

    Science.gov (United States)

    Zhang, Zhengwu; Descoteaux, Maxime; Zhang, Jingwen; Girard, Gabriel; Chamberland, Maxime; Dunson, David; Srivastava, Anuj; Zhu, Hongtu

    2018-05-15

    Advances in understanding the structural connectomes of human brain require improved approaches for the construction, comparison and integration of high-dimensional whole-brain tractography data from a large number of individuals. This article develops a population-based structural connectome (PSC) mapping framework to address these challenges. PSC simultaneously characterizes a large number of white matter bundles within and across different subjects by registering different subjects' brains based on coarse cortical parcellations, compressing the bundles of each connection, and extracting novel connection weights. A robust tractography algorithm and streamline post-processing techniques, including dilation of gray matter regions, streamline cutting, and outlier streamline removal are applied to improve the robustness of the extracted structural connectomes. The developed PSC framework can be used to reproducibly extract binary networks, weighted networks and streamline-based brain connectomes. We apply the PSC to Human Connectome Project data to illustrate its application in characterizing normal variations and heritability of structural connectomes in healthy subjects. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. Pengaruh Penggunaan Formalin terhadap Kerusakan Protein Daging Ikan Tuna (Thunus sp)

    OpenAIRE

    Apituley, Daniel A. N.

    2012-01-01

    Formaldehyde is used on handling and processing of fishery product by some fisher at some coastal region of Indonesia was one that promotes protein oxidation and modification of protein structure of fish meat which give direct impact on nutritional quality of fish primarily the amino acids. This experiment was done in vitro experiment by using model of protein preparat of red and white meat of tuna. The purpose of this research was to study the effect of formaldehyde concentration and impact ...

  10. Oligonucleotide indexing of DNA barcodes: identification of tuna and other scombrid species in food products

    Directory of Open Access Journals (Sweden)

    Botti Sara

    2010-08-01

    Full Text Available Abstract Background DNA barcodes are a global standard for species identification and have countless applications in the medical, forensic and alimentary fields, but few barcoding methods work efficiently in samples in which DNA is degraded, e.g. foods and archival specimens. This limits the choice of target regions harbouring a sufficient number of diagnostic polymorphisms. The method described here uses existing PCR and sequencing methodologies to detect mitochondrial DNA polymorphisms in complex matrices such as foods. The reported application allowed the discrimination among 17 fish species of the Scombridae family with high commercial interest such as mackerels, bonitos and tunas which are often present in processed seafood. The approach can be easily upgraded with the release of new genetic diversity information to increase the range of detected species. Results Cocktail of primers are designed for PCR using publicly available sequences of the target sequence. They are composed of a fixed 5' region and of variable 3' cocktail portions that allow amplification of any member of a group of species of interest. The population of short amplicons is directly sequenced and indexed using primers containing a longer 5' region and the non polymorphic portion of the cocktail portion. A 226 bp region of CytB was selected as target after collection and screening of 148 online sequences; 85 SNPs were found, of which 75 were present in at least two sequences. Primers were also designed for two shorter sub-fragments that could be amplified from highly degraded samples. The test was used on 103 samples of seafood (canned tuna and scomber, tuna salad, tuna sauce and could successfully detect the presence of different or additional species that were not identified on the labelling of canned tuna, tuna salad and sauce samples. Conclusions The described method is largely independent of the degree of degradation of DNA source and can thus be applied to

  11. Oligonucleotide indexing of DNA barcodes: identification of tuna and other scombrid species in food products.

    Science.gov (United States)

    Botti, Sara; Giuffra, Elisabetta

    2010-08-23

    DNA barcodes are a global standard for species identification and have countless applications in the medical, forensic and alimentary fields, but few barcoding methods work efficiently in samples in which DNA is degraded, e.g. foods and archival specimens. This limits the choice of target regions harbouring a sufficient number of diagnostic polymorphisms. The method described here uses existing PCR and sequencing methodologies to detect mitochondrial DNA polymorphisms in complex matrices such as foods. The reported application allowed the discrimination among 17 fish species of the Scombridae family with high commercial interest such as mackerels, bonitos and tunas which are often present in processed seafood. The approach can be easily upgraded with the release of new genetic diversity information to increase the range of detected species. Cocktail of primers are designed for PCR using publicly available sequences of the target sequence. They are composed of a fixed 5' region and of variable 3' cocktail portions that allow amplification of any member of a group of species of interest. The population of short amplicons is directly sequenced and indexed using primers containing a longer 5' region and the non polymorphic portion of the cocktail portion. A 226 bp region of CytB was selected as target after collection and screening of 148 online sequences; 85 SNPs were found, of which 75 were present in at least two sequences. Primers were also designed for two shorter sub-fragments that could be amplified from highly degraded samples. The test was used on 103 samples of seafood (canned tuna and scomber, tuna salad, tuna sauce) and could successfully detect the presence of different or additional species that were not identified on the labelling of canned tuna, tuna salad and sauce samples. The described method is largely independent of the degree of degradation of DNA source and can thus be applied to processed seafood. Moreover, the method is highly flexible

  12. Population structure and recruitment of penaeid shrimps in ...

    African Journals Online (AJOL)

    Population structure and recruitment of penaeid shrimps in mozambique. ... This study characterizes the population structure and identifies nursery areas and recruitment seasons of penaeid shrimps in the ... AJOL African Journals Online.

  13. POPULATION STRUCTURES OF FOUR TREE SPECIES IN LOGGED-OVER TROPICAL FOREST IN SOUTH PAPUA, INDONESIA: AN INTEGRAL PROJECTION MODEL APPROACH

    Directory of Open Access Journals (Sweden)

    Relawan kuswandi

    2015-12-01

    Full Text Available Selective logging has been taking place in Papua for several decades. In contrast, very little is known about the stand structure in post-logged forest. Hence, this paper investigates stand structures in logged-over area of tropical forest in South Papua. Four species were selected in three one-hectare permanent sample plots (PSPs: Vatica rassak, Syzygium sp, Litsea timoriana and Canarium asperum. PSPs were located in the forest concession area of PT. Tunas Sawaerma in Assiki, Boven Digul, in South Papua. Data sets comprised measurements made in 2005 and 2012 consisting of species, diameter at breast height (DBH, mortality and number of tree of each species. Integral Projection Models (IPMs were developed, taking into account mortality, growth, recruitment and fecundity. Results show the pattern of stand structures of the four species were more or less similar, i.e. more individual trees were present in the small diameter classes than in the larger diameter classes. The general pattern of the individual distribution of the four species is the typical reverse-J shape. Syzygium sp. has a greater number of individuals in the small diameter classes than the other three species. Population growth rates (λ are above one, indicating that the stand structures of the population dynamics of the four species are recuperating. Conclusively, these results suggest that species composition and population structure in these logged-over forests are recovering increasingly.

  14. Bioenergetics, Trophic Ecology, and Niche Separation of Tunas.

    Science.gov (United States)

    Olson, R J; Young, J W; Ménard, F; Potier, M; Allain, V; Goñi, N; Logan, J M; Galván-Magaña, F

    Tunas are highly specialized predators that have evolved numerous adaptations for a lifestyle that requires large amounts of energy consumption. Here we review our understanding of the bioenergetics and feeding dynamics of tunas on a global scale, with an emphasis on yellowfin, bigeye, skipjack, albacore, and Atlantic bluefin tunas. Food consumption balances bioenergetics expenditures for respiration, growth (including gonad production), specific dynamic action, egestion, and excretion. Tunas feed across the micronekton and some large zooplankton. Some tunas appear to time their life history to take advantage of ephemeral aggregations of crustacean, fish, and molluscan prey. Ontogenetic and spatial diet differences are substantial, and significant interdecadal changes in prey composition have been observed. Diet shifts from larger to smaller prey taxa highlight ecosystem-wide changes in prey availability and diversity and provide implications for changing bioenergetics requirements into the future. Where tunas overlap, we show evidence of niche separation between them; resources are divided largely by differences in diet percentages and size ranges of prey taxa. The lack of long-term data limits the ability to predict impacts of climate change on tuna feeding behaviour. We note the need for systematic collection of feeding data as part of routine monitoring of these species, and we highlight the advantages of using biochemical techniques for broad-scale analyses of trophic relations. We support the continued development of ecosystem models, which all too often lack the regional-specific trophic data needed to adequately investigate climate and fishing impacts. © 2016 Elsevier Ltd. All rights reserved.

  15. Characterization of Fish Skin Gelatin Yellowfin Tuna

    Directory of Open Access Journals (Sweden)

    Mala Nurilmala

    2017-08-01

    Full Text Available Gelatin is one of the products which become a necessity for various industries, i.e. food and non-food industries. The application of gelatin has been increasing year by year in Indonesia. However, there is nogelatin industry in Indonesia so far. Thus, it is necessary to find an alternative source of gelatin, especially from fishery by products.Thus, the purpose of this research was to extract fish skin gelatin of yellowfin tuna with temperature treatments (55, 65 and 75oC. In addition, the properties of resulted gelatin were determined including yield, pH, gel strength, viscosity, functional groups, molecular weight profiles, and amino acid composition. The extraction at 75oC was chosen as the best result. The yield was 17%; pH 5.3; gel strength 1789.55 gf, viscosity 104.2 Cp, respectively. There was functional group amide A, I, II, dan III. SDS-PAGE showed β, α1 dan α2 bands for tuna skin gelatin. In addition, the main amino acids were glycine and proline.

  16. Economic Impacts of Climate Change on Tuna Fisheries in Fiji Islands and Kiribati

    Energy Technology Data Exchange (ETDEWEB)

    Aaheim, Asbjoern; Sygna, Linda

    2000-06-01

    This paper discusses the possible economic consequences of a change in the tuna fisheries in the Pacific Ocean resulting from climate change. On the background of Lehodey's (2000) study of potential changes in the tuna fisheries, we survey possible economic impacts in terms of quantities and values and give examples of macroeconomic impacts. The two main effects of climate change on tuna fishing are likely to be a decline in the total stock and a migration of the stock westwards. This will lead to various changes in the catch in different countries. The price of the fish in the export market may also change as a result. The Pacific islands are generally dependent on fisheries, and may therefore be vulnerable to these changes, although some will probably gain while others will lose. Based on a very simple macroeconomic model, it is shown that the resulting effects for the national economy in general may diverge substantially from the expected. This applies, in particular, if the national economies are inflexible and a large part of the population relies on subsistence production, which is the case for many developing countries. (author)

  17. First attempt to assess the viability of bluefin tuna spawning events in offshore cages located in an a priori favourable larval habitat

    Directory of Open Access Journals (Sweden)

    Patricia Reglero

    2013-10-01

    Full Text Available Most of the Atlantic bluefin tuna caught by the purse-seine fleet in the Mediterranean Sea are transferred alive into transport cages and towed to coastal facilities where they are fattened. This major fishery is targeting aggregations of reproductive bluefin tuna that continue spawning within the transport cages. Our study is the first attempt to assess the viability of the spawning events within transport cages placed offshore in a priori favourable locations for larval survival. The study was conducted in June 2010 in the Balearic Sea, a main spawning area for bluefin tuna in the Mediterranean. The location of two transport cages, one with wild and one with captive tuna, coincide with the situation of the chlorophyll front using satellite imagery as a proxy for the salinity front between resident surface waters and those of recent Atlantic origin. The results showed that bluefin tuna eggs were spawned almost every day within the two cages but few or no larvae were found. The expected larval densities estimated after applying mortality curves to the daily egg densities observed in the cages were higher than the sampled larval densities. The trajectories of the eggs after hatching estimated from a particle tracking model based on observed geostrophic currents and a drifter deployed adjacent to the cage suggest that larvae were likely to be caught close to the cages within the sampling dates. Spawning events in captive tuna in transport cages may hatch into larvae though they may experience higher mortality rates than expected in natural populations. The causes of the larval mortality are further discussed in the text. Such studies should be repeated in other spawning areas in the Mediterranean if spawning in cages located offshore in areas favourable a priori for larval survival is likely to be considered a management measurement to minimize the impact of purse-seine fishing on tuna.

  18. Population genetic structure analysis in endangered Hordeum ...

    African Journals Online (AJOL)

    Administrator

    2011-09-07

    Sep 7, 2011 ... populations are grown by few local farmers in low-input farming systems. Based on 117 random ... Triticeae of the Poaceae (Graminae) family found throughout the ... populations and phylogeography is made easy by the.

  19. Polimorfisme Enzim Glucose-6-Phosphate Isomerase pada Tiga Populasi Tuna Sirip Kuning (Thunnus albacares)

    OpenAIRE

    Permana, Gusti Ngurah; Hutapea, Jhon H.; Moria, Sari Budi; Haryanti, Haryanti

    2006-01-01

    Samples of yellowfin tuna (Thunnus albacares) were taken from three locations Bali, North Sulawesi and North Maluku. The glucose-6-phosphate isomerase (GPI) was analyzed from liver using allozyme electrophoresis method. Polymorphism of GPI enzyme was observed and four alleles (A, B ,C, D) were found in Bali population, three alleles (A,B,C) were found in North Maluku and North Sulawesi populations. Heterozygosity values, from Bali, North Maluku and North Sulawesi were 0.419; 0.417; 0.143 resp...

  20. Tuna Cannery Points, Tutuila AS, 2007, US EPA Region 9

    Data.gov (United States)

    U.S. Environmental Protection Agency — American Samoa's primary industry is tuna processing by the Samoa Packing Co., user of the "Chicken of the Sea" label, and StarKist Samoa. Canneries thrive in this...

  1. Spatial and population genetic structure of microsatellites in white pine

    Science.gov (United States)

    Paula E. Marquardt; Bryan K. Epperson

    2004-01-01

    We evaluated the population genetic structure of seven microsatellite loci for old growth and second growth populations of eastern white pine (Pinus strobus). From each population, located within Hartwick Pines State Park, Grayling, Michigan, USA, 120-122 contiguous trees were sampled for genetic analysis. Within each population, genetic diversity...

  2. Visualising the demographic factors which shape population age structure

    Directory of Open Access Journals (Sweden)

    Tom Wilson

    2016-09-01

    Full Text Available Background: The population pyramid is one of the most popular tools for visualising population age structure. However, it is difficult to discern from the diagram the relative effects of different demographic components on the size of age-specific populations, making it hard to understand exactly how a population's age structure is formed. Objective: The aim of this paper is to introduce a type of population pyramid which shows how births, deaths, and migration have shaped a population's age structure. Methods: Births, deaths, and population data were obtained from the Human Mortality Database and the Australian Bureau of Statistics. A variation on the conventional population pyramid, termed here a components-of-change pyramid, was created. Based on cohort population accounts, it illustrates how births, deaths, and net migration have created the population of each age group. A simple measure which summarises the impact of net migration on age structure is also suggested. Results: Example components-of-change pyramids for several countries and subnational regions are presented, which illustrate how births, deaths, and net migration have fashioned current population age structures. The influence of migration is shown to vary greatly between populations. Conclusions: The new type of pyramid aids interpretation of a population's age structure and helps to understand its demographic history over the last century.

  3. Underground population defense structures in China

    Energy Technology Data Exchange (ETDEWEB)

    Wukasch, E.

    The design and construction ofunderground shelters to protect the Chinese population in the event of nuclear war are described. Built in the style of World War II air raid shelters and designed as neighborhood defense facilities, these are not judged to be adequate for nuclear defense needs, particularly the needs of urban populations. However, 80% of China's population is rural and 1/3 of this has lived underground for centuries in cliff dwellings and atrium houses. It is, therefore, concluded that China's rural population has a better chance the the population of any other country for long-term survival from the later consequences, as well as the immediate shock, of an urban nuclear attack. (LCL)

  4. Genetic structure of Potentilla acaulis (Rosaceae) populations ...

    African Journals Online (AJOL)

    Jane

    2011-07-18

    Jul 18, 2011 ... populations based on randomly amplified polymorphic. DNA (RAPD) in habitat ..... the correlation between ΦST values and genetic distances was highly ... Propagule recruitment from genets of perennial clonal plants could ...

  5. Estimating population age structure using otolith morphometrics

    DEFF Research Database (Denmark)

    Doering-Arjes, P.; Cardinale, M.; Mosegaard, Henrik

    2008-01-01

    known-age fish individuals. Here we used known-age Atlantic cod (Gadus morhua) from the Faroe Bank and Faroe Plateau stocks. Cod populations usually show quite large variation in growth rates and otolith shape. We showed that including otolith morphometrics into ageing processes has the potential...... populations. The intercalibration method was successful but generalization from one stock to another remains problematic. The development of an otolith growth model is needed for generalization if an operational method for different populations is required in the future....... to make ageing objective, accurate, and fast. Calibration analysis indicated that a known-age sample from the same population and environment is needed to obtain robust calibration; using a sample from a different stock more than doubles the error rate, even in the case of genetically highly related...

  6. Coexistence of competing stage-structured populations.

    KAUST Repository

    Fujiwara, Masami; Pfeiffer, Georgia; Boggess, May; Day, Sarah; Walton, Jay

    2011-01-01

    -use overlap. The former ratio, which we define as fitness, can be equalized by adjusting organisms' life history strategies, thereby promoting coexistence. We conclude that in addition to niche differentiation among populations, the life history strategies

  7. Projecting the impacts of climate change on skipjack tuna abundance and spatial distribution.

    Science.gov (United States)

    Dueri, Sibylle; Bopp, Laurent; Maury, Olivier

    2014-03-01

    Climate-induced changes in the physical, chemical, and biological environment are expected to increasingly stress marine ecosystems, with important consequences for fisheries exploitation. Here, we use the APECOSM-E numerical model (Apex Predator ECOSystem Model - Estimation) to evaluate the future impacts of climate change on the physiology, spatial distribution, and abundance of skipjack tuna, the worldwide most fished species of tropical tuna. The main novelties of our approach lie in the mechanistic link between environmental factors, metabolic rates, and behavioral responses and in the fully three dimensional representation of habitat and population abundance. Physical and biogeochemical fields used to force the model are provided by the last generation of the IPSL-CM5 Earth System Model run from 1990 to 2100 under a 'business-as-usual' scenario (RCP8.5). Our simulations show significant changes in the spatial distribution of skipjack tuna suitable habitat, as well as in their population abundance. The model projects deterioration of skipjack habitat in most tropical waters and an improvement of habitat at higher latitudes. The primary driver of habitat changes is ocean warming, followed by food density changes. Our projections show an increase of global skipjack biomass between 2010 and 2050 followed by a marked decrease between 2050 and 2095. Spawning rates are consistent with population trends, showing that spawning depends primarily on the adult biomass. On the other hand, growth rates display very smooth temporal changes, suggesting that the ability of skipjack to keep high metabolic rates in the changing environment is generally effective. Uncertainties related to our model spatial resolution, to the lack or simplification of key processes and to the climate forcings are discussed. © 2013 John Wiley & Sons Ltd.

  8. Etiologi Penyebab Malformasi Tunas Ranting Kakao di Kulonprogo, DIY dan Segayung, Jawa Tengah

    Directory of Open Access Journals (Sweden)

    Susamto Somowiyarjo

    2014-12-01

    insektisida hasilnya tunas muda yang tumbuh berikutnya tidak menunjukan adanya gejala malformasi. Diduga bahwa malformasi pada tunas dan ranting tersebut disebabkan oleh racun yang ditularkan oleh serangga. Penelitian lebih lanjut untuk karakterisasi penyebab penyakit secara molekuler saat ini sedang dilakukan.

  9. Cytochrome Oxidase I (COI) sequence conservation and variation patterns in the yellowfin and longtail tunas

    Digital Repository Service at National Institute of Oceanography (India)

    Kunal, S.P.; GirishKumar

    within and between tuna Thunnus species and its application to species identification. J Fish Biol. 58, 1646–1657. 8 Terol, J., Mascarell, R., Fernandez-Pedrosa, V., Perez-Alonso, M. (2002) Statistical validation of the identification of tuna...

  10. Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna

    OpenAIRE

    Nakamura, Yoji; Mori, Kazuki; Saitoh, Kenji; Oshima, Kenshiro; Mekuchi, Miyuki; Sugaya, Takuma; Shigenobu, Yuya; Ojima, Nobuhiko; Muta, Shigeru; Fujiwara, Atushi; Yasuike, Motoshige; Oohara, Ichiro; Hirakawa, Hideki; Chowdhury, Vishwajit Sur; Kobayashi, Takanori

    2013-01-01

    Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing tec...

  11. 50 CFR 216.95 - Official mark for “Dolphin-safe” tuna products.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Official mark for âDolphin-safeâ tuna... AND IMPORTING OF MARINE MAMMALS Dolphin Safe Tuna Labeling § 216.95 Official mark for “Dolphin-safe... Department of Commerce that may be used to label tuna products that meet the “dolphin-safe” standards set...

  12. Trophic impact of Atlantic bluefin tuna migrations in the North Sea

    DEFF Research Database (Denmark)

    Mariani, Patrizio; Andersen, Ken Haste; Lindegren, Martin

    2017-01-01

    and the stability of the fish community. The impact of a migrating top-predator is investigated here for Atlantic bluefin tuna in the North Sea. Bluefin tuna has been absent from the region for half-century, but recent years have seen recovery of migrations and a return of bluefin tuna in the area. We use a size...

  13. Feeding Partitioning among Tuna Taken in Surface and Mid-water ...

    African Journals Online (AJOL)

    Crustaceans were the almost exclusive food source of surface-swimming bigeye tuna, with the stomatopod (Natosquilla investigatoris) being the sole prey item recorded in this category. The diet of deep-swimming yellowfin tuna was balanced between epipelagic fish, crustaceans and cephalopods. Bigeye tuna fed ...

  14. Extensive population genetic structure in the giraffe

    Directory of Open Access Journals (Sweden)

    Grether Gregory F

    2007-12-01

    Full Text Available Abstract Background A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (Giraffa camelopardalis are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation. Results By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations. Conclusion Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate in situ and ex situ management, not only of pelage morphs, but also of local populations.

  15. Population structure and genetic diversity of Sudanese native chickens

    African Journals Online (AJOL)

    The objectives of this study were to analyze genetic diversity and population structure of Sudanese native chicken breeds involved in a conservation program. Five Sudanese native chicken breeds were compared with populations studied previously, which included six purebred lines, six African populations and one ...

  16. Population Genetic Structure and Gene Flow Among Nigerian Goats ...

    African Journals Online (AJOL)

    Population Genetic structure in 200 indigenous goats sampled across four states from the South-Western and South Southern region of Nigeria was assessed using 7 microsatellite DNA markers. Observed Analysis of molecular genetic variation (AMOVA) was higher within populations (3.47) than among populations (1.84) ...

  17. Genetic diversity and population structure of sweet cassava using ...

    African Journals Online (AJOL)

    The objective of this study was to evaluate the population structure and genetic diversity among 66 sweet cassava (Manihot esculenta Crantz) traditional accessions collected in Maringa, Parana, Brazil, using microsatellite molecular markers. Population structure was analyzed by means of genetic distances and ...

  18. Genetic diversity and population structure of Chinese honeybees ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of Chinese honeybees (Apis cerana) under microsatellite markers. T Ji, L Yin, G Chen. Abstract. Using 21 microsatellite markers and PCR method, the polymorphisms of 20 Apis cerana honeybee populations across China was investigated and the genetic structure and diversity of ...

  19. A Structure for Population Education: Goals, Generalizations, and Behavioral Objectives.

    Science.gov (United States)

    Lane, Mary Turner; Wileman, Ralph E.

    This book is written to assist anyone who wants to learn about, teach, or plan curricula for population education. A structure is provided that educators can use for first graders or for high school students. Chapter 1 identifies the population phenomenon and the need to study it. Chapter 2 gives the elements of the structure: goals,…

  20. Modeling evolutionary games in populations with demographic structure

    DEFF Research Database (Denmark)

    Li, Xiang-Yi; Giaimo, Stefano; Baudisch, Annette

    2015-01-01

    interactions, but usually omits life history and the demographic structure of the population. Here we show how an integration of both aspects can substantially alter the underlying evolutionary dynamics. We study the replicator dynamics of strategy interactions in life stage structured populations. Individuals...

  1. Some epidemiological and clinical characteristics of solid malignant tumors in children from Las Tunas

    Directory of Open Access Journals (Sweden)

    Silvio Laffita Estévez

    2015-11-01

    Full Text Available Background: cancer has kept up as the second cause of death in Las Tunas pediatric population.Objective: to characterize clinical and epidemiological variables of the cases diagnosed with solid malignant tumors in children seen and treated in the onco-pediatric consultation of “Mártires de Las Tunas” Pediatric Hospital from 2010 to 2014.Methods: a descriptive and retrospective study was carried out in 62 patients with solid malignant tumors in the pediatric population of Las Tunas province, from January, 2010 to December, 2014. The variables considered were: presumptive diagnosis, age, family history of tumors, clinical signs of alarm related to the tumor at the moment of diagnosis and investigations to confirm the diagnosis.  Results: non-Hodgkin lymphoma was the most frequently diagnosed tumor, with a 19, 35% of the patients. The most affected age group was between 11 and 14 years old, with a 33, 87%. The 16, 13% of the patients had family history of solid malignant tumors. The most frequent form of presentation was the abdominal tumor, with 29, 03 %. Abdominal ultrasound and computerized axial tomography were the most used complementary diagnostic means, both in the 17, 74% of the patients. Biopsy was used to confirm the 96, 77% of the cases.Conclusions: the clinical and epidemiological variables were characterized in pediatric patients diagnosed with solid malignant tumors in Las Tunas. Children between 11 and 14 years old and family history of malignant tumors were the most significant findings.

  2. Radiation hydrolysate of tuna cooking juice with enhanced antioxidant properties

    International Nuclear Information System (INIS)

    Choi, Jong-il; Sung, Nak-Yun; Lee, Ju-Woon

    2012-01-01

    Tuna protein hydrolysates are of increasing interest because of their potential application as a source of bioactive peptides. Large amounts of tuna cooking juice with proteins and extracts are produced during the process of tuna canning, and these cooking juice wastes cause environmental problems. Therefore, in this study, cooking juice proteins were hydrolyzed by irradiation for their utilization as functional additives. The degree of hydrolysis of tuna cooking juice protein increased from 0% to 15.1% at the absorbed doses of 50 kGy. To investigate the antioxidant activity of the hydrolysate, it was performed the ferric reducing antioxidant power (FRAP) assay, and the lipid peroxidation inhibitory and superoxide radical scavenging activities were measured. The FRAP values increased from 1470 μM to 1930 μM and IC 50 on superoxide anion was decreased from 3.91 μg/mL to 1.29 μg/mL at 50 kGy. All of the antioxidant activities were increased in the hydrolysate, suggesting that radiation hydrolysis, which is a simple process that does not require an additive catalysts or an inactivation step, is a promising method for food and environmental industries. - Highlights: ► Radiation was applied for the hydrolysis of tuna cooking juice protein. ► The degree of hydrolysis were increased by irradiation and the antioxidant activity of hydrolysate was higher than protein. ► This result suggest that radiation is useful method for the hydrolysis of protein.

  3. Population structure of Han nationality in Central-Southern China.

    Science.gov (United States)

    Liu, Qiu-Ling; Chen, Ye-Fei; He, Xin; Shi, Yan-Wei; Wu, Wei-Wei; Zhao, Hu; Lu, De-Jian

    2017-07-01

    Knowledge of population structure is very important for forensic genetics. However, the population substructure in Central-Southern China Han nationality has still not been fully described. In this study, we investigated the genetic diversity of 15 forensic autosomal STR loci from 6879 individuals in 12 Han populations subdivided by administrative provinces in Central-Southern China. The statistical analysis of genetic variation showed that genetic differentiation among these populations was very small with a F st value of 0.0009. The Discriminant Analysis of Principal Components (DAPC) showed that there were no obvious population clusters in Central-Southern China Han population. In practice, the population structure effect in Central-Southern China Han population can be negligible in forensic identification and paternity testing. Copyright © 2017. Published by Elsevier B.V.

  4. Pulsed adiabatic structure and complete population transfer

    International Nuclear Information System (INIS)

    Shore, B.W.

    1992-10-01

    Population can be transferred between atomic or molecular energy states in a variety of ways. The basic idea of adiabatic transfer, discussed in many textbooks, is as follows. One begins with an atom that is in some single energy state (an eigenstate of an initial Hamiltonian). This energy state is one of many possible states, known variously as the unperturbed states or basis states or diabatic states. Next one begins to change the Hamiltonian very slowly. The changes may occur in either the diagonal elements (the basis state energies) or in the off-diagonal elements (interactions between basis states). If there are off-diagonal elements then the Hamiltonian will no longer commute with the original one. Because the Hamiltonian is no longer the one that was used to define the original basis states, it will cause these states to become mixed. However, if the change is sufficiently slow, the system can remain in a single eigenstate of the changing Hamiltonian -- an adiabatic state, composed of a combination of basis states. Finally, at some later time, one examines the system once again in the original basis. One finds that the population has undergone a change, and now resides in a different unperturbed state. One has produced population transfer. There are many illustrative examples of adiabatic passage, both theory and experiment. The author mentions briefly two common examples, inelastic collisions between atoms, and the static Stark effect in Rydberg atoms, before continuing with the main objective, a discussion of adiabatic passage induced by laser pulses

  5. Dynamical community structure of populations evolving on genotype networks

    International Nuclear Information System (INIS)

    Capitán, José A.; Aguirre, Jacobo; Manrubia, Susanna

    2015-01-01

    Neutral evolutionary dynamics of replicators occurs on large and heterogeneous networks of genotypes. These networks, formed by all genotypes that yield the same phenotype, have a complex architecture that conditions the molecular composition of populations and their movements on genome spaces. Here we consider as an example the case of populations evolving on RNA secondary structure neutral networks and study the community structure of the network revealed through dynamical properties of the population at equilibrium and during adaptive transients. We unveil a rich hierarchical community structure that, eventually, can be traced back to the non-trivial relationship between RNA secondary structure and sequence composition. We demonstrate that usual measures of modularity that only take into account the static, topological structure of networks, cannot identify the community structure disclosed by population dynamics

  6. Development of functional canned and pouched tuna products added inulin for commercial production.

    Science.gov (United States)

    Rueangwatcharin, U; Wichienchot, S

    2015-08-01

    Four formulas of canned tuna in spring water and tuna in mayonnaise and pouched tuna in salad cream and tuna in thousand island cream with added inulin were developed for commercial production. The effects of the addition of a prebiotic (inulin, Orafti®-HP) on the color and sensory properties of these products were studied. For inulin concentrations studied (3, 5, 7 and 10 %, w/w) caused more intensed yellow and red colors. Hedonic sensory values of tuna packed in spring water and in mayonnaise showed no significant differences (p > 0.05) among products with different inulin addition levels (3, 5, 7 and 10 %, w/w) in terms of color, flavor, sweetness and overall characteristics. However, when packed in thousand island cream, significant differences (p < 0.05) in color and overall characteristics were found when inulin was added higher than 7 %. Tuna in salad cream showed significant differences (p < 0.05) in color, flavor, sweetness and overall characteristics at higher than 7 % inulin. The panelists showed acceptable overall liking scores at upto 7 % inulin of all tuna products. The thermal sterilization process resulted in approximately 20 % decrease in final inulin content. The calculated residual fructans of finished products at shelf life of 3 years were 3.01, 2.78, 2.90 and 2.84 % for tuna in spring water, tuna in mayonnaise, tuna in thousand island and tuna in salad cream, respectively. Considering formula cost in a commercial production and the recommended daily intake (RDI) of inulin in the finished product at end of shelf life (≥3 g/d), an addition of 5 % inulin for tuna in spring water and 7 % inulin for tuna in mayonnaise, tuna in thousand island and tuna in salad cream are recommended.

  7. Population structure and genetic diversity of native and invasive populations of Solanum rostratum (Solanaceae.

    Directory of Open Access Journals (Sweden)

    Jiali Zhao

    Full Text Available We investigate native and introduced populations of Solanum rostratum, an annual, self-compatible plant that has been introduced around the globe. This study is the first to compare the genetic diversity of Solanum rostratum between native and introduced populations. We aim to (1 determine the level of genetic diversity across the studied regions; (2 explore the likely origins of invasive populations in China; and (3 investigate whether there is the evidence of multiple introductions into China.We genotyped 329 individuals at 10 microsatellite loci to determine the levels of genetic diversity and to investigate population structure of native and introduced populations of S. rostratum. We studied five populations in each of three regions across two continents: Mexico, the U.S.A. and China.We found the highest genetic diversity among Mexican populations of S. rostratum. Genetic diversity was significantly lower in Chinese and U.S.A. populations, but we found no regional difference in inbreeding coefficients (F IS or population differentiation (F ST. Population structure analyses indicate that Chinese and U.S.A. populations are more closely related to each other than to sampled Mexican populations, revealing that introduced populations in China share an origin with the sampled U.S.A. populations. The distinctiveness between some introduced populations indicates multiple introductions of S. rostratum into China.

  8. Stability patterns for a size-structured population model and its stage-structured counterpart

    DEFF Research Database (Denmark)

    Zhang, Lai; Pedersen, Michael; Lin, Zhigui

    2015-01-01

    In this paper we compare a general size-structured population model, where a size-structured consumer feeds upon an unstructured resource, to its simplified stage-structured counterpart in terms of equilibrium stability. Stability of the size-structured model is understood in terms of an equivale...... to the population level....

  9. Population structure analysis using rare and common functional variants

    Directory of Open Access Journals (Sweden)

    Ding Lili

    2011-11-01

    Full Text Available Abstract Next-generation sequencing technologies now make it possible to genotype and measure hundreds of thousands of rare genetic variations in individuals across the genome. Characterization of high-density genetic variation facilitates control of population genetic structure on a finer scale before large-scale genotyping in disease genetics studies. Population structure is a well-known, prevalent, and important factor in common variant genetic studies, but its relevance in rare variants is unclear. We perform an extensive population structure analysis using common and rare functional variants from the Genetic Analysis Workshop 17 mini-exome sequence. The analysis based on common functional variants required 388 principal components to account for 90% of the variation in population structure. However, an analysis based on rare variants required 532 significant principal components to account for similar levels of variation. Using rare variants, we detected fine-scale substructure beyond the population structure identified using common functional variants. Our results show that the level of population structure embedded in rare variant data is different from the level embedded in common variant data and that correcting for population structure is only as good as the level one wishes to correct.

  10. STOMACH CONTENT OF THREE TUNA SPECIES IN THE EASTERN INDIAN OCEAN

    Directory of Open Access Journals (Sweden)

    Bram Setyadji

    2012-12-01

    Full Text Available Feeding habit of tuna in Indian Ocean has been described around Sri Lanka, Indian Waters, Andaman Sea, western Indian Ocean (Seychelles Islands, western equatorial Indian Ocean whereas the tunas feeding habit study in Eastern Indian Oceanis merely in existence. The purpose of this study is to investigate the stomach content of three tuna species (bigeye tuna, yellowfin tuna, and skipjack tuna, apex predator in the southern part of Eastern Indian Ocean. The study was conducted in March – April, 2010 on the basis of catches of commercial tuna longline vessel based in Port of Benoa. A total of 53 individual fishes were collected, consisting of bigeye tuna (Thunnus obesus, yellowfin tuna (Thunnus albacores, and skipjack tuna (Katsuwonus pelamis. Stomach specimens were collected and analyzed.Analysis was conducted on the basis of index of preponderance method. The diet of the three tuna species showed fishes as the main diet (56–82%, followed by cephalopods (squids as the complementary diet (0–8%, and crustaceans (shrimps as the additional diet (2–4%. Fish prey composed of 6 families i.e. Alepisauridae, Bramidae, Carangidae, Clupeidae, Engraulidae, and Scombridae.

  11. Earthworm ecology affects the population structure of their Verminephrobacter symbionts

    DEFF Research Database (Denmark)

    Macedo Viana, Flavia Daniela; Jensen, Christopher Erik; Macey, Michael

    2016-01-01

    from two contrasting ecological types of earthworm hosts: the high population density, fast reproducing compost worms, Eisenia andrei and E. fetida, and the low-density, slow reproducing Aporrectodea tuberculata, commonly found in garden soils; for both types, three distinct populations were...... across host individuals from the same population. Thus, host ecology shapes the population structure of the Verminephrobacter symbionts. The homogeneous symbiont populations in the compost worms indicate that Verminephrobacter can be transferred bi-parentally or via leaky horizontal transmission in high...

  12. Population activity structure of excitatory and inhibitory neurons.

    Directory of Open Access Journals (Sweden)

    Sean R Bittner

    Full Text Available Many studies use population analysis approaches, such as dimensionality reduction, to characterize the activity of large groups of neurons. To date, these methods have treated each neuron equally, without taking into account whether neurons are excitatory or inhibitory. We studied population activity structure as a function of neuron type by applying factor analysis to spontaneous activity from spiking networks with balanced excitation and inhibition. Throughout the study, we characterized population activity structure by measuring its dimensionality and the percentage of overall activity variance that is shared among neurons. First, by sampling only excitatory or only inhibitory neurons, we found that the activity structures of these two populations in balanced networks are measurably different. We also found that the population activity structure is dependent on the ratio of excitatory to inhibitory neurons sampled. Finally we classified neurons from extracellular recordings in the primary visual cortex of anesthetized macaques as putative excitatory or inhibitory using waveform classification, and found similarities with the neuron type-specific population activity structure of a balanced network with excitatory clustering. These results imply that knowledge of neuron type is important, and allows for stronger statistical tests, when interpreting population activity structure.

  13. Population activity structure of excitatory and inhibitory neurons.

    Science.gov (United States)

    Bittner, Sean R; Williamson, Ryan C; Snyder, Adam C; Litwin-Kumar, Ashok; Doiron, Brent; Chase, Steven M; Smith, Matthew A; Yu, Byron M

    2017-01-01

    Many studies use population analysis approaches, such as dimensionality reduction, to characterize the activity of large groups of neurons. To date, these methods have treated each neuron equally, without taking into account whether neurons are excitatory or inhibitory. We studied population activity structure as a function of neuron type by applying factor analysis to spontaneous activity from spiking networks with balanced excitation and inhibition. Throughout the study, we characterized population activity structure by measuring its dimensionality and the percentage of overall activity variance that is shared among neurons. First, by sampling only excitatory or only inhibitory neurons, we found that the activity structures of these two populations in balanced networks are measurably different. We also found that the population activity structure is dependent on the ratio of excitatory to inhibitory neurons sampled. Finally we classified neurons from extracellular recordings in the primary visual cortex of anesthetized macaques as putative excitatory or inhibitory using waveform classification, and found similarities with the neuron type-specific population activity structure of a balanced network with excitatory clustering. These results imply that knowledge of neuron type is important, and allows for stronger statistical tests, when interpreting population activity structure.

  14. Training set optimization under population structure in genomic selection.

    Science.gov (United States)

    Isidro, Julio; Jannink, Jean-Luc; Akdemir, Deniz; Poland, Jesse; Heslot, Nicolas; Sorrells, Mark E

    2015-01-01

    Population structure must be evaluated before optimization of the training set population. Maximizing the phenotypic variance captured by the training set is important for optimal performance. The optimization of the training set (TRS) in genomic selection has received much interest in both animal and plant breeding, because it is critical to the accuracy of the prediction models. In this study, five different TRS sampling algorithms, stratified sampling, mean of the coefficient of determination (CDmean), mean of predictor error variance (PEVmean), stratified CDmean (StratCDmean) and random sampling, were evaluated for prediction accuracy in the presence of different levels of population structure. In the presence of population structure, the most phenotypic variation captured by a sampling method in the TRS is desirable. The wheat dataset showed mild population structure, and CDmean and stratified CDmean methods showed the highest accuracies for all the traits except for test weight and heading date. The rice dataset had strong population structure and the approach based on stratified sampling showed the highest accuracies for all traits. In general, CDmean minimized the relationship between genotypes in the TRS, maximizing the relationship between TRS and the test set. This makes it suitable as an optimization criterion for long-term selection. Our results indicated that the best selection criterion used to optimize the TRS seems to depend on the interaction of trait architecture and population structure.

  15. Population activity structure of excitatory and inhibitory neurons

    Science.gov (United States)

    Doiron, Brent

    2017-01-01

    Many studies use population analysis approaches, such as dimensionality reduction, to characterize the activity of large groups of neurons. To date, these methods have treated each neuron equally, without taking into account whether neurons are excitatory or inhibitory. We studied population activity structure as a function of neuron type by applying factor analysis to spontaneous activity from spiking networks with balanced excitation and inhibition. Throughout the study, we characterized population activity structure by measuring its dimensionality and the percentage of overall activity variance that is shared among neurons. First, by sampling only excitatory or only inhibitory neurons, we found that the activity structures of these two populations in balanced networks are measurably different. We also found that the population activity structure is dependent on the ratio of excitatory to inhibitory neurons sampled. Finally we classified neurons from extracellular recordings in the primary visual cortex of anesthetized macaques as putative excitatory or inhibitory using waveform classification, and found similarities with the neuron type-specific population activity structure of a balanced network with excitatory clustering. These results imply that knowledge of neuron type is important, and allows for stronger statistical tests, when interpreting population activity structure. PMID:28817581

  16. Dynamics of a structured neuron population

    International Nuclear Information System (INIS)

    Pakdaman, Khashayar; Salort, Delphine; Perthame, Benoît

    2010-01-01

    We study the dynamics of assemblies of interacting neurons. For large fully connected networks, the dynamics of the system can be described by a partial differential equation reminiscent of age-structure models used in mathematical ecology, where the 'age' of a neuron represents the time elapsed since its last discharge. The nonlinearity arises from the connectivity J of the network. We prove some mathematical properties of the model that are directly related to qualitative properties. On the one hand, we prove that it is well-posed and that it admits stationary states which, depending upon the connectivity, can be unique or not. On the other hand, we study the long time behaviour of solutions; both for small and large J, we prove the relaxation to the steady state describing asynchronous firing of the neurons. In the middle range, numerical experiments show that periodic solutions appear expressing re-synchronization of the network and asynchronous firing

  17. Population genetic structure in wild and aquaculture populations of Hemibarbus maculates inferred from microsatellites markers

    Directory of Open Access Journals (Sweden)

    Linlin Li

    2017-03-01

    Full Text Available The objective of this study was to investigate 4 aquaculture populations Shanghai (SH, Hangzhou (HZ, Kaihua (KH and Xianju (XJ and one wild population Yingshan (YS of spotted barbell (Hemibarbus maculates to assess their genetic diversity level and investigate the genetic structure of the populations. The dendrogram and STRUCTURE revealed that the populations XJ, KH, and HZ jointly formed one cluster, to which the populations SH and YS were sequentially adhered. The genetic diversity of the cultured populations maintained better, possible due to favourable hatchery conditions that decreased the effect of environmental selection present in wild populations. The results of the present study will contribute to the management of spotted barbell genetic resources, but also demonstrates how the genetic diversity of freshwater species is vulnerable to human activity.

  18. Human population structure detection via multilocus genotype clustering

    Directory of Open Access Journals (Sweden)

    Starmer Joshua

    2007-06-01

    Full Text Available Abstract Background We describe a hierarchical clustering algorithm for using Single Nucleotide Polymorphism (SNP genetic data to assign individuals to populations. The method does not assume Hardy-Weinberg equilibrium and linkage equilibrium among loci in sample population individuals. Results We show that the algorithm can assign sample individuals highly accurately to their corresponding ethnic groups in our tests using HapMap SNP data and it is also robust to admixed populations when tested with Perlegen SNP data. Moreover, it can detect fine-scale population structure as subtle as that between Chinese and Japanese by using genome-wide high-diversity SNP loci. Conclusion The algorithm provides an alternative approach to the popular STRUCTURE program, especially for fine-scale population structure detection in genome-wide association studies. This is the first successful separation of Chinese and Japanese samples using random SNP loci with high statistical support.

  19. A general modeling framework for describing spatially structured population dynamics

    Science.gov (United States)

    Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

    2017-01-01

    Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance

  20. Analysis of genetic diversity and population structure in upland ...

    Indian Academy of Sciences (India)

    Mulugeta Seyoum

    2018-06-09

    Jun 9, 2018 ... diversity and population structure at DNA level, 302 elite upland cotton germplasm accessions ...... conservation of cotton germplasm in China (English abstract). ... and Alishah O. 2011 Inter simple sequence repeats (ISSR).

  1. Genetic diversity and population structure of endangered Aquilaria ...

    Indian Academy of Sciences (India)

    2015-12-03

    Dec 3, 2015 ... ... Aromatic and Economic Plants, CSIR - North-East Institute of Science and Technology ... and population structure is receiving tremendous attention for effective .... unreliable detection and to increase the quality of data. The.

  2. The population genomics of begomoviruses: global scale population structure and gene flow

    Directory of Open Access Journals (Sweden)

    Prasanna HC

    2010-09-01

    Full Text Available Abstract Background The rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people. Results We focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations. Conclusions Although geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could

  3. DISKRIMINASI KELAMIN PADA IKAN TUNA SIRIP KUNING, Yellowfin tuna MENGGUNAKAN ANALISIS DOT BLOT DAN ELISA

    Directory of Open Access Journals (Sweden)

    Gusti Ngurah Permana

    2014-08-01

    Full Text Available Pemahaman tentang penentuan jenis kelamin dalam populasi induk merupakan hal yang sangat penting bagi keberhasilan program pembenihan. Pengukuran reaksi antibodi dan aktivitas hormon testosterone, serta estradiol adalah metode dengan potensi yang secara akurat dapat menentukan jenis kelamin ikan tanpa mematikan ikan. Tujuan penelitian ini adalah untuk mengetahui akurasi metode dot blot dan ELISA dengan 11-ketotestorsterone (11-KT yang tersedia secara komersial EIA-kit untuk membedakan jenis kelamin ikan tuna sirip kuning. Hasil analisis menunjukkan bahwa metode dot blot menghasilkan ekspresi vitelogenin tampak jelas pada individu betina dan efek plasma terlihat transparan, jika dibandingkan dengan individu jantan. Interpretasi dari metode ini memerlukan pengalaman dan keahlian dalam akurasi pembacaan hasil. Aktivitas hormon 11-KT dengan sampel klip sirip dan plasma memberikan hasil yang baik dengan aktivitas hormon terlihat jelas.

  4. Genetic diversity and population structure of leaf-nosed bat ...

    African Journals Online (AJOL)

    Genetic variation and population structure of the leaf-nosed bat Hipposideros speoris were estimated using 16S rRNA sequence and microsatellite analysis. Twenty seven distinct mitochondrial haplotypes were identified from 186 individuals, sampled from eleven populations. FST test revealed significant variations ...

  5. Structured populations with distributed recruitment : from PDE to delay formulation

    NARCIS (Netherlands)

    Calsina, Àngel; Diekmann, Odo; Farkas, József Z.

    2016-01-01

    In this work, first, we consider a physiologically structured population model with a distributed recruitment process. That is, our model allows newly recruited individuals to enter the population at all possible individual states, in principle. The model can be naturally formulated as a first-order

  6. Genetic structure of populations and differentiation in forest trees

    Science.gov (United States)

    Raymond P. Guries; F. Thomas Ledig

    1981-01-01

    Electrophoretic techniques permit population biologists to analyze genetic structure of natural populations by using large numbers of allozyme loci. Several methods of analysis have been applied to allozyme data, including chi-square contingency tests, F-statistics, and genetic distance. This paper compares such statistics for pitch pine (Pinus rigida...

  7. Population structure and expansion of kuruma shrimp ( Penaeus ...

    African Journals Online (AJOL)

    Sequence analyses on the specific intron from the elongation factor-1α gene were conducted to examine the population genetic structure and expansion of kuruma shrimp (Penaeus japonicus) off Taiwan. Five populations including 119 individuals were separately sampled from the north of East China Sea (ECS), west of ...

  8. Genetic structure of West Greenland populations of lumpfish Cyclopterus lumpus

    DEFF Research Database (Denmark)

    Mayoral, Elsa Garcia; Olsen, M.; Hedeholm, R.

    2016-01-01

    In this study, 11 microsatellite markers were used to determine the structure of West Greenlandic lumpfish Cyclopterus lumpus populations across six spawning locations spanning >1500 km and compared with neighbouring populations in Canada and Iceland. To evaluate whether data allow for identifica...

  9. Plasmodium vivax Diversity and Population Structure across Four Continents.

    Science.gov (United States)

    Koepfli, Cristian; Rodrigues, Priscila T; Antao, Tiago; Orjuela-Sánchez, Pamela; Van den Eede, Peter; Gamboa, Dionicia; van Hong, Nguyen; Bendezu, Jorge; Erhart, Annette; Barnadas, Céline; Ratsimbasoa, Arsène; Menard, Didier; Severini, Carlo; Menegon, Michela; Nour, Bakri Y M; Karunaweera, Nadira; Mueller, Ivo; Ferreira, Marcelo U; Felger, Ingrid

    2015-01-01

    Plasmodium vivax is the geographically most widespread human malaria parasite. To analyze patterns of microsatellite diversity and population structure across countries of different transmission intensity, genotyping data from 11 microsatellite markers was either generated or compiled from 841 isolates from four continents collected in 1999-2008. Diversity was highest in South-East Asia (mean allelic richness 10.0-12.8), intermediate in the South Pacific (8.1-9.9) Madagascar and Sudan (7.9-8.4), and lowest in South America and Central Asia (5.5-7.2). A reduced panel of only 3 markers was sufficient to identify approx. 90% of all haplotypes in South Pacific, African and SE-Asian populations, but only 60-80% in Latin American populations, suggesting that typing of 2-6 markers, depending on the level of endemicity, is sufficient for epidemiological studies. Clustering analysis showed distinct clusters in Peru and Brazil, but little sub-structuring was observed within Africa, SE-Asia or the South Pacific. Isolates from Uzbekistan were exceptional, as a near-clonal parasite population was observed that was clearly separated from all other populations (FST>0.2). Outside Central Asia FST values were highest (0.11-0.16) between South American and all other populations, and lowest (0.04-0.07) between populations from South-East Asia and the South Pacific. These comparisons between P. vivax populations from four continents indicated that not only transmission intensity, but also geographical isolation affect diversity and population structure. However, the high effective population size results in slow changes of these parameters. This persistency must be taken into account when assessing the impact of control programs on the genetic structure of parasite populations.

  10. Bluefin tuna fishing and ranching: a difficult management problem

    NARCIS (Netherlands)

    Stefano, de V.; Heijden, van der P.G.M.

    2007-01-01

    The fish processing industry and consumers in Japan are willing to pay high (and sometimes outrageous) prices for fresh bluefin tuna with fat content and flesh colour just right to be served raw as sashimi or sushi. This willingness was and still is the economic incentive for a high fishing pressure

  11. Radiation hydrolysate of tuna cooking juice with enhanced antioxidant properties

    Science.gov (United States)

    Choi, Jong-il; Sung, Nak-Yun; Lee, Ju-Woon

    2012-08-01

    Tuna protein hydrolysates are of increasing interest because of their potential application as a source of bioactive peptides. Large amounts of tuna cooking juice with proteins and extracts are produced during the process of tuna canning, and these cooking juice wastes cause environmental problems. Therefore, in this study, cooking juice proteins were hydrolyzed by irradiation for their utilization as functional additives. The degree of hydrolysis of tuna cooking juice protein increased from 0% to 15.1% at the absorbed doses of 50 kGy. To investigate the antioxidant activity of the hydrolysate, it was performed the ferric reducing antioxidant power (FRAP) assay, and the lipid peroxidation inhibitory and superoxide radical scavenging activities were measured. The FRAP values increased from 1470 μM to 1930 μM and IC50 on superoxide anion was decreased from 3.91 μg/mL to 1.29 μg/mL at 50 kGy. All of the antioxidant activities were increased in the hydrolysate, suggesting that radiation hydrolysis, which is a simple process that does not require an additive catalysts or an inactivation step, is a promising method for food and environmental industries.

  12. A full lifecycle bioenergetic model for bluefin tuna.

    NARCIS (Netherlands)

    Jusup, M.; Klanjscek, T.; Matsuda, H.; Kooijman, S.A.L.M.

    2011-01-01

    We formulated a full lifecycle bioenergetic model for bluefin tuna relying on the principles of Dynamic Energy Budget theory. Traditional bioenergetic models in fish research deduce energy input and utilization from observed growth and reproduction. In contrast, our model predicts growth and

  13. Production of aspartic peptidases by Aspergillus spp. using tuna ...

    African Journals Online (AJOL)

    The production of extracellular aspartic peptidase by the fungi Aspergillus niger and Aspergillus awamori was carried out in a shake flask and in stirred tank submerged fermentations using tuna cooked wastewater, an industrial effluent, as nitrogen source for culture medium. In stirred tank fermentation, biomass production ...

  14. Trace elements in the kidney tissue of Bluefin Tuna ( Thunnus ...

    African Journals Online (AJOL)

    Trace elements, namely lead (Pb), copper (Cu), manganese (Mn), nickel (Ni), zinc (Zn), and iron (Fe), found in kidney tissues were analyzed and compared between wild/fattened and female/male bluefin tuna (BFT) in the Eastern Mediterranean region of Turkey. One hundred (that is, 50 female and 50 male) individual ...

  15. Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient

    OpenAIRE

    Vangestel, C; Mergeay, Joachim; Dawson, D. A; Callens, T; Vandomme, V; Lens, L

    2012-01-01

    House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierar...

  16. DISTRIBUSI SPASIAL DAN TEMPORAL IKAN TUNA MATA BESAR (Thunnus obesus DI SAMUDERA HINDIA BAGIAN TIMUR

    Directory of Open Access Journals (Sweden)

    Irwan Jatmiko

    2016-03-01

    Full Text Available Ikan tuna mata besar (Thunnus obesus merupakan salah satu hasil tangkapan yang penting bagi industri perikanan di Indonesia. Penelitian ini bertujuan untuk mengetahui distribusi spasial dan temporal ikan tuna mata besar di Samudera Hindia Bagian Timur. Pengumpulan data dilakukan oleh pemantau ilmiah (scientific observers pada kapal rawai tuna yang berbasis di Pelabuhan Benoa Bali, mulai Agustus 2005 hingga November 2013. Ikan tuna mata besar yang tertangkap sebanyak 5.340 ekor dan dari jumlah tersebut sebanyak 5.253 ekor diukur panjangnya. Distribusi spasial ikan tuna mata besar yang tertangkap rawai tuna Indonesia membentang dari 0°-33° LS dan 76°-128° BT. Persentase tertinggi ikan tuna mata besar dengan panjang >110 cm (Lm terdapat di sebelah barat Sumatera Barat dan di sebelah selatan Jawa Timur. Laju pancing menurut bulan penagkapan menunjukkan perbedaan yang nyata dengan laju pancing tertinggi terjadi pada Agustus sebesar 0,54 ekor/100 mata pancing. Nelayan direkomendasikan untuk melakukan operasi penangkapan di daerah dengan persentase ukuran panjang ikan tuna mata besar >110 cm (Lm tertinggi, sehingga species tersebut mempunyai kesempatan untuk melakukan pemijahan minimal sekali sepanjang hidupnya. Hal ini dimaksudkan untuk menjaga kelestarian sumberdaya ikan tuna mata besar di Samudera Hindia. Big eye tuna (Thunnus obesus is one of the important catch of the fishing industry in Indonesia. The study is aimed to investigate the spatial and temporal distribution of big eye tuna in the Eastern Indian Ocean. Data were collected by scientific observers on tuna long line vessels which were mainly based in Port of Benoa Bali from August 2005 to November 2013. Total number of big eye tuna caught were 5,340 individuals and as many as 5,253 of them were measured in length. The spatial distribution of  big eye tuna caught by Indonesia tuna long line are in the area between 0°-33° S and 76°-128° E. The highest percentage of big eye tuna with

  17. Penanganan penyu yang tertangkap rawai tuna di Samudera Hindia

    Directory of Open Access Journals (Sweden)

    Budi Nugraha

    2017-03-01

    Full Text Available Turtle is one of the vulnerable of megafauna and as a by-catch in tuna longline fisheries, however, management practices have not been done yet. This paper described the efforts to avoid the capture of turtles on the tuna longline fishery and its handling recommendation. It has been written based on the research results and observer programs of activities that have been implemented since 2005. It’s also including a literature review rules and regulations regarding the management of sea turtles. The record results during 2005 - 2014 conducted by an independent scientific board on tuna longline in the Indian Ocean with 72 times number of setting and 89,441number of hooks. There are 105 turtles caught, which are leatherback, olive ridley turtles, hawksbill, loggerhead sea turtles as well as the unknown green turtle where the current status of turtles in the Indian Ocean is in a state of vulnerable, endangered, critically even endangered. The olive ridley turtle, loggerhead and leatherback turtles are in a vulnerable status. While, the green turtles are in a state endangered and even hawksbill in a state extremely endangered. Policy measures for handling of turtles in tuna longline fishery needs to be taken in order to be implemented include the socialization of the use of intensified circle hooks and if necessary the government issued regulations regarding the use of circle hooks, the implementation of the placement of fishing monitoring (observer aboard the tuna longline in order to assist the skippers monitoring the catch of turtles and turtle handling training for the skippers and crew in order to hold the caught turtles can be handled directly on the boat to reduce the mortality turtles which can be released back into the sea alive. Penyu merupakan salah satu biota yang rawan punah dan sebagai hasil tangkapan sampingan pada perikanan rawai tuna dimana pengelolaannya belum banyak dilakukan. Makalah ini membahas tentang upaya bagaimana

  18. Competition in size-structured populations: mechanisms inducing cohort formation and population cycles

    NARCIS (Netherlands)

    de Roos, A.M.; Persson, L.

    2003-01-01

    In this paper we investigate the consequences of size-dependent competition among the individuals of a consumer population by analyzing the dynamic properties of a physiologically structured population model. Only 2 size-classes of individuals are distinguished: juveniles and adults. Juveniles and

  19. Stage-Structured Population Dynamics of AEDES AEGYPTI

    Science.gov (United States)

    Yusoff, Nuraini; Budin, Harun; Ismail, Salemah

    Aedes aegypti is the main vector in the transmission of dengue fever, a vector-borne disease affecting world population living in tropical and sub-tropical countries. Better understanding of the dynamics of its population growth will help in the efforts of controlling the spread of this disease. In looking at the population dynamics of Aedes aegypti, this paper explored the stage-structured modeling of the population growth of the mosquito using the matrix population model. The life cycle of the mosquito was divided into five stages: eggs, larvae, pupae, adult1 and adult2. Developmental rates were obtained for the average Malaysian temperature and these were used in constructing the transition matrix for the matrix model. The model, which was based only on temperature, projected that the population of Aedes aegypti will blow up with time, which is not realistic. For further work, other factors need to be taken into account to obtain a more realistic result.

  20. ESTIMATION OF YELLOWFIN TUNA PRODUCTION LANDED IN BENOA PORT WITH WEIGHT-WEIGHT, LENGTH-WEIGHT RELATIONSHIPS AND CONDITION FACTOR APPROACHES

    Directory of Open Access Journals (Sweden)

    Irwan Jatmiko

    2017-01-01

    Full Text Available Yellowfin tuna (Thunnus albacares is one of the important catch for the fishing industry in Indonesia. Length-weight relationship study is one of important tools to support fisheries management. However it could not be done to yellowfin tuna landed in Benoa port since they are in the form of gilled-gutted condition. The objectives of this study are to determine the relationship between gilled-gutted weight (GW and whole weight (WW, to calculate length weight relationship between fork length (FL and estimated whole weight (WW and to assess the relative condition factor (Kn of yellowfin tuna in Eastern Indian Ocean. Data were collected from three landing sites i.e. Malang, East Java; Benoa, Bali and Kupang, East Nusa Tenggara from January 2013 to February 2014. Linear regression analysis applied to test the significance baseline between weight-weight relationships and log transformed length weight relationship. Relative condition factor (Kn used to identify fish condition among length groups and months. The results showed a significant positive linear relationships between whole weight (WW and gilled-gutted weight (GW of T. albacares (p<0.001. There was a significant positive linier relationships between log transformed fork length and log transformed whole weight of T. albacares (p<0.001. Relative condition factor (Kn showed declining pattern along with length increase and varied among months. The findings from this study provide data for management of yellowfin tuna stock and population.

  1. Effect of Population Structure Change on Carbon Emission in China

    Directory of Open Access Journals (Sweden)

    Wen Guo

    2016-03-01

    Full Text Available This paper expanded the Logarithmic Mean Divisia Index (LMDI model through the introduction of urbanization, residents’ consumption, and other factors, and decomposed carbon emission changes in China into carbon emission factor effect, energy intensity effect, consumption inhibitory factor effect, urbanization effect, residents’ consumption effect, and population scale effect, and then explored contribution rates and action mechanisms of the above six factors on change in carbon emissions in China. Then, the effect of population structure change on carbon emission was analyzed by taking 2003–2012 as a sample period, and combining this with the panel data of 30 provinces in China. Results showed that in 2003–2012, total carbon emission increased by 4.2117 billion tons in China. The consumption inhibitory factor effect, urbanization effect, residents’ consumption effect, and population scale effect promoted the increase in carbon emissions, and their contribution ratios were 27.44%, 12.700%, 74.96%, and 5.90%, respectively. However, the influence of carbon emission factor effect (−2.54% and energy intensity effect (−18.46% on carbon emissions were negative. Population urbanization has become the main population factor which affects carbon emission in China. The “Eastern aggregation” phenomenon caused the population scale effect in the eastern area to be significantly higher than in the central and western regions, but the contribution rate of its energy intensity effect (−11.10 million tons was significantly smaller than in the central (−21.61 million tons and western regions (−13.29 million tons, and the carbon emission factor effect in the central area (−3.33 million tons was significantly higher than that in the eastern (−2.00 million tons and western regions (−1.08 million tons. During the sample period, the change in population age structure, population education structure, and population occupation structure

  2. Comparative population structure of cavity-nesting sea ducks

    Science.gov (United States)

    Pearce, John M.; Eadie, John M.; Savard, Jean-Pierre L.; Christensen, Thomas K.; Berdeen, James; Taylor, Eric J.; Boyd, Sean; Einarsson, Árni

    2014-01-01

    A growing collection of mtDNA genetic information from waterfowl species across North America suggests that larger-bodied cavity-nesting species exhibit greater levels of population differentiation than smaller-bodied congeners. Although little is known about nest-cavity availability for these species, one hypothesis to explain differences in population structure is reduced dispersal tendency of larger-bodied cavity-nesting species due to limited abundance of large cavities. To investigate this hypothesis, we examined population structure of three cavity-nesting waterfowl species distributed across much of North America: Barrow's Goldeneye (Bucephala islandica), Common Goldeneye (B. clangula), and Bufflehead (B. albeola). We compared patterns of population structure using both variation in mtDNA control-region sequences and band-recovery data for the same species and geographic regions. Results were highly congruent between data types, showing structured population patterns for Barrow's and Common Goldeneye but not for Bufflehead. Consistent with our prediction, the smallest cavity-nesting species, the Bufflehead, exhibited the lowest level of population differentiation due to increased dispersal and gene flow. Results provide evidence for discrete Old and New World populations of Common Goldeneye and for differentiation of regional groups of both goldeneye species in Alaska, the Pacific Northwest, and the eastern coast of North America. Results presented here will aid management objectives that require an understanding of population delineation and migratory connectivity between breeding and wintering areas. Comparative studies such as this one highlight factors that may drive patterns of genetic diversity and population trends.

  3. Genetic population structure of Shoal Bass within their native range

    Science.gov (United States)

    Taylor, Andrew T.; Tringali, Michael D.; Sammons, Steven M.; Ingram, Travis R.; O'Rouke, Patrick M.; Peterson, Douglas L.; Long, James M.

    2018-01-01

    Endemic to the Apalachicola River basin of the southeastern USA, the Shoal Bass Micropterus cataractae is a fluvial‐specialist sport fish that is imperiled because of anthropogenic habitat alteration. To counter population declines, restorative stocking efforts are becoming an increasingly relevant management strategy. However, population genetic structure within the species is currently unknown, but it could influence management decisions, such as brood source location. Leveraging a collaborative effort to collect and genotype specimens with 16 microsatellite loci, our objective was to characterize hierarchical population structure and genetic differentiation of the Shoal Bass across its native range, including an examination of structuring mechanisms, such as relatedness and inbreeding levels. Specimens identified as Shoal Bass were collected from 13 distinct sites (N ranged from 17 to 209 per location) and were then taxonomically screened to remove nonnative congeners and hybrids (pure Shoal Bass N ranged from 13 to 183 per location). Our results revealed appreciable population structure, with five distinct Shoal Bass populations identifiable at the uppermost hierarchical level that generally corresponded with natural geographic features and anthropogenic barriers. Substructure was recovered within several of these populations, wherein differences appeared related to spatial isolation and local population dynamics. An analysis of molecular variance revealed that 3.6% of the variation in our data set was accounted for among three larger river drainages, but substructure within each river drainage also explained an additional 8.9% of genetic variation, demonstrating that management at a scale lower than the river drainage level would likely best conserve genetic diversity. Results provide a population genetic framework that can inform future management decisions, such as brood source location, so that genetic diversity within and among populations is

  4. Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient.

    Science.gov (United States)

    Vangestel, C; Mergeay, J; Dawson, D A; Callens, T; Vandomme, V; Lens, L

    2012-09-01

    House sparrow (Passer domesticus) populations have suffered major declines in urban as well as rural areas, while remaining relatively stable in suburban ones. Yet, to date no exhaustive attempt has been made to examine how, and to what extent, spatial variation in population demography is reflected in genetic population structuring along contemporary urbanization gradients. Here we use putatively neutral microsatellite loci to study if and how genetic variation can be partitioned in a hierarchical way among different urbanization classes. Principal coordinate analyses did not support the hypothesis that urban/suburban and rural populations comprise two distinct genetic clusters. Comparison of FST values at different hierarchical scales revealed drift as an important force of population differentiation. Redundancy analyses revealed that genetic structure was strongly affected by both spatial variation and level of urbanization. The results shown here can be used as baseline information for future genetic monitoring programmes and provide additional insights into contemporary house sparrow dynamics along urbanization gradients.

  5. Accounting for age uncertainty in growth modeling, the case study of yellowfin tuna (Thunnus albacares of the Indian Ocean.

    Directory of Open Access Journals (Sweden)

    Emmanuelle Dortel

    Full Text Available Age estimates, typically determined by counting periodic growth increments in calcified structures of vertebrates, are the basis of population dynamics models used for managing exploited or threatened species. In fisheries research, the use of otolith growth rings as an indicator of fish age has increased considerably in recent decades. However, otolith readings include various sources of uncertainty. Current ageing methods, which converts an average count of rings into age, only provide periodic age estimates in which the range of uncertainty is fully ignored. In this study, we describe a hierarchical model for estimating individual ages from repeated otolith readings. The model was developed within a Bayesian framework to explicitly represent the sources of uncertainty associated with age estimation, to allow for individual variations and to include knowledge on parameters from expertise. The performance of the proposed model was examined through simulations, and then it was coupled to a two-stanza somatic growth model to evaluate the impact of the age estimation method on the age composition of commercial fisheries catches. We illustrate our approach using the sagittal otoliths of yellowfin tuna of the Indian Ocean collected through large-scale mark-recapture experiments. The simulation performance suggested that the ageing error model was able to estimate the ageing biases and provide accurate age estimates, regardless of the age of the fish. Coupled with the growth model, this approach appeared suitable for modeling the growth of Indian Ocean yellowfin and is consistent with findings of previous studies. The simulations showed that the choice of the ageing method can strongly affect growth estimates with subsequent implications for age-structured data used as inputs for population models. Finally, our modeling approach revealed particularly useful to reflect uncertainty around age estimates into the process of growth estimation and it can

  6. Genetic population structure of the vulnerable bog fritillary butterfly.

    Science.gov (United States)

    Vandewoestijne, S; Baguette, M

    2004-01-01

    Populations of the bog fritillary butterfly Proclossiana eunomia (Lepidoptera, Nymphalidae) occur in patchy habitat in central and western Europe. P. eunomia is a vulnerable species in the Belgian Ardennes and the number of occupied sites has significantly decreased in this region since the 1960s. RAPD (random amplified polymorphic DNA) markers were used to study the consequences of habitat loss and fragmentation on the genetic population structure of this species. Gene diversity was lower in populations with smaller population sizes. Genetic subdivision was high (Fst=0.0887) considering the small spatial scale of this study (150 km2). The most geographically isolated population was also the most genetically differentiated one. The genetic population structure and genetic differentiation detected in this study were explained by (1) differences in altitude of the sampled locations and, (2) lower dispersal propensity and dispersal rate in fragmented landscapes versus continuous landscapes. Results from the RAPD analyses were compared with a previous allozyme based study on the same populations. The results of this study suggest that increased fragmentation has lead to a greater genetic differentiation between remaining P. eunomia populations.

  7. Assessing population genetic structure via the maximisation of genetic distance

    Directory of Open Access Journals (Sweden)

    Toro Miguel A

    2009-11-01

    Full Text Available Abstract Background The inference of the hidden structure of a population is an essential issue in population genetics. Recently, several methods have been proposed to infer population structure in population genetics. Methods In this study, a new method to infer the number of clusters and to assign individuals to the inferred populations is proposed. This approach does not make any assumption on Hardy-Weinberg and linkage equilibrium. The implemented criterion is the maximisation (via a simulated annealing algorithm of the averaged genetic distance between a predefined number of clusters. The performance of this method is compared with two Bayesian approaches: STRUCTURE and BAPS, using simulated data and also a real human data set. Results The simulations show that with a reduced number of markers, BAPS overestimates the number of clusters and presents a reduced proportion of correct groupings. The accuracy of the new method is approximately the same as for STRUCTURE. Also, in Hardy-Weinberg and linkage disequilibrium cases, BAPS performs incorrectly. In these situations, STRUCTURE and the new method show an equivalent behaviour with respect to the number of inferred clusters, although the proportion of correct groupings is slightly better with the new method. Re-establishing equilibrium with the randomisation procedures improves the precision of the Bayesian approaches. All methods have a good precision for FST ≥ 0.03, but only STRUCTURE estimates the correct number of clusters for FST as low as 0.01. In situations with a high number of clusters or a more complex population structure, MGD performs better than STRUCTURE and BAPS. The results for a human data set analysed with the new method are congruent with the geographical regions previously found. Conclusion This new method used to infer the hidden structure in a population, based on the maximisation of the genetic distance and not taking into consideration any assumption about Hardy

  8. Patterns of admixture and population structure in native populations of Northwest North America.

    Directory of Open Access Journals (Sweden)

    Paul Verdu

    2014-08-01

    Full Text Available The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

  9. Population genetic structure in natural and reintroduced beaver (Castor fiber populations in Central Europe

    Directory of Open Access Journals (Sweden)

    Kautenburger, R.

    2008-12-01

    Full Text Available Castor fiber Linnaeus, 1758 is the only indigenous species of the genus Castor in Europe and Asia. Due to extensive hunting until the beginning of the 20th century, the distribution of the formerly widespread Eurasian beaver was dramatically reduced. Only a few populations remained and these were in isolated locations, such as the region of the German Elbe River. The loss of genetic diversity in small or captive populations throughgenetic drift and inbreeding is a severe conservation problem. However, the reintroduction of beaver populations from several regions in Europe has shown high viability and populations today are growing fast. In the present study we analysed the population genetic structure of a natural and two reintroduced beaver populations in Germany and Austria. Furthermore, we studied the genetic differentiation between two beaver species, C. fiber and the American beaver (C. canadensis, using RAPD (Random Amplified Polymorphic DNA as a genetic marker. The reintroduced beaver populations of different origins and the autochthonous population of the Elbe River showed a similar low genetic heterogeneity. There was an overall high genetic similarity in the species C. fiber, and no evidence was found for a clear subspecific structure in the populations studied.

  10. The scale of population structure in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Alexander Platt

    2010-02-01

    Full Text Available The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This level of outcrossing greatly limits observed heterozygosity but is sufficient to generate considerable local haplotypic diversity. We also find that in its native Eurasian range A. thaliana exhibits continuous isolation by distance at every geographic scale without natural breaks corresponding to classical notions of populations. By contrast, in North America, where it exists as an exotic species, A. thaliana exhibits little or no population structure at a continental scale but local isolation by distance that extends hundreds of km. This suggests a pattern for the development of isolation by distance that can establish itself shortly after an organism fills a new habitat range. It also raises questions about the general applicability of many standard population genetics models. Any model based on discrete clusters of interchangeable individuals will be an uneasy fit to organisms like A. thaliana which exhibit continuous isolation by distance on many scales.

  11. Modeling structured population dynamics using data from unmarked individuals

    Science.gov (United States)

    Grant, Evan H. Campbell; Zipkin, Elise; Thorson, James T.; See, Kevin; Lynch, Heather J.; Kanno, Yoichiro; Chandler, Richard; Letcher, Benjamin H.; Royle, J. Andrew

    2014-01-01

    The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark–recapture data. We extended recently developed N-mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders (Desmognathus fuscus) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark–recapture) and extensive (e.g., counts) data sources.

  12. Population structure of larch forests in the Urals

    Energy Technology Data Exchange (ETDEWEB)

    Putenikhin, V.P.; Farukshina, G.G. [Russian Academy of Sciences, Ufa (Russian Federation). Botanical Garden Inst.

    1995-12-31

    The variability and population structure of larch (Larix sukaczewii Dyl.) naturally growing in the Urals was studied on the basis of biometric analysis of generative organs. The obtained results point to the existence of 11 phenotypically different local populations of Larix sukaczewii in the Urals. Four populations are identified in the South Urals: Marginal, central, high-mountainous, south-uralian and Bashkircis-uralian. Middle-uralian, Perm cis-uralian, central north-uralian and high-mountainous north-uralian populations are determined in the Middle and the North Urals. Three populations of Larix sukaczewii are identified in the Sub-Polar and the Polar Urals: Subpolar-uralian, Pechora-Thiman cisuralian and polar-uralian. 8 refs, 2 tabs

  13. Population structure of larch forests in the Urals

    Energy Technology Data Exchange (ETDEWEB)

    Putenikhin, V P; Farukshina, G G [Russian Academy of Sciences, Ufa (Russian Federation). Botanical Garden Inst.

    1996-12-31

    The variability and population structure of larch (Larix sukaczewii Dyl.) naturally growing in the Urals was studied on the basis of biometric analysis of generative organs. The obtained results point to the existence of 11 phenotypically different local populations of Larix sukaczewii in the Urals. Four populations are identified in the South Urals: Marginal, central, high-mountainous, south-uralian and Bashkircis-uralian. Middle-uralian, Perm cis-uralian, central north-uralian and high-mountainous north-uralian populations are determined in the Middle and the North Urals. Three populations of Larix sukaczewii are identified in the Sub-Polar and the Polar Urals: Subpolar-uralian, Pechora-Thiman cisuralian and polar-uralian. 8 refs, 2 tabs

  14. Correlations in the population structure of music, genes and language

    Science.gov (United States)

    Brown, Steven; Savage, Patrick E.; Ko, Albert Min-Shan; Stoneking, Mark; Ko, Ying-Chin; Loo, Jun-Hun; Trejaut, Jean A.

    2014-01-01

    We present, to our knowledge, the first quantitative evidence that music and genes may have coevolved by demonstrating significant correlations between traditional group-level folk songs and mitochondrial DNA variation among nine indigenous populations of Taiwan. These correlations were of comparable magnitude to those between language and genes for the same populations, although music and language were not significantly correlated with one another. An examination of population structure for genetics showed stronger parallels to music than to language. Overall, the results suggest that music might have a sufficient time-depth to retrace ancient population movements and, additionally, that it might be capturing different aspects of population history than language. Music may therefore have the potential to serve as a novel marker of human migrations to complement genes, language and other markers. PMID:24225453

  15. Age structure changes and extraordinary lifespan in wild medfly populations.

    Science.gov (United States)

    Carey, James R; Papadopoulos, Nikos T; Müller, Hans-Georg; Katsoyannos, Byron I; Kouloussis, Nikos A; Wang, Jane-Ling; Wachter, Kenneth; Yu, Wei; Liedo, Pablo

    2008-06-01

    The main purpose of this study was to test the hypotheses that major changes in age structure occur in wild populations of the Mediterranean fruit fly (medfly) and that a substantial fraction of individuals survive to middle age and beyond (> 3-4 weeks). We thus brought reference life tables and deconvolution models to bear on medfly mortality data gathered from a 3-year study of field-captured individuals that were monitored in the laboratory. The average time-to-death of captured females differed between sampling dates by 23.9, 22.7, and 37.0 days in the 2003, 2004, and 2005 field seasons, respectively. These shifts in average times-to-death provided evidence of changes in population age structure. Estimates indicated that middle-aged medflies (> 30 days) were common in the population. A surprise in the study was the extraordinary longevity observed in field-captured medflies. For example, 19 captured females but no reference females survived in the laboratory for 140 days or more, and 6 captured but no reference males survived in the laboratory for 170 days or more. This paper advances the study of aging in the wild by introducing a new method for estimating age structure in insect populations, demonstrating that major changes in age structure occur in field populations of insects, showing that middle-aged individuals are common in the wild, and revealing the extraordinary lifespans of wild-caught individuals due to their early life experience in the field.

  16. Chronic irradiation as an ecological factor affecting genetic population structure

    International Nuclear Information System (INIS)

    Kal'chenko, V.A.; Kalabushkin, B.A.; Rubanovich, A.V.

    1991-01-01

    Genetic structure of two Centaurea scabiosa L. populations was studied by frequency distribution of leucine aminopeptidase (LAP) locus genotypes. The experimental population has been growing under conditions of chronic irradiation, with the dose per generation amounting to 1.2 to 25.5 Gy. In it, mutational variants are observed with a frequency of 5.4.10(-3)-4.5.10(-2) per generation (as compared to control population frequency at 5.4.10(-4)). Indexes for heterozygosity, mean number of genotypes, and effective number of alleles were higher in the experimental population. Segregation analysis revealed no differences in viability in the control population, and all genotypic combinations were found to be nearly neutral. In the experimental population, however, significant differences in relative viability of the genotypes were disclosed. The relative viability of heterozygotes for mutant allele C' was nearly maximum, while heterozygotes for other mutant alleles showed minimum viability. We reach the conclusion that the differences in genetic structure of the populations under investigation can be explained by the chronic irradiation factor that brought out differences in adaptability of both normal and mutant genotypes. The suggestion is that intra-locus interactions of the C' allele with normal alleles determine plant resistance to a wide range of unfavorable environmental conditions

  17. Detailed genetic structure of European bitterling populations in Central Europe

    Directory of Open Access Journals (Sweden)

    Veronika Bartáková

    2015-11-01

    Full Text Available The European bitterling (Rhodeus amarus is a small cyprinid fish whose populations declined markedly between 1950 and 1980. However, its range currently expands, partly due to human-assisted introductions. We determined the genetic variability and detailed spatial structure among bitterling populations in Central Europe and tested alternative hypotheses about colonization of this area. Twelve polymorphic microsatellite loci on a large sample of 688 individuals had been used to analyse genetic variability and population structure. Samples originated from 27 localities with emphasis on area of the Czech Republic where three major sea drainages (Black, Baltic, and Northern Sea meet. Highly variable level of intrapopulation genetic variability had generally been detected and a recent decrease in numbers (“bottleneck” had been indicated by genetic data among six populations. High level of interpopulation differentiation was identified even within the basins. There was a significant role of genetic drift and indications of low dispersal ability of R. amarus. Surprisingly, the Odra River was inhabited by two distinct populations without any genetic signatures of a secondary contact. Czech part of the Odra (Baltic basin was colonized from the Danubian refugium (similarly to adjacent Danubian basin rivers including the Morava, while Polish part of the Odra was genetically similar to the populations in the Vistula River (Baltic basin, that has been colonized by a different (Eastern phylogeographic lineage of R. amarus. Most Czech R. amarus populations were colonized from the Danubian refugium, suggesting potential for a human-mediated colonization of the Odra or Elbe Rivers by R. amarus. One Elbe basin population was genetically mixed from the two (Danubian and Eastern phylogeographic lineages. In general the Czech populations of R. amarus were genetically stable except for a single population which has probably been recently introduced. This research

  18. Hubungan Antara Body Image Dan Self-esteem Pada Dewasa Awal Tuna Daksa

    OpenAIRE

    Sari, Dahlia Nur Permata

    2012-01-01

    Penelitian ini meneliti mengenai pengaruh body image terhadap selfesteem pada dewasa awal tuna daksa. Hipotesis pada penelitian ini adalah adanya hubungan positif antara body image dan self-esteem pada dewasa awal tuna daksa. Semakin positif body image maka semakin tinggi self-esteem yang dimiliki, begitu juga sebaliknya, semakin negatif body image maka semakin rendah self-esteem yang dimiliki. Sampel penelitian sebanyak 30 dewasa awal tuna daksa yang memiliki cacat tubuh seteleh kelahiran. D...

  19. Ethnicity and Population Structure in Personal Naming Networks

    Science.gov (United States)

    Mateos, Pablo; Longley, Paul A.; O'Sullivan, David

    2011-01-01

    Personal naming practices exist in all human groups and are far from random. Rather, they continue to reflect social norms and ethno-cultural customs that have developed over generations. As a consequence, contemporary name frequency distributions retain distinct geographic, social and ethno-cultural patterning that can be exploited to understand population structure in human biology, public health and social science. Previous attempts to detect and delineate such structure in large populations have entailed extensive empirical analysis of naming conventions in different parts of the world without seeking any general or automated methods of population classification by ethno-cultural origin. Here we show how ‘naming networks’, constructed from forename-surname pairs of a large sample of the contemporary human population in 17 countries, provide a valuable representation of cultural, ethnic and linguistic population structure around the world. This innovative approach enriches and adds value to automated population classification through conventional national data sources such as telephone directories and electoral registers. The method identifies clear social and ethno-cultural clusters in such naming networks that extend far beyond the geographic areas in which particular names originated, and that are preserved even after international migration. Moreover, one of the most striking findings of this approach is that these clusters simply ‘emerge’ from the aggregation of millions of individual decisions on parental naming practices for their children, without any prior knowledge introduced by the researcher. Our probabilistic approach to community assignment, both at city level as well as at a global scale, helps to reveal the degree of isolation, integration or overlap between human populations in our rapidly globalising world. As such, this work has important implications for research in population genetics, public health, and social science adding new

  20. Structure of the New England herring gull population

    Science.gov (United States)

    Kadlec, J.A.; Drury, W.H.

    1968-01-01

    Measurements of the rates of population increase, reproduction, and mortality together with an observed age ratio, were used to analyze the population of the Herring Gull in New England. Data from sporadic censuses prior to this study, aerial censuses by the authors, and National Audubon Society Christmas Bird Count indicated that the New England breeding population has been doubling every 12 to 15 years since the early 1900's. This increase has involved founding new colonies and expanding the breeding range There is evidence that 15 to 30% of the adults do not breed in any given year. Sixty-one productivity measurements on 43 islands from 1963 through 1966, involving almost 13,000 nests, showed that from 0.8 to 1.4 young/breeding pair/year is the usual range of rate of production. The age distribution in the population was determined by classifying Herring Gulls by plumage category on an aerial census of the coast from Tampico, Mexico, to Cape Sable, Nova Scotia. Of the 622,000 gulls observed, 68% were adults, 17% were second- and third-year birds, and 15% were first-year birds. Mortality rates derived from band recovery data were too high to be consistent with the observed rate of population growth, productivity, and age structure. Loss of bands increasing to the rate of about 20%/year 5 years after banding eliminates most of the discrepancy. The age structure and rate of population increase indicate a mortality rate of 4 to 9% for gulls 2 years old or older, compared with the 25 to 30% indicated by band recoveries. The population structure we have developed fits everything we have observed about Herring Gull population dynamics, except mortality based on band recoveries.

  1. Diversity and population structure of red rice germplasm in Bangladesh.

    Directory of Open Access Journals (Sweden)

    M Z Islam

    Full Text Available While the functionality and healthy food value of red rice have increased its popularity, such that market demand for it is expected to rise, most strains suffer from low grain yield. To perform diversity and population structure analyses of red rice germplasm, therefore, becomes essential for improving yields for commercial production. In this study, fifty red rice germplasm from the Bangladesh Rice Research Institute (BRRI genebank were characterized both morphologically and genetically using fifty simple sequence repeat (SSR markers. Overall, 162 alleles were detected by the markers with the detected allele number varying from two to seven. Additionally, 22 unique alleles were identified for use as a germplasm diagnostic tool. The highest and lowest polymorphic information content (PIC indices were 0.75 and 0.04 found in markers RM282 and RM304, respectively, and genetic diversity was moderate, varying from 0.05 to 0.78 (average: 0.35. While phylogenetic cluster analysis of the fifteen distance-based agro-morphological traits divided the germplasm into five clusters (I, II, III, IV and V, a similar SSR analysis yielded only three major groups (I, II, and III, and a model-based population structure analysis yielded four (A, B, C and D. Both principal component and neighbors joining tree analysis from the population structure method showed the tested germplasm as highly diverse in structure. Moreover, an analysis of molecular variance (AMOVA, as well as a pairwise FST analysis, both indicated significant differentiation (ranging from 0.108 to 0.207 among all pairs of populations, suggesting that all four population structure groups differed significantly. Populations A and D were the most differentiated from each other by FST. Findings from this study suggest that the diverse germplasm and polymorphic trait-linked SSR markers of red rice are suitable for the detection of economically desirable trait loci/genes for use in future molecular

  2. Diversity and population structure of red rice germplasm in Bangladesh.

    Science.gov (United States)

    Islam, M Z; Khalequzzaman, M; Prince, M F R K; Siddique, M A; Rashid, E S M H; Ahmed, M S U; Pittendrigh, B R; Ali, M P

    2018-01-01

    While the functionality and healthy food value of red rice have increased its popularity, such that market demand for it is expected to rise, most strains suffer from low grain yield. To perform diversity and population structure analyses of red rice germplasm, therefore, becomes essential for improving yields for commercial production. In this study, fifty red rice germplasm from the Bangladesh Rice Research Institute (BRRI) genebank were characterized both morphologically and genetically using fifty simple sequence repeat (SSR) markers. Overall, 162 alleles were detected by the markers with the detected allele number varying from two to seven. Additionally, 22 unique alleles were identified for use as a germplasm diagnostic tool. The highest and lowest polymorphic information content (PIC) indices were 0.75 and 0.04 found in markers RM282 and RM304, respectively, and genetic diversity was moderate, varying from 0.05 to 0.78 (average: 0.35). While phylogenetic cluster analysis of the fifteen distance-based agro-morphological traits divided the germplasm into five clusters (I, II, III, IV and V), a similar SSR analysis yielded only three major groups (I, II, and III), and a model-based population structure analysis yielded four (A, B, C and D). Both principal component and neighbors joining tree analysis from the population structure method showed the tested germplasm as highly diverse in structure. Moreover, an analysis of molecular variance (AMOVA), as well as a pairwise FST analysis, both indicated significant differentiation (ranging from 0.108 to 0.207) among all pairs of populations, suggesting that all four population structure groups differed significantly. Populations A and D were the most differentiated from each other by FST. Findings from this study suggest that the diverse germplasm and polymorphic trait-linked SSR markers of red rice are suitable for the detection of economically desirable trait loci/genes for use in future molecular breeding programs.

  3. GENETIC IDENTIFICATION FOR TUNA AND RAINBOW RUNNER CAPTURE IN NORTH BALI WATERS

    Directory of Open Access Journals (Sweden)

    Gusti Ngurah Permana

    2006-06-01

    Full Text Available Gondol Research Institute for Mariculture identification of tuna and rainbow runner was an objective in this current study. Samples of five species were collected from territorial water of North Bali. The method used in this study was allozyme electrophoresis. The results showed that buffer of CAPM-6 (citric acid aminoprophylmorpholine resulted in a sharp and clear banding pattern. The species could be differentiated in six diagnostic isozyme patterns Idh* (isocitrate dehydrogenase, 6Pgd* (6 phosphogluconate dehydrogenase, Gpi* (glucose phosphate isomerase, Mdh* (malate dehydrogenase, Est* (esterase, and Sp* (sarcoplasmic protein. All species were in Hardy-weinberg equilibrium. Heterozygosities of species were ranged from 0.00 to 0.099. Yellowfin tuna has the highest heterozigosity compared with the other species. Clustering samples according to pairs revealed that genetic distance of Bullet tuna (A. rochei and Eastern little tuna (E. affinis had small value (0.001. By contrast, the largest value was observed between yellowfin tuna, T. albacares and rainbow runner, E. bipunnulata (0.007. This value indicated that Bullet tuna (A. rochei and Eastern little tuna (E. affinis closed relation, while among yellowfin tuna, skipjack tuna, and rainbow runner, were separated phylogenically.

  4. Population and evolutionary dynamics in spatially structured seasonally varying environments.

    Science.gov (United States)

    Reid, Jane M; Travis, Justin M J; Daunt, Francis; Burthe, Sarah J; Wanless, Sarah; Dytham, Calvin

    2018-03-25

    Increasingly imperative objectives in ecology are to understand and forecast population dynamic and evolutionary responses to seasonal environmental variation and change. Such population and evolutionary dynamics result from immediate and lagged responses of all key life-history traits, and resulting demographic rates that affect population growth rate, to seasonal environmental conditions and population density. However, existing population dynamic and eco-evolutionary theory and models have not yet fully encompassed within-individual and among-individual variation, covariation, structure and heterogeneity, and ongoing evolution, in a critical life-history trait that allows individuals to respond to seasonal environmental conditions: seasonal migration. Meanwhile, empirical studies aided by new animal-tracking technologies are increasingly demonstrating substantial within-population variation in the occurrence and form of migration versus year-round residence, generating diverse forms of 'partial migration' spanning diverse species, habitats and spatial scales. Such partially migratory systems form a continuum between the extreme scenarios of full migration and full year-round residence, and are commonplace in nature. Here, we first review basic scenarios of partial migration and associated models designed to identify conditions that facilitate the maintenance of migratory polymorphism. We highlight that such models have been fundamental to the development of partial migration theory, but are spatially and demographically simplistic compared to the rich bodies of population dynamic theory and models that consider spatially structured populations with dispersal but no migration, or consider populations experiencing strong seasonality and full obligate migration. Second, to provide an overarching conceptual framework for spatio-temporal population dynamics, we define a 'partially migratory meta-population' system as a spatially structured set of locations that can

  5. Evolutionary snowdrift game incorporating costly punishment in structured populations

    Science.gov (United States)

    Chan, Nat W. H.; Xu, C.; Tey, Siew Kian; Yap, Yee Jiun; Hui, P. M.

    2013-01-01

    The role of punishment and the effects of a structured population in promoting cooperation are important issues. Within a recent model of snowdrift game (SG) incorporating a costly punishing strategy (P), we study the effects of a population connected through a square lattice. The punishers, who carry basically a cooperative (C) character, are willing to pay a cost α so as to punish a non-cooperative (D) opponent by β. Depending on α, β, the cost-to-benefit ratio r in SG, and the initial conditions, the system evolves into different phases that could be homogeneous or inhomogeneous. The spatial structure imposes geometrical constraint on how one agent is affected by neighboring agents. Results of extensive numerical simulations, both for the steady state and the dynamics, are presented. Possible phases are identified and discussed, and isolated phases in the r-β space are identified as special local structures of strategies that are stable due to the lattice structure. In contrast to a well-mixed population where punishers are suppressed due to the cost of punishment, the altruistic punishing strategy can flourish and prevail for appropriate values of the parameters, implying an enhancement in cooperation by imposing punishments in a structured population. The system could evolve to a phase corresponding to the coexistence of C, D, and P strategies at some particular payoff parameters, and such a phase is absent in a well-mixed population. The pair approximation, a commonly used analytic approach, is extended from a two-strategy system to a three-strategy system. We show that the pair approximation can, at best, capture the numerical results only qualitatively. Due to the improper way of including spatial correlation imposed by the lattice structure, the approximation does not give the frequencies of C, D, and P accurately and fails to give the homogeneous AllD and AllP phases.

  6. An age structured model for obesity prevalence dynamics in populations

    Directory of Open Access Journals (Sweden)

    Gilberto González Parra

    2010-08-01

    Full Text Available Objective. Modeling the correlation of the development of obesity in a population with age and time and predict the dynamics of the correlation of the development of obesity in a population with age and time under different scenarios in Valencia (Spain. Materials and methods. An age structured mathematical model is used to describe the future dynamics of obesity prevalence for different ages in human population with excess weight. Simulation of the model with parameters estimated using the Health Survey of the Region of Valencia 2000 (4.319 interviews and Health Survey of the Region of Valencia 2005 (4.012 interviews. The model considers only overweight and obese populations since these subpopulations are the most relevant on obesity health concern. Results. The model allows predicting and studying the prevalence of obesity for each age. Results showed an increasing trend of obesity in the following years in well accordance with the trend observed in several countries. Conclusions. Based on the numerical simulations it is possible to conclude that the age structured mathematical model is suitable to forecast the obesity epidemic in each age group in different countries. Additionally, this type of models may be applied to study other characteristics of other populations such animal populations.

  7. Population genetic structure and demographic history of small ...

    African Journals Online (AJOL)

    Population genetic structure and demographic history of small yellow croaker, ... diversity (0.0112 ± 0.0061 to 0.0141 ± 0.0075) were detected in the species. ... into two closely related clades, but did not appear to have any geographic ...

  8. Changes in population structures of the major species in selected ...

    African Journals Online (AJOL)

    The study was carried out in six satellite lakes by making investigations on fish collected from experimental and artisanal fisheries. The fishes were analysed for length frequencies, weight and numbers caught to determine the population structure of the fishes. Indiscriminate fishing by deploying illegal gears and increased ...

  9. Review: Genetic diversity and population structure of cotton ...

    African Journals Online (AJOL)

    Cotton (Gossypium spp.) is the world's leading natural fiber crop and is cultivated in diverse temperate and tropical areas. In this sense, molecular markers are important tools for polymorphism identification in genetic diversity analyses. The objective of this study was to evaluate genetic diversity and population structure in ...

  10. Molecular epidemiology and population structure of bovine Streptococcus uberis

    DEFF Research Database (Denmark)

    Rato, M G; Bexiga, R; Nunes, S F

    2008-01-01

    The molecular epidemiology and population structure of 30 bovine subclinical mastitis field isolates of Streptococcus uberis, collected from 6 Portuguese herds (among 12 farms screened) during 2002 and 2003, were examined by using pulsed-field gel electrophoresis (PFGE) for clustering of the isol...

  11. Genetic structure and diversity within and among six populations of ...

    African Journals Online (AJOL)

    Yomi

    2010-04-24

    Apr 24, 2010 ... Genetic structure and diversity within and among six populations of .... Lyopholized samples were ground to a fine powder. DNA extraction ..... 22(3): 287-292. Pei YL, Zou, YP, Yin Z, Wang XQ, Zhang ZX, Hong DY (1995).

  12. Population genetic structure of coral reef species Plectorhinchus ...

    African Journals Online (AJOL)

    The population genetic structure and the dispersal ability of Plectorhinchus flavomaculatus from South China Sea were examined with a 464 bp segment of mtDNA control region. A total of 116 individuals were collected from 12 coral reefs in Xisha, Zhongsha and Nansha archipelagos and 22 haplotypes were obtained.

  13. Population structure and genetic trends for indigenous African beef ...

    African Journals Online (AJOL)

    The aim of this study was to investigate population structure and genetic trends based on pedigree and performance records of five indigenous African beef cattle breeds (Afrikaner, Boran, Drakensberger, Nguni and Tuli) in South Africa. Pedigree completeness over six generations was higher than 88.5% in the first ...

  14. Genetic diversity, population structure and marker trait associations ...

    Indian Academy of Sciences (India)

    Supplementary data: Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum). Ashok Badigannavar and Gerald O. Myers. J. Genet. 94, 87–94. Table 1. List of cotton germplasm lines used in this study. Germplasm no. Cultivar. Region. Germplasm no. Cultivar.

  15. Dynamique de structuration spatio-temporelle des populations de ...

    African Journals Online (AJOL)

    Dynamique de structuration spatio-temporelle des populations de familles de macroinvertébrés dans un continuum lac de barrage-effluent-fleuve issu de périmètre irrigué. Bassin de la Volta (Burkina Faso)

  16. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    Genetic diversity and population structure of maize landraces from Côte ... However, no study on the genetic diversity of the species has been performed to date. ... The cross between two individuals from different groups might help exploit the ...

  17. Comparison of the population structure and life-history parameters ...

    African Journals Online (AJOL)

    Blacktail seabream Diplodus capensis were sampled from proximate (10 km apart) exploited and unexploited areas in southern Angola to compare their population structures and life-history parameters. Females dominated the larger size and older age classes in the unexploited area. In the exploited area the length and ...

  18. Dynamic optimal foraging theory explains vertical migrations of bigeye tuna

    DEFF Research Database (Denmark)

    Thygesen, Uffe Høgsbro; Sommer, Lene; Evans, Karen

    2016-01-01

    Bigeye tuna are known for remarkable daytime vertical migrations between deep water, where food is abundant but the water is cold, and the surface, where water is warm but food is relatively scarce. Here we investigate if these dive patterns can be explained by dynamic optimal foraging theory...... behaves such as to maximize its energy gains. The model therefore provides insight into the processes underlying observed behavioral patterns and allows generating predictions of foraging behavior in unobserved environments...

  19. Population Genetic Structure of the People of Qatar

    Science.gov (United States)

    Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A.; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W.; Fuller, Jennifer; Hackett, Neil R.; Crystal, Ronald G.; Clark, Andrew G.

    2010-01-01

    People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari. PMID:20579625

  20. Population structure and cultural geography of a folktale in Europe

    Science.gov (United States)

    Ross, Robert M.; Greenhill, Simon J.; Atkinson, Quentin D.

    2013-01-01

    Despite a burgeoning science of cultural evolution, relatively little work has focused on the population structure of human cultural variation. By contrast, studies in human population genetics use a suite of tools to quantify and analyse spatial and temporal patterns of genetic variation within and between populations. Human genetic diversity can be explained largely as a result of migration and drift giving rise to gradual genetic clines, together with some discontinuities arising from geographical and cultural barriers to gene flow. Here, we adapt theory and methods from population genetics to quantify the influence of geography and ethnolinguistic boundaries on the distribution of 700 variants of a folktale in 31 European ethnolinguistic populations. We find that geographical distance and ethnolinguistic affiliation exert significant independent effects on folktale diversity and that variation between populations supports a clustering concordant with European geography. This pattern of geographical clines and clusters parallels the pattern of human genetic diversity in Europe, although the effects of geographical distance and ethnolinguistic boundaries are stronger for folktales than genes. Our findings highlight the importance of geography and population boundaries in models of human cultural variation and point to key similarities and differences between evolutionary processes operating on human genes and culture. PMID:23390109

  1. Convergent evolution in mechanical design of lamnid sharks and tunas.

    Science.gov (United States)

    Donley, Jeanine M; Sepulveda, Chugey A; Konstantinidis, Peter; Gemballa, Sven; Shadwick, Robert E

    2004-05-06

    The evolution of 'thunniform' body shapes in several different groups of vertebrates, including whales, ichthyosaurs and several species of large pelagic fishes supports the view that physical and hydromechanical demands provided important selection pressures to optimize body design for locomotion during vertebrate evolution. Recognition of morphological similarities between lamnid sharks (the most well known being the great white and the mako) and tunas has led to a general expectation that they also have converged in their functional design; however, no quantitative data exist on the mechanical performance of the locomotor system in lamnid sharks. Here we examine the swimming kinematics, in vivo muscle dynamics and functional morphology of the force-transmission system in a lamnid shark, and show that the evolutionary convergence in body shape and mechanical design between the distantly related lamnids and tunas is much more than skin deep; it extends to the depths of the myotendinous architecture and the mechanical basis for propulsive movements. We demonstrate that not only have lamnids and tunas converged to a much greater extent than previously known, but they have also developed morphological and functional adaptations in their locomotor systems that are unlike virtually all other fishes.

  2. A full lifecycle bioenergetic model for bluefin tuna.

    Directory of Open Access Journals (Sweden)

    Marko Jusup

    Full Text Available We formulated a full lifecycle bioenergetic model for bluefin tuna relying on the principles of Dynamic Energy Budget theory. Traditional bioenergetic models in fish research deduce energy input and utilization from observed growth and reproduction. In contrast, our model predicts growth and reproduction from food availability and temperature in the environment. We calibrated the model to emulate physiological characteristics of Pacific bluefin tuna (Thunnus orientalis, hereafter PBT, a species which has received considerable scientific attention due to its high economic value. Computer simulations suggest that (i the main cause of different growth rates between cultivated and wild PBT is the difference in average body temperature of approximately 6.5°C, (ii a well-fed PBT individual can spawn an average number of 9 batches per spawning season, (iii food abundance experienced by wild PBT is rather constant and sufficiently high to provide energy for yearly reproductive cycle, (iv energy in reserve is exceptionally small, causing the weight-length relationship of cultivated and wild PBT to be practically indistinguishable and suggesting that these fish are poorly equipped to deal with starvation, (v accelerated growth rate of PBT larvae is connected to morphological changes prior to metamorphosis, while (vi deceleration of growth rate in the early juvenile stage is related to efficiency of internal heat production. Based on these results, we discuss a number of physiological and ecological traits of PBT, including the reasons for high Feed Conversion Ratio recorded in bluefin tuna aquaculture.

  3. Structural Approaches to Sequence Evolution Molecules, Networks, Populations

    CERN Document Server

    Bastolla, Ugo; Roman, H. Eduardo; Vendruscolo, Michele

    2007-01-01

    Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.

  4. Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of Southern Africa

    Directory of Open Access Journals (Sweden)

    Khulekhani Sedwell Khanyile

    2015-02-01

    Full Text Available Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterised and utilized. Surveys that can reveal a population’s genetic structure and provide an insight into its demographic history will give valuable information to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n =146, Malawi (n =30 and Zimbabwe (n =136 were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29-0.36, was observed between SNP markers that were less than 10kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK and 0.24 (VD at SNP marker interval of 500kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective population

  5. Shallow Population Genetic Structures of Thread-sail Filefish (Stephanolepis cirrhifer) Populations from Korean Coastal Waters.

    Science.gov (United States)

    Yoon, M; Park, W; Nam, Y K; Kim, D S

    2012-02-01

    Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population F ST values (-0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups (F CT = 0.028, p<0.05), and no genetic variation within groups (0.53%; F SC = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

  6. Shallow Population Genetic Structures of Thread-sail Filefish ( Populations from Korean Coastal Waters

    Directory of Open Access Journals (Sweden)

    M. Yoon

    2012-02-01

    Full Text Available Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076 and nucleotide diversities (0.014 to 0.019, and low levels of genetic differentiation among populations inferred from pairwise population FST values (−0.007 to 0.107, support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA revealed weak but significant genetic structures among three groups (FCT = 0.028, p<0.05, and no genetic variation within groups (0.53%; FSC = 0.005, p = 0.23. These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

  7. Population structure and infectious disease risk in southern Africa.

    Science.gov (United States)

    Uren, Caitlin; Möller, Marlo; van Helden, Paul D; Henn, Brenna M; Hoal, Eileen G

    2017-06-01

    The KhoeSan populations are the earliest known indigenous inhabitants of southern Africa. The relatively recent expansion of Bantu-speaking agropastoralists, as well as European colonial settlement along the south-west coast, dramatically changed patterns of genetic diversity in a region which had been largely isolated for thousands of years. Owing to this unique history, population structure in southern Africa reflects both the underlying KhoeSan genetic diversity as well as differential recent admixture. This population structure has a wide range of biomedical and sociocultural implications; such as changes in disease risk profiles. Here, we consolidate information from various population genetic studies that characterize admixture patterns in southern Africa with an aim to better understand differences in adverse disease phenotypes observed among groups. Our review confirms that ancestry has a direct impact on an individual's immune response to infectious diseases. In addition, we emphasize the importance of collaborative research, especially for populations in southern Africa that have a high incidence of potentially fatal infectious diseases such as HIV and tuberculosis.

  8. An age-structured population balance model for microbial dynamics

    Directory of Open Access Journals (Sweden)

    Duarte M.V.E.

    2003-01-01

    Full Text Available This work presents an age-structured population balance model (ASPBM for a bioprocess in a continuous stirred-tank fermentor. It relates the macroscopic properties and dynamic behavior of biomass to the operational parameters and microscopic properties of cells. Population dynamics is governed by two time- and age-dependent density functions for living and dead cells, accounting for the influence of substrate and dissolved oxygen concentrations on cell division, aging and death processes. The ASPBM described biomass and substrate oscillations in aerobic continuous cultures as experimentally observed. It is noteworthy that a small data set consisting of nonsegregated measurements was sufficient to adjust a complex segregated mathematical model.

  9. Global population structure and demographic history of the grey seal

    DEFF Research Database (Denmark)

    Klimova, A.; Phillips, C. D.; Fietz, Katharina

    2014-01-01

    Although the grey seal Halichoerus grypus is one of the most familiar and intensively studied of all pinniped species, its global population structure remains to be elucidated. Little is also known about how the species as a whole may have historically responded to climate-driven changes in habitat...... a little over 10 000 years ago, consistent with the last proposed isolation of the Baltic Sea. Approximate Bayesian computation also identified genetic signals consistent with postglacial population expansion across much of the species range, suggesting that grey seals are highly responsive to changes...

  10. Estimating spatio-temporal dynamics of size-structured populations

    DEFF Research Database (Denmark)

    Kristensen, Kasper; Thygesen, Uffe Høgsbro; Andersen, Ken Haste

    2014-01-01

    with simple stock dynamics, to estimate simultaneously how size distributions and spatial distributions develop in time. We demonstrate the method for a cod population sampled by trawl surveys. Particular attention is paid to correlation between size classes within each trawl haul due to clustering...... of individuals with similar size. The model estimates growth, mortality and reproduction, after which any aspect of size-structure, spatio-temporal population dynamics, as well as the sampling process can be probed. This is illustrated by two applications: 1) tracking the spatial movements of a single cohort...

  11. Population structure of barley landrace populations and gene-flow with modern varieties.

    Directory of Open Access Journals (Sweden)

    Elisa Bellucci

    Full Text Available Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population. We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.

  12. A Spatial Framework for Understanding Population Structure and Admixture.

    Science.gov (United States)

    Bradburd, Gideon S; Ralph, Peter L; Coop, Graham M

    2016-01-01

    Geographic patterns of genetic variation within modern populations, produced by complex histories of migration, can be difficult to infer and visually summarize. A general consequence of geographically limited dispersal is that samples from nearby locations tend to be more closely related than samples from distant locations, and so genetic covariance often recapitulates geographic proximity. We use genome-wide polymorphism data to build "geogenetic maps," which, when applied to stationary populations, produces a map of the geographic positions of the populations, but with distances distorted to reflect historical rates of gene flow. In the underlying model, allele frequency covariance is a decreasing function of geogenetic distance, and nonlocal gene flow such as admixture can be identified as anomalously strong covariance over long distances. This admixture is explicitly co-estimated and depicted as arrows, from the source of admixture to the recipient, on the geogenetic map. We demonstrate the utility of this method on a circum-Tibetan sampling of the greenish warbler (Phylloscopus trochiloides), in which we find evidence for gene flow between the adjacent, terminal populations of the ring species. We also analyze a global sampling of human populations, for which we largely recover the geography of the sampling, with support for significant histories of admixture in many samples. This new tool for understanding and visualizing patterns of population structure is implemented in a Bayesian framework in the program SpaceMix.

  13. 50 CFR 216.92 - Dolphin-safe requirements for tuna harvested in the ETP by large purse seine vessels.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Dolphin-safe requirements for tuna... MAMMALS REGULATIONS GOVERNING THE TAKING AND IMPORTING OF MARINE MAMMALS Dolphin Safe Tuna Labeling § 216.92 Dolphin-safe requirements for tuna harvested in the ETP by large purse seine vessels. (a) U.S...

  14. Population estimates of extended family structure and size.

    Science.gov (United States)

    Garceau, Anne; Wideroff, Louise; McNeel, Timothy; Dunn, Marsha; Graubard, Barry I

    2008-01-01

    Population-based estimates of biological family size can be useful for planning genetic studies, assessing how distributions of relatives affect disease associations with family history and estimating prevalence of potential family support. Mean family size per person is estimated from a population-based telephone survey (n = 1,019). After multivariate adjustment for demographic variables, older and non-White respondents reported greater mean numbers of total, first- and second-degree relatives. Females reported more total and first-degree relatives, while less educated respondents reported more second-degree relatives. Demographic differences in family size have implications for genetic research. Therefore, periodic collection of family structure data in representative populations would be useful. Copyright 2008 S. Karger AG, Basel.

  15. Evolutionary genomics and population structure of Entamoeba histolytica

    Directory of Open Access Journals (Sweden)

    Koushik Das

    2014-11-01

    Full Text Available Amoebiasis caused by the gastrointestinal parasite Entamoeba histolytica has diverse disease outcomes. Study of genome and evolution of this fascinating parasite will help us to understand the basis of its virulence and explain why, when and how it causes diseases. In this review, we have summarized current knowledge regarding evolutionary genomics of E. histolytica and discussed their association with parasite phenotypes and its differential pathogenic behavior. How genetic diversity reveals parasite population structure has also been discussed. Queries concerning their evolution and population structure which were required to be addressed have also been highlighted. This significantly large amount of genomic data will improve our knowledge about this pathogenic species of Entamoeba.

  16. Population structure and genomic inbreeding in nine Swiss dairy cattle populations.

    Science.gov (United States)

    Signer-Hasler, Heidi; Burren, Alexander; Neuditschko, Markus; Frischknecht, Mirjam; Garrick, Dorian; Stricker, Christian; Gredler, Birgit; Bapst, Beat; Flury, Christine

    2017-11-07

    Domestication, breed formation and intensive selection have resulted in divergent cattle breeds that likely exhibit their own genomic signatures. In this study, we used genotypes from 27,612 autosomal single nucleotide polymorphisms to characterize population structure based on 9214 sires representing nine Swiss dairy cattle populations: Brown Swiss (BS), Braunvieh (BV), Original Braunvieh (OB), Holstein (HO), Red Holstein (RH), Swiss Fleckvieh (SF), Simmental (SI), Eringer (ER) and Evolèner (EV). Genomic inbreeding (F ROH ) and signatures of selection were determined by calculating runs of homozygosity (ROH). The results build the basis for a better understanding of the genetic development of Swiss dairy cattle populations and highlight differences between the original populations (i.e. OB, SI, ER and EV) and those that have become more popular in Switzerland as currently reflected by their larger populations (i.e. BS, BV, HO, RH and SF). The levels of genetic diversity were highest and lowest in the SF and BS breeds, respectively. Based on F ST values, we conclude that, among all pairwise comparisons, BS and HO (0.156) differ more than the other pairs of populations. The original Swiss cattle populations OB, SI, ER, and EV are clearly genetically separated from the Swiss cattle populations that are now more common and represented by larger numbers of cows. Mean levels of F ROH ranged from 0.027 (ER) to 0.091 (BS). Three of the original Swiss cattle populations, ER (F ROH : 0.027), OB (F ROH : 0.029), and SI (F ROH : 0.039), showed low levels of genomic inbreeding, whereas it was much higher in EV (F ROH : 0.074). Private signatures of selection for the original Swiss cattle populations are reported for BTA4, 5, 11 and 26. The low levels of genomic inbreeding observed in the original Swiss cattle populations ER, OB and SI compared to the other breeds are explained by a lesser use of artificial insemination and greater use of natural service. Natural service

  17. Can Cooperative Management of Tuna Fisheries in the Western Pacific Solve the Growth Overfishing Problem?

    NARCIS (Netherlands)

    Bailey, M.L.; Rashid Sumaila, U.; Martell, S.J.D.

    2013-01-01

    Tuna fisheries in the western and central Pacific Ocean are important globally for both food and economic security. Yellowfin and bigeye tuna stocks in this region are declining, in part due to the juvenile bycatch of these species by the purse seine fishery using floating objects and fish

  18. 77 FR 73969 - International Fisheries; Pacific Tuna Fisheries; Fishing Restrictions in the Eastern Pacific Ocean

    Science.gov (United States)

    2012-12-12

    ... overfishing of the stock. DATES: Comments must be submitted in writing by January 11, 2013. A public hearing... effort quotas are an important step for reducing the overfishing of bluefin tuna. In 2011, NMFS determined overfishing is occurring on Pacific bluefin tuna based on stock assessment results of the...

  19. 76 FR 283 - International Fisheries; Pacific Tuna Fisheries; Vessel Capacity Limit in the Purse Seine Fishery...

    Science.gov (United States)

    2011-01-04

    ... of implementing a capacity management regime, the United States chose to further limit its fleet... Inter-American Tropical Tuna Commission (IATTC) Resolution on the Capacity of the Tuna Fleet Operating.... industry consistent with the IATTC management framework. DATES: These regulations become effective on...

  20. 77 FR 24669 - Atlantic Highly Migratory Species; Public Conference Call Regarding Recreational Yellowfin Tuna...

    Science.gov (United States)

    2012-04-25

    ... collection in the U.S. recreational yellowfin tuna fishery and the relationship to international yellowfin...-XB162 Atlantic Highly Migratory Species; Public Conference Call Regarding Recreational Yellowfin Tuna... Administration (NOAA), Commerce. ACTION: Notice of public conference call. SUMMARY: In order to better inform the...

  1. Argentine Population Genetic Structure: Large Variance in Amerindian Contribution

    Science.gov (United States)

    Seldin, Michael F.; Tian, Chao; Shigeta, Russell; Scherbarth, Hugo R.; Silva, Gabriel; Belmont, John W.; Kittles, Rick; Gamron, Susana; Allevi, Alberto; Palatnik, Simon A.; Alvarellos, Alejandro; Paira, Sergio; Caprarulo, Cesar; Guillerón, Carolina; Catoggio, Luis J.; Prigione, Cristina; Berbotto, Guillermo A.; García, Mercedes A.; Perandones, Carlos E.; Pons-Estel, Bernardo A.; Alarcon-Riquelme, Marta E.

    2011-01-01

    Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies. PMID:17177183

  2. Genetic population structure of sympatric and allopatric populations of Baltic ciscoes (Coregonus albula complex, Teleostei, Coregonidae).

    Science.gov (United States)

    Mehner, Thomas; Pohlmann, Kirsten; Elkin, Che; Monaghan, Michael T; Nitz, Barbara; Freyhof, Jörg

    2010-03-29

    Teleost fishes of the Coregonidae are good model systems for studying postglacial evolution, adaptive radiation and ecological speciation. Of particular interest is whether the repeated occurrence of sympatric species pairs results from in-situ divergence from a single lineage or from multiple invasions of one or more different lineages. Here, we analysed the genetic structure of Baltic ciscoes (Coregonus albula complex), examining 271 individuals from 8 lakes in northern Germany using 1244 polymorphic AFLP loci. Six lakes had only one population of C. albula while the remaining two lakes had C. albula as well as a sympatric species (C. lucinensis or C. fontanae). AFLP demonstrated a significant population structure (Bayesian thetaB = 0.22). Lower differentiation between allopatric (thetaB = 0.028) than sympatric (0.063-0.083) populations contradicts the hypothesis of a sympatric origin of taxa, and there was little evidence for stocking or ongoing hybridization. Genome scans found only three loci that appeared to be under selection in both sympatric population pairs, suggesting a low probability of similar mechanisms of ecological segregation. However, removal of all non-neutral loci decreased the genetic distance between sympatric pairs, suggesting recent adaptive divergence at a few loci. Sympatric pairs in the two lakes were genetically distinct from the six other C. albula populations, suggesting introgression from another lineage may have influenced these two lakes. This was supported by an analysis of isolation-by-distance, where the drift-gene flow equilibrium observed among allopatric populations was disrupted when the sympatric pairs were included. While the population genetic data alone can not unambiguously uncover the mode of speciation, our data indicate that multiple lineages may be responsible for the complex patterns typically observed in Coregonus. Relative differences within and among lakes raises the possibility that multiple lineages may be

  3. Insular Celtic population structure and genomic footprints of migration.

    Directory of Open Access Journals (Sweden)

    Ross P Byrne

    2018-01-01

    Full Text Available Previous studies of the genetic landscape of Ireland have suggested homogeneity, with population substructure undetectable using single-marker methods. Here we have harnessed the haplotype-based method fineSTRUCTURE in an Irish genome-wide SNP dataset, identifying 23 discrete genetic clusters which segregate with geographical provenance. Cluster diversity is pronounced in the west of Ireland but reduced in the east where older structure has been eroded by historical migrations. Accordingly, when populations from the neighbouring island of Britain are included, a west-east cline of Celtic-British ancestry is revealed along with a particularly striking correlation between haplotypes and geography across both islands. A strong relationship is revealed between subsets of Northern Irish and Scottish populations, where discordant genetic and geographic affinities reflect major migrations in recent centuries. Additionally, Irish genetic proximity of all Scottish samples likely reflects older strata of communication across the narrowest inter-island crossing. Using GLOBETROTTER we detected Irish admixture signals from Britain and Europe and estimated dates for events consistent with the historical migrations of the Norse-Vikings, the Anglo-Normans and the British Plantations. The influence of the former is greater than previously estimated from Y chromosome haplotypes. In all, we paint a new picture of the genetic landscape of Ireland, revealing structure which should be considered in the design of studies examining rare genetic variation and its association with traits.

  4. Population Structure of Pseudocercospora fijiensis in Costa Rica Reveals Shared Haplotype Diversity with Southeast Asian Populations.

    Science.gov (United States)

    Saville, Amanda; Charles, Melodi; Chavan, Suchitra; Muñoz, Miguel; Gómez-Alpizar, Luis; Ristaino, Jean Beagle

    2017-12-01

    Pseudocercospora fijiensis is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20 to 80% yield loss in the absence of fungicides in banana crops. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared with Honduran and global populations to better understand migration patterns and inform management strategies. In total, 118 isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared with a previously published global dataset of populations of P. fijiensis. The Costa Rican and Honduran populations shared haplotype diversity with haplotypes from Southeast Asia, Oceania, and the Americas but not Africa for all but one of the six loci studied. Gene flow and shared haplotype diversity was found in Honduran and Costa Rican populations of the pathogen. The data indicate that the haplotypic diversity observed in Costa Rican populations of P. fijiensis is derived from dispersal from initial outbreak sources in Honduras and admixtures between genetically differentiated sources from Southeast Asia, Oceania, and the Americas.

  5. Population structure of Nellore cattle in northeastern Brazil

    Directory of Open Access Journals (Sweden)

    Ana Carla Borges Barbosa

    2013-09-01

    Full Text Available The objective of this study was to evaluate the population genetic structure of Nellore cattle in northeastern Brazil. Pedigree information was collected from 175,231 animals born from 1967 to 2007. Probability of gene origin, inbreeding, average relatedness coefficient (AR, completeness pedigree, effective population size and generation interval were calculated. Generation interval was high due to the long period of time animals were used as reproducers. The bottleneck effect was evidenced as a result of intensive use of limited breeders over the last years. Low values were observed ​​in the effective number of founder animals (434 and ancestors (427 comparing with the number on the base (175,231 and reference populations (130,038. Generally, the variability explained by the founders and ancestors is considered low. The average coefficient of inbreeding (0.11% and AR (0.14% estimated for this population is considered low and can be partly explained by the increased population effective number in recent periods; however, it may be underestimated by shallow pedigree.

  6. Perilaku Tuna Fungsi Auditor: Pengujian atas Karakteristik Personal dan Penilai Kinerja Auditor

    Directory of Open Access Journals (Sweden)

    Aprina Nugrahesthy Sulistya Hapsari

    2016-12-01

      Fenomena perilaku tuna fungsi yang dilakukan oleh auditor makin dianggap lazim di lingkup audit. Hubungan antara karakteristik personal, karakteristik non personal dan perilaku tuna fungsi menjadi sesuatu hal yang menarik untuk diteliti. Penelitian ini menguji hubungan antara karakteristik personal berupa locus of control, tingkat kinerja pribadi karyawan, komitmen organisasi dan turnover intention dan penilai kinerja auditor sebagai faktor diluar karakteristik personal terhadap penerimaan perilaku tuna fungsi dalam lingkup audit. Pengumpulan data dilakukan melalui kuisioner dari responden yaitu auditor di KAP Kota Semarang dan Surakarta dengan metode convenience sampling karena populasi auditor yang bekerja tidak diketahui dengan pasti. Analisis data dengan menggunakan Model Persamaan Struktural. Hasil dari pengujian hipotesis mengindikasikan bahwa tidak ada hubungan antara karakteristik personal dengan penerimaan perilaku tuna fungsi dalam ruang lingkup audit. Sementara itu di lain sisi terdapat hubungan antara penilai kinerja auditor dengan penerimaan perilaku tuna fungsi dalam ruang lingkup audit.

  7. Population genetic structure of the people of Qatar.

    Science.gov (United States)

    Hunter-Zinck, Haley; Musharoff, Shaila; Salit, Jacqueline; Al-Ali, Khalid A; Chouchane, Lotfi; Gohar, Abeer; Matthews, Rebecca; Butler, Marcus W; Fuller, Jennifer; Hackett, Neil R; Crystal, Ronald G; Clark, Andrew G

    2010-07-09

    People of the Qatar peninsula represent a relatively recent founding by a small number of families from three tribes of the Arabian Peninsula, Persia, and Oman, with indications of African admixture. To assess the roles of both this founding effect and the customary first-cousin marriages among the ancestral Islamic populations in Qatar's population genetic structure, we obtained and genotyped with Affymetrix 500k SNP arrays DNA samples from 168 self-reported Qatari nationals sampled from Doha, Qatar. Principal components analysis was performed along with samples from the Human Genetic Diversity Project data set, revealing three clear clusters of genotypes whose proximity to other human population samples is consistent with Arabian origin, a more eastern or Persian origin, and individuals with African admixture. The extent of linkage disequilibrium (LD) is greater than that of African populations, and runs of homozygosity in some individuals reflect substantial consanguinity. However, the variance in runs of homozygosity is exceptionally high, and the degree of identity-by-descent sharing generally appears to be lower than expected for a population in which nearly half of marriages are between first cousins. Despite the fact that the SNPs of the Affymetrix 500k chip were ascertained with a bias toward SNPs common in Europeans, the data strongly support the notion that the Qatari population could provide a valuable resource for the mapping of genes associated with complex disorders and that tests of pairwise interactions are particularly empowered by populations with elevated LD like the Qatari. Copyright 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  8. Population age structure and asset returns: an empirical investigation.

    Science.gov (United States)

    Poterba, J M

    1998-10-01

    "This paper investigates the association between population age structure, particularly the share of the population in the 'prime saving years' 45-60, and the returns on stocks and bonds. The paper is motivated by the claim that the aging of the 'Baby Boom' cohort in the United States is a key factor in explaining the recent rise in asset values. It also addresses the associated claim that asset prices will decline when this large cohort reaches retirement age and begins to reduce its asset holdings. This paper begins by considering household age-asset accumulation profiles. Data from the Survey of Consumer Finances suggest that while cross-sectional age-wealth profiles peak for households in their early 60s, cohort data on the asset ownership of the same households show a much less pronounced peak.... The paper then considers the historical relationship between demographic structure and real returns on Treasury bills, long-term government bonds, and corporate stock. The results do not suggest any robust relationship between demographic structure and asset returns.... The paper concludes by discussing factors such as international capital flows and forward-looking behavior on the part of market participants that could weaken the relationship between age structure and asset returns in a single nation." excerpt

  9. Lack of Population Structure in Coriander Populations Based on SDS (Seed Storage Protein Page Analysis

    Directory of Open Access Journals (Sweden)

    Gülsüm Yaldiz

    2016-08-01

    Full Text Available Genetic variation is prerequisite for plant breeding. Nothing information existed in the literature for available diversity of Coriander accession in Turkey. Plant breeding activities are negligible in Turkey. So in order to start effective plant breeding program in Turkey, information on the available genetic diversity is viable. Therefore we planned to study the genetic variation and population structure of 29 Coriander accessions by seed storage protein (SDS. SDS analysis elaborated the lack of population structure and genetic bottleneck in the Coriander accessions in Turkey. Based on the results of this study, it was clear that sampling strategy was not appropriate and plant introduction should be made from different sources and diverse genotypes should be used as parents to initialize the effective Turkish Coriander breeding program.

  10. Evaluation of three harvest control rules for Bigeye Tuna ( Thunnus obesus) fisheries in the Indian Ocean

    Science.gov (United States)

    Tong, Yuhe; Chen, Xinjun; Kolody, Dale

    2014-10-01

    The stock of Bigeye tuna ( Thunnus obesus) in the Indian Ocean supports an important international fishery and is considered to be fully exploited. The responsible management agency, the Indian Ocean Tuna Commission (IOTC), does not have an explicit management decision-making framework in place to prevent over-fishing. In this study, we evaluated three harvest control rules, i) constant fishing mortality (CF), from 0.2 to 0.6, ii) constant catch (CC), from 60000 to 140000 t, and iii) constant escapement (CE), from 0.3 to 0.7. The population dynamics simulated by the operating model was based on the most recent stock assessment using Stock Synthesis version III (SS3). Three simulation scenarios (low, medium and high productivity) were designed to cover possible uncertainty in the stock assessment and biological parameters. Performances of three harvest control rules were compared on the basis of three management objectives (over 3, 10 and 25 years): i) the probability of maintaining spawning stock biomass above a level that can sustain maximum sustainable yield (MSY) on average, ii) the probability of achieving average catches between 0.8 MSY and 1.0 MSY, and iii) inter-annual variability in catches. The constant escapement strategy ( CE=0.5), constant fishing mortality strategy ( F=0.4) and constant catch ( CC=80000) were the most rational among the respective management scenarios. It is concluded that the short-term annual catch is suggested at 80000 t, and the potential total allowable catch for a stable yield could be set at 120000 t once the stock had recovered successfully. All the strategies considered in this study to achieve a `tolerable' balance between resource conservation and utilization have been based around the management objectives of the IOTC.

  11. Mitochondrial DNA structure of an isolated Tunisian Berber population and its relationship with Mediterranean populations.

    Science.gov (United States)

    Ben Halim, Nizar; Hsouna, Sana; Lasram, Khaled; Chargui, Mariem; Khemira, Laaroussi; Saidane, Rachid; Abdelhak, Sonia; Kefi, Rym

    2018-02-01

    Douiret is an isolated Berber population from South-Eastern Tunisia. The strong geographic and cultural isolation characterising this population might have contributed to remarkable endogamy and consanguinity, which were practiced for several centuries. The objective of this study is to evaluate the mitochondrial DNA (mtDNA) genetic structure of Douiret and to compare it to other Mediterranean populations with a special focus on major haplogroup T. Genomic DNA was extracted from blood samples of 58 unrelated individuals collected from the different patrilineal lineages of the population. The hypervariable region 1 of the mtDNA was amplified and sequenced. For comparative analyses, additional HVS1 sequences (n = 4857) were compiled from previous studies. The maternal background of the studied sample from Douiret was mainly of Eurasian origin (74%) followed by Sub-Saharan (17%) and North African (3%) lineages. Douiret harbours the highest frequency of haplogroup T in the Mediterranean region, assigned to the unique subclade T1a (38%). Phylogenetic analysis showed an outlier position of Douiret at the Mediterranean level. The genetic structure of Douiret highlights the presence of founders, most likely of Near/Middle Eastern origin, who conquered this area during the Middle/Late Upper Palaeolithic and Neolithic dispersals.

  12. Genetic diversity, population structure, and traditional culture of Camellia reticulata.

    Science.gov (United States)

    Xin, Tong; Huang, Weijuan; De Riek, Jan; Zhang, Shuang; Ahmed, Selena; Van Huylenbroeck, Johan; Long, Chunlin

    2017-11-01

    Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio-economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi-structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province. We collected plant material ( n  = 190 individuals) from five populations at study sites using single-dose AFLP markers in order to access the genetic diversity within and between populations. A total of 387 DNA fragments were produced by four AFLP primer sets. All DNA fragments were found to be polymorphic (100%). A relatively high level of genetic diversity was revealed in C. reticulata samples at both the species ( H sp  = 0.3397, I sp  = 0.5236) and population (percentage of polymorphic loci = 85.63%, H pop  = 0.2937, I pop  = 0.4421) levels. Findings further revealed a relatively high degree of genetic diversity within C. reticulata populations (Analysis of Molecular Variance = 96.31%). The higher genetic diversity within populations than among populations of C. reticulata from different geographies is likely due to the cultural and social influences associated with its long cultivation history for esthetic and culinary purposes by diverse sociolinguistic groups. This study highlights the influence of human management, socio-economic factors, and other cultural variables on the genetic and morphological diversity of C. reticulata at a regional level. Findings emphasize the important role of traditional culture on the conservation and utilization of plant genetic diversity.

  13. Periodic matrix models for seasonal dynamics of structured populations with application to a seabird population.

    Science.gov (United States)

    Cushing, J M; Henson, Shandelle M

    2018-02-03

    For structured populations with an annual breeding season, life-stage interactions and behavioral tactics may occur on a faster time scale than that of population dynamics. Motivated by recent field studies of the effect of rising sea surface temperature (SST) on within-breeding-season behaviors in colonial seabirds, we formulate and analyze a general class of discrete-time matrix models designed to account for changes in behavioral tactics within the breeding season and their dynamic consequences at the population level across breeding seasons. As a specific example, we focus on egg cannibalism and the daily reproductive synchrony observed in seabirds. Using the model, we investigate circumstances under which these life history tactics can be beneficial or non-beneficial at the population level in light of the expected continued rise in SST. Using bifurcation theoretic techniques, we study the nature of non-extinction, seasonal cycles as a function of environmental resource availability as they are created upon destabilization of the extinction state. Of particular interest are backward bifurcations in that they typically create strong Allee effects in population models which, in turn, lead to the benefit of possible (initial condition dependent) survival in adverse environments. We find that positive density effects (component Allee effects) due to increased adult survival from cannibalism and the propensity of females to synchronize daily egg laying can produce a strong Allee effect due to a backward bifurcation.

  14. Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

    Directory of Open Access Journals (Sweden)

    Mallikarjuna Rao eKovi

    2015-11-01

    Full Text Available Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US] from the second generation of the two divergently selected populations and an unselected control population were genotyped using 278 genome-wide SNPs derived from Lolium perenne L. transcriptome sequence. Our studies showed that the HF and LF populations are very divergent after selection for freezing tolerance, whereas the HF and US populations are more similar. Linkage disequilibrium (LD decay varied across the seven chromosomes and the conspicuous pattern of LD between the HF and LF population confirmed their divergence in freezing tolerance. Furthermore, two Fst outlier methods; finite island model (fdist by LOSITAN and hierarchical structure model using ARLEQUIN detected six loci under directional selection. These outlier loci are most probably linked to genes involved in freezing tolerance, cold adaptation and abiotic stress and might be the potential marker resources for breeding perennial ryegrass cultivars with improved freezing tolerance.

  15. An analysis of the basic population structure of Shanghai Municipality.

    Science.gov (United States)

    Shen, A

    1984-01-01

    This paper analyzes the changes in Shanghai's population structure over the last 30 years in the 4 aspects of age structure, sex composition, urban and rural composition, and labor and employment structure. In 1953 those of the 0 to 6 age group accounted for 21.2% of the total population; in 1957 the group represented a proportion of 24.6%. Since the 1960s, especially after the 1970s, the family planning program gradually took effect, and the birthrate of the entire municipality fell drastically. The number of school-age children in 1979 was 1 1/2 times more than the same age group in 1953; there should be no worry that population control may result in a shortage of manpower to meet the needs of the work force and the armed forces either toward the end of this century or at the beginning of the next. The economy in China is underdeveloped, production and technology remain at a low level, average wages for employees are low, and for a long time the low living standard of the people has shown little sign of improvement. The problem is mainly manifest in the following areas: 1) distribution of the work force in heavy and light industries is not sufficiently rational, 2) the distribution of the work force between captial construction and transport and communications on the 1 hand and the national economy on the other is out of proportion, 3) the distribution of the work force between commerce, service trades, and public utilities on the 1 hand and the national economy on the other is disproportionated, and 4) the distribution of the work force between undertakings of culture, education, scientific research, health, and medical care on the 1 hand and economic construction on the other is improper. How to control population growth and adjust parts of the population structure to suit the national economic development poses a problem that calls for further in-depth study and analysis to resolve it step by step.

  16. El Niño revisited: the influence of El Niño Southern Oscillation on the world's largest tuna fisheries.

    Science.gov (United States)

    Receveur, A.; Simon, N.; Menkes, C.; Tremblay-Boyer, L.; Senina, I.; Lehodey, P.

    2016-12-01

    El Niño Southern Oscillation (ENSO) drives global climate on inter-annual scales and impacts the ecosystem structure in the warm-pool and cold-tongue of the Pacific Ocean. During the El Niño phase of ENSO, the warm-pool can stretch from the western equatorial Pacific to the eastern Pacific allowing species associated with the warm-pool to correspondingly spread eastwards. Conversely, during the la Niña phase the warm-pool is pushed to the far western equatorial Pacific by the cold-tongue allowing species associated with this ecosystem to spread westwards. Consequently, ENSO dynamics are likely to be critical for understanding the ecological processes supporting fisheries in the equatorial Pacific Ocean. Surface inhabiting tuna, such as skipjack, are thought to track the convergence of the warm-pool and cold-tongue with fishing vessels tracking this tuna behavior. Given the reliance of Pacific Island economies on tuna fisheries, knowing when tunas are more likely to be present in high density in their territorial waters is beneficial for harvest control policies such as effort trading between nations. We use the SEAPODYM model to investigate the response of bigeye and skipjack tuna species to the phases of ENSO. SEAPODYM is an age structured model that integrates fisheries dependent and independent data with environmental data. We analyze the outputs of SEAPODYM using wavelets to assess the impact of environmental and biotic variables on the abundance and distribution of adult and juvenile age classes and to study time series cycle and temporal lags to ENSO. The main result for skipjack is the eastward or westward movement of the biomass pattern which is significantly lagged with the warm pool ENSO displacement. That lag ranges from 8 months for juvenile up to 18 months for adults. Such delayed response, can be traced in the model. Higher temperature in the central Pacific during El Niño leads to better recruitment which leads to lagged increase of juvenile

  17. Population structure of fishes from an urban stream

    Directory of Open Access Journals (Sweden)

    Naiara Zanatta

    2017-05-01

    Full Text Available The aim of this study was to identify the population structure of the ichthyofauna in an urban stream within an environmental protection area in southern Brazil. Quarterly samplings were conducted between October 2009 and August 2010. Poecilia reticulata was the most abundant species, followed by Hypostomus ancistroides and Rhamdia quelen. It was found a higher proportion of adults instead of juveniles from P. reticulata and R. quelen populations, while the opposite was recorded for H. ancistroides. Sex ratio of 1:1 was found for H. ancistroides, but differed significantly for P. reticulata and R. quelen. Females of P. reticulata and R. quelen reached higher length than males in the smaller and higher length-classes, while H. ancistroides females were only longer in initial length-classes. It was recorded higher occurrence of mature and maturing individuals. Mature individuals of H. ancistroides were sampled in October, and P. reticulata and R. quelen throughout the sampling period. Despite adverse environmental conditions, the occurrence of juveniles indicates reproductive activity for these species. Population structure studies in degraded systems are urgent, since life-history features of species may suffer changes due to anthropic impacts. Providing such information contributes to decision making and management of degraded systems.

  18. A Malthusian curb on spatial structure in microorganism populations.

    Science.gov (United States)

    Martin, A P

    2004-10-07

    That all organisms are born in the company of a parent but die alone is a fundamental biological asymmetry. It has been suggested that this provides a deep-rooted source of spatial pattern formation for microorganisms even at the scale of the population. Such a theory, however, neglects the strong influence in nature of the limited and spatially variable availability of food. The tendency, first recognized by Thomas Malthus in the 18th century, of a population to out-strip its food resources will eventually lead, through local starvation, to the suppression of a heterogeneity growing within a population. Using a generic model it is demonstrated that including local food limitation of breeding strongly dampens spatial structure otherwise resulting from birth and death. The extent of this damping is shown to be a function of the strength of the coupling between organisms and their food and of the total abundance of organic material. Moreover, this work provides an example of a density-dependent process acting to diminish spatial structure rather than to create it and highlights the rich variety of behaviour that is missed by continuum models which fail to represent such local dynamics.

  19. Competition in size-structured populations: mechanisms inducing cohort formation and population cycles.

    Science.gov (United States)

    de Roos, André M; Persson, Lennart

    2003-02-01

    In this paper we investigate the consequences of size-dependent competition among the individuals of a consumer population by analyzing the dynamic properties of a physiologically structured population model. Only 2 size-classes of individuals are distinguished: juveniles and adults. Juveniles and adults both feed on one and the same resource and hence interact by means of exploitative competition. Juvenile individuals allocate all assimilated energy into development and mature on reaching a fixed developmental threshold. The combination of this fixed threshold and the resource-dependent developmental rate, implies that the juvenile delay between birth and the onset of reproduction may vary in time. Adult individuals allocate all assimilated energy to reproduction. Mortality of both juveniles and adults is assumed to be inversely proportional to the amount of energy assimilated. In this setting we study how the dynamics of the population are influenced by the relative foraging capabilities of juveniles and adults. In line with results that we previously obtained in size-structured consumer-resource models with pulsed reproduction, population cycles primarily occur when either juveniles or adults have a distinct competitive advantage. When adults have a larger per capita feeding rate and are hence competitively superior to juveniles, population oscillations occur that are primarily induced by the fact that the duration of the juvenile period changes with changing food conditions. These cycles do not occur when the juvenile delay is a fixed parameter. When juveniles are competitively superior, two different types of population fluctuations can occur: (1) rapid, low-amplitude fluctuations having a period of half the juvenile delay and (2) slow, large-amplitude fluctuations characterized by a period, which is roughly equal to the juvenile delay. The analysis of simplified versions of the structured model indicates that these two types of oscillations also occur if

  20. Multi-layered population structure in Island Southeast Asians

    Science.gov (United States)

    Mörseburg, Alexander; Pagani, Luca; Ricaut, Francois-Xavier; Yngvadottir, Bryndis; Harney, Eadaoin; Castillo, Cristina; Hoogervorst, Tom; Antao, Tiago; Kusuma, Pradiptajati; Brucato, Nicolas; Cardona, Alexia; Pierron, Denis; Letellier, Thierry; Wee, Joseph; Abdullah, Syafiq; Metspalu, Mait; Kivisild, Toomas

    2016-01-01

    The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here, we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognised major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers. Given the extensive presence of trade goods, cultural and linguistic evidence of Indian influence in Southeast Asia starting from 2.5 kya, we also detect traces of a South Asian signature in different populations in the region dating to the last couple of thousand years. PMID:27302840

  1. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

  2. An evaluation of management strategies for Atlantic tuna stocks

    Directory of Open Access Journals (Sweden)

    L. T. Kell

    2003-04-01

    Full Text Available International agreements for the International Commission for the Conservation of Atlantic Tunas (ICCAT convention area imply that Atlantic tuna stocks should be managed by strategies based on maximum sustainable yield (MSY; however, there is concern whether this will actually ensure sustainability with sufficiently high probability consistent with the principals of the precautionary approach. Therefore, the performance of MSY management strategies based on current assessment procedures was evaluated using a computer simulation framework. The framework includes the data collection, assessment, prediction, and management processes, as well as the implementation of management regulations. It therefore provides an integrated way to evaluate the relative importance of and the interactions between each component of the system with regard to the overall success of the management strategy. The study elucidates guidelines about assessment and management that are general enough to be applied to all tunas in the Atlantic Ocean. It does so by comparing different hypotheses about management and assessment for three stocks (North Atlantic albacore, Atlantic bigeye and East Atlantic skipjack, which are representative of the variety encountered (i.e. from data rich to poor and tropical to temperate waters in ICCAT stocks. Management performance was especially sensitive to the carrying capacity of the stock. The type of proxy used for MSY was more important to the success of the procedure than the frequency of assessment or the number of indices used in the assessment. Whilst the procedure was successful at achieving the management objectives for albacore, it was only partially successful for bigeye and was too conservative for skipjack.

  3. Tuna cannery energy conservation interventions: Technical/economic feasibility study

    Energy Technology Data Exchange (ETDEWEB)

    Florio, G. (Calabria Univ. Arcavacata di Rende (Italy). Dipt. di Meccanica)

    An energy audit was conducted on a 230,000 can (x 80 g)/day tuna cannery to determine where technically and economically feasible energy savings interventions could be made. The plant is equipped with an oil fired boiler which supplies steam for cooking and sterilization purposes. In the energy/cost analysis, it was found that the most significant and cost effective energy savings could be obtained by the substitution of the four sterilization chambers with three sets of twin sterilization/heat exchange chambers.

  4. Diversification and Population Structure in Common Beans (Phaseolus vulgaris L.)

    Science.gov (United States)

    Blair, Matthew W.; Soler, Alvaro; Cortés, Andrés J.

    2012-01-01

    Wild accessions of crops and landraces are valuable genetic resources for plant breeding and for conserving alleles and gene combinations in planta. The primary genepool of cultivated common beans includes wild accessions of Phaseolus vulgaris. These are of the same species as the domesticates and therefore are easily crossable with cultivated accessions. Molecular marker assessment of wild beans and landraces is important for the proper utilization and conservation of these important genetic resources. The goal of this research was to evaluate a collection of wild beans with fluorescent microsatellite or simple sequence repeat markers and to determine the population structure in combination with cultivated beans of all known races. Marker diversity in terms of average number of alleles per marker was high (13) for the combination of 36 markers and 104 wild genotypes that was similar to the average of 14 alleles per marker found for the 606 cultivated genotypes. Diversity in wild beans appears to be somewhat higher than in cultivated beans on a per genotype basis. Five populations or genepools were identified in structure analysis of the wild beans corresponding to segments of the geographical range, including Mesoamerican (Mexican), Guatemalan, Colombian, Ecuadorian-northern Peruvian and Andean (Argentina, Bolivia and Southern Peru). The combined analysis of wild and cultivated accessions showed that the first and last of these genepools were related to the cultivated genepools of the same names and the penultimate was found to be distinct but not ancestral to the others. The Guatemalan genepool was very novel and perhaps related to cultivars of race Guatemala, while the Colombian population was also distinct. Results suggest geographic isolation, founder effects or natural selection could have created the different semi-discrete populations of wild beans and that multiple domestications and introgression were involved in creating the diversity of cultivated beans

  5. Diversification and population structure in common beans (Phaseolus vulgaris L..

    Directory of Open Access Journals (Sweden)

    Matthew W Blair

    Full Text Available Wild accessions of crops and landraces are valuable genetic resources for plant breeding and for conserving alleles and gene combinations in planta. The primary genepool of cultivated common beans includes wild accessions of Phaseolus vulgaris. These are of the same species as the domesticates and therefore are easily crossable with cultivated accessions. Molecular marker assessment of wild beans and landraces is important for the proper utilization and conservation of these important genetic resources. The goal of this research was to evaluate a collection of wild beans with fluorescent microsatellite or simple sequence repeat markers and to determine the population structure in combination with cultivated beans of all known races. Marker diversity in terms of average number of alleles per marker was high (13 for the combination of 36 markers and 104 wild genotypes that was similar to the average of 14 alleles per marker found for the 606 cultivated genotypes. Diversity in wild beans appears to be somewhat higher than in cultivated beans on a per genotype basis. Five populations or genepools were identified in structure analysis of the wild beans corresponding to segments of the geographical range, including Mesoamerican (Mexican, Guatemalan, Colombian, Ecuadorian-northern Peruvian and Andean (Argentina, Bolivia and Southern Peru. The combined analysis of wild and cultivated accessions showed that the first and last of these genepools were related to the cultivated genepools of the same names and the penultimate was found to be distinct but not ancestral to the others. The Guatemalan genepool was very novel and perhaps related to cultivars of race Guatemala, while the Colombian population was also distinct. Results suggest geographic isolation, founder effects or natural selection could have created the different semi-discrete populations of wild beans and that multiple domestications and introgression were involved in creating the diversity of

  6. Petrological and geochemical studies of alkaline rocks from continental Brazil. The tunas massif, state of Parana

    International Nuclear Information System (INIS)

    Gomes, C.B.; Barbieri, M.

    1987-01-01

    The Tunas massif, outcropping 80 km from the city of Curitiba, Parana State, southern Brazil, covers about 22 km 2 . It intruded into Precambrian metaigneous and metasedimentary units about 80 Ma ago (K/Ar and Rb/Sr data); five subcircular volcanic structures are recognized. Syenites and alkali syenites (plus some pulaskites) are the main rock-types, with subordinate alkali gabbros, syenogabbros, essexites and syenodiorites; small late syenitic dikes are also found. Magmatic breccias containing clasts of all rock-types are widespread. Main minerals are feldspars (both alkali feldspars and plagioclases, varying from bytownite to more sodic members), Ca-pyroxenes (Ti-salites grading towards ferrosalites and aegirine-augites), amphiboles (mainly pargasites, although kaersutites and katophorites are also present), Fe-biotites (sometimes enriched in Ti), olivines (hortonolites to ferrohortonolites), quartz and feldspathoids (both fresh and altered nephelines and sodalites); main accessories are Ti-magnetites (with exsolved ilmenite) and apatite. In the AFM diagram, whole rock chemistry depicts a typical alkaline trend. Binary variation diagrams (D.I. vs. several elements) show positive correlation for Si, Na and K, and negative slopes for Mg and Ca. The variation in the amounts of Ni, Cr and V with differentiation can be explained by withdrawal of olivine, Ca-pyroxenes and magnetite, and that of Sr and Ba by the fractionation of feldspars. The rocks are also relatively enriched in REE, a trend which is more pronounced for the light REE. Mass balance calculations show that the overall differentiation trend of the Tunas rocks can be explained by crystal fractionation, although several complexities arise and point to more complex genetic patterns. Isotopic Rb/Sr ratios are consistent with a mantle origin for the parental magma; dike rocks, however, with 87 Sr 86 Sr i = 0.70777 - 0.70806, were probably contaminated by crustal material. (author) [pt

  7. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

    Directory of Open Access Journals (Sweden)

    Reem Joukhadar

    2017-12-01

    Full Text Available Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to

  8. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat.

    Science.gov (United States)

    Joukhadar, Reem; Daetwyler, Hans D; Bansal, Urmil K; Gendall, Anthony R; Hayden, Matthew J

    2017-01-01

    Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT) germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to assist with

  9. Population structure of Salmonella investigated by amplified fragment length polymorphism

    DEFF Research Database (Denmark)

    Torpdahl, M.; Ahrens, Peter

    2004-01-01

    Aims: This study was undertaken to investigate the usefulness of amplified fragment length polymorphism (AFLP) in determining the population structure of Salmonella. Methods and Results: A total of 89 strains were subjected to AFLP analysis using the enzymes BglII and BspDI, a combination...... that is novel in Salmonella. Both species S. bongori and S. enterica and all subsp. of S. enterica were represented with emphasis on S. enterica subsp. enterica using a local strain collection and strains from the Salmonella Reference Collection B (SARB). The amplified fragments were used in a band...

  10. Temporal structure of neuronal population oscillations with empirical model decomposition

    International Nuclear Information System (INIS)

    Li Xiaoli

    2006-01-01

    Frequency analysis of neuronal oscillation is very important for understanding the neural information processing and mechanism of disorder in the brain. This Letter addresses a new method to analyze the neuronal population oscillations with empirical mode decomposition (EMD). Following EMD of neuronal oscillation, a series of intrinsic mode functions (IMFs) are obtained, then Hilbert transform of IMFs can be used to extract the instantaneous time frequency structure of neuronal oscillation. The method is applied to analyze the neuronal oscillation in the hippocampus of epileptic rats in vivo, the results show the neuronal oscillations have different descriptions during the pre-ictal, seizure onset and ictal periods of the epileptic EEG at the different frequency band. This new method is very helpful to provide a view for the temporal structure of neural oscillation

  11. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Science.gov (United States)

    Al-Hamidhi, Salama; H Tageldin, Mohammed; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

    2015-01-01

    Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075, θ = 0.07) were

  12. Genetic Diversity and Population Structure of Theileria annulata in Oman.

    Directory of Open Access Journals (Sweden)

    Salama Al-Hamidhi

    Full Text Available Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia. A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST' = 0.075,

  13. Genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV)

    DEFF Research Database (Denmark)

    Snow, M.; Bain, N.; Black, J.

    2004-01-01

    The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders this the m......The nucleotide sequences of a specific region of the nucleoprotein gene were compared in order to investigate the genetic population structure of marine viral haemorrhagic septicaemia virus (VHSV). Analysis of the sequence from 128 isolates of diverse geographic and host origin renders...... this the most comprehensive molecular epidemiological study of marine VHSV conducted to date. Phylogenetic analysis of nucleoprotein gene sequences confirmed the existence of the 4 major genotypes previously identified based on N- and subsequent G-gene based analyses. The range of Genotype I included subgroups...... of isolates associated with rainbow trout aquaculture (Genotype la) and those from the Baltic marine environment (Genotype Ib) to emphasise the relatively close genetic relationship between these isolates. The existence of an additional genotype circulating within the Baltic Sea (Genotype II) was also...

  14. Global pollution monitoring of butyltin compounds using skipjack tuna as a bioindicator

    International Nuclear Information System (INIS)

    Ueno, D.; Inoue, S.; Takahashi, S.; Ikeda, K.; Tanaka, H.; Subramanian, A.N.; Fillmann, G.; Lam, P.K.S.; Zheng, J.; Muchtar, M.; Prudente, M.; Chung, K.; Tanabe, S.

    2004-01-01

    Global pollution monitoring of butyltin in offshore water and open sea were conducted using skipjack tuna as a bioindicator. - Butyltin compounds (BTs) including mono- (MBT), di- (DBT), tri-butyltin (TBT) and total tin (ΣSn), were determined in the liver of skipjack tuna (Katsuwonus pelamis) collected from Asian offshore waters (off-Japan, the Japan Sea, off-Taiwan, the East China Sea, the South China Sea, off-Philippines, off-Indonesia, the Bay of Bengal), off-Seychelles, off-Brazil and open seas (the North Pacific). BTs were detected in all the skipjack tuna collected, suggesting widespread contamination of BTs even in offshore waters and open seas on a global scale. Considering specific accumulation, Sex-, body length- differences and migration of skipjack tuna did not seem to affect BT concentrations, indicating rapid reflection of the pollution levels in seawater where and when they were collected. Skipjack tuna is a suitable bioindicator for monitoring the global distribution of BTs in offshore waters and open seas. High concentrations of BTs were observed in skipjack tuna from offshore waters around Japan, a highly developed and industrialized region (up to 400 ng/g wet weight). Moreover skipjack tuna collected from offshore waters around Asian developing countries also revealed the levels comparable to those in Japan (up to 270 ng/g wet weight) which may be due to the recent improvement in economic status in Asian developing countries. High percentages (almost 90%) of BTs in total tin (ΣSn: sum of inorganic tin+organic tin) were found in the liver of skipjack tuna from offshore waters around Asian developing countries. This finding suggests that the anthropogenic BTs represent the major source of Sn accumulation in skipjack tuna from these regions

  15. Global pollution monitoring of butyltin compounds using skipjack tuna as a bioindicator

    Energy Technology Data Exchange (ETDEWEB)

    Ueno, D.; Inoue, S.; Takahashi, S.; Ikeda, K.; Tanaka, H.; Subramanian, A.N.; Fillmann, G.; Lam, P.K.S.; Zheng, J.; Muchtar, M.; Prudente, M.; Chung, K.; Tanabe, S

    2004-01-01

    Global pollution monitoring of butyltin in offshore water and open sea were conducted using skipjack tuna as a bioindicator. - Butyltin compounds (BTs) including mono- (MBT), di- (DBT), tri-butyltin (TBT) and total tin ({sigma}Sn), were determined in the liver of skipjack tuna (Katsuwonus pelamis) collected from Asian offshore waters (off-Japan, the Japan Sea, off-Taiwan, the East China Sea, the South China Sea, off-Philippines, off-Indonesia, the Bay of Bengal), off-Seychelles, off-Brazil and open seas (the North Pacific). BTs were detected in all the skipjack tuna collected, suggesting widespread contamination of BTs even in offshore waters and open seas on a global scale. Considering specific accumulation, Sex-, body length- differences and migration of skipjack tuna did not seem to affect BT concentrations, indicating rapid reflection of the pollution levels in seawater where and when they were collected. Skipjack tuna is a suitable bioindicator for monitoring the global distribution of BTs in offshore waters and open seas. High concentrations of BTs were observed in skipjack tuna from offshore waters around Japan, a highly developed and industrialized region (up to 400 ng/g wet weight). Moreover skipjack tuna collected from offshore waters around Asian developing countries also revealed the levels comparable to those in Japan (up to 270 ng/g wet weight) which may be due to the recent improvement in economic status in Asian developing countries. High percentages (almost 90%) of BTs in total tin ({sigma}Sn: sum of inorganic tin+organic tin) were found in the liver of skipjack tuna from offshore waters around Asian developing countries. This finding suggests that the anthropogenic BTs represent the major source of Sn accumulation in skipjack tuna from these regions.

  16. Skipjack tuna as a bioindicator of contamination by perfluorinated compounds in the oceans.

    Science.gov (United States)

    Hart, Kimberly; Kannan, Kurunthachalam; Tao, Lin; Takahashi, Shin; Tanabe, Shinsuke

    2008-09-15

    Perfluorinated chemicals (PFCs) have emerged as global environmental contaminants. Studies have reported the widespread occurrence of PFCs in biota from marine coastal waters and in remote polar regions. However, few studies have reported the distribution of PFCs in biota from offshore waters and open oceans. In this study, concentrations of nine PFCs were determined in the livers of 60 skipjack tuna (Katsuwonus pelamis) collected from offshore waters and the open ocean along the Pacific Rim, including the Sea of Japan, the East China Sea, the Indian Ocean, and the Western North Pacific Ocean, during 1997-1999. At least one of the nine PFCs was found in every tuna sample analyzed. Overall, perfluorooctanesulfonate (PFOS) and perfluoroundecanoic acid (PFUnDA) were the predominant compounds found in livers of tuna at concentrations of ocean locations, concentrations of PFUnDA were greater than the concentrations of PFOS. The profiles and concentrations of PFCs in tuna livers suggest that the sources in East Asia are dominated by long-chain perfluorocarboxylates, especially PFUnDA. High concentrations of PFUnDA in tuna may indicate a shift in sources of PFCs in East Asia. The spatial distribution of PFOS in skipjack tuna reflected the concentrations previously reported in seawater samples from the Pacific and Indian Oceans, suggesting that tuna are good bioindicators of pollution by PFOS. Despite its predominance in ocean waters, PFOA was rarely found in tuna livers, indicative of the low bioaccumulation potential of this compound. Our study establishes baseline concentrations of PFCs in skipjack tuna from the oceans of the Asia-Pacific region, enabling future temporal trend studies of PFCs in oceans.

  17. KAPASITAS PENANGKAPAN PANCING ULUR TUNA DI KEPULAUAN BANDA NEIRA

    Directory of Open Access Journals (Sweden)

    Baihaqi Baihaqi

    2016-04-01

    Fishing capacity is an approach to fishery management relating to restrictions on fishing effort capacity. The effort capacity is determined by several variables such as vessel  and engine sizes, the size of the nets, and fishing tool technology. Study of fishing capacity based fisheries management is an alternative approach to control the input factors that are not efficiently used in fishing effort. Through the research capacity, it is expected to know the level of technical efficiency of fishing tuna fishing fleet in the Banda Sea. Fishing capacity was examined using analysis technique Data Envelopment Analysis (DEA using a linear programming. The results show that the tuna line fisheries in the Banda Neira with single output approach (catch weight, was generally at the level of efficiency that is far under from the optimal level with the current input has exceeded the optimal capacity. To achieve the production potential of the third fishing grounds, reductions of the capacity of 33%, 42% and 45% for Hatta Island, Manukang Island and Rhum Island, respectively should be done.

  18. Treatment of tuna cooking juices by nano filtration

    International Nuclear Information System (INIS)

    Walha, K. a.; Ben Amar, R.; Bourseau, P.; Jaouen, P.

    2009-01-01

    Canned tuna is among the largest commercial canned fishery product in Tunisia. This industry rejects many aqueous effluents (washing, thawing, rinsing and cooking waters). Cooking juice represents 50 pour cent of the total effluent volume. It has a high organic load and a very high salt content. For consequence, discarding directly the effluent in the environment is not possible and need further treatment. However, the juice seems to contain interesting flavour compounds. In this work, a membrane process system consisting in nano filtration was used to reduce the pollution load and to concentrate flavour compounds of tuna cooking juice. The NF membrane tested in this work concentrate the organic matter since the retentions are high, starting at 74 pour cent for total circulation and increasing up to 85 pour cent for volume reduction factor (VRF) of 5. The membrane undergoes severe fouling, it can be effectively cleaned through a complete basic-acid washing cycle. The effect of three chemical reagents was studied for the regeneration of the fouled membrane. In the future, we will focus on the concentrates obtained by NF: sensory analysis with a panel of trained tasters and analysis of aromatic molecules should allow to value the quality of the flavouring concentrates.

  19. Atlantic Bluefin Tuna (Thunnus thynnus) Biometrics and Condition.

    Science.gov (United States)

    Rodriguez-Marin, Enrique; Ortiz, Mauricio; Ortiz de Urbina, José María; Quelle, Pablo; Walter, John; Abid, Noureddine; Addis, Piero; Alot, Enrique; Andrushchenko, Irene; Deguara, Simeon; Di Natale, Antonio; Gatt, Mark; Golet, Walter; Karakulak, Saadet; Kimoto, Ai; Macias, David; Saber, Samar; Santos, Miguel Neves; Zarrad, Rafik

    2015-01-01

    The compiled data for this study represents the first Atlantic and Mediterranean-wide effort to pool all available biometric data for Atlantic bluefin tuna (Thunnus thynnus) with the collaboration of many countries and scientific groups. Biometric relationships were based on an extensive sampling (over 140,000 fish sampled), covering most of the fishing areas for this species in the North Atlantic Ocean and Mediterranean Sea. Sensitivity analyses were carried out to evaluate the representativeness of sampling and explore the most adequate procedure to fit the weight-length relationship (WLR). The selected model for the WLRs by stock included standardized data series (common measurement types) weighted by the inverse variability. There was little difference between annual stock-specific round weight-straight fork length relationships, with an overall difference of 6% in weight. The predicted weight by month was estimated as an additional component in the exponent of the weight-length function. The analyses of monthly variations of fish condition by stock, maturity state and geographic area reflect annual cycles of spawning and feeding behavior. We update and improve upon the biometric relationships for bluefin currently used by the International Commission for the Conservation of Atlantic Tunas, by incorporating substantially larger datasets than ever previously compiled, providing complete documentation of sources and employing robust statistical fitting. WLRs and other conversion factors estimated in this study differ from the ones used in previous bluefin stock assessments.

  20. Population structure, migration, and diversifying selection in the Netherlands

    Science.gov (United States)

    Abdellaoui, Abdel; Hottenga, Jouke-Jan; Knijff, Peter de; Nivard, Michel G; Xiao, Xiangjun; Scheet, Paul; Brooks, Andrew; Ehli, Erik A; Hu, Yueshan; Davies, Gareth E; Hudziak, James J; Sullivan, Patrick F; van Beijsterveldt, Toos; Willemsen, Gonneke; de Geus, Eco J; Penninx, Brenda W J H; Boomsma, Dorret I

    2013-01-01

    Genetic variation in a population can be summarized through principal component analysis (PCA) on genome-wide data. PCs derived from such analyses are valuable for genetic association studies, where they can correct for population stratification. We investigated how to capture the genetic population structure in a well-characterized sample from the Netherlands and in a worldwide data set and examined whether (1) removing long-range linkage disequilibrium (LD) regions and LD-based SNP pruning significantly improves correlations between PCs and geography and (2) whether genetic differentiation may have been influenced by migration and/or selection. In the Netherlands, three PCs showed significant correlations with geography, distinguishing between: (1) North and South; (2) East and West; and (3) the middle-band and the rest of the country. The third PC only emerged with minimized LD, which also significantly increased correlations with geography for the other two PCs. In addition to geography, the Dutch North–South PC showed correlations with genome-wide homozygosity (r=0.245), which may reflect a serial-founder effect due to northwards migration, and also with height (♂: r=0.142, ♀: r=0.153). The divergence between subpopulations identified by PCs is partly driven by selection pressures. The first three PCs showed significant signals for diversifying selection (545 SNPs - the majority within 184 genes). The strongest signal was observed between North and South for the functional SNP in HERC2 that determines human blue/brown eye color. Thus, this study demonstrates how to increase ancestry signals in a relatively homogeneous population and how those signals can reveal evolutionary history. PMID:23531865

  1. Population structure of humpback whales in the western and central South Pacific Ocean as determined by vocal exchange among populations.

    Science.gov (United States)

    Garland, Ellen C; Goldizen, Anne W; Lilley, Matthew S; Rekdahl, Melinda L; Garrigue, Claire; Constantine, Rochelle; Hauser, Nan Daeschler; Poole, M Michael; Robbins, Jooke; Noad, Michael J

    2015-08-01

    For cetaceans, population structure is traditionally determined by molecular genetics or photographically identified individuals. Acoustic data, however, has provided information on movement and population structure with less effort and cost than traditional methods in an array of taxa. Male humpback whales (Megaptera novaeangliae) produce a continually evolving vocal sexual display, or song, that is similar among all males in a population. The rapid cultural transmission (the transfer of information or behavior between conspecifics through social learning) of different versions of this display between distinct but interconnected populations in the western and central South Pacific region presents a unique way to investigate population structure based on the movement dynamics of a song (acoustic) display. Using 11 years of data, we investigated an acoustically based population structure for the region by comparing stereotyped song sequences among populations and years. We used the Levenshtein distance technique to group previously defined populations into (vocally based) clusters based on the overall similarity of their song display in space and time. We identified the following distinct vocal clusters: western cluster, 1 population off eastern Australia; central cluster, populations around New Caledonia, Tonga, and American Samoa; and eastern region, either a single cluster or 2 clusters, one around the Cook Islands and the other off French Polynesia. These results are consistent with the hypothesis that each breeding aggregation represents a distinct population (each occupied a single, terminal node) in a metapopulation, similar to the current understanding of population structure based on genetic and photo-identification studies. However, the central vocal cluster had higher levels of song-sharing among populations than the other clusters, indicating that levels of vocal connectivity varied within the region. Our results demonstrate the utility and value of

  2. Effects of demographic structure on key properties of stochastic density-independent population dynamics.

    Science.gov (United States)

    Vindenes, Yngvild; Sæther, Bernt-Erik; Engen, Steinar

    2012-12-01

    The development of stochastic demography has largely been based on age structured populations, although other types of demographic structure, especially permanent and dynamic heterogeneity, are likely common in natural populations. The combination of stochasticity and demographic structure is a challenge for analyses of population dynamics and extinction risk, because the population structure will fluctuate around the stable structure and the population size shows transient fluctuations. However, by using a diffusion approximation for the total reproductive value, density-independent dynamics of structured populations can be described with only three population parameters: the expected population growth rate, the environmental variance and the demographic variance. These parameters depend on population structure via the state-specific vital rates and transition rates. Once they are found, the diffusion approximation represents a substantial reduction in model complexity. Here, we review and compare the key population parameters across a wide range of demographic structure, from the case of no structure to the most general case of dynamic heterogeneity, and for both discrete and continuous types. We focus on the demographic variance, but also show how environmental stochasticity can be included. This study brings together results from recent models, each considering a specific type of population structure, and places them in a general framework for structured populations. Comparison across different types of demographic structure reveals that the reproductive value is an essential concept for understanding how population structure affects stochastic dynamics and extinction risk. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Evolutionary game dynamics in a growing structured population

    Energy Technology Data Exchange (ETDEWEB)

    Poncela, Julia; Gomez-Gardenes, Jesus; Moreno, Yamir [Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, E-50009 Zaragoza (Spain); Traulsen, Arne [Emmy-Noether Group for Evolutionary Dynamics, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306 Ploen (Germany)], E-mail: traulsen@evolbio.mpg.de

    2009-08-15

    We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful in the past. The latter depends on the dynamics of strategies in the game, which we implement following the so-called Fermi rule such that the limits of weak and strong strategy selection can be explored. Our framework allows to address general evolutionary games. With only two parameters describing the preferential attachment and the intensity of selection, we describe a wide range of network structures and evolutionary scenarios. Our results show that even for moderate payoff preferential attachment, over represented hubs arise. Interestingly, we find that while the networks are growing, high levels of cooperation are attained, but the same network structure does not promote cooperation as a static network. Therefore, the mechanism of payoff preferential attachment is different to those usually invoked to explain the promotion of cooperation in static, already-grown networks.

  4. Evolutionary game dynamics in a growing structured population

    International Nuclear Information System (INIS)

    Poncela, Julia; Gomez-Gardenes, Jesus; Moreno, Yamir; Traulsen, Arne

    2009-01-01

    We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful in the past. The latter depends on the dynamics of strategies in the game, which we implement following the so-called Fermi rule such that the limits of weak and strong strategy selection can be explored. Our framework allows to address general evolutionary games. With only two parameters describing the preferential attachment and the intensity of selection, we describe a wide range of network structures and evolutionary scenarios. Our results show that even for moderate payoff preferential attachment, over represented hubs arise. Interestingly, we find that while the networks are growing, high levels of cooperation are attained, but the same network structure does not promote cooperation as a static network. Therefore, the mechanism of payoff preferential attachment is different to those usually invoked to explain the promotion of cooperation in static, already-grown networks.

  5. Discrimination of juvenile yellowfin (Thunnus albacares and bigeye (T. obesus Tunas using mitochondrial DNA control region and liver morphology.

    Directory of Open Access Journals (Sweden)

    Ivane R Pedrosa-Gerasmio

    Full Text Available Yellowfin tuna, Thunnus albacares (Bonnaterre, 1788 and bigeye tuna, Thunnus obesus (Lowe, 1839 are two of the most economically important tuna species in the world. However, identification of their juveniles, especially at sizes less than 40 cm, is very difficult, often leading to misidentification and miscalculation of their catch estimates. Here, we applied the mitochondrial DNA control region D-loop, a recently validated genetic marker used for identifying tuna species (Genus Thunnus, to discriminate juvenile tunas caught by purse seine and ringnet sets around fish aggregating devices (FADs off the Southern Iloilo Peninsula in Central Philippines. We checked individual identifications using the Neighbor-Joining Method and compared results with morphometric analyses and the liver phenotype. We tested 48 specimens ranging from 13 to 31 cm fork length. Morpho-meristic analyses suggested that 12 specimens (25% were bigeye tuna and 36 specimens (75% were yellowfin tuna. In contrast, the genetic and liver analyses both showed that 5 specimens (10% were bigeye tuna and 43 (90% yellowfin tuna. This suggests that misidentification can occur even with highly stringent morpho-meristic characters and that the mtDNA control region and liver phenotype are excellent markers to discriminate juveniles of yellowfin and bigeye tunas.

  6. Population structure of humpback whales in the western and central South Pacific Ocean as determined by vocal exchange among populations

    OpenAIRE

    Garland, E.C.; Goldizen, A.W.; Lilley, M.S.; Rekdahl, M.L.; Garrigue, Claire; Constantine, R.; Hauser, N.D.; Poole, M.M.; Robbins, J.; Noad, M.J.

    2015-01-01

    For cetaceans, population structure is traditionally determined by molecular genetics or photographically identified individuals. Acoustic data, however, has provided information on movement and population structure with less effort and cost than traditional methods in an array of taxa. Male humpback whales (Megaptera novaeangliae) produce a continually evolving vocal sexual display, or song, that is similar among all males in a population. The rapid cultural transmission (the transfer of inf...

  7. Dispersal and population structure of a New World predator, the army ant Eciton burchellii

    DEFF Research Database (Denmark)

    Berghoff, S M; Kronauer, D J C; Edwards, K J

    2008-01-01

    barriers, which might have severe impacts on population structure and lead to population decline. Using nuclear microsatellite markers and mitochondrial sequences, we investigated genetic differentiation in a fragmented population in the Panama Canal area. While nuclear markers showed little...

  8. Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand.

    Science.gov (United States)

    Mohan, Vathsala; Stevenson, Mark; Marshall, Jonathan; Fearnhead, Paul; Holland, Barbara R; Hotter, Grant; French, Nigel P

    2013-08-01

    A repeated cross-sectional study was conducted to determine the prevalence of Campylobacter spp. and the population structure of C. jejuni in European starlings and ducks cohabiting multiple public access sites in an urban area of New Zealand. The country's geographical isolation and relatively recent history of introduction of wild bird species, including the European starling and mallard duck, create an ideal setting to explore the impact of geographical separation on the population biology of C. jejuni, as well as potential public health implications. A total of 716 starling and 720 duck fecal samples were collected and screened for C. jejuni over a 12 month period. This study combined molecular genotyping, population genetics and epidemiological modeling and revealed: (i) higher Campylobacter spp. isolation in starlings (46%) compared with ducks (30%), but similar isolation of C. jejuni in ducks (23%) and starlings (21%), (ii) significant associations between the isolation of Campylobacter spp. and host species, sampling location and time of year using logistic regression, (iii) evidence of population differentiation, as indicated by FST , and host-genotype association with clonal complexes CC ST-177 and CC ST-682 associated with starlings, and clonal complexes CC ST-1034, CC ST-692, and CC ST-1332 associated with ducks, and (iv) greater genetic diversity and genotype richness in ducks compared with starlings. These findings provide evidence that host-associated genotypes, such as the starling-associated ST-177 and ST-682, represent lineages that were introduced with the host species in the 19th century. The isolation of sequence types associated with human disease in New Zealand indicate that wild ducks and starlings need to be considered as a potential public health risk, particularly in urban areas. © 2013 The Authors. Microbiology Open published by John Wiley & Sons Ltd.

  9. Toxoplasma and Africa: One Parasite, Two Opposite Population Structures.

    Science.gov (United States)

    Galal, Lokman; Ajzenberg, Daniel; Hamidović, Azra; Durieux, Marie-Fleur; Dardé, Marie-Laure; Mercier, Aurélien

    2018-02-01

    Exploring the genetic diversity of Toxoplasma gondii is essential for an understanding of its worldwide distribution and the determinants of its evolution. Africa remains one of the least studied areas of the world regarding T. gondii genetic diversity. This review has compiled published data on T. gondii strains from Africa to generate a comprehensive map of their continent-wide geographical distribution. The emerging picture about T. gondii strain distribution in Africa suggests a geographical separation of the parasite populations across the continent. We discuss the potential role of a number of factors in shaping this structure. We finally suggest the next steps towards a better understanding of Toxoplasma epidemiology in Africa in light of the strains circulating on this continent. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Cognitive and brain structural changes in a lung cancer population.

    Science.gov (United States)

    Simó, Marta; Root, James C; Vaquero, Lucía; Ripollés, Pablo; Jové, Josep; Ahles, Tim; Navarro, Arturo; Cardenal, Felipe; Bruna, Jordi; Rodríguez-Fornells, Antoni

    2015-01-01

    No study has examined structural brain changes specifically associated with chemotherapy in a lung cancer population. The aim of this cross-sectional study was to assess differences in brain structure between small-cell lung cancer patients (C+) following chemotherapy, non-small-cell lung cancer patients (C-) before chemotherapy and healthy controls (HC). Twenty-eight small-cell lung cancer patients underwent a neuropsychological assessment and a structural magnetic resonance imaging, including T1-weighted and diffusion tensor imaging to examine gray matter density and white matter (WM) integrity, respectively, 1 month following completion of platinum-based chemotherapy. This group was compared with 20 age and education-matched non-small-cell lung cancer patients before receiving chemotherapy and 20 HC. Both C+ and C- groups exhibited cognitive impairment compared with the HC group. The C+ group performed significantly worse than HC in verbal fluency and visuospatial subtests; C- performed significantly worse than both C+ and HC in verbal memory. Voxel-based morphometry analysis revealed lower gray matter density in the insula and parahippocampal gyrus bilaterally, and left anterior cingulate cortex in C+ compared with HC. Diffusion tensor imaging indices showed focal decreased WM integrity in left cingulum and bilateral inferior longitudinal fasciculus in the C+ group and more widespread decreased integrity in the C- group compared with the HC group. This study demonstrates that lung cancer patients exhibit cognitive impairment before and after chemotherapy. Before the treatment, C- showed verbal memory deficits as well as a widespread WM damage. Following treatment, the C+ group performed exhibited lower visuospatial and verbal fluency abilities, together with structural gray matter and WM differences in bilateral regions integrating the paralimbic system.

  11. Interactive diversity promotes the evolution of cooperation in structured populations

    International Nuclear Information System (INIS)

    Su, Qi; Li, Aming; Zhou, Lei; Wang, Long

    2016-01-01

    Evolutionary games on networks traditionally assume that each individual adopts an identical strategy to interact with all its neighbors in each generation. Considering the prevalent diversity of individual interactions in the real society, here we propose the concept of interactive diversity, which allows individuals to adopt different strategies against different neighbors in each generation. We investigate the evolution of cooperation based on the edge dynamics rather than the traditional nodal dynamics in networked systems. The results show that, without invoking any other mechanisms, interactive diversity drives the frequency of cooperation to a high level for a wide range of parameters in both well-mixed and structured populations. Even in highly connected populations, cooperation still thrives. When interactive diversity and large topological heterogeneity are combined together, however, in the relaxed social dilemma, cooperation level is lower than that with just one of them, implying that the combination of many promotive factors may make a worse outcome. By an analytical approximation, we get the condition under which interactive diversity provides more advantages for cooperation than traditional evolutionary dynamics does. Numerical simulations validating the approximation are also presented. Our work provides a new line to explore the latent relation between the ubiquitous cooperation and individuals’ distinct responses in different interactions. The presented results suggest that interactive diversity should receive more attention in pursuing mechanisms fostering cooperation. (paper)

  12. Genetic population structure of muskellunge in the Great Lakes

    Science.gov (United States)

    Kapuscinski, Kevin L.; Sloss, Brian L.; Farrell, John M.

    2013-01-01

    We quantified genetic relationships among Muskellunge Esox masquinongy from 15 locations in the Great Lakes to determine the extent and distribution of measurable population structure and to identify appropriate spatial scales for fishery management and genetic conservation. We hypothesized that Muskellunge from each area represented genetically distinct populations, which would be evident from analyses of genotype data. A total of 691 Muskellunge were sampled (n = 10–127/site) and genetic data were collected at 13 microsatellite loci. Results from a suite of analyses (including pairwise genetic differentiation, Bayesian admixture prediction, analysis of molecular variance, and tests of isolation by distance) indicated the presence of nine distinct genetic groups, including two that were approximately 50 km apart. Geographic proximity and low habitat complexity seemed to facilitate genetic similarity among areas, whereas Muskellunge from areas of greater habitat heterogeneity exhibited high differentiation. Muskellunge from most areas contained private alleles, and mean within-area genetic variation was similar to that reported for other freshwater fishes. Management programs aimed at conserving the broader diversity and long-term sustainability of Muskellunge could benefit by considering the genetically distinct groups as independent fisheries, and individual spawning and nursery habitats could subsequently be protected to conserve the evolutionary potential of Muskellunge.

  13. Evolutionary Dynamics of Collective Action in Structured Populations

    Science.gov (United States)

    Santos, Marta Daniela de Almeida

    The pervasiveness of cooperation in Nature is not easily explained. If evolution is characterized by competition and survival of the fittest, why should selfish individuals cooperate with each other? Evolutionary Game Theory (EGT) provides a suitable mathematical framework to study this problem, central to many areas of science. Conventionally, interactions between individuals are modeled in terms of one-shot, symmetric 2-Person Dilemmas of Cooperation, but many real-life situations involve decisions within groups with more than 2 individuals, which are best-dealt in the framework of N-Person games. In this Thesis, we investigate the evolutionary dynamics of two paradigmatic collective social dilemmas - the N-Person Prisoner's Dilemma (NPD) and the N-Person Snowdrift Game (NSG) on structured populations, modeled by networks with diverse topological properties. Cooperative strategies are just one example of the many traits that can be transmitted on social networks. Several recent studies based on empirical evidence from a medical database have suggested the existence of a 3 degrees of influence rule, according to which not only our "friends", but also our friends' friends, and our friends' friends' friends, have a non-trivial influence on our decisions. We investigate the degree of peer influence that emerges from the spread of cooperative strategies, opinions and diseases on populations with distinct underlying networks of contacts. Our results show that networks naturally entangle individuals into interactions of many-body nature and that for each network class considered different processes lead to identical degrees of influence. None

  14. Keragaman Spesies Ikan Tuna di Pasar Ikan Kedonganan Bali dengan Analisis Sekuen Kontrol Daerah Mitokondria DNA (SPECIES DIVERSITY OF TUNA FISH USING MITOCHONDRIAL DNA CONTROL REGION SEQUENCE ANALYSIS AT KEDONGANAN FISH MARKET

    Directory of Open Access Journals (Sweden)

    Daud Steven Triyomi Hariyanto

    2015-10-01

    Full Text Available Tuna is an export commodity which has very high economic value. However, some tuna speciesare threatened with extinction. The purpose of this study was to identify the tuna species that aresold in Kedonganan Fish Market. The research method was polymerase chain reaction technique(PCR using the marker sequence mitochondrial DNA control region. Samples were obtained fromthe Fish Market tuna Kedonganan, Kuta, Badung, Bali. The total number of samples are 28specimens. Sequence from each sample was obtained through sequencing techniques. Sequencesobtained were run in BLAST (Basic Local Alignment Search Tool and subsequently analyzed withMEGA 5 for species confirmation. Three species of tuna that are identified in the Kedonganan FishMarket is: Thunnus albacares, T. obesus, and Katsuwonus pelamis. All three species have highgenetic variation HD = 1. This study needed to be continued with more number of samples todetermine the species of tuna sold in Kedonganan Fish Market.

  15. The Southern Oscillation, Hypoxia, and the Eastern Pacific Tuna Fishery

    Science.gov (United States)

    Webster, D.; Kiefer, D.; Lam, C. H.; Harrison, D. P.; Armstrong, E. M.; Hinton, M.; Luo, L.

    2012-12-01

    The Eastern Pacific tuna fishery, which is one of the world's major fisheries, covers thousands of square kilometers. The vessels of this fishery are registered in more than 30 nations and largely target bigeye (Thunnus obesus), skipjack (Katsuwonus pelamis), and yellowfin (T. albacores) tuna. In both the Pelagic Habitat Analysis Module project, which is sponsored by NASA, and the Fishscape project, which is sponsored by NSF, we have attempted to define the habitat of the three species by matching a 50 year time series on fish catch and effort with oceanographic information obtained from satellite imagery and from a global circulation model. The fishery time series, which was provided by the Inter-American Tropical Tuna Commission, provided spatial maps of catch and effort at monthly time steps; the satellite imagery of the region consisted of sea surface temperature, chlorophyll, and height from GHRSST, SEAWiFS, and AVISO products, and the modeled flow field at selected depths was output from ECCO-92 simulations from 1992 to present. All information was integrated and analyzed within the EASy marine geographic information system. This GIS will also provides a home for the Fishscape spatial simulation model of the coupled dynamics of the ocean, fish, fleets, and markets. This model will then be applied to an assessment of the potential ecological and economic impacts of climate change, technological advances in fleet operations, and increases in fuel costs. We have determined by application of EOF analysis that the ECCO-2 simulation of sea surface height fits well with that of AVISO imagery; thus, if driven properly by predictions of future air-sea exchange, the model should provide good estimates of circulation patterns. We have also found that strong El Nino events lead to strong recruitment of all three species and strong La Nina events lead to weak recruitment. Finally, we have found that the general spatial distribution of the Eastern Pacific fishing grounds

  16. SWFSC/MMTD/ETP: Dolphin-Tuna Tracking Studies (DTTS) 1992-1993

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This research was designed to better understand the nature of the dolphin-tuna bond in the eastern tropical Pacific Ocean. In this study, researchers attempted to...

  17. 75 FR 33531 - Atlantic Highly Migratory Species; Atlantic Bluefin Tuna Fisheries

    Science.gov (United States)

    2010-06-14

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration 50 CFR Part 635 RIN 0648-XW79 Atlantic Highly Migratory Species; Atlantic Bluefin Tuna Fisheries AGENCY: National Marine..., recent Large Pelagics Survey estimates indicate that charter/headboat BFT landings constitute...

  18. Population Structure and Genomic Breed Composition in an Angus-Brahman Crossbred Cattle Population.

    Science.gov (United States)

    Gobena, Mesfin; Elzo, Mauricio A; Mateescu, Raluca G

    2018-01-01

    Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus-Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA) and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus-Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage-indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals. This was most likely due

  19. Population Structure and Genomic Breed Composition in an Angus–Brahman Crossbred Cattle Population

    Directory of Open Access Journals (Sweden)

    Mesfin Gobena

    2018-03-01

    Full Text Available Crossbreeding is a common strategy used in tropical and subtropical regions to enhance beef production, and having accurate knowledge of breed composition is essential for the success of a crossbreeding program. Although pedigree records have been traditionally used to obtain the breed composition of crossbred cattle, the accuracy of pedigree-based breed composition can be reduced by inaccurate and/or incomplete records and Mendelian sampling. Breed composition estimation from genomic data has multiple advantages including higher accuracy without being affected by missing, incomplete, or inaccurate records and the ability to be used as independent authentication of breed in breed-labeled beef products. The present study was conducted with 676 Angus–Brahman crossbred cattle with genotype and pedigree information to evaluate the feasibility and accuracy of using genomic data to determine breed composition. We used genomic data in parametric and non-parametric methods to detect population structure due to differences in breed composition while accounting for the confounding effect of close familial relationships. By applying principal component analysis (PCA and the maximum likelihood method of ADMIXTURE to genomic data, it was possible to successfully characterize population structure resulting from heterogeneous breed ancestry, while accounting for close familial relationships. PCA results offered additional insight into the different hierarchies of genetic variation structuring. The first principal component was strongly correlated with Angus–Brahman proportions, and the second represented variation within animals that have a relatively more extended Brangus lineage—indicating the presence of a distinct pattern of genetic variation in these cattle. Although there was strong agreement between breed proportions estimated from pedigree and genetic information, there were significant discrepancies between these two methods for certain animals

  20. Coexistence of structured populations with size-based prey selection

    DEFF Research Database (Denmark)

    Hartvig, Martin; Andersen, Ken Haste

    2013-01-01

    Abstract Species with a large adult-offspring size ratio and a preferred predator–prey mass ratio undergo ontogenetic trophic niche shift(s) throughout life. Trophic interactions between such species vary throughout life, resulting in different species-level interaction motifs depending on the ma......Abstract Species with a large adult-offspring size ratio and a preferred predator–prey mass ratio undergo ontogenetic trophic niche shift(s) throughout life. Trophic interactions between such species vary throughout life, resulting in different species-level interaction motifs depending...... on the maximum adult sizes and population size distributions. We explore the assembly and potential for coexistence of small communities where all species experience ontogenetic trophic niche shifts. The life-history of each species is described by a physiologically structured model and species identity...... there is a large scope for coexistence of two species, the scope for coexistence of three species is limited and we conclude that further trait differentiation is required for coexistence of more species-rich size-structured communities....

  1. A population on the edge: genetic diversity and population structure of the world's northernmost harbour seals (Phoca vitulina)

    DEFF Research Database (Denmark)

    Andersen, Liselotte Wesley; Lydersen, Christian; Frie, Anne Kirstine

    2011-01-01

    insight into consequences of population declines in a broader conservation context. The harbour seal population at Svalbard is the world's northernmost harbour seal population. Nothing is known about the genetic diversity, distinctiveness or origin of this small, marginalized mammalian population. Thus......  It is crucial to examine the genetic diversity and structure of small, isolated populations, especially those at the edge of their distribution range, because they are vulnerable to stochastic processes if genetic diversity is low and isolation level high, and because such populations provide...... microsatellites and variation in the D-loop. Each of the four locations was a genetically distinct population. The Svalbard population was highly genetically distinct, had reduced genetic diversity, received limited gene flow, had a rather low effective population size and showed an indication of having...

  2. Tuna Park Shopping Centre A comparative study of marketing communication tools

    OpenAIRE

    Wongrattanavichit, Teewin; Wang, Haiyan

    2008-01-01

    Date: 2008 June 08 Course: Master thesis Authors: Haiyan Wang, Teewin Wongrattanavichit Tutor: Jan Löwstedt Title: The study of marketing communication effectiveness and customer perception of Tuna Park shopping centre Introduction: The research about the effectiveness of marketing communication tool and customer perception was studied in Tuna Park shopping center, Eskilstuna. The marketing strategy and objective was to compare with the results from the questionnaire in order to measure the e...

  3. Precooking as a Control for Histamine Formation during the Processing of Tuna: An Industrial Process Validation.

    Science.gov (United States)

    Adams, Farzana; Nolte, Fred; Colton, James; De Beer, John; Weddig, Lisa

    2018-02-23

    An experiment to validate the precooking of tuna as a control for histamine formation was carried out at a commercial tuna factory in Fiji. Albacore tuna ( Thunnus alalunga) were brought on board long-line catcher vessels alive, immediately chilled but never frozen, and delivered to an on-shore facility within 3 to 13 days. These fish were then allowed to spoil at 25 to 30°C for 21 to 25 h to induce high levels of histamine (>50 ppm), as a simulation of "worst-case" postharvest conditions, and subsequently frozen. These spoiled fish later were thawed normally and then precooked at a commercial tuna processing facility to a target maximum core temperature of 60°C. These tuna were then held at ambient temperatures of 19 to 37°C for up to 30 h, and samples were collected every 6 h for histamine analysis. After precooking, no further histamine formation was observed for 12 to 18 h, indicating that a conservative minimum core temperature of 60°C pauses subsequent histamine formation for 12 to 18 h. Using the maximum core temperature of 60°C provided a challenge study to validate a recommended minimum core temperature of 60°C, and 12 to 18 h was sufficient to convert precooked tuna into frozen loins or canned tuna. This industrial-scale process validation study provides support at a high confidence level for the preventive histamine control associated with precooking. This study was conducted with tuna deliberately allowed to spoil to induce high concentrations of histamine and histamine-forming capacity and to fail standard organoleptic evaluations, and the critical limits for precooking were validated. Thus, these limits can be used in a hazard analysis critical control point plan in which precooking is identified as a critical control point.

  4. The Genetic Structure of Wild Orobanche cumana Wallr. (Orobanchaceae Populations in Eastern Bulgaria Reflects Introgressions from Weedy Populations

    Directory of Open Access Journals (Sweden)

    Rocío Pineda-Martos

    2014-01-01

    Full Text Available Orobanche cumana is a holoparasitic plant naturally distributed from central Asia to south-eastern Europe, where it parasitizes wild Asteraceae species. It is also an important parasitic weed of sunflower crops. The objective of this research was to investigate genetic diversity, population structure, and virulence on sunflower of O. cumana populations parasitizing wild plants in eastern Bulgaria. Fresh tissue of eight O. cumana populations and mature seeds of four of them were collected in situ on wild hosts. Genetic diversity and population structure were studied with SSR markers and compared to weedy populations. Two main gene pools were identified in Bulgarian populations, with most of the populations having intermediate characteristics. Cross-inoculation experiments revealed that O. cumana populations collected on wild species possessed similar ability to parasitize sunflower to those collected on sunflower. The results were explained on the basis of an effective genetic exchange between populations parasitizing sunflower crops and those parasitizing wild species. The occurrence of bidirectional gene flow may have an impact on wild populations, as new physiological races continuously emerge in weedy populations. Also, genetic variability of wild populations may favour the ability of weedy populations to overcome sunflower resistance mechanisms.

  5. The Genetic Structure of Wild Orobanche cumana Wallr. (Orobanchaceae) Populations in Eastern Bulgaria Reflects Introgressions from Weedy Populations

    Science.gov (United States)

    Pineda-Martos, Rocío; Pujadas-Salvà, Antonio J.; Fernández-Martínez, José M.; Stoyanov, Kiril; Pérez-Vich, Begoña

    2014-01-01

    Orobanche cumana is a holoparasitic plant naturally distributed from central Asia to south-eastern Europe, where it parasitizes wild Asteraceae species. It is also an important parasitic weed of sunflower crops. The objective of this research was to investigate genetic diversity, population structure, and virulence on sunflower of O. cumana populations parasitizing wild plants in eastern Bulgaria. Fresh tissue of eight O. cumana populations and mature seeds of four of them were collected in situ on wild hosts. Genetic diversity and population structure were studied with SSR markers and compared to weedy populations. Two main gene pools were identified in Bulgarian populations, with most of the populations having intermediate characteristics. Cross-inoculation experiments revealed that O. cumana populations collected on wild species possessed similar ability to parasitize sunflower to those collected on sunflower. The results were explained on the basis of an effective genetic exchange between populations parasitizing sunflower crops and those parasitizing wild species. The occurrence of bidirectional gene flow may have an impact on wild populations, as new physiological races continuously emerge in weedy populations. Also, genetic variability of wild populations may favour the ability of weedy populations to overcome sunflower resistance mechanisms. PMID:25143963

  6. Banning is not enough: The complexities of oceanic shark management by tuna regional fisheries management organizations

    Directory of Open Access Journals (Sweden)

    Mariana Travassos Tolotti

    2015-07-01

    Full Text Available Recently, declining populations of several pelagic shark species have led to global conservation concerns surrounding this group. As a result, a series of species-specific banning measures have been implemented by Regional Fishery Management Organizations (RFMOs in charge of tuna fisheries, which include retention bans, finning bans and trading bans. There are both positive and negative aspects to most management measures, but generally, the positive aspects outweigh the negatives, ensuring the measure is beneficial to the resource and its users in the long term. Banning measures are a good first step towards the conservation of pelagic shark species, especially since they improve conservation awareness among fishers, managers and the public. Measures that impose total bans, however, can lead to negative impacts that may jeopardize the populations they were intended to protect. The majority of pelagic shark catches are incidental and most sharks die before they reach the vessel or after they are released. The legislation set out by RFMOs only prevents retention but not the actual capture or the mortality that may occur as a result. Managers should be fully aware that the development and implementation of mitigation measures are critical for a more effective conservation strategy.

  7. Stable isotopes indicate population structuring in the southwest Atlantic population of right whales (Eubalaena australis.

    Directory of Open Access Journals (Sweden)

    Morgana Vighi

    Full Text Available From the early 17th century to the 1970s southern right whales, Eubalaena australis, were subject to intense exploitation along the Atlantic coast of South America. Catches along this coast recorded by whalers originally formed a continuum from Brazil to Tierra del Fuego. Nevertheless, the recovery of the population has apparently occurred fragmentarily, and with two main areas of concentration, one off southern Brazil (Santa Catarina and another off central Argentina (Peninsula Valdés. This pattern suggests some level of heterogeneity amongst the population, which is apparently contradicted by records that traced individuals moving throughout the whole geographical extension covered by the species in the Southwest Atlantic. To test the hypothesis of the potential occurrence of discrete subpopulations exploiting specific habitats, we investigated N, C and O isotopic values in 125 bone samples obtained from whaling factories operating in the early 1970s in southern Brazil (n=72 and from contemporary and more recent strandings occurring in central Argentina (n=53. Results indicated significant differences between the two sampling areas, being δ13C and δ18O values significantly higher in samples from southern Brazil than in those from central Argentina. This variation was consistent with isotopic baselines from the two areas, indicating the occurrence of some level of structure in the Southwest Atlantic right whale population and equally that whales more likely feed in areas commonly thought to exclusively serve as nursing grounds. Results aim at reconsidering of the units currently used in the management of the southern right whale in the Southwest Atlantic Ocean. In the context of the current die-off affecting the species in Peninsula Valdés, these results also highlight the necessity to better understand movements of individuals and precisely identify their feeding areas.

  8. CULTURAL MEMORY OF VICTORY OF LAS TUNAS CITY' LODGES FROM 1930 TO 1945 / MEMORIA CULTURAL DE LAS LOGIAS DE VICTORIA DE LAS TUNAS 1930-1945

    Directory of Open Access Journals (Sweden)

    Milena Medina Pérez

    2012-09-01

    Full Text Available The cultural memory of the lodges of Victoria de Las Tunas (1930-1945, it constitutes the topic of the present investigation. The thematic of the lodges has been approached for studious and investigating, not alone of the town but of several parts of the world. Still when these studies exist, the related with the cultural memory of the lodges of the territory, is in the pages of the documents of the time that which leaves to the light starting from this investigation, to show yesterday's Tunas, rich in histories and anecdotes. In the town during the investigated period the lodges Masonic Children of Hiram existed, Vicente García No. 27, the young AJEF, the lodge Teosófica Esperanza, the Children of East No. 54 of the Odd Independent Fellows, the lodge Cucalambé of the Odd United Fellows and the lodge Victoria de Las Tunas No. 78 of the Luz's Order Gentlemen.

  9. Quality Changes of Light Flesh Tuna at Water of Tomini Bay, Gorontalo Province

    Directory of Open Access Journals (Sweden)

    Wila Rumina Nento

    2015-01-01

    Full Text Available Tuna is one of the mainstay fisheries commodities that involve many of the ordinary fishermen. The handling usually still not follows the principles of good handling that causing the poor quality as the result.The aims of this research were to analyze and to determine the quality of tuna meat (the abdominal wall, dorsal fin, and caudal fin. Raw material yellowfin tuna meat prepared for the light, the meat section of the abdominal wall, dorsal fin, and caudal fin. The result of organoleptic analysis showed that the tuna meat was above the minimum value for the criteria of fresh fish. The result of TVB analysis showed that the meat on the caudal fin had the highest value and significantly different with the other, but still exist on the safe limits and on the fresh category. For the result of analysis in histamine, it shown that at the fourth hour the meat at the dorsal fin had the histamine content which were above the minimum that have been recommended. For the result of analysis in peroxide number, it shown that the tuna meat did not sustain the fat damage until the fourth hour after the catching process. And for the result of analysis in TPC, it showed that at the fourth hour the tuna meat on the pectoral fin had the highest number of total colony and significantly different with the other.Keywords: handling, histamine, light flesh, microbiology, yellowfin

  10. Validation of the method spectrophotometer in the histamine determination in fresh tuna (Thunnus Tunna)

    International Nuclear Information System (INIS)

    Chacon Silva, F.

    1998-01-01

    The objective of this study was to validate the spectrophotometer method described by Bateman et al. (1994) for the histamine determination in fresh tuna (Thunnus Tunna) and to evaluate the histamine concentration in samples of fresh tuna. To fulfill the recently exposed objectives, the figures of merit were determined like they are it: recovery limits of detection, sensibility and repetitive of the method spectrophotometry and applied the analysis at twenty samples of fresh tuna for copy of the Metropolitan area and three sample like reference of fresh tuna stored 4 degree centigrade by 15 days. The histamine recovery you determines enriching seven ours of fresh tuna with histamine to two levels different 0.613 mg/L and 2.21 mg/L. three samples were left without enriching and you subtract the average to the native histamine. You determines the one it limits of detection using the standard deviation to three levels of concentration of histamine 1.37 mg/L, 2.22 mg/L and 3.22 mg/L, the minimum quantity of hi stamina that you can determine for the method spectrophotometry settling down. The repetitive you determines using the standard deviation for 100 among the average of the histamine values, in seven you replies independent of the same sample. You determines the histamine content, in the fresh tuna Thunnus Tunna of the expends of the Metropolitan Area and in samples of reference stored 4 degrees centigrade by 15 days [es

  11. Characterization of the Boundary Layer on Full-Scale Bluefin Tuna

    Science.gov (United States)

    Amaral, Brian; Cipolla, Kimberly; Henoch, Charles

    2014-11-01

    The physics that enable tuna to cross large expanses of ocean while feeding and avoiding predators is not presently understood, and could involve complex control of turbulent boundary layer transition and drag reduction. Typical swimming speeds of Bluefin tuna are 1-2 m/s, but can be higher during strong accelerations. The goal of this work is to experimentally determine the approximate lateral location at which transition to turbulence occurs on the tuna for various speeds. The question is whether laminar flow or an advanced propulsion mechanism (or both) allows them to swim at high speeds. Uncertainties include the surface roughness of the skin, local favorable and adverse pressure gradients, and discontinuities such as the open mouth or juncture at the fins. Historically, much of the fluid mechanics work in the area of fish locomotion has focused on vortex shedding issues rather than the boundary layer. Here, the focus is obtaining information on the boundary layer characteristics of a rigid tuna model. A full scale model of a Pacific Bluefin tuna was fabricated using a mold made from an actual deceased tuna, preserving the surface features and details of the appendages. The model was instrumented with 32 wall pressure sensors and experiments performed in a tow tank. Results from flow visualization, drag and wall pressure measurements over a range of speeds and varying angles of attack will be presented.

  12. Predation and physical environment structure the density and population size structure of zebra mussels

    OpenAIRE

    Naddafi, Rahmat; Pettersson, Kurt; Eklöv, Peter

    2010-01-01

    The zebra mussel (Dreissena polymorpha) provides one example of successful invaders in novel environments. However, little attention has been devoted to exploring the factors regulating zebra mussel density and population size structure at the local scale. We tested effects of physicochemical factors and fish predation on the density of zebra mussels at several sites and between years in a natural lake. Water depth and roach (Rutilus rutilus) density were the most important variables affectin...

  13. Plasmodium vivax Population Structure and Transmission Dynamics in Sabah Malaysia

    Science.gov (United States)

    Abdullah, Noor Rain; Barber, Bridget E.; William, Timothy; Norahmad, Nor Azrina; Satsu, Umi Rubiah; Muniandy, Prem Kumar; Ismail, Zakiah; Grigg, Matthew J.; Jelip, Jenarun; Piera, Kim; von Seidlein, Lorenz; Yeo, Tsin W.; Anstey, Nicholas M.; Price, Ric N.; Auburn, Sarah

    2013-01-01

    Despite significant progress in the control of malaria in Malaysia, the complex transmission dynamics of P. vivax continue to challenge national efforts to achieve elimination. To assess the impact of ongoing interventions on P. vivax transmission dynamics in Sabah, we genotyped 9 short tandem repeat markers in a total of 97 isolates (8 recurrences) from across Sabah, with a focus on two districts, Kota Marudu (KM, n = 24) and Kota Kinabalu (KK, n = 21), over a 2 year period. STRUCTURE analysis on the Sabah-wide dataset demonstrated multiple sub-populations. Significant differentiation (F ST  = 0.243) was observed between KM and KK, located just 130 Km apart. Consistent with low endemic transmission, infection complexity was modest in both KM (mean MOI  = 1.38) and KK (mean MOI  = 1.19). However, population diversity remained moderate (H E  = 0.583 in KM and H E  = 0.667 in KK). Temporal trends revealed clonal expansions reflecting epidemic transmission dynamics. The haplotypes of these isolates declined in frequency over time, but persisted at low frequency throughout the study duration. A diverse array of low frequency isolates were detected in both KM and KK, some likely reflecting remnants of previous expansions. In accordance with clonal expansions, high levels of Linkage Disequilibrium (I A S >0.5 [P<0.0001] in KK and KM) declined sharply when identical haplotypes were represented once (I A S  = 0.07 [P = 0.0076] in KM, and I A S = -0.003 [P = 0.606] in KK). All 8 recurrences, likely to be relapses, were homologous to the prior infection. These recurrences may promote the persistence of parasite lineages, sustaining local diversity. In summary, Sabah's shrinking P. vivax population appears to have rendered this low endemic setting vulnerable to epidemic expansions. Migration may play an important role in the introduction of new parasite strains leading to epidemic expansions, with important implications for malaria

  14. Addressing wild turkey population declines using structured decision making

    Science.gov (United States)

    Robinson, Kelly F.; Fuller, Angela K.; Schiavone, Michael V.; Swift, Bryan L.; Diefenbach, Duane R.; Siemer, William F.; Decker, Daniel J.

    2017-01-01

    We present a case study from New York, USA, of the use of structured decision making (SDM) to identify fall turkey harvest regulations that best meet stakeholder objectives, in light of recent apparent declines in abundance of wild turkeys in the northeastern United States. We used the SDM framework to incorporate the multiple objectives associated with turkey hunting, stakeholder desires, and region-specific ecological and environmental factors that could influence fall harvest. We identified a set of 4 fall harvest regulations, composed of different season lengths and bag limits, and evaluated their relative achievement of the objectives. We used a stochastic turkey population model, statistical modeling, and expert elicitation to evaluate the consequences of each harvest regulation on each of the objectives. We conducted a statewide mail survey of fall turkey hunters in New York to gather the necessary information to evaluate tradeoffs among multiple objectives associated with hunter satisfaction. The optimal fall harvest regulation was a 2-week season and allowed for the harvest of 1 bird/hunter. This regulation was the most conservative of those evaluated, reflecting the concerns about recent declines in turkey abundance among agency wildlife biologists and the hunting public. Depending on the region of the state, the 2-week, 1-bird regulation was predicted to result in 7–32% more turkeys on the landscape after 5 years. The SDM process provided a transparent framework for setting fall turkey harvest regulations and reduced potential stakeholder conflict by explicitly taking the multiple objectives of different stakeholder groups into account.

  15. DAYA SAING EKSPOR TUNA KALENG INDONESIA DI UNI EROPA TAHUN 2003-2013

    Directory of Open Access Journals (Sweden)

    Umar Wahono

    2017-06-01

    Full Text Available Perbedaan tarif yang diberikan antara Indonesia yang lebih tinggi sebesar 20.5% dibandingkan dengan negara pesaing utamanya yang tergabung dalang Africa, Caribbean, Pasific (ACP Countries dengan pelayanan tarif impor hingga 0% ke pasar Uni Eropa (UE. Keadaan ini mampu menyebabkan menghilangnya distorsi perbedaan harga sesungguhnya yang seharusnya menjadi keuntungan lebih atas keunggulan komparatif yang dimiliki. Hal ini mampu melemahkan daya saing komoditi ekspor akibat dampak kenaikan harga terhadap tarif. Penelitian ini bertujuan untuk gambaran daya saing komoditas tuna kaleng Indonesia terhadap negara pesaingnya dipasar UE pada periode 2003-2013. Metode yang digunakan dalam penelitin ini adalah metode Revealed Comparative Advantage (RCA yang kemudian nilai RCA dikomparasikan tiap-tiap negara pengekspor utama tuna kaleng di pasar UE untuk melihat posisi daya saing relatifnya. Sedangkan untuk mendekomposisikan determinan pertumbuhan ekspor tuna kaleng Indonesia ke UE digunankan metode Constant Market Share (CMS. Hasil perhitungan nilai RCA tuna kaleng Indonesia periode 2003-2013 di pasar UE memiliki daya saing dengan rata-rata nilai RCA 4.27. Namun masih dibawah rata-rata nilai RCA negara ACP Countries. Perbedaan pelayanan tarif impor oleh UE untuk komoditas tuna kaleng Indonesia tidak berdampak terhadap penurunan daya saing. The difference between the rates given Indonesia which is higher by 20.5% compared to its main competitor countries that joined the mastermind Africa, Caribbean, Pacific (ACP Countries with service import tariffs to 0% to the European Union (EU. This situation is capable of causing the disappearance of the distortion of the true price difference should be more advantages over comparative advantage. It is capable of undermining the competitiveness of export commodities due to the impact of price increases on tariffs. This study aims to illustrate the competitiveness of commodities Indonesian canned tuna to the EU market of

  16. Using Genome-Wide SNPs to Detect Structure in High-Diversity and Low-Divergence Populations of Severely Impacted Eastern Tropical Pacific Spinner (Stenella longirostris And Pantropical Spotted Dolphins (S. attenuata

    Directory of Open Access Journals (Sweden)

    Matthew Steven Leslie

    2016-12-01

    Full Text Available Millions of spinner (Stenella longirostris and pantropical spotted dolphins (Stenella attenuata died since the 1960’s as bycatch in tuna nets in the eastern tropical Pacific Ocean. Despite three decades of protection, they show little-to-no sign of recovery (although recent fisheries-independent abundance estimates are not available. In efforts to establish biologically meaningful management boundaries for recovery, endemic subspecies and multiple stocks have been proposed. However, genetic differentiation among most of these units has been difficult to identify, possibly due to low statistical power stemming from large historical abundances, ongoing gene flow, and recent divergence. We tested for genetic structure at multiple hierarchical levels by analyzing the largest dataset to date brought to bear on these questions. Single nucleotide polymorphisms (SNPs were collected from nuclear DNA regions associated with the restriction enzyme site PstI from 72 spinner dolphins and 58 pantropical spotted dolphins using genotype-by-sequencing (GBS. Our results support the current subspecies for both species and indicate stock-level separation for Tres Marias spinner dolphins and the two offshore pantropical spotted dolphin stocks in this area. Although bycatch has been reduced a small fraction of pre-protection levels, incidental mortality continues to impact these populations. Our results are important for the ongoing management and recovery of these highly-impacted pelagic dolphins in the eastern tropical Pacific Ocean.

  17. The migration game in habitat network: the case of tuna

    DEFF Research Database (Denmark)

    Mariani, Patrizio; Krivan, Vlastimil; MacKenzie, Brian

    2016-01-01

    migration in direction of increasing fitness should lead to the ideal free distribution (IFD) which is the evolutionary stable strategy of the habitat selection game. We introduce a migration game which focuses on migrating dynamics leading to the IFD for age-structured populations and in time varying...

  18. The migration game in habitat network: the case of tuna

    Czech Academy of Sciences Publication Activity Database

    Mariani, P.; Křivan, Vlastimil; MacKenzie, B. R.; Mullon, C.

    2016-01-01

    Roč. 9, č. 2 (2016), s. 219-232 ISSN 1874-1738 Institutional support: RVO:60077344 Keywords : structured population * ideal free distribution * game theory Subject RIV: EH - Ecology, Behaviour Impact factor: 1.221, year: 2016 http://link.springer.com/article/10.1007%2Fs12080-015-0290-8

  19. JENIS, UKURAN DAN DAERAH PENANGKAPAN HIU THRESHER (FAMILI ALOPIIDAE YANG TERTANGKAP RAWAI TUNA DI SAMUDERA HINDIA

    Directory of Open Access Journals (Sweden)

    Agustinus Anung Widodo

    2016-03-01

    Full Text Available Sebagai anggota Indian Ocean Tuna Commision (IOTC Indonesia wajib mengadopsi isi Resolusi IOTC 10/12 yang mengatur pengelolaan sumberdaya ikan hiu thresher (famili Alopiidae. Secara spesifik Indonesia belum melaksanakan pengelolaan sumberdaya hiu thresher karena spesies tersebut belum mendapatkan perhatian serius. Tulisan ini bermaksud menyampaikan hasil penelitian tentang ikan hiu thresher (Famili Alopiidae yang tertangkap rawai tuna di Samudera Hindia berbasis di Cilacap. Data diperoleh dari kegiatan pengambilan contoh di pelabuhan tahun 2010, kegiatan observasi di atas kapal rawai tuna bulan Januari 2010 dan laporan statistik PPS Cilacap tahun 2006-2010. Hasil kajian menunjukkan bahwa: (a di perairan Indonesia ada dua spesies dari tiga spesies hiu thresher yang ada di dunia, yaitu hiu monyet atau pelagic thresher (Alopias pelagicus Nakamura 1935 dan hiu paitan atau bigeye thresher (A. superciliosus Lowe 1840. Satu spesies lainnya yang belum pernah ditemukan adalah thinfin thresher (A.vulpinus Bonnaterre1788.  Dilihat dari teknologi rawai tuna yang digunakan, daerah sebaran hiu thresher sama dengan tuna di Samudera Hindia, sehingga sulit untuk menghindari tidak tertangkapnya hiu thresher oleh rawai tuna. Jumlah dari jenis hiu monyet yang tertangkap rawai tuna di Samudera Hindia berkisar 0,1-0,6 % dan hiu paitan berkisar 0,1-1,3 % dari total tangkapan. Ukuran hiu thresher yang tertangkap rawai tuna umumnya ikan yang telah dewasa (berkisar 54-74% dan diduga telah mengalami pemijahan. Hampir semua bagian hiu thresher dimanfaatkan sebagai bahan pangan dan farmasi. Selain dipasarkan di dalam negeri, ikan hiu thresher juga diekspor terutama siripnya ke manca negara dan terbanyak ke China.   As a member of IOTC, Indonesia is obliged to implement all IOTC’s resolutions including resolution 10/12 on the conservation of thresher sharks (Family Alopiidae caught in association with fisheries in the IOTC area of competence. Indonsia has not

  20. Continental-scale assessment of genetic diversity and population structure in quaking aspen (Populus tremuloides)

    Science.gov (United States)

    Colin M. Callahan; Carol A. Rowe; Ronald J. Ryel; John D. Shaw; Michael D. Madritch; Karen E. Mock

    2013-01-01

    Aspen populations in the south-western portion of the range are consistent with expectations for a historically stable edge, with low within-population diversity, significant geographical population structuring, and little evidence of northward expansion. Structuring within the southwestern cluster may result from distinct gene pools separated during the Pleistocene...

  1. 15 CFR 50.10 - Fee structure for special population censuses.

    Science.gov (United States)

    2010-01-01

    ... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Fee structure for special population... § 50.10 Fee structure for special population censuses. The Bureau of the Census is authorized to conduct special population censuses at the request of and at the expense of the community concerned. To...

  2. Geographic population structure analysis of worldwide human populations infers their biogeographical origins

    Science.gov (United States)

    Elhaik, Eran; Tatarinova, Tatiana; Chebotarev, Dmitri; Piras, Ignazio S.; Maria Calò, Carla; De Montis, Antonella; Atzori, Manuela; Marini, Monica; Tofanelli, Sergio; Francalacci, Paolo; Pagani, Luca; Tyler-Smith, Chris; Xue, Yali; Cucca, Francesco; Schurr, Theodore G.; Gaieski, Jill B.; Melendez, Carlalynne; Vilar, Miguel G.; Owings, Amanda C.; Gómez, Rocío; Fujita, Ricardo; Santos, Fabrício R.; Comas, David; Balanovsky, Oleg; Balanovska, Elena; Zalloua, Pierre; Soodyall, Himla; Pitchappan, Ramasamy; GaneshPrasad, ArunKumar; Hammer, Michael; Matisoo-Smith, Lisa; Wells, R. Spencer; Acosta, Oscar; Adhikarla, Syama; Adler, Christina J.; Bertranpetit, Jaume; Clarke, Andrew C.; Cooper, Alan; Der Sarkissian, Clio S. I.; Haak, Wolfgang; Haber, Marc; Jin, Li; Kaplan, Matthew E.; Li, Hui; Li, Shilin; Martínez-Cruz, Begoña; Merchant, Nirav C.; Mitchell, John R.; Parida, Laxmi; Platt, Daniel E.; Quintana-Murci, Lluis; Renfrew, Colin; Lacerda, Daniela R.; Royyuru, Ajay K.; Sandoval, Jose Raul; Santhakumari, Arun Varatharajan; Soria Hernanz, David F.; Swamikrishnan, Pandikumar; Ziegle, Janet S.

    2014-01-01

    The search for a method that utilizes biological information to predict humans’ place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an accuracy of 700 km in Europe, they were inaccurate elsewhere. Here we describe the Geographic Population Structure (GPS) algorithm and demonstrate its accuracy with three data sets using 40,000–130,000 SNPs. GPS placed 83% of worldwide individuals in their country of origin. Applied to over 200 Sardinians villagers, GPS placed a quarter of them in their villages and most of the rest within 50 km of their villages. GPS’s accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing. PMID:24781250

  3. Population structure of Pacific Common Eiders breeding in Alaska

    Science.gov (United States)

    Petersen, M.R.; Flint, P.L.

    2002-01-01

    We used satellite telemetry to study the migration routes and wintering areas of two allopatric breeding populations of Pacific Common Eiders (Somateria mollissima v-nigrum) in Alaska: the Yukon-Kuskokwim Delta, and the western Beaufort Sea coast. Only 6% (2 of 36) of females wintered within the wintering area of the other breeding population. Both breeding populations wintered in the closest available ice-free habitat, perhaps to minimize migratory distance. Two Beaufort Sea females wintered in areas used by Yukon-Kuskokwim Delta females, implying potential gene flow among breeding areas. Yet, we conclude that these two populations are largely geographically isolated throughout the annual cycle and the environmental factors influencing survival and reproduction likely differ between these groups of birds. Thus, regardless of the potential gene flow among breeding populations, we suggest that birds from these two breeding areas should be managed as separate populations. ?? The Cooper Ornithological Society 2002.

  4. Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna.

    Science.gov (United States)

    Nakamura, Yoji; Mori, Kazuki; Saitoh, Kenji; Oshima, Kenshiro; Mekuchi, Miyuki; Sugaya, Takuma; Shigenobu, Yuya; Ojima, Nobuhiko; Muta, Shigeru; Fujiwara, Atushi; Yasuike, Motoshige; Oohara, Ichiro; Hirakawa, Hideki; Chowdhury, Vishwajit Sur; Kobayashi, Takanori; Nakajima, Kazuhiro; Sano, Motohiko; Wada, Tokio; Tashiro, Kosuke; Ikeo, Kazuho; Hattori, Masahira; Kuhara, Satoru; Gojobori, Takashi; Inouye, Kiyoshi

    2013-07-02

    Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values, the open-ocean lifestyle of tuna, in which effective sensing systems such as color vision are required for capture of prey, has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna, we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis), using next-generation sequencing technology. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS), UV-sensitive (short-wavelength sensitive 1; SWS1), blue-sensitive (SWS2), rhodopsin (RH1), and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e., blue shift). Pacific bluefin tuna has at least five RH2 paralogs, the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover, phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus, Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1, RH2, and SWS2), which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and, thereby, could help to improve the technology to culture such fish in captivity for resource management.

  5. A validated methodology for genetic identification of tuna species (genus Thunnus.

    Directory of Open Access Journals (Sweden)

    Jordi Viñas

    2009-10-01

    Full Text Available Tuna species of the genus Thunnus, such as the bluefin tunas, are some of the most important and yet most endangered trade fish in the world. Identification of these species in traded forms, however, may be difficult depending on the presentation of the products, which may hamper conservation efforts on trade control. In this paper, we validated a genetic methodology that can fully distinguish between the eight Thunnus species from any kind of processed tissue.After testing several genetic markers, a complete discrimination of the eight tuna species was achieved using Forensically Informative Nucleotide Sequencing based primarily on the sequence variability of the hypervariable genetic marker mitochondrial DNA control region (mtDNA CR, followed, in some specific cases, by a second validation by a nuclear marker rDNA first internal transcribed spacer (ITS1. This methodology was able to distinguish all tuna species, including those belonging to the subgenus Neothunnus that are very closely related, and in consequence can not be differentiated with other genetic markers of lower variability. This methodology also took into consideration the presence of introgression that has been reported in past studies between T. thynnus, T. orientalis and T. alalunga. Finally, we applied the methodology to cross-check the species identity of 26 processed tuna samples.Using the combination of two genetic markers, one mitochondrial and another nuclear, allows a full discrimination between all eight tuna species. Unexpectedly, the genetic marker traditionally used for DNA barcoding, cytochrome oxidase 1, could not differentiate all species, thus its use as a genetic marker for tuna species identification is questioned.

  6. Population structure of Vibrio fischeri within the light organs of Euprymna scolopes squid from Two Oahu (Hawaii) populations.

    Science.gov (United States)

    Wollenberg, M S; Ruby, E G

    2009-01-01

    We resolved the intraspecific diversity of Vibrio fischeri, the bioluminescent symbiont of the Hawaiian sepiolid squid Euprymna scolopes, at two previously unexplored morphological and geographical scales. These scales ranged from submillimeter regions within the host light organ to the several kilometers encompassing two host populations around Oahu. To facilitate this effort, we employed both novel and standard genetic and phenotypic assays of light-organ symbiont populations. A V. fischeri-specific fingerprinting method and five phenotypic assays were used to gauge the genetic richness of V. fischeri populations; these methods confirmed that the symbiont population present in each adult host's light organ is polyclonal. Upon statistical analysis of these genetic and phenotypic population data, we concluded that the characteristics of symbiotic populations were more similar within individual host populations than between the two distinct Oahu populations of E. scolopes, providing evidence that local geographic symbiont population structure exists. Finally, to better understand the genesis of symbiont diversity within host light organs, the process of symbiosis initiation in newly hatched juvenile squid was examined both experimentally and by mathematical modeling. We concluded that, after the juvenile hatches, only one or two cells of V. fischeri enter each of six internal epithelium-lined crypts present in the developing light organ. We hypothesize that the expansion of different, crypt-segregated, clonal populations creates the polyclonal adult light-organ population structure observed in this study. The stability of the luminous-bacterium-sepiolid squid mutualism in the presence of a polyclonal symbiont population structure is discussed in the context of contemporary evolutionary theory.

  7. Projections of climate-driven changes in tuna vertical habitat based on species-specific differences in blood oxygen affinity.

    Science.gov (United States)

    Mislan, K A S; Deutsch, Curtis A; Brill, Richard W; Dunne, John P; Sarmiento, Jorge L

    2017-10-01

    Oxygen concentrations are hypothesized to decrease in many areas of the ocean as a result of anthropogenically driven climate change, resulting in habitat compression for pelagic animals. The oxygen partial pressure, pO 2 , at which blood is 50% saturated (P 50 ) is a measure of blood oxygen affinity and a gauge of the tolerance of animals for low ambient oxygen. Tuna species display a wide range of blood oxygen affinities (i.e., P 50 values) and therefore may be differentially impacted by habitat compression as they make extensive vertical movements to forage on subdaily time scales. To project the effects of end-of-the-century climate change on tuna habitat, we calculate tuna P 50 depths (i.e., the vertical position in the water column at which ambient pO 2 is equal to species-specific blood P 50 values) from 21st century Earth System Model (ESM) projections included in the fifth phase of the Climate Model Intercomparison Project (CMIP5). Overall, we project P 50 depths to shoal, indicating likely habitat compression for tuna species due to climate change. Tunas that will be most impacted by shoaling are Pacific and southern bluefin tunas-habitat compression is projected for the entire geographic range of Pacific bluefin tuna and for the spawning region of southern bluefin tuna. Vertical shifts in P 50 depths will potentially influence resource partitioning among Pacific bluefin, bigeye, yellowfin, and skipjack tunas in the northern subtropical and eastern tropical Pacific Ocean, the Arabian Sea, and the Bay of Bengal. By establishing linkages between tuna physiology and environmental conditions, we provide a mechanistic basis to project the effects of anthropogenic climate change on tuna habitats. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

  8. Genetic diversity and population genetic structure of the only population of Aoluguya Reindeer (Rangifer tarandus) in China.

    Science.gov (United States)

    Ju, Yan; Liu, Huamiao; Rong, Min; Zhang, Ranran; Dong, Yimeng; Zhou, Yongna; Xing, Xiumei

    2018-04-16

    Aoluguya Reindeer is the only reindeer species in China and currently approximately 1000 Aoluguya Reindeer remain semi-domesticated. A relative low diversity estimate was found by investigating genetic variability and demographic history of its population. Mismatch distribution curve of its nucleotide sequences and neutral test indicate its population has not experienced expansion. Genetic diversity and population structure were also analysed by using its mtDNA and microsatellites technology. Statistical results of these analyses showed there were varying degrees of population inbreeding and suggested that gene flow existed among its populations at one time. Three mutation models were also used to detect the bottleneck effect of reindeer population. The genetic variation of eight populations is relatively small. In addition, the clustering program STRUCTURE was used to analyse Aoluguya Reindeer population structure, to determine its optimal K and first time to analyse the phylogenetic status of Aoluguya Reindeer among other reindeer subspecies. It is recommended that the government establish a natural conservation area in Aoluguya Reindeer growing geography, forbade the trade and hunting of Aoluguya Reindeer, and strengthen the protection of this endangered species.

  9. Analysis of genetic diversity and population structure among exotic ...

    African Journals Online (AJOL)

    The same clustering pattern was also found in the PCoA analysis. In all the geographical populations, genotypes from the same country were often in different clusters and likewise accessions from different countries often clustered together indicating the possibility of exchange of materials between countries. Population ...

  10. Population genetic structure of the sidespot barb, Barbus neefi, from ...

    African Journals Online (AJOL)

    Allozyme analysis was used to determine patterns of genetic variation within and between populations of Barbus neefi. The products of 29 loci were analysed, with 17 loci being monomorphic in all populations. The genetic variability estimates compared well with values reported in the literature. The percentage of ...

  11. Genetic variation and population structure of willowy flounder ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-11-05

    Nov 5, 2008 ... based on morphological features, and a piece of muscle tissue was obtained from .... The value within Niigata population (0.9%) was the lowest among the .... Ibaraki population could also get direct recruitment of larvae from ...

  12. Effect of tuna skin gelatin-based coating enriched with seaweed extracts on the quality of tuna fillets during storage at 4 °C

    Directory of Open Access Journals (Sweden)

    Milene Vala

    2017-10-01

    Full Text Available Nowadays, consumers demand high quality food products with an extended shelf-life without chemical additives. Edible coatings (EC containing natural compounds are a promising preservation technology for raw seafood without compromising fresh-like appeal and nutritional content.The aim of this work was to evaluate the effect of Thunnus obesus skin gelatin-based EC containing Codium spp. or Fucus vesiculosus extracts on raw tuna preservation. Three gelatin-based EC (gelatin (5 % + glycerol (25 %; gelatin (5 % + Codium spp. (1 % + glycerol (25 %; gelatin (5 % + Fucus vesiculosus (1 % + glycerol (25 % were applied directly on the surface of tuna fillets. Functional properties of gelatin and gelatin-based EC containing seaweed extracts were also studied. The gelatin was extracted by an acid-swelling process in the presence/absence of pepsin, followed by subsequent heating/refrigeration, after a pre-treatment with NaOH. The type of acid, temperature and concentration of NaOH greatly influence the process yield. The higher extraction yield was achieved using acetic acid in the presence of pepsin by subsequent refrigeration, especially when skins were previously treated with NaOH (0.2 M. Tuna quality was assessed over 12 days of storage at 4 ± 1 °C in terms of chemical and microbial indices. Results showed that tuna skin gelatin-based EC avoids tuna deterioration. Microbial growth, assessed by total viable counts, and total volatile basic nitrogen were maintained below the maximum limits recommended, contrarily to the control. Additionally, the use of EC increased the stability of red colour during storage. 

  13. Evaluating alternative management strategies for bigeye tuna, Thunnus obesus, in the Indian Ocean

    Directory of Open Access Journals (Sweden)

    Yuhe Tong

    2013-09-01

    Full Text Available Bigeye tuna (Thunnus obesus support a large commercial fishery in the Indian Ocean. However, explicit management strategies and harvest control rules are yet to be developed for the management of this fishery. We used a stochastic age-structured production model as an operating model to evaluate several potential management strategies under different assumptions of stock productivity. Five management strategies—constant fishing mortality, constant catch, quasi-constant catch, constant escapement, and status-dependent strategies—were evaluated and compared using the performance indicators including average catch, average spawning stock biomass, variation in catch, average fishing mortality and lowest biomass during the time period considered in the simulation. This study shows that (1 for the constant catch strategy, an annual catch of 90000 t would result in a low risk of stock being overfished while obtaining a stable catch; (2 for the constant fishing mortality strategy fishing mortality of 0.3 per year could yield a higher catch, but might have a high probability (64% of stock dropping below the spawning stock biomass (SSB that could achieve maximum sustainable yield (SSBmsy; and (3 for the quasi-constant catch strategy an annual catch of 110000 t was sustainable if the current SSB was higher than SSBmsy. Constant escapement and status-dependent strategies were robust with respect to different levels of virgin recruitment and steepness. This study suggests that it is important to incorporate uncertainties associated with key life history, fisheries and management processes in evaluating management strategies.

  14. Characteristics and nutritional value of whole wheat cracker fortified with tuna bone bio-calcium powder.

    Science.gov (United States)

    Benjakul, Soottawat; Karnjanapratum, Supatra

    2018-09-01

    Whole wheat cracker fortified with tuna bone bio-calcium (Bio-Ca) powder was developed as health-promoting food rich in calcium. Fortification with different levels of Bi-Ca, over the range of 0-50% of whole wheat flour (w/w) on quality and sensory properties of crackers, were determined. Color, thickness, weight and textural properties of crackers varied with the different levels of Bio-Ca powder added, but it was found that up to 30% could be added without detrimental effect on sensory properties. Scanning electron microscopic images showed that the developed crackers were less porous and had a denser structure, compared to the control. Based on scanning electron microscopy-energy dispersive X-ray spectroscopic (SEM-EDX), the cracker containing Bio-Ca powder had calcium and phosphorous distribution with higher intensity, compared to the control. The fortified crackers were rich in calcium and phosphorous with higher protein content but lower fat, carbohydrate, cholesterol and energy value, compared to the control. Copyright © 2018 Elsevier Ltd. All rights reserved.

  15. Age structure of the population in Belgium and social security.

    Science.gov (United States)

    Dooghe, G

    1991-01-01

    The effects of demographic aging and of various socioeconomic factors on the social security system in Belgium are explored. "Special attention is given to the impact of the ageing of the population on the pension problem. Based on a simple formula a series of percentages of taxation have been calculated as a function of shifts in the proportion of retired vs. active population and in the proportion of the average income vs. the average amount of pension. One of the conclusions is that the progressive ageing of the population will become the most significant factor in the growth of social expenditures." excerpt

  16. Stable isotopes provide insight into population structure and segregation in eastern North Atlantic sperm whales

    DEFF Research Database (Denmark)

    Borrell, Asunción; Velásquez Vacca, Adriana; Pinela, Ana M.

    2013-01-01

    In pelagic species inhabiting large oceans, genetic differentiation tends to be mild and populations devoid of structure. However, large cetaceans have provided many examples of structuring. Here we investigate whether the sperm whale, a pelagic species with large population sizes and reputedly......, use of habitat and/or migratory destinations are dissimilar between whales from the two regions and suggest that the North Atlantic population of sperm whales is more structured than traditionally accepted....

  17. Screening of biodiesel production from waste tuna oil (Thunnus sp.), seaweed Kappaphycus alvarezii and Gracilaria sp.

    Science.gov (United States)

    Alamsjah, Mochammad Amin; Abdillah, Annur Ahadi; Mustikawati, Hutami; Atari, Suci Dwi Purnawa

    2017-09-01

    Biodiesel has several advantages over solar. Compared to solar, biodiesel has more eco-friendly characteristic and produces lower greenhouse gas emissions. Biodiesel that is made from animal fats can be produced from fish oil, while other alternative sources from vegetable oils are seaweed Kappaphycus alvarezii and Gracilaria sp. Waste tuna oil (Thunnus sp.) in Indonesia is commonly a side product of tuna canning industries known as tuna precook oil; on the other hand, seaweed Gracilaria sp. and Kappaphycus alvarezii are commonly found in Indonesia's seas. Seaweed waste that was used in the present study was 100 kg and in wet condition, and the waste oil was 10 liter. The seaweed was extracted with soxhletation method that used n-hexane as the solvent. To produce biodiesel, trans esterification was performed on the seaweed oil that was obtained from the soxhletation process and waste tuna oil. Biodiesel manufactured from seaweed K. alvarezii obtained the best score in flash point, freezing point, and viscosity test. However, according to level of manufacturing efficiency, biodiesel from waste tuna oil is more efficient and relatively easier compared to biodiesel from waste K. alvarezii and Gracilaria sp.

  18. Modelling the spatial behaviour of a tropical tuna purse seine fleet.

    Directory of Open Access Journals (Sweden)

    Tim K Davies

    Full Text Available Industrial tuna fisheries operate in the Indian, Atlantic and Pacific Oceans, but concerns over sustainability and environmental impacts of these fisheries have resulted in increased scrutiny of how they are managed. An important but often overlooked factor in the success or failure of tuna fisheries management is the behaviour of fishers and fishing fleets. Uncertainty in how a fishing fleet will respond to management or other influences can be reduced by anticipating fleet behaviour, although to date there has been little research directed at understanding and anticipating the human dimension of tuna fisheries. The aim of this study was to address gaps in knowledge of the behaviour of tuna fleets, using the Indian Ocean tropical tuna purse seine fishery as a case study. We use statistical modelling to examine the factors that influence the spatial behaviour of the purse seine fleet at broad spatiotemporal scales. This analysis reveals very high consistency between years in the use of seasonal fishing grounds by the fleet, as well as a forcing influence of biophysical ocean conditions on the distribution of fishing effort. These findings suggest strong inertia in the spatial behaviour of the fleet, which has important implications for predicting the response of the fleet to natural events or management measures (e.g., spatial closures.

  19. Reduced fine-scale spatial genetic structure in grazed populations of Dianthus carthusianorum.

    Science.gov (United States)

    Rico, Y; Wagner, H H

    2016-11-01

    Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations.

  20. Application of the Oxidation-Reduction Potential (ORP) for Pre-grading Tuna Freshness On-board

    Science.gov (United States)

    Cheevaporanapivat, Mongkol; Sakai, Hisaharu; Mine, Yuuji; Watanabe, Manabu; Suzuki, Toru

    Application of ORP as a rapid indicator for grading tuna's freshness on the ship was studied. The long line trawling process was used for catching the sample tuna in the South Pacific Ocean. All captured sample tuna were weighed, gender identified and investigated for their mortality, then measured ORP and K value. Three species of tuna were caught: blue marlin (Makaira mazara), yellow fin tuna (Thunnus albacares), and swordfish (Xiphia gladius). Most of the fish captured were male and they had been dead after picking onboard. The measured ORP values of blue marlin varied in the range of 0.295-0.362 Volt, with pH between 5.35-5.84. Both ORP and pH of swordfish was similar to that of blue marlin. But for yellow fin tuna, the ORP value was about the same as blue marlin while its pH was significantly higher. ORP value in all species tended to increase with pH of the fish meat decrease. It is interesting that ORP value of tuna increased in correlation with K value. These results suggested that ORP and pH change, which are measured in the short time, are the effective indicators for grading tuna's freshness on-board.

  1. Evaluation of the proximate quality of the combination of Tuna (Thunnus albacares) and white oyster mushroom (Pleurotus ostreatus) nuggets

    Science.gov (United States)

    Yufidasari, H. S.; Prihanto, A. A.; Nurdiani, R.; Jaziri, A. A.

    2018-04-01

    Nugget is a processed meat product which has great market demand but need variations to increase its nutritional content. Tuna is rich in omega-3 protein, vitamins, and minerals. White oyster mushrooms have high nutritional content which are about 23-33% protein, 36-68 % carbohydrates and 12-22 % amino acids. The purpose of this research is to evaluate the chemical quality of Tuna nugget (Thunnus albacores) with combination of white oyster mushroom (Pleurotus ostreatus). Complete Randomized Design (RAL) with parameters of Tuna and white oyster mushroom formulation, TJ1 (70 % Tuna: 30 % white oyster mushroom), TJ2 (50 % Tuna: 50 % white oyster mushroom), TJ3 (30 % Tuna: 70 % white oyster mushroom), and Control or K Treatment (100 % Tuna) is used. Results of Tuna nuggets with white oyster mushroom combination showed the highest value of water content in TJ3 50.14 %, protein K 19.6 %, fat TJ3 22.98 %, ash K 3.99 % and 2.47 % crude fiber. From these results, there is a need for further research on fat, ash and coarse fiber content that is used in the manufacture of fish nuggets combined with oyster mushrooms because it failed to meet Indonesian National Standard (SNI).

  2. Genetic structure of populations of Mugil cephalus using RAPD ...

    African Journals Online (AJOL)

    Dr.Suresh

    2013-10-30

    , Andhra Pradesh and. Tamil Nadu in India was studied using randomly amplified polymorphic DNA (RAPD) markers. Five selective primers provided distinct and consistent RAPD profiles in all the four populations. The bands.

  3. DEMOGRAPHY AND SPATIAL POPULATION STRUCTURE IN CALIFORNIA TIGER SALAMANDER

    Science.gov (United States)

    Although the causes of many amphibian declines remain mysterious, there is general agreement that human habitat alteration represents the greatest threat to amphibian populations. In January 2000 the US Fish and Wildlife Service proposed listing Santa Barbara County California Ti...

  4. Genetic variation and population structure of interleukin genes ...

    Indian Academy of Sciences (India)

    ... phylogenetic analysis based on genetic distances between populations agreed with known social and cultural data ... thus, impact on community genetics (Bittles 2001, 2002). ... reflect an interaction between evolutionary and demographic.

  5. Similar levels of diversity and population Structure in superflock and ...

    African Journals Online (AJOL)

    superflock cichlid fishes from Lake Victoria, Africa. ... Tropical Freshwater Biology ... We use DNA microsatellite loci to estimate neutral genetic diversity and the level of gene flow among populations of two cichlid species from southern Lake Victoria, ...

  6. SIR dynamics in structured populations with heterogeneous connectivity

    OpenAIRE

    Volz, Erik

    2005-01-01

    Most epidemic models assume equal mixing among members of a population. An alternative approach is to model a population as random network in which individuals may have heterogeneous connectivity. This paper builds on previous research by describing the exact dynamical behavior of epidemics as they occur in random networks. A system of nonlinear differential equations is presented which describes the behavior of epidemics spreading through random networks with arbitrary degree distributions. ...

  7. Population structure and genetic variability of mainland and insular populations of the Neotropical water rat, Nectomys squamipes (Rodentia, Sigmodontinae

    Directory of Open Access Journals (Sweden)

    Francisca C. Almeida

    2005-12-01

    Full Text Available Seven microsatellite loci were used to investigate the genetic variability and structure of six mainland and two island populations of the Neotropical water rat Nectomys squamipes, a South American semi-aquatic rodent species with a wide distribution. High levels of variability were found within mainland populations while island populations were less variable but the more differentiated in respect to allele number and frequency. The time of biological divergence between mainland and island populations coincided with geological data. A significant geographic structure was found in mainland populations (theta = 0.099; rho = 0.086 although the degree of differentiation was relatively low in respect to the distance between surveyed localities (24 to 740 km. Genetic and geographic distances were not positively correlated as previously found with random amplified polymorphic DNA (RAPD markers. Significant but low genetic differentiation in the mainland and lack of isolation by distance can be explained by large population size and/or recent population expansion. Additionally, the agreement between the age of geologic events (sea level fluctuations and divergence times for insular populations points to a good reference for molecular clock calibration to associate recent environmental changes and the distribution pattern of small mammals in the Brazilian Atlantic Forest.

  8. Karakteristik Ikan Tuna sirip biru selatan (Thunnus maccoyii Hasil Tangkapan Kapal Rawai Tuna yang didaratkan di Pelabuhan Benoa

    Directory of Open Access Journals (Sweden)

    I Gede Adi Swastana

    2016-07-01

    Full Text Available Southern bluefin tuna (SBT is scientifically known Thunnus maccoyii, and just live in the southern hemisphere. SBT fish classified as the most exploited tuna fish in the southeastern part of the Indian Ocean, so it is protected by the International Union for the Conservation of Nature (IUCN. The aim of this study is too collected of SBT fish caught during January which is the peak of SBT landing in Benoa port. The study was conducted base on data sampling, observation and interviews on 33 ships were landing SBT fish during January 2016. Based on observations from 33 vessels, we found that the total of SBT fish that landed in Benoa port during January 2016 is 251 fresh fish and 366 frozen fish. However just 251 SBT fresh fish were sampled, and the result indicated the fresh SBT fish is dominated by weigh between 61-70 kg with number 61 fish with a total weight of 19.28 tonne. The SBT were caught dominated by fish that has FL (fork lenght ranging between 151-160 cm with number 69 fish. While the smallest SBT range between 131-140 cm with the number of 5 fish. These results indicate that SBT fish caught in the Souetheast Indian Ocean during January 2016 is generaly relative small fish (130–160 cm FL with a number of 163 fish and mature SBT fish (FL > 162 cm with a number of 88 and young SBT (FL < 130 cm with a number of 5 fish. Based on morphometric analysis, eyeball diameter of SBT range 6-8 cm, the length lateral head from the tip of the mouth to behind the gill cover ranging 46-54 cm, the length of body from the early dorsal or in front of the first dorsal fin ranging between 38-47 cm, the height of fish at the end of the anal or at the end ranging between 34-39 cm, the high of caudal peduncle ranging between 4-5 cm, th length of the dorsal base of the tail fish ranging between 53-63 cm, and the length of the base of tail anal from anal to tail ranging between 41-51 cm. Base on size and age composition, it is shown that the growth of SBT

  9. Karakteristik Ikan Tuna sirip biru selatan (Thunnus maccoyii Hasil Tangkapan Kapal Rawai Tuna yang didaratkan di Pelabuhan Benoa

    Directory of Open Access Journals (Sweden)

    I Gede Adi Swastana

    2016-12-01

    Full Text Available Southern bluefin tuna (SBT is scientifically known Thunnus maccoyii, and just live in the southern hemisphere. SBT fish classified as the most exploited tuna fish in the southeastern part of the Indian Ocean, so it is protected by the International Union for the Conservation of Nature (IUCN. The aim of this study is too collected of SBT fish caught during January which is the peak of SBT landing in Benoa port. The study was conducted base on data sampling, observation and interviews on 33 ships were landing SBT fish during January 2016. Based on observations from 33 vessels, we found that the total of SBT fish that landed in Benoa port during January 2016 is 251 fresh fish and 366 frozen fish. However just 251 SBT fresh fish were sampled, and the result indicated the fresh SBT fish is dominated by weigh between 61-70 kg with number 61 fish with a total weight of 19.28 tonne. The SBT were caught dominated by fish that has FL (fork lenght ranging between 151-160 cm with number 69 fish. While the smallest SBT range between 131-140 cm with the number of 5 fish. These results indicate that SBT fish caught in the Souetheast Indian Ocean during January 2016 is generaly relative small fish (130–160 cm FL with a number of 163 fish and mature SBT fish (FL > 162 cm with a number of 88 and young SBT (FL < 130 cm with a number of 5 fish. Based on morphometric analysis, eyeball diameter of SBT range 6-8 cm, the length lateral head from the tip of the mouth to behind the gill cover ranging 46-54 cm, the length of body from the early dorsal or in front of the first dorsal fin ranging between 38-47 cm, the height of fish at the end of the anal or at the end ranging between 34-39 cm, the high of caudal peduncle ranging between 4-5 cm, th length of the dorsal base of the tail fish ranging between 53-63 cm, and the length of the base of tail anal from anal to tail ranging between 41-51 cm. Base on size and age composition, it is shown that the growth of SBT

  10. Génesis de la medicina familiar en Las Tunas

    Directory of Open Access Journals (Sweden)

    Maritza Rodríguez Peña

    2014-08-01

    Full Text Available Se realizó una investigación desde los presupuestos de la historia social integral, con el objetivo de analizar momentos importantes de la historia de la medicina familiar en la localidad de Las Tunas. Para la investigación se consultaron diversas fuentes documentales, orales, iconográficas, patrimoniales y bibliográficas, entre ellas la obra de los historiadores de la ciudad y del Ministerio de Salud Pública, así como resultados científicos de proyectos de investigación. Los métodos empleados partieron de la observación, el análisis histórico-lógico, la síntesis, la inducción y la deducción de la información, que permitieron la sistematización y determinación de los momentos más importantes de este proceso desde su origen en la comunidad primitiva, transitando por diferentes etapas hasta 1984, con la puesta en práctica del Programa del Médico y la Enfermera de la Familia, para el fortalecimiento de la atención primaria de salud, con marcado acento preventivo

  11. Population Structure and Evolution after Speciation of the Hokkaido Salamander (Hynobius retardatus.

    Directory of Open Access Journals (Sweden)

    Masatoshi Matsunami

    Full Text Available The Hokkaido salamander (Hynobius retardatus is endemic to Hokkaido Island, Japan, and shows intriguing flexible phenotypic plasticity and regional morphological diversity. However, to date, allozymes and partial mitochondria DNA sequences have provided only an outline of its demographic histories and the pattern of its genetic diversification. To understand the finer details of the population structure of this species and its evolution since speciation, we genotyped five regional populations by using 12 recently developed microsatellite polymorphic markers. We found a clear population structure with low gene flow among the five populations, but a close genetic relationship between the Teshio and Kitami populations. Our demographic analysis suggested that Teshio and Erimo had the largest effective population sizes among the five populations. These findings regarding the population structure and demography of H. retardatus improve our understanding of the faunal phylogeography on Hokkaido Island and also provide fundamental genetic information that will be useful for future studies.

  12. Sea otter population structure and ecology in Alaska

    Science.gov (United States)

    Bodkin, James L.; Monson, Daniel H.

    2002-01-01

    Sea otters are the only fully marine otter. They share a common ancestry with the Old World land otters, but their route of dispersal to the New World is uncertain. The historic range of the species is along the northern Pacific Ocean rim, between central Baja California and the islands of northern Japan. Because they forage almost exclusively on bottom-dwelling marine invertebrates such as clams, snails, crabs, and sea urchins, they predominantly occur near shore. Their offshore distribution is limited by their diving ability; although they are capable of diving to more than 100 meters deep, most of their feeding takes place between the shoreline and depths of 40 meters. They are social animals, generally resting in protected bays or kelp forests in groups, commonly referred to as rafts. Because they are gregarious, possess a fine fur, and occur primarily near shore, they have been exploited by humans for as long as they have co-occupied coastal marine communities.During the late Pleistocene, glacial advances and retreats in the northern latitudes likely influenced genetic exchange within the sea otter’s northern range. When the glaciers were at their maximum, ice sheets extended over large coastal areas, isolating sea otter populations and causing local extinctions. During periods of glacial retreat, sea otters likely recolonized the newly available habitats, allowing exchange of individuals and gene flow between populations.Beginning in about 1750, sea otter populations underwent dramatic declines as a direct result of commercial harvest for their furs. Explorations by Vitus Bering led to the discovery of abundant sea otter populations in the Aleutian Islands. The early harvest, conducted by Russians with enslaved Aleut hunters, began in the eastern Aleutians. Eventually the harvest became multinational and contributed significantly to the exploration and settlement of the North Pacific coastline by Europeans. There were two distinct periods of harvest

  13. Economic consequences of population size, structure and growth.

    Science.gov (United States)

    Lee, R

    1983-01-01

    There seems to be 4 major approaches to conceptualizing and modeling demographic influences on economic and social welfare. These approaches are combined in various ways to construct richer and more comprehensive models. The basic approaches are: demographic influences on household or family behavior; population growth and reproducible capital; population size and fixed factors; and population and advantages of scale. These 4 models emphasize the supply side effects of population. A few of the ways in which these theories have been combined are sketched. Neoclassical growth models often have been combined with age distributed populations of individuals (or households), assumed to pursue optimal life cycle consumption and saving. In some well known development models, neoclassical growth models for the modern sector are linked by labor markets and migration to fixed factor (land) models of the traditional (agricultural) sector. A whole series of macro simulation models for developed and developing countries was based on single sector neoclassical growth models with age distributed populations. Yet, typically the household level foundations of assumed age distribution effects were not worked out. Simon's (1977) simulation models are in a class by themselves, for they are the only models that attempt to incorporate all the kinds of effects discussed. The economic demography of the individual and family cycle, as it is affected by regimes of fertility, mortality, and nuptiality, taken as given, are considered. The examination touches on many of the purported consequences of aggregate population growth and age composition, since so many of these are based implicitly or explicitly on assertions about micro level behavior. Demographic influences on saving and consumption, on general labor supply and female labor supply, and on problems of youth and old age dependency frequently fall in this category. Finally, attention is focused specifically on macro economic issues in

  14. Population structure of the Southeast Asian river catfish Mystus nemurus.

    Science.gov (United States)

    Usmani, S; Tan, S G; Siraj, S S; Yusoff, K

    2003-12-01

    A total of 143 microsatellites were isolated from Mystus nemurus using a 5' anchored polymerase chain reaction technique or the random amplified hybridization microsatellite method, the first set of microsatellite markers developed for the Southeast Asian river catfish. Twenty polymorphic microsatellite loci were used as markers for population characterization of M. nemurus from six different geographical locations in Malaysia (Perak, Kedah, Johor, UPM, Sarawak and Terengganu). The number of alleles per locus ranged from 2 to 11 with 6.3 as the average number of alleles per locus. Characterization of the populations showed relatively high levels of genetic variation compared with previous studies using allozyme markers. The highest genetic similarity was found between Perak and Kedah, while the highest genetic distance was found between Terengganu and Kedah. The majority of clustering was in accordance with geographical locations and the histories of the populations. Microsatellite analysis indicated that the Sarawak population might be genetically closer to the Peninsular Malaysian populations than has been previously shown by other molecular marker studies.

  15. Brain morphology and immunohistochemical localization of the gonadotropin-releasing hormone in the bluefin tuna, Thunnus thynnus

    Directory of Open Access Journals (Sweden)

    G Palmieri

    2009-08-01

    Full Text Available The present study was focused on the morphology of the diencephalic nuclei (likely involved in reproductive functions as well as on the distribution of GnRH (gonadotropin-releasing hormone in the rhinencephalon, telencephalon and the diencephalon of the brain of bluefin tuna (Thunnus thynnus by means of immunohistochemistry. Bluefin tuna has an encephalization quotient (QE similar to that of other large pelagic fish. Its brain exhibits well-developed optic tecta and corpus cerebelli. The diencephalic neuron cell bodies involved in reproductive functions are grouped in two main nuclei: the nucleus preopticus-periventricularis and the nucleus lateralis tuberis. The nucleus preopticus-periventricularis consists of the nucleus periventricularis and the nucleus preopticus consisting of a few sparse multipolar neurons in the rostral part and numerous cells closely packed and arranged in several layers in its aboral part. The nucleus lateralis tuberis is located in the ventral-lateral area of the diencephalon and is made up of a number of large multipolar neurones. Four different polyclonal primary antibodies against salmon (sGnRH, chicken (cGnRH-II (cGnRH-II 675, cGnRH-II 6 and sea bream (sbGnRH were employed in the immunohistochemical experiments. No immunoreactive structures were found with anti sbGnRH serum. sGnRH and cGnRH-II antisera revealed immunoreactivity in the perikarya of the olfactory bulbs, preopticus-periventricular nucleus, oculomotor nucleus and midbrain tegmentum. The nucleus lateralis tuberis showed immunostaining only with anti-sGnRH serum. Nerve fibres immunoreactive to cGnRH and sGnRH sera were found in the olfactory bulbs, olfactory nerve and neurohypophysis. The significance of the distribution of the GnRHimmunoreactive neuronal structures is discussed.

  16. Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population.

    Science.gov (United States)

    Tay, Chin Yen; Mitchell, Hazel; Dong, Quanjiang; Goh, Khean-Lee; Dawes, Ian W; Lan, Ruiting

    2009-06-19

    Helicobacter pylori is a major gastric bacterial pathogen. This pathogen has been shown to follow the routes of human migration by their geographical origin and currently the global H. pylori population has been divided into six ancestral populations, three from Africa, two from Asia and one from Europe. Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recent H. pylori migration and admixture. Seventy eight H. pylori isolates, including 27 Chinese, 35 Indian and 16 Malay isolates from Malaysia were analysed by multilocus sequence typing (MLST) of seven housekeeping genes and compared with the global MLST data. STRUCTURE analysis assigned the isolates to previously identified H. pylori ancestral populations, hpEastAsia, hpAsia2 and hpEurope, and revealed a new subpopulation, hspIndia, within hpAsia2. Statistical analysis allowed us to identify population segregation sites that divide the H. pylori populations and the subpopulations. The majority of Malay isolates were found to be grouped together with Indian isolates. The majority of the Malay and Indian H. pylori isolates share the same origin while the Malaysian Chinese H. pylori is distinctive. The Malay population, known to have a low infection rate of H. pylori, was likely to be initially H. pylori free and gained the pathogen only recently from cross infection from other populations.

  17. Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population

    Directory of Open Access Journals (Sweden)

    Dawes Ian W

    2009-06-01

    Full Text Available Abstract Background Helicobacter pylori is a major gastric bacterial pathogen. This pathogen has been shown to follow the routes of human migration by their geographical origin and currently the global H. pylori population has been divided into six ancestral populations, three from Africa, two from Asia and one from Europe. Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recent H. pylori migration and admixture. Results Seventy eight H. pylori isolates, including 27 Chinese, 35 Indian and 16 Malay isolates from Malaysia were analysed by multilocus sequence typing (MLST of seven housekeeping genes and compared with the global MLST data. STRUCTURE analysis assigned the isolates to previously identified H. pylori ancestral populations, hpEastAsia, hpAsia2 and hpEurope, and revealed a new subpopulation, hspIndia, within hpAsia2. Statistical analysis allowed us to identify population segregation sites that divide the H. pylori populations and the subpopulations. The majority of Malay isolates were found to be grouped together with Indian isolates. Conclusion The majority of the Malay and Indian H. pylori isolates share the same origin while the Malaysian Chinese H. pylori is distinctive. The Malay population, known to have a low infection rate of H. pylori, was likely to be initially H. pylori free and gained the pathogen only recently from cross infection from other populations.

  18. Global trophic ecology of yellowfin, bigeye, and albacore tunas: Understanding predation on micronekton communities at ocean-basin scales

    Science.gov (United States)

    Duffy, Leanne M.; Kuhnert, Petra M.; Pethybridge, Heidi R.; Young, Jock W.; Olson, Robert J.; Logan, John M.; Goñi, Nicolas; Romanov, Evgeny; Allain, Valerie; Staudinger, Michelle D.; Abecassis, Melanie; Choy, C. Anela; Hobday, Alistair J.; Simier, Monique; Galván-Magaña, Felipe; Potier, Michel; Ménard, Frederic

    2017-06-01

    Predator-prey interactions for three commercially valuable tuna species: yellowfin (Thunnus albacares), bigeye (T. obesus), and albacore (T. alalunga), collected over a 40-year period from the Pacific, Indian, and Atlantic Oceans, were used to quantitatively assess broad, macro-scale trophic patterns in pelagic ecosystems. Analysis of over 14,000 tuna stomachs, using a modified classification tree approach, revealed for the first time the global expanse of pelagic predatory fish diet and global patterns of micronekton diversity. Ommastrephid squids were consistently one of the top prey groups by weight across all tuna species and in most ocean bodies. Interspecific differences in prey were apparent, with epipelagic scombrid and mesopelagic paralepidid fishes globally important for yellowfin and bigeye tunas, respectively, while vertically-migrating euphausiid crustaceans were important for albacore tuna in the Atlantic and Pacific Oceans. Diet diversity showed global and regional patterns among tuna species. In the central and western Pacific Ocean, characterized by low productivity, a high diversity of micronekton prey was detected while low prey diversity was evident in highly productive coastal waters where upwelling occurs. Spatial patterns of diet diversity were most variable in yellowfin and bigeye tunas while a latitudinal diversity gradient was observed with lower diversity in temperate regions for albacore tuna. Sea-surface temperature was a reasonable predictor of the diets of yellowfin and bigeye tunas, whereas chlorophyll-a was the best environmental predictor of albacore diet. These results suggest that the ongoing expansion of warmer, less productive waters in the world's oceans may alter foraging opportunities for tunas due to regional changes in prey abundances and compositions.

  19. Gamma Irradiation Effects On Thiamin And Riboflavin On Fresh Tuna (Thunnus thynnus) And Salmon (Onchorhynchus gorbuscha)

    International Nuclear Information System (INIS)

    Tanhindarto, Rindy P.; Fox, J.B.; Lakritz, L.; Thayer, D.W.

    2002-01-01

    An experiment have been conducted on the effect of gamma irradiation on thiamine and riboflavin in fresh tuna and salmon. Samples were irradiated at (20 ± 0,5) oC by gamma rays with doses of 0; 2,5 and 5 kGy. The purpose of the present experiment was to study on changes of thiamine and riboflavin contents on extraction of fresh tuna and salmon after and before irradiation. The results showed that irradiation up to 2,5 kGy changed the thiamine and riboflavin contents on fresh tuna as well as their destruction which was significantly increasing caused by irradiated treatment with the dose of 5 kGy. The fresh salmon did not significantly change of the thiamine and riboflavin contents treated by irradiation up to 5 kGy

  20. Leaching of Oil from Tuna Fish Liver by Using Solvent of Methyl-Ethyl Ketone

    Directory of Open Access Journals (Sweden)

    Mirna Rahmah Lubis

    2013-12-01

    Full Text Available Research of oil leaching from Tuna Fish Liver has been carried out by extracting of tuna fish liver in soxhlet by using methyl-ethyl ketone as solvent. Liver of fresh tuna fish is blended, put into soxhlet, and extracted at temperatures of 60oC, 65oC, 70oC, 75oC, and 80oC. After obtaining the oil, separation between solvent and oil is carried out by distillation. Oil obtained is analyzed by testing the yield, acid number, Iodine value, viscosity, and its impurities content. Yield obtained is influenced by temperature and time of leaching. Both variables indicates that the higher the variables, the more fish liver oil obtained. Maximum yield obtained is 25.552% at operating condition of leaching temperature 80oC, and leaching duration of 5 hours.

  1. Autolytic degradation of skipjack tuna during heating as affected by initial quality and processing conditions.

    Science.gov (United States)

    Stagg, Nicola J; Amato, Penny M; Giesbrecht, Francis; Lanier, Tyre C

    2012-02-01

    Several factors were studied as affecting protein degradation and texture of skipjack tuna muscle following ambient pressure thermal processing (precooking). These included degree of mushy tuna syndrome (MTS) evidenced in the raw meat, raw meat pH, abusive thawing/holding, and precooking temperature/time. Slurries and intact pieces from frozen skipjack tuna, either tempered for 2 h or thawed and held at 25 °C for 22 h (abusive treatment) were heated at temperatures ranging from 40 to 80 °C for up to 2 h, and also at 90 °C for 1 h, with or without prior adjustment of pH to 5 or 7 to favor cathepsin or calpain activity, respectively. Proteolysis of precooked samples was monitored by Lowry assay and SDS-PAGE; cooked texture of intact meat was measured using a Kramer shear press and by sensory profile analysis. Proteolysis maximally occurred in slurries of skipjack tuna muscle that had been abusively stored (22 h at 25 °C) and adjusted to pH 5 prior to heating at 55 °C. Intact pieces of tuna abusively thawed/held for 22 h with subsequent heating at 55 °C also evidenced the most proteolysis and were the least firm in texture. Raw fish that evidenced higher severity of MTS when raw displayed higher levels of proteolysis prior to cooking, which were further increased after cooking at 55 °C. The kinetic data presented here can be used to optimize processing conditions for skipjack tuna canning to minimize textural degradation and optimize quality. © 2012 Institute of Food Technologists®

  2. Genetic structure of natural populations: Final technical report

    International Nuclear Information System (INIS)

    Ayala, F.J.

    1987-01-01

    We determined the LD 50 for individuals with any one of four genetic constitutions. The LD 50 was in kR units (S and F refer to the two common alleles found in natural populations and N is a mull allele) S/S 5.31, F/F 4.61, S/F 4.19, N/N 3.16. These results are as expected under the hypothesis the SOD is involved in radio-resistance and the degree of protection is a function of SOD specific activity. S codes for an allozyme that has the highest in vitro specific activity while N reduces the amount of enzyme to 3.5% of the normal level. Natural selection experiments in population cages were carried out for 13 generations. In control populations, the frequency of the S allele decreases from the initial frequency of 0.50 to an equilibrium value 0.1 to 0.2 in about 10 generations. In populations with the larvae receiving 4 KR in each generation, s reaches an equilibrium frequency of 0.6; when the irradiation was no longer applied, the frequency of S started declining, eventually reaching 0.1 to 0.2. These results corroborate the hypothesis that SOD protects against irradiation and that the degree of protection is correlated by the in vitro specific activity of the allozymes. 29 refs., 4 tabs

  3. The population structure of Ukraine in relation to the ...

    African Journals Online (AJOL)

    Background: The taste sensitivity to phenylthiocarbamide (PTC) is one of the classical genetic markers in human studies. PTC is of great interest from the medical point of view since a number of associations of the taster status with human diseases have been found. The aim of our study was to evaluate the population ...

  4. Euphausiid population structure and grazing in the Antarctic Polar ...

    African Journals Online (AJOL)

    The daily ration estimates of autotrophic carbon for the euphausiids suggest that phytoplankton represent a minor component in their diets, with only the sub-adult E. vallentini consuming sufficient phytoplankton to meet their daily carbon requirements. Keywords: euphausiid; ingestion; Polar Frontal Zone; population ...

  5. Genetic diversity and population structure of 10 Chinese indigenous ...

    Indian Academy of Sciences (India)

    This program uses a Monte Carlo Markov chain. (MCMC) algorithm to ... tal population, measured as FST value, for the 29 loci var- ied from 0.002 (SMO11) to .... linked to loci affecting morphological, productive or adap- tive traits of selective ...

  6. Population structure and growth of polydorid polychaetes that infest ...

    African Journals Online (AJOL)

    Polydorid polychaetes can infest cultured abalone thereby reducing productivity. In order to effectively control these pests, their reproductive biology must be understood. The population dynamics and reproduction of polydorids infesting abalone Haliotis midae from two farms in South Africa is described using a ...

  7. Analysis of genetic structure in Melia volkensii (Gurke.) populations ...

    African Journals Online (AJOL)

    Administrator

    2Farm Forestry Programme, Kenya Forestry Research Institute, P. O. Box 20412, Nairobi, Kenya. Accepted 5 ... were used to estimate genetic distances between populations and for construction of neighbour-joining phenograms. Analysis of Molecular Variance (AMOVA) indicated significant genetic differentiation between ...

  8. Genetic variability and structure of an isolated population of ...

    Indian Academy of Sciences (India)

    Rosa-Laura Heredia-Bobadilla

    2017-11-15

    Nov 15, 2017 ... Journal of Genetics, Vol. 96, No. 6, December 2017 ... or international status of protection. The mole ... populations by a matrix of agriculture and urbanization, can be considered ...... BioScience 38, 471–479. Lemos-Espinal ...

  9. Geographical structure and differential natural selection among North European populations

    DEFF Research Database (Denmark)

    McEvoy, Brian P; Montgomery, Grant W; McRae, Allan F

    2009-01-01

    polymorphism, in 2099 individuals from populations of Northern European origin (Ireland, United Kingdom, Netherlands, Denmark, Sweden, Finland, Australia, and HapMap European-American). The major trends (PC1 and PC2) demonstrate an ability to detect geographic substructure, even over a small area like...

  10. The Population Structure of African Cultivated Rice Oryza glaberrima (Steud.)

    DEFF Research Database (Denmark)

    Semon, Mande; Nielsen, Rasmus; Jones, Monty P.

    2005-01-01

    Genome-wide linkage disequilibrium (LD) was investigated for 198 accessions of Oryza glaberrima using 93 nuclear microsatellite markers. Significantly elevated levels of LD were detected, even among distantly located markers. Free recombination among loci at the population genetic level was shown...

  11. Strong Migration Limit for Games in Structured Populations: Applications to Dominance Hierarchy and Set Structure

    Directory of Open Access Journals (Sweden)

    Dhaker Kroumi

    2015-09-01

    Full Text Available In this paper, we deduce a condition for a strategy S1 to be more abundant on average at equilibrium under weak selection than another strategy S2 in a population structured into a finite number of colonies of fixed proportions as the population size tends to infinity. It is assumed that one individual reproduces at a time with some probability depending on the payoff received in pairwise interactions within colonies and between colonies and that the offspring replaces one individual chosen at random in the colony into which the offspring migrates. It is shown that an expected weighted average equilibrium frequency of S1 under weak symmetric strategy mutation between S1 and S2 is increased by weak selection if an expected weighted payoff of S1 near neutrality exceeds the corresponding expected weighted payoff of S2. The weights are given in terms of reproductive values of individuals in the different colonies in the neutral model. This condition for S1 to be favoured by weak selection is obtained from a strong migration limit of the genealogical process under neutrality for a sample of individuals, which is proven using a two-time scale argument. The condition is applied to games between individuals in colonies with linear or cyclic dominance and between individuals belonging to groups represented by subsets of a given set.

  12. Demography and genetic structure of a recovering grizzly bear population

    Science.gov (United States)

    Kendall, K.C.; Stetz, J.B.; Boulanger, J.; Macleod, A.C.; Paetkau, David; White, Gary C.

    2009-01-01

    Grizzly bears (brown bears; Ursus arctos) are imperiled in the southern extent of their range worldwide. The threatened population in northwestern Montana, USA, has been managed for recovery since 1975; yet, no rigorous data were available to monitor program success. We used data from a large noninvasive genetic sampling effort conducted in 2004 and 33 years of physical captures to assess abundance, distribution, and genetic health of this population. We combined data from our 3 sampling methods (hair trap, bear rub, and physical capture) to construct individual bear encounter histories for use in Huggins-Pledger closed mark-recapture models. Our population estimate, N?? = 765 (95% CI = 715-831) was more than double the existing estimate derived from sightings of females with young. Based on our results, the estimated known, human-caused mortality rate in 2004 was 4.6% (95% CI = 4.2-4.9%), slightly above the 4% considered sustainable; however, the high proportion of female mortalities raises concern. We used location data from telemetry, confirmed sightings, and genetic sampling to estimate occupied habitat. We found that grizzly bears occupied 33,480 km2 in the Northern Continental Divide Ecosystem (NCDE) during 1994-2007, including 10,340 km beyond the Recovery Zone. We used factorial correspondence analysis to identify potential barriers to gene flow within this population. Our results suggested that genetic interchange recently increased in areas with low gene flow in the past; however, we also detected evidence of incipient fragmentation across the major transportation corridor in this ecosystem. Our results suggest that the NCDE population is faring better than previously thought, and they highlight the need for a more rigorous monitoring program.

  13. Landlocked Arctic charr ( Salvelinus alpinus ) population structure and lake morphometry in Greenland - is there a connection?

    DEFF Research Database (Denmark)

    Riget, F.; Jeppesen, E.; Landkildehus, F.

    2000-01-01

    correlated with lake volume. Our study indicates that the charr population structure became more complex with increasing lake size. Moreover, the population structure seemed to be influenced by lake-water transparency and the presence or absence of three-spined stickleback (Gasterosteus aculeatus)...

  14. Reducing the Bitterness of Tuna (Euthynnus pelamis) Dark Meat with Lactobacillus casei subsp. casei ATCC 393

    OpenAIRE

    Ernani S. Sant’Anna; Luiz H. Beirão; Fabiano Cleber Bertoldi

    2004-01-01

    During the process of canning tuna fish, considerable amounts of dark tuna meat are left over because of its bitterness, which are then used in the production of animal food. Fermentation with Lactobacillus casei subsp. casei ATCC 393 was used as an alternative to reduce this bitter taste. Samples of meat were prepared, vacuum packed and then stored at –18 °C. The frozen dark meat was used immediately after defrosting and the experiment was carried out with 2 and 4 % of NaCl with the addition...

  15. The Real maccoyii: Identifying Tuna Sushi with DNA Barcodes – Contrasting Characteristic Attributes and Genetic Distances

    Science.gov (United States)

    Lowenstein, Jacob H.; Amato, George; Kolokotronis, Sergios-Orestis

    2009-01-01

    Background The use of DNA barcodes for the identification of described species is one of the least controversial and most promising applications of barcoding. There is no consensus, however, as to what constitutes an appropriate identification standard and most barcoding efforts simply attempt to pair a query sequence with reference sequences and deem identification successful if it falls within the bounds of some pre-established cutoffs using genetic distance. Since the Renaissance, however, most biological classification schemes have relied on the use of diagnostic characters to identify and place species. Methodology/Principal Findings Here we developed a cytochrome c oxidase subunit I character-based key for the identification of all tuna species of the genus Thunnus, and compared its performance with distance-based measures for identification of 68 samples of tuna sushi purchased from 31 restaurants in Manhattan (New York City) and Denver, Colorado. Both the character-based key and GenBank BLAST successfully identified 100% of the tuna samples, while the Barcode of Life Database (BOLD) as well as genetic distance thresholds, and neighbor-joining phylogenetic tree building performed poorly in terms of species identification. A piece of tuna sushi has the potential to be an endangered species, a fraud, or a health hazard. All three of these cases were uncovered in this study. Nineteen restaurant establishments were unable to clarify or misrepresented what species they sold. Five out of nine samples sold as a variant of “white tuna” were not albacore (T. alalunga), but escolar (Lepidocybium flavorunneum), a gempylid species banned for sale in Italy and Japan due to health concerns. Nineteen samples were northern bluefin tuna (T. thynnus) or the critically endangered southern bluefin tuna (T. maccoyii), though nine restaurants that sold these species did not state these species on their menus. Conclusions/Significance The Convention on International Trade

  16. Synthesis of Monoacylglycerol Rich in Polyunsaturated Fatty Acids from Tuna Oil with Immobilized Lipase AK

    DEFF Research Database (Denmark)

    Pawongrat, Ratchapol; Xu, Xuebing; H-Kittikun, Aran

    2007-01-01

    The aim of this study was to produce monoacylglycerols (MAG) rich in polyunsaturated fatty acids (PUFA), especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), by glycerolysis of tuna oil with lipase AK from Pseudomonas fluorescence immobilized on Accurel EP-100 (IM-AK). tert...... on tuna oil. The temperature was controlled at 45 degrees C. Under these conditions, with a 24 h reaction, the yield of MAG was 24.6%, but containing 56.0 wt% PUFA (EPA and DHA). Stability of the IM-AK was also studied. The hydrolytic activity of the enzyme remained at 88% and 80% of initial activity...

  17. The concentration and variability of selenium and mercury measured in vacuum-packed tuna fish

    International Nuclear Information System (INIS)

    Brockman, J.D.; Sharp, N.; Ngwenyama, R.A.; Shelnutt, L.D.; McElroy, J.A.

    2009-01-01

    Methylmercury (meHg) is a known toxin commonly found in fish. Fish is also a rich source of the trace nutrient selenium which has been hypothesized to modify the toxicity of meHg. We analyzed 28 samples of commercially packaged albacore and light tuna fish for selenium and mercury using standard comparator instrumental neutron activation analysis. Significant differences in the concentration of mercury and selenium were associated with the type of fish, brand and batch. Fish consumers should vary the brand of tuna fish to avoid routine consumption of a brand high in mercury. (author)

  18. ObStruct: a method to objectively analyse factors driving population structure using Bayesian ancestry profiles.

    Directory of Open Access Journals (Sweden)

    Velimir Gayevskiy

    Full Text Available Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 Saccharomyces cerevisiae from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses.

  19. Population Structure Analysis of Bull Genomes of European and Western Ancestry

    DEFF Research Database (Denmark)

    Chung, Neo Christopher; Szyda, Joanna; Frąszczak, Magdalena

    2017-01-01

    Since domestication, population bottlenecks, breed formation, and selective breeding have radically shaped the genealogy and genetics of Bos taurus. In turn, characterization of population structure among diverse bull (males of Bos taurus) genomes enables detailed assessment of genetic resources...... and origins. By analyzing 432 unrelated bull genomes from 13 breeds and 16 countries, we demonstrate genetic diversity and structural complexity among the European/Western cattle population. Importantly, we relaxed a strong assumption of discrete or admixed population, by adapting latent variable models...... harboring largest genetic differentiation suggest positive selection underlying population structure. We carried out gene set analysis using SNP annotations to identify enriched functional categories such as energy-related processes and multiple development stages. Our population structure analysis of bull...

  20. Into the depth of population genetics: pattern of structuring in mesophotic red coral populations

    Science.gov (United States)

    Costantini, Federica; Abbiati, Marco

    2016-03-01

    Deep-sea reef-building corals are among the most conspicuous invertebrates inhabiting the hard-bottom habitats worldwide and are particularly susceptible to human threats. The precious red coral ( Corallium rubrum, L. 1758) has a wide bathymetric distribution, from shallow up to 800 m depth, and represents a key species in the Mediterranean mesophotic reefs. Several studies have investigated genetic variability in shallow-water red coral populations, while geographic patterns in mesophotic habitats are largely unknown. This study investigated genetic variability of C. rubrum populations dwelling between 55 and 120 m depth, from the Ligurian to the Ionian Sea along about 1500 km of coastline. A total of 18 deep rocky banks were sampled. Colonies were analyzed by means of a set of microsatellite loci and the putative control region of the mitochondrial DNA. Collected data were compared with previous studies. Both types of molecular markers showed high genetic similarity between populations within the northern (Ligurian Sea and Tuscan Archipelago) and the southern (Tyrrhenian and Ionian seas) study areas. Variability in habitat features between the sampling sites did not affect the genetic variability of the populations. Conversely, the patchy distribution of suitable habitats affected populations' connectivity within and among deep coral banks. Based on these results and due to the emphasis on red coral protection in the Mediterranean Sea by international institutions, red coral could be promoted as a `focal species' to develop management plans for the conservation of deep coralligenous reefs, a reservoir of marine biodiversity.

  1. The genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    SAM

    2014-07-16

    Jul 16, 2014 ... polymorphic molecular markers for use in hybridization and variety development. Genomic ... The model-based cluster analysis of SSR diversity in the ...... clusters of individuals using the software STRUCTURE: A simulation.

  2. Genetic structure and variability within and among populations of the ...

    African Journals Online (AJOL)

    Lalouta

    2014-01-01

    Jan 1, 2014 ... The clustering analysis performed with 'structure' detected the absence of .... tance of molecular information in the establishment of genetic improvement ... applied using a Markov Chain Monte Carlo simulation (100 batches,.

  3. Genetic diversity and population structure of maize landraces from ...

    African Journals Online (AJOL)

    pc

    2016-11-02

    Nov 2, 2016 ... useful in selection. The cross between two individuals from different groups might help exploit the ... primers used are labeled with different colored .... with a view to detect a structuring of accessions in genetically different ...

  4. Landscape structure mediates the effects of a stressor on field vole populations

    DEFF Research Database (Denmark)

    Dalkvist, Trine; Sibly, Richard M.; Topping, Christopher John

    2013-01-01

    Spatio-temporal landscape heterogeneity has rarely been considered in population-level impact assessments. Here we test whether landscape heterogeneity is important by examining the case of a pesticide applied seasonally to orchards which may affect non-target vole populations, using a validated ...... results show that accurate prediction of population impact cannot be achieved without taking account of landscape structure. The specifics of landscape structure and habitat connectivity are likely always important in mediating the effects of stressors....

  5. Alu polymorphic insertions reveal genetic structure of north Indian populations.

    Science.gov (United States)

    Tripathi, Manorama; Tripathi, Piyush; Chauhan, Ugam Kumari; Herrera, Rene J; Agrawal, Suraksha

    2008-10-01

    The Indian subcontinent is characterized by the ancestral and cultural diversity of its people. Genetic input from several unique source populations and from the unique social architecture provided by the caste system has shaped the current genetic landscape of India. In the present study 200 individuals each from three upper-caste and four middle-caste Hindu groups and from two Muslim populations in North India were examined for 10 polymorphic Alu insertions (PAIs). The investigated PAIs exhibit high levels of polymorphism and average heterozygosity. Limited interpopulation variance and genetic flow in the present study suggest admixture. The results of this study demonstrate that, contrary to common belief, the caste system has not provided an impermeable barrier to genetic exchange among Indian groups.

  6. Transferrin variation and genetic structure of reindeer populations in Scandinavia

    Directory of Open Access Journals (Sweden)

    Knut H. Røed

    1987-06-01

    Full Text Available Polyacrylamide gel electrophoresis was used to analyse transferrin variation in herds of semi-domestic reindeer from Scandinavia. The results are compared with previously reported values for other populations of both semi-domestic and wild reindeer using the same techniques as in the present study. In all populations the number of alleles was high, ranging from seven to eleven, and the heterozygosity was correspondingly high, with a mean of 0.749. This high genetic variation in all populations suggests that inbreeding is not widespread among Scandinavian reindeer. The pattern of allele frequency distribution indicates a high degree of genetic heterogeneity in the transferrin locus, both between the different semi-domestic herds and between the different wild populations. The mean value of genetic distance was 0.069 between semi-domestic herds and 0.091 between wild populations. Between semi-domestic and wild populations the genetic distance was particularly high, with a mean of 0.188. This high value was mainly due to a different pattern in the distribution of the two most common transferrin alleles: Tfu was most common among semi-domestic herds, while TfEI was most common among wild populations. These differences in transferrin allele distribution are discussed in relation to possible different origins of semi-domestic and wild reindeer in Scandinavia, or alternatively, to different selection forces acting on transferrin genotypes in semi-domestic and wild populations.Transferrin-variasjon og genetisk struktur hos rein i Skandinavia.Abstact in Norwegian / Sammendrag: Transferrin-variasjon i tamreinflokker ble analysert ved hjelp av polyacrylamid gel elektroforese. Resultatene er sammenlignet med verdier som tidligere er beskrevet for både tamrein og villrein hvor det ble benyttet samme metode som i denne undersøkelsen. I alle populasjonene ble det registrert et høyt antall alleler (7-11 og heterozygositeten var tilsvarende høy med en

  7. Sus scrofa: Population Structure, Reproduction and Condition in Tropical North Eastern Australia

    Directory of Open Access Journals (Sweden)

    NELSON, John E.

    2009-01-01

    Full Text Available Three feral pig populations inhabiting contrasting environments along the north easterncoast of Australia have been investigated with respect to population structure, individual condition andreproduction. The population on Prince of Wales Island contains a large proportion of juvenile andsub-adult pigs but lacks pigs in the higher age classes. Individuals also breed at an earlier age thananimals of the mainland populations. Pig populations on Cape York Peninsula show a largerproportion of older animals and feral pigs living in rainforest habitats show a low proportion ofanimals in very young and very old age classes. Pigs from the lowland rainforest population are inbetter condition than those of the other populations for most of the year, reflecting the availability offood all year round in this environment. Differences in the population structure of the threepopulations are discussed with respect to fecundity and several mortality factors such as predation anddiseases/parasites.

  8. Should I stay or should I go? Dispersal and population structure in small, isolated desert populations of West African crocodiles.

    Directory of Open Access Journals (Sweden)

    Guillermo Velo-Antón

    Full Text Available The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa. We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4 and microsatellite markers (32 loci and a subset of 12 loci. Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure and considerable genetic differentiation between sub-basins (FST range: 0.12-0.24 with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments.

  9. Relationships between tuna catch and variable frequency oceanographic conditions

    Directory of Open Access Journals (Sweden)

    F. I. Ormaza-González

    2016-08-01

    Full Text Available Skipjack (Katsuwunus pelamis, yellow fin (Thunnus albacares and albacore (Thunnus alulunga tunas landed in the Eastern Pacific Ocean (EPO countries and Ecuador were correlated to the Indexes Oceanic El Niño (ONI and Multivariate Enso Index (MEI. The temporal series 1983–2012, and 1977–1999 (warm Pacific Decadal Oscillation, PDO, and 2000–2012 (cold PDO were analyzed. Linear correlation showed that at least 11 % of the total landings were associated with the MEI, with a slightly negative gradient from cold to warm conditions. When non-linear regression (n  =  6, the R2 was higher up to 0.304 (MEI, r =  0.551. The correlation shows high spread from −0.5 to +0.5 for both MEI/ONI; the highest landings occurred at 0.34–0.45; both indexes suggested that at extreme values < −1.0 and > 1.1 total landings tend to decrease. Landings were associated up to 21.9 % (MEI in 2000–2012, 1983–1999 rendered lower R2 (< 0.09; i.e., during cold PDO periods there was a higher association between landings and oceanographic conditions. For the non-linear regression (n  =  6 a R2 of 0.374 (MEI and 0.408 (ONI were registered, for the 2000–2012, a higher R2 was observed in 1983–1999, 0.443 and 0.711 for MEI and ONI respectively, suggesting that is better to analyze split series (1983–1999, 2000–2012 than as a whole (1983–2012, due to noise produced by the transition from hot to cold PDOs. The highest landings were in the range −0.2 to 0.5 for MEI/ONI. The linear regression of skipjack landings in Ecuador gave an R2 of 0.140 (MEI and 0.066 (ONI and the non-linear were 0.440 and 0.183 respectively. Total landings in the EPO associated to oceanographic events of high and low frequencies could be used somehow as predictors of the high El Niño o La Niña. There is a clear evidence that tuna fish biomass are at higher levels when the PDO is on cold phase (2000–2030 and vice versa on warm phase (1980–1999. The

  10. Whole-genome sequence variation, population structure and demographic history of the Dutch population

    NARCIS (Netherlands)

    Francioli, Laurent C.; Menelaou, Andronild; Pulit, Sara L.; Van Dijk, Freerk; Palamara, Pier Francesco; Elbers, Clara C.; Neerincx, Pieter B. T.; Ye, Kai; Guryev, Victor; Kloosterman, Wigard P.; Deelen, Patrick; Abdellaoui, Abdel; Van Leeuwen, Elisabeth M.; Van Oven, Mannis; Vermaat, Martijn; Li, Mingkun; Laros, Jeroen F. J.; Karssen, Lennart C.; Kanterakis, Alexandros; Amin, Najaf; Hottenga, Jouke Jan; Lameijer, Eric-Wubbo; Kattenberg, Mathijs; Dijkstra, Martijn; Byelas, Heorhiy; Van Settenl, Jessica; Van Schaik, Barbera D. C.; Bot, Jan; Nijman, Isaac J.; Renkens, Ivo; Marscha, Tobias; Schonhuth, Alexander; Hehir-Kwa, Jayne Y.; Handsaker, Robert E.; Polak, Paz; Sohail, Mashaal; Vuzman, Dana; Hormozdiari, Fereydoun; Van Enckevort, David; Mei, Hailiang; Koval, Vyacheslav; Moed, Ma-Tthijs H.; Van der Velde, K. Joeri; Rivadeneira, Fernando; Estrada, Karol; Medina-Gomez, Carolina; Isaacs, Aaron; Platteel, Mathieu; Swertz, Morris A.; Wijmenga, Cisca

    Whole-genome sequencing enables complete characterization of genetic variation, but geographic clustering of rare alleles demands many diverse populations be studied. Here we describe the Genome of the Netherlands (GoNL) Project, in which we sequenced the whole genomes of 250 Dutch parent-offspring

  11. Whole-genome sequence variation, population structure and demographic history of the Dutch population

    NARCIS (Netherlands)

    The Genome of the Netherlands Consortium; T. Marschall (Tobias); A. Schönhuth (Alexander)

    2014-01-01

    htmlabstractWhole-genome sequencing enables complete characterization of genetic variation, but geographic clustering of rare alleles demands many diverse populations be studied. Here we describe the Genome of the Netherlands (GoNL) Project, in which we sequenced the whole genomes of 250 Dutch

  12. FLUKTUASI DAN KOMPOSISI HASIL TANGKAPAN TUNA NERITIK TERTANGKAP JARING INSANG DI PERAIRAN LAUT CINA SELATAN

    Directory of Open Access Journals (Sweden)

    Arief Wujdi

    2016-03-01

    Full Text Available Saat ini tuna neritik merupakan komoditas penting perikanan di Indonesia, namun ketersediaan data dan informasi hasil tangkapan jenis tuna ini masih tergolong kurang. Penelitian ini bertujuan untuk memperoleh informasi mengenai sebaran daerah penangkapan, fluktuasi hasil tangkapan tuna neritik yang tertangkap jaring insang yang beroperasi di Laut Cina Selatan. Pengumpulan data dilakukan melalui program enumerasi monitoring hasil tangkapan harian di Pemangkat pada tahun 2011-2012. Hasil menunjukkan daerah penangkapan tersebar di perairan Laut Cina Selatan pada koordinat 01°03’ LS-04°57’ LU; dan 104°65’-110°00’ BT. Hasil tangkapan jenis tuna neritik menunjukan variasi yang cenderung sama dimana puncak hasil tangkapan terjadi pada bulan Oktober dan November. Pola CPUE berfluktuasi dan cenderung mengalami peningkatan dan puncaknya terjadi pada bulan November 2011 dan 2012, yaitu 402,85 dan 444,57 kg/hari/trip. Secara statistik hasil tangkapan pada periode 2011-2012 tidak berbeda nyata (p<0,05. Komposisi hasil tangkapan bulanan jenis tuna neritik bervariasi berdasarkan atas spesies yang didominasi oleh Euthynnus affinis (49,7% diikuti dengan Thunnus tonggol (33,4%; Scomberomorus commerson (15,9%; dan Scomberomorus guttatus (1%. Kelimpahan Euthynnus affinis terjadi pada musim timur hingga musim peralihan 2 (Juni- November, sedangkan kelimpahan Thunnus tonggol terjadi pada musim barat (Januari-Februari. Nowadays, neritic tuna just become an important commodity Indonesia. However, the information about catch of tuna neritic species in Indonesia still quite lacks. This This study aims to obtain information about catch fluctuation, monthly catch per unit of effort, and catch composition of neritic tuna species caught by gill net operated in the South China Sea. Data was collected by daily catch monitoring program by enumerator in Pemangkat during period 2011-2012. The result showed that gillnetter fishing ground is scattered between 01°03

  13. High genetic diversity and low population structure in Porter's sunflower (Helianthus porteri).

    Science.gov (United States)

    Gevaert, Scott D; Mandel, Jennifer R; Burke, John M; Donovan, Lisa A

    2013-01-01

    Granite outcrops in the southeastern United States are rare and isolated habitats that support edaphically controlled communities dominated by herbaceous plants. They harbor rare and endemic species that are expected to have low genetic variability and high population structure due to small population sizes and their disjunct habitat. We test this expectation for an annual outcrop endemic, Helianthus porteri (Porter's sunflower). Contrary to expectation, H. porteri has relatively high genetic diversity (H e = 0.681) and relatively low genetic structure among the native populations (F ST = 0.077) when compared to 5 other Helianthus species (N = 288; 18 expressed sequence tag-SSR markers). These findings suggest greater gene flow than expected. The potential for gene flow is supported by the analysis of transplant populations established with propagules from a common source in 1959. One population established close to a native population (1.5 km) at the edge of the natural range is genetically similar to and shares rare alleles with the adjacent native population and is distinct from the central source population. In contrast, a transplant population established north of the native range has remained similar to the source population. The relatively high genetic diversity and low population structure of this species, combined with the long-term success of transplanted populations, bode well for its persistence as long as the habitat persists.

  14. Population structure and effective/census population size ratio in threatened three-spined stickleback populations from an isolated river basin in northwest Spain.

    Science.gov (United States)

    Pérez-Figueroa, A; Fernández, C; Amaro, R; Hermida, M; San Miguel, E

    2015-08-01

    Variability at 20 microsatellite loci was examined to assess the population genetic structure, gene flow, and effective population size (N(e)) in three populations of three-spined stickleback (Gasterosteus aculeatus) from the upper basin of the Miño River in Galicia, NW Spain, where this species is threatened. The three populations showed similar levels of genetic diversity. There is a significant genetic differentiation between the three populations, but also significant gene flow. N(e) estimates based on linkage disequilibrium yielded values of 355 for the Miño River population and 241 and 311 for the Rato and Guisande Rivers, respectively, although we expect that these are overestimates. N(e) estimates based on temporal methods, considering gene flow or not, for the tributaries yielded values of 30-56 and 47-56 for the Rato and Guisande Rivers, respectively. Estimated census size (N(c)) for the Rato River was 880 individuals. This yielded a N(e)/N(c) estimate of 3-6 % for temporal estimation of N(e), which is within the empirical range observed in freshwater fishes. We suggest that the three populations analyzed have a sufficient level of genetic diversity with some genetic structure. Additionally, the absence of physical barriers suggests that conservation efforts and monitoring should focus in the whole basin as a unit.

  15. A genomic overview of the population structure of Salmonella.

    Directory of Open Access Journals (Sweden)

    Nabil-Fareed Alikhan

    2018-04-01

    Full Text Available For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST] corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST, core genome MLST (cgMLST, and whole genome MLST (wgMLST and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs. eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.

  16. A genomic overview of the population structure of Salmonella.

    Science.gov (United States)

    Alikhan, Nabil-Fareed; Zhou, Zhemin; Sergeant, Martin J; Achtman, Mark

    2018-04-01

    For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.

  17. Harvesting Renewable Resources of Population with Size Structure and Diffusion

    Directory of Open Access Journals (Sweden)

    Qiang-Jun Xie

    2014-01-01

    Full Text Available The aim of this work is to explore the optimal exploitation way for a biological resources model incorporating individual’s size difference and spatial effects. The existence of a unique nonnegative solution to the state system is shown by means of Banach’s fixed point theorem, and the continuous dependence of the population density with the harvesting effort is given. The optimal harvesting strategy is established via normal cone and adjoint system technique. Some conditions are found to assure that there is only one optimal policy.

  18. The genetic diversity and population structure of common bean ...

    African Journals Online (AJOL)

    The STRUCTURE result was confirmed by Principal Coordinate analysis (PCoA) which also clustered beans in three groups. Most Andean genotypes were included in K3.1 and Mesoamerican genotypes belonged to the K3.2 and K3.3 subgroups. This study sets the stage for further analyses for agronomic traits such as ...

  19. Population structures of Astragalus filipes collections from western North America

    Science.gov (United States)

    B. Shaun Bushman; Kishor Bhattarai; Douglas A. Johnson

    2010-01-01

    The majority of species used for revegetation in semi-arid western rangelands of North America are grasses, with few forbs and nearly no legumes. Astragalus filipes (Torr. Ex A. Gray) is a western North American legume and a promising candidate for use in rangeland revegetation, but assessments of plant species diversity and structure are necessary to determine which...

  20. Foveal shape and structure in a normal population.

    Science.gov (United States)

    Tick, Sarah; Rossant, Florence; Ghorbel, Itebeddine; Gaudric, Alain; Sahel, José-Alain; Chaumet-Riffaud, Philippe; Paques, Michel

    2011-07-29

    The shape of the human fovea presents important but still poorly characterized variations. In this study, the variability of the shape and structure of normal foveae were examined. In a group of 110 eyes of 57 healthy adults, the shape and structure of the fovea were analyzed by automated segmentation of retinal layer on high-resolution optical coherence tomography scans. In an additional group of 10 normal eyes of 10 patients undergoing fluorescein angiography, the size of the foveal avascular zone (FAZ) was correlated to foveal shape. From the thickest to the thinnest fovea, there was a structural continuum ranging from a shallow pit with continuity of the inner nuclear layer (INL) over the center (seven eyes; 6.7%), to a complete separation of inner layers overlying a flat and thinner central outer nuclear layer (ONL; eight eyes; 7.3%). Central foveal thickness correlated inversely to the degree of inner layer separation and to the surface of the FAZ. Foveal structure strongly correlates with its neurovascular organization. The findings support a developmental model in which the size of the FAZ determines the extent of centrifugal migration of inner retinal layers, which counteracts in some way the centripetal packing of cone photoreceptors.

  1. Genetic polymorphism and population structure of Echinococcus ortleppi.

    Science.gov (United States)

    Addy, F; Wassermann, M; Banda, F; Mbaya, H; Aschenborn, J; Aschenborn, O; Koskei, P; Umhang, G; DE LA Rue, M; Elmahdi, I E; Mackenstedt, U; Kern, P; Romig, T

    2017-04-01

    The zoonotic cestode Echinococcus ortleppi (Lopez-Neyra and Soler Planas, 1943) is mainly transmitted between dogs and cattle. It occurs worldwide but is only found sporadically in most regions, with the notable exception of parts of southern Africa and South America. Its epidemiology is little understood and the extent of intraspecific variability is unknown. We have analysed in the present study the genetic diversity among 178 E. ortleppi isolates from sub-Saharan Africa, Europe and South America using the complete mitochondrial cox1 (1608 bp) and nad1 (894 bp) DNA sequences. Genetic polymorphism within the loci revealed 15 cox1 and six nad1 haplotypes, respectively, and 20 haplotypes of the concatenated genes. Presence of most haplotypes was correlated to geographical regions, and only one haplotype had a wider spread in both eastern and southern Africa. Intraspecific microvariance was low in comparison with Echinococcus granulosus sensu stricto, despite the wide geographic range of examined isolates. In addition, the various sub-populations showed only subtle deviation from neutrality and were mostly genetically differentiated. This is the first insight into the population genetics of the enigmatic cattle adapted Echinococcus ortleppi. It, therefore, provides baseline data for biogeographical comparison among E. ortleppi endemic regions and for tracing its translocation paths.

  2. Spawning Dynamics and Size Related Trends in Reproductive Parameters of Southern Bluefin Tuna, Thunnus maccoyii.

    Directory of Open Access Journals (Sweden)

    Jessica H Farley

    Full Text Available Knowledge of spawning behaviour and fecundity of fish is important for estimating the reproductive potential of a stock and for constructing appropriate statistical models for assessing sustainable catch levels. Estimates of length-based reproductive parameters are particularly important for determining potential annual fecundity as a function of fish size, but they are often difficult to estimate reliably. Here we provide new information on the reproductive dynamics of southern bluefin tuna (SBT Thunnus maccoyii through the analysis of fish size and ovary histology collected on the spawning ground in 1993-1995 and 1999-2002. These are used to refine previous parameter estimates of spawning dynamics and investigate size related trends in these parameters. Our results suggest that the small SBT tend to arrive on the spawning ground slightly later and depart earlier in the spawning season relative to large fish. All females were mature and the majority were classed as spawning capable (actively spawning or non-spawning with a very small proportion classed as regressing. The fraction of females spawning per day decreased with fish size, but once females start a spawning episode, they spawned daily irrespective of size. Mean batch fecundity was estimated directly at 6.5 million oocytes. Analysis of ovary histology and ovary weight data indicated that relative batch fecundity, and the duration of spawning and non-spawning episodes, increased with fish size. These reproductive parameter estimates could be used with estimates of residency time on the spawning ground as a function of fish size (if known and demographic data for the spawning population to provide a time series of relative annual fecundity for SBT.

  3. Discovering where bluefin tuna, Thunnus thynnus, might go: using environmental and fishery data to map potential tuna habitat in the eastern Mediterranean Sea

    OpenAIRE

    Dimitrios Damalas; Persefoni Megalofonou

    2012-01-01

    Based on a dataset derived from commercial fisheries in the eastern Mediterranean Sea in 1998-2005, we applied generalized additive models (GAMs) to investigate the relative influence of a range of environmental factors on catch rates of Atlantic bluefin tuna (Thunnus thynnus Linnaeus, 1785). GAM analyses were conducted by separately modelling (1) the probability of making a catch (encountering a school), and (2) the positive catch rates (school size). Results suggested intra-annual variation...

  4. Estimating demographic contributions to effective population size in an age-structured wild population experiencing environmental and demographic stochasticity.

    Science.gov (United States)

    Trask, Amanda E; Bignal, Eric M; McCracken, Davy I; Piertney, Stuart B; Reid, Jane M

    2017-09-01

    A population's effective size (N e ) is a key parameter that shapes rates of inbreeding and loss of genetic diversity, thereby influencing evolutionary processes and population viability. However, estimating N e , and identifying key demographic mechanisms that underlie the N e to census population size (N) ratio, remains challenging, especially for small populations with overlapping generations and substantial environmental and demographic stochasticity and hence dynamic age-structure. A sophisticated demographic method of estimating N e /N, which uses Fisher's reproductive value to account for dynamic age-structure, has been formulated. However, this method requires detailed individual- and population-level data on sex- and age-specific reproduction and survival, and has rarely been implemented. Here, we use the reproductive value method and detailed demographic data to estimate N e /N for a small and apparently isolated red-billed chough (Pyrrhocorax pyrrhocorax) population of high conservation concern. We additionally calculated two single-sample molecular genetic estimates of N e to corroborate the demographic estimate and examine evidence for unobserved immigration and gene flow. The demographic estimate of N e /N was 0.21, reflecting a high total demographic variance (σ2dg) of 0.71. Females and males made similar overall contributions to σ2dg. However, contributions varied among sex-age classes, with greater contributions from 3 year-old females than males, but greater contributions from ≥5 year-old males than females. The demographic estimate of N e was ~30, suggesting that rates of increase of inbreeding and loss of genetic variation per generation will be relatively high. Molecular genetic estimates of N e computed from linkage disequilibrium and approximate Bayesian computation were approximately 50 and 30, respectively, providing no evidence of substantial unobserved immigration which could bias demographic estimates of N e . Our analyses identify

  5. Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

    Directory of Open Access Journals (Sweden)

    Federica Costantini

    Full Text Available While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.

  6. Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

    Science.gov (United States)

    Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

    2013-01-01

    While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.

  7. Ancestral informative marker selection and population structure visualization using sparse Laplacian eigenfunctions.

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    Full Text Available Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the similar underlying population structure efficiently. Employing a standard Support Vector Machine (SVM to predict individuals' continental memberships on HGDP dataset of seven continents, we demonstrate that the selected SNPs by our method are more informative but less redundant than those selected by PCA. Our algorithm is a promising tool in genome-wide association studies and population genetics, facilitating the selection of structure informative markers, efficient detection of population substructure and ancestral inference.

  8. Population structure age of Paraná state between 1970 and 2010

    Directory of Open Access Journals (Sweden)

    Eduardo de Pintor

    2014-06-01

    Full Text Available The theory of demographic transition began with an effort of Frank Notestein (1945 to understand the demographic changes that were occurring in Western Europe since the late nineteenth century. The demographic transition is the transition between two scenarios of population growth, which changes the age structure of the population. The aim of the article is to discuss the evolution of population structure age of Paraná state between 1970 and 2010. The changes in the age structure of the Paraná indicate a reduction in the share of young population and increasing aging population, an increase in the relative weight of the elderly population. Public policies on education, health, social security and labor market should consider the current change in the age structure. Thus, the aim of this study was to analyze the change in the age structure of the population of the state of Paraná. For this we used data Censuses of the Brazilian Institute of Geography and Statistics (IBGE on the age distribution of urban and rural Paraná and its Mesoregions. It was concluded that the change in structure occurs group widespread in all Mesoregions state. However, it occurs unevenly between urban and rural population.

  9. Food web framework for size-structured populations

    DEFF Research Database (Denmark)

    Hartvig, Martin; Andersen, Ken Haste; Beyer, Jan

    2011-01-01

    . Parameter values are determined from cross-species analysis of fish communities as life-history omnivory is widespread in aquatic systems, but may be reparameterised for other systems. An ensemble of food webs is generated and the resulting communities are analysed at four levels of organisation: community......We synthesise traditional unstructured food webs, allometric body size scaling, trait-based modelling, and physiologically structured modelling to provide a novel and ecologically relevant tool for size-structured food webs. The framework allows food web models to include ontogenetic growth...... level, species level, trait level, and individual level. The model may be solved analytically by assuming that the community spectrum follows a power law. The analytical solution provides a baseline expectation of the results of complex food web simulations, and agrees well with the predictions...

  10. Population structure of Aggarwals of north India as revealed by molecular markers.

    Science.gov (United States)

    Gupta, Vipin; Khadgawat, Rajesh; Ng, Hon Keung Tony; Kumar, Satish; Rao, Vadlamudi Raghavendra; Sachdeva, Mohinder Pal

    2010-12-01

    Using molecular genetic data on Aggarwals (Vaish/Vysya), an endogamous population group of north India, we provide evidence of its homogeneous unstratified population structure. We found the mean average heterozygosity value of 0.33 for 14 single nucleotide polymorphisms belonging to four genes (TCF7L2-, HHEX-, KCNJ11-, and ADIPOQ-) in the Aggarwal population (sample of 184 individuals) and tried to evaluate the genomic efficiency of endogamy in this population with the help of clan-based stratified analysis. We concluded that the sociocultural identity of the endogamous population groups could act as a robust proxy maker for inferring their homogeneity and population structure in India, which is ideal also for population selection for future genome-wide association studies in the country.

  11. Urban habitat fragmentation and genetic population structure of bobcats in coastal southern California

    Science.gov (United States)

    Ruell, E.W.; Riley, S.P.D.; Douglas, M.R.; Antolin, M.F.; Pollinger, J.R.; Tracey, J.A.; Lyren, L.M.; Boydston, E.E.; Fisher, R.N.; Crooks, K.R.

    2012-01-01

    Although habitat fragmentation is recognized as a primary threat to biodiversity, the effects of urban development on genetic population structure vary among species and landscapes and are not yet well understood. Here we use non-invasive genetic sampling to compare the effects of fragmentation by major roads and urban development on levels of dispersal, genetic diversity, and relatedness between paired bobcat populations in replicate landscapes in coastal southern California. We hypothesized that bobcat populations in sites surrounded by urbanization would experience reduced functional connectivity relative to less isolated nearby populations. Our results show that bobcat genetic population structure is affected by roads and development but not always as predicted by the degree that these landscape features surround fragments. Instead, we suggest that urban development may affect functional connectivity between bobcat populations more by limiting the number and genetic diversity of source populations of migrants than by creating impermeable barriers to dispersal.

  12. Population structure, fluctuating asymmetry and genetic variability in an endemic and highly isolated Astyanax fish population (Characidae

    Directory of Open Access Journals (Sweden)

    Maria Claudia Gross

    2004-01-01

    Full Text Available Morphological and chromosomal markers were used to infer the structure and genetic variability of a population of fish of the genus Astyanax, geographically isolated at sinkhole 2 of Vila Velha State Park, Paraná, Brazil. Two morphotypes types were observed, the standard phenotype I and phenotype II which showed an anatomical alteration probably due to an inbreeding process. Fluctuating asymmetry (FA analysis of different characters showed low levels of morphological variation among the population from sinkhole 2 and in another population from the Tibagi river (Paraná, Brazil. The Astyanax karyotype was characterized in terms of chromosomal morphology, constitutive heterochromatin and nucleolar organizer regions. Males and females presented similar karyotypes (2n=48, 6M+18SM+14ST+10A with no evidence of a sex chromosome system. One female from sinkhole 2 was a natural triploid with 2n=3x=72 chromosomes (9M+27SM+21ST+15A. The data are discussed regarding the maintenance of population structure and their evolutionary importance, our data suggesting that Astyanax from the Vila Velha State Park sinkhole 2 is a recently isolated population.

  13. Colony social organization and population genetic structure of an introduced population of formosan subterranean termite from New Orleans, Louisiana.

    Science.gov (United States)

    Husseneder, Claudia; Messenger, Matthew T; Su, Nan-Yao; Grace, J Kenneth; Vargo, Edward L

    2005-10-01

    The Formosan subterranean termite, Coptotermes formosanus Shiraki, is an invasive species in many parts of the world, including the U.S. mainland. The reasons for its invasive success may have to do with the flexible social and spatial organization of colonies. We investigated the population and breeding structure of 14 C. formosanus colonies in Louis Armstrong Park, New Orleans, LA. This population has been the focus of extensive study for many years, providing the opportunity to relate aspects of colony breeding structure to previous findings on colony characteristics such as body weight and number of workers, wood consumption, and intercolony aggression. Eight colonies were headed by a single pair of outbred reproductives (simple families), whereas six colonies were headed by low numbers of multiple kings and/or queens that were likely the neotenic descendants of the original colony (extended families). Within the foraging area of one large extended family colony, we found genetic differentiation among different collection sites, suggesting the presence of separate reproductive centers. No significant difference between simple family colonies and extended family colonies was found in worker body weight, soldier body weight, foraging area, population size, or wood consumption. However, level of inbreeding within colonies was negatively correlated with worker body weight and positively correlated with wood consumption. Also, genetic distance between colonies was positively correlated with aggression levels, suggesting a genetic basis to nestmate discrimination cues in this termite population. No obvious trait associated with colony reproductive structure was found that could account for the invasion success of this species.

  14. Genetic diversity and population structure in Polygonum cespitosum: insights to an ongoing plant invasion.

    Directory of Open Access Journals (Sweden)

    Silvia Matesanz

    Full Text Available Molecular markers can help elucidate how neutral evolutionary forces and introduction history contribute to genetic variation in invaders. We examined genetic diversity, population structure and colonization patterns in the invasive Polygonum cespitosum, a highly selfing, tetraploid Asian annual introduced to North America. We used nine diploidized polymorphic microsatellite markers to study 16 populations in the introduced range (northeastern North America, via the analyses of 516 individuals, and asked the following questions: 1 Do populations have differing levels of within-population genetic diversity? 2 Do populations form distinct genetic clusters? 3 Does population structure reflect either geographic distances or habitat similarities? We found low heterozygosity in all populations, consistent with the selfing mating system of P. cespitosum. Despite the high selfing levels, we found substantial genetic variation within and among P. cespitosum populations, based on the percentage of polymorphic loci, allelic richness, and expected heterozygosity. Inferences from individual assignment tests (Bayesian clustering and pairwise FST values indicated high among-population differentiation, which indicates that the effects of gene flow are limited relative to those of genetic drift, probably due to the high selfing rates and the limited seed dispersal ability of P. cespitosum. Population structure did not reflect a pattern of isolation by distance nor was it related to habitat similarities. Rather, population structure appears to be the result of the random movement of propagules across the introduced range, possibly associated with human dispersal. Furthermore, the high population differentiation, genetic diversity, and fine-scale genetic structure (populations founded by individuals from different genetic sources in the introduced range suggest that multiple introductions to this region may have occurred. High genetic diversity may further

  15. Vector-borne disease risk indexes in spatially structured populations.

    Directory of Open Access Journals (Sweden)

    Jorge Velázquez-Castro

    2018-02-01

    Full Text Available There are economic and physical limitations when applying prevention and control strategies for urban vector borne diseases. Consequently, there are increasing concerns and interest in designing efficient strategies and regulations that health agencies can follow in order to reduce the imminent impact of viruses like Dengue, Zika and Chikungunya. That includes fumigation, abatization, reducing the hatcheries, picking up trash, information campaigns. A basic question that arise when designing control strategies is about which and where these ones should focus. In other words, one would like to know whether preventing the contagion or decrease vector population, and in which area of the city, is more efficient. In this work, we propose risk indexes based on the idea of secondary cases from patch to patch. Thus, they take into account human mobility and indicate which patch has more chance to be a corridor for the spread of the disease and which is more vulnerable, i.e. more likely to have cases?. They can also indicate the neighborhood where hatchery control will reduce more the number of potential cases. In order to illustrate the usefulness of these indexes, we run a set of numerical simulations in a mathematical model that takes into account the urban mobility and the differences in population density among the areas of a city. If we label by i a particular neighborhood, the transmission risk index (TRi measures the potential secondary cases caused by a host in that neighborhood. The vector transmission risk index (VTRi measures the potential secondary cases caused by a vector. Finally, the vulnerability risk index (VRi measures the potential secondary cases in the neighborhood. Transmission indexes can be used to give geographical priority to some neighborhoods when applying prevention and control measures. On the other hand, the vulnerability index can be useful to implement monitoring campaigns or public health investment.

  16. Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites

    DEFF Research Database (Denmark)

    Pham, Lan Doan; Do, Duy Ngoc; Binh, Nguyen Trong

    2013-01-01

    Cattle play a very important role in agriculture and food security in Vietnam. A high level of cattle diversity exists and serves different needs of Vietnamese cattle keepers but has not yet been molecularly characterized. This study evaluates the genetic diversity and structure of Vietnamese...... geographic distances. Structure analysis indicated five homogeneous clusters. The Brahman, Lang Son, Ha Giang and U Dau Riu cattle were assigned to independent clusters while Nghe An, Thanh Hoa and Phu Yen cattle were grouped in a single cluster. We conclude that Vietnamese indigenous cattle have high levels...

  17. Reducing the Bitterness of Tuna (Euthynnus pelamis Dark Meat with Lactobacillus casei subsp. casei ATCC 393

    Directory of Open Access Journals (Sweden)

    Ernani S. Sant’Anna

    2004-01-01

    Full Text Available During the process of canning tuna fish, considerable amounts of dark tuna meat are left over because of its bitterness, which are then used in the production of animal food. Fermentation with Lactobacillus casei subsp. casei ATCC 393 was used as an alternative to reduce this bitter taste. Samples of meat were prepared, vacuum packed and then stored at –18 °C. The frozen dark meat was used immediately after defrosting and the experiment was carried out with 2 and 4 % of NaCl with the addition of 2 and 4 % of glucose, respectively. The dark tuna meat was inoculated with lactic acid bacteria (LAB and fermented at 10 °C for 30 days. The fermentation process was monitored through bacteriological and chemical analyses, when an increase of acidity and the corresponding decrease of pH were observed due to the prevalence of LAB. Sensorial analysis, using a test of multiple comparison, was carried out with pastes of fermented dark tuna meat and presented a significant difference when compared to the paste control, indicating the reduction of bitter taste.

  18. Microbiological quality and safety of Skipjack tuna loins (Katsuwonus Pelamis intented for canning

    Directory of Open Access Journals (Sweden)

    Francesco Casalinuovo

    2018-03-01

    Full Text Available Tuna is a food widely consumed fresh and canned as well. After catching and filleting, a pre-cooking step is normally followed by freezing and shipping to canning industry as loins. The aim of this paper was to assess the microbiological quality and safety of tuna loins (50 samples imported by an Italian canned tuna producer from two different FAO fishing areas. Total bacterial count (TBC, Coliforms, Enterobacteriaceae, Escherichia coli, Listeria monocytogenes, Salmonella, Staphylococcus aureus, Vibrio parahaemolyticus, Vibrio cholera, pH measurement, S. aureus enterotoxin and histamine levels were evaluated. Significant differences were evidenced for TBC, Enterobacteriaceae, E. coli, Coliforms and pH between fishing areas. Staphylococcus aureus was detected in all the samples tested at 1 to 3 Log cfu/g; Staphylococcus warneri, S. saprophyticus, S. epidermidis, S. hominis, S. intermedius, S. vitulinus and S. sciuri were also identified. Listeria monocytogenes, Salmonella, Vibrio parahaemolyticus, Vibrio cholera and Staphylococcus aureus enterotoxin were not detected. Histamine ranged between 0 to 5 mg/kg. The tuna loins analysed in this paper have to be considered safe; staphylococci presence represents a possible concern and has to been taken in account when risk analysis is carried out.

  19. Gender Transformations and Colonial Displacements in Laura Antillano's "Tuna de mar"

    Science.gov (United States)

    Reid, Alana

    2015-01-01

    This paper examines the trajectories of two characters in Laura Antillano's short story, "Tuna de mar" (1991), as they navigate interrelated systems of power and attempt to position themselves closer to, or further away from, the margins. Set in the late eighteenth century, the tale features a female protagonist who escapes prostitution…

  20. Nisin Migration in Shelf Stable, Tuna-Filled Tortillas During Storage

    Science.gov (United States)

    2014-09-22

    INGREDIENTS AND PROCESSING ..........................................................................4 2.4 TUNA WRAP STORAGE...Leung, 1986 and Taub, 2003), meat (Pavey, 1972; Powers, 1981; Yang, 1997 and Richardson, 1995), seafood (Dymsza, 1979), eggs (Richardson, 2008 and...Incorporation of Preservatives, such as nitrites and antioxidants. (4) Thermal pasteurization by baking. (5) Appropriate Packaging, such as the

  1. 77 FR 19175 - Atlantic Highly Migratory Species; 2012 Atlantic Bluefin Tuna Quota Specifications

    Science.gov (United States)

    2012-03-30

    ...). Attachments to electronic comments will be accepted in Microsoft Word or Excel, WordPerfect, or Adobe PDF file... active member of the International Commission for the Conservation of Atlantic Tunas (ICCAT), the United States implements binding ICCAT recommendations to comply with this international treaty. ATCA authorizes...

  2. 78 FR 2273 - Canned Tuna Deviating From Identity Standard; Temporary Permit for Market Testing

    Science.gov (United States)

    2013-01-10

    ... introduces or causes the introduction of one or more of the test products into interstate commerce, but not... permit covers limited interstate marketing tests of products identified as ``no drain canned tuna... permit provides for the temporary marketing of a total 533,333 cases of 12 x 4 ounce cans (totaling 6.4...

  3. Biogenic amine content, histamine-forming bacteria, and adulteration of pork in tuna sausage products.

    Science.gov (United States)

    Kung, Hsien-Feng; Tsai, Yung-Hsiang; Chang, Shih-Chih; Hong, Tang-Yao

    2012-10-01

    Twenty-five tuna sausage products were purchased from retail markets in Taiwan. The rates of occurrence of biogenic amines, histamine-forming bacteria, and adulteration by pork and poultry were determined. The average content of various biogenic amines in all tested samples was less than 2.0 mg/100 g (Makaira nigricans (blue marlin).

  4. Pelagic shark bycatch in the tuna- and swordfish-directed longline ...

    African Journals Online (AJOL)

    The capture of pelagic sharks as bycatch of the South African pelagic longline fleet targeting tuna Thunnus spp. and swordfish Xiphias gladius was investigated during the period 1998–2005. In all, 26 species were caught, of which six are listed by the International Union for Conservation of Nature (IUCN) as Vulnerable and ...

  5. CONCENTRATION AND RECOVERY OF PROTEIN FROM TUNA COOKING JUICE BY FORWARD OSMOSIS

    Directory of Open Access Journals (Sweden)

    KHONGNAKORN W.

    2016-07-01

    Full Text Available Tuna cooking processing plants generate large amount of cooking juice containing a significant content of protein. Recovery and concentrating process of this valuable compound together with a low energy consumption process are of interest regarding full utilization concept and green process approach. Forward osmosis (FO was employed in this work to recover and concentrate tuna cooking juice. FO process could increase the protein concentration up to 9% with an average permeate flux of 2.54 L/m2h. The permeate flux however tended to decrease as protein concentration increased due to the impact of osmotic pressure of the feed and fouling on the membrane surface. Since tuna cooking juice consists of protein and minerals, membrane analyses indicated that fouling was more severe compared to the fouling caused by standard bovine serum albumin pure protein. However, the presence of minerals rendered it a quicker and lower energy process by comparison. These results indicated that FO is a promising technique in the recovery and concentration of tuna cooking juice protein.

  6. V ITER chrání zimu tuna stříbra

    Czech Academy of Sciences Publication Activity Database

    Řípa, Milan

    Říjen (2016) ISSN 2464-7888 Institutional support: RVO:61389021 Keywords : fusion * tokamak * ITER * thermal shield * silver * superconductivity Subject RIV: BL - Plasma and Gas Discharge Physics http://www.3pol.cz/cz/rubriky/jaderna-fyzika-a-energetika/1922-v-iter-chrani-zimu-tuna-stribra

  7. 77 FR 21015 - Atlantic Highly Migratory Species; Atlantic Bluefin Tuna Fisheries

    Science.gov (United States)

    2012-04-09

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration 50 CFR Part 635 [Docket No. 110210132-1275-02] RIN 0648-XB116 Atlantic Highly Migratory Species; Atlantic Bluefin Tuna Fisheries AGENCY... to their ability to attract customers. In addition, 2011 Large Pelagics Survey estimates indicate...

  8. 78 FR 20258 - Atlantic Highly Migratory Species; Atlantic Bluefin Tuna Fisheries

    Science.gov (United States)

    2013-04-04

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration 50 CFR Part 635 [Docket No. 120306154-2241-02] RIN 0648-XC593 Atlantic Highly Migratory Species; Atlantic Bluefin Tuna Fisheries AGENCY... retention limit is vital to their ability to attract customers. In addition, 2012 Large Pelagics Survey...

  9. 76 FR 18416 - Atlantic Highly Migratory Species; Atlantic Bluefin Tuna Fisheries

    Science.gov (United States)

    2011-04-04

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration 50 CFR Part 635 [Docket No. 100317152-0176-01] RIN 0648-XA327 Atlantic Highly Migratory Species; Atlantic Bluefin Tuna Fisheries AGENCY... ability to attract customers. In addition, recent Large Pelagics Survey estimates indicate that charter...

  10. Closing the Incentive Gap: The Role of Public and Private Actors in Governing Indonesia's Tuna Fisheries

    NARCIS (Netherlands)

    Bailey, M.L.; Miller, A.M.M.; Bush, S.R.; Zwieten, van P.A.M.; Wiryawan, B.

    2016-01-01

    Indonesia is one of the world's largest tuna producing countries, yet regulatory oversight remains weak and management is poor. Incentive-based approaches are a way to improve state-based resource management, but they often require strong government regulation. In this paper, we use principal–agent

  11. Quantitative analysis on dose to humans as a result of consuming tuna fish contaminated by cesium radionuclides

    International Nuclear Information System (INIS)

    Khani, J.; Donev, J.M.K.C.

    2014-01-01

    Quantitative empirical data is presented on the dose exposure to North Americans consuming tuna fish that have accumulated concentrations of radioactive isotopes. The two particular radioactive isotopes of interest are cesium-137 and cesium-134. Though biological effects of radiation are a widely debatable topic, the consumption of tuna fish does not support significant increased risk of cancer to humans. An important comparison is made between the elevated levels of radioactive cesium concentrations to naturally occurring radionuclides, namely potassium-40 and polonium-210. It is calculated that naturally occurring radioactive isotopes are in the orders of magnitude greater than the cesium radionuclides in tuna fish. (author)

  12. Quantitative analysis on dose to humans as a result of consuming tuna fish contaminated by cesium radionuclides

    Energy Technology Data Exchange (ETDEWEB)

    Khani, J.; Donev, J.M.K.C., E-mail: jykhani@ucalgary.ca, E-mail: jason.donev@ucalgary.ca [Univ. of Calgary, Calgary, AB (Canada)

    2014-07-01

    Quantitative empirical data is presented on the dose exposure to North Americans consuming tuna fish that have accumulated concentrations of radioactive isotopes. The two particular radioactive isotopes of interest are cesium-137 and cesium-134. Though biological effects of radiation are a widely debatable topic, the consumption of tuna fish does not support significant increased risk of cancer to humans. An important comparison is made between the elevated levels of radioactive cesium concentrations to naturally occurring radionuclides, namely potassium-40 and polonium-210. It is calculated that naturally occurring radioactive isotopes are in the orders of magnitude greater than the cesium radionuclides in tuna fish. (author)

  13. Microvessel organization and structure in experimental brain tumors: microvessel populations with distinctive structural and functional properties.

    Science.gov (United States)

    Schlageter, K E; Molnar, P; Lapin, G D; Groothuis, D R

    1999-11-01

    We studied microvessel organization in five brain tumor models (ENU, MSV, RG-2, S635cl15, and D-54MG) and normal brain, including microvessel diameter (LMVD), intermicrovessel distance (IMVD), microvessel density (MVD), surface area (S(v)), and orientation. LMVD and IMVD were larger and MVD was lower in tumors than normal brain. S(v) in tumors overlapped normal brain values and orientation was random in both tumors and brain. ENU and RG-2 tumors and brain were studied by electron microscopy. Tumor microvessel wall was thicker than that of brain. ENU and normal brain microvessels were continuous and nonfenestrated. RG-2 microvessels contained fenestrations and endothelial gaps; the latter had a maximum major axis of 3.0 microm. Based on anatomic measurements, the pore area of RG-2 tumors was estimated at 7.4 x 10(-6) cm(2) g(-1) from fenestrations and 3.5 x 10(-5) cm(2) g(-1) from endothelial gaps. Increased permeability of RG-2 microvessels to macromolecules is most likely attributable to endothelial gaps. Three microvessel populations may occur in brain tumors: (1) continuous nonfenestrated, (2) continuous fenestrated, and (3) discontinuous (with or without fenestrations). The first group may be unique to brain tumors; the latter two are similar to microvessels found in systemic tumors. Since structure-function properties of brain tumor microvessels will affect drug delivery, studies of microvessel function should be incorporated into clinical trials of brain tumor therapy, especially those using macromolecules. Copyright 1999 Academic Press.

  14. The Application of Contagious Disease Epidemiological Models to Known Population Structure and Movement

    Science.gov (United States)

    2016-03-01

    concept model ( Ebola ) • Time-varying disease transmission rate () Influenza model • Population structure represented via finite scale-free network...I N S T I T U T E F O R D E F E N S E A N A L Y S E S The Application of Contagious Disease Epidemiological Models to Known Population Structure ...Known Population Structure and Movement Julia K. Burr Robert L. Cubeta Lucas A. LaViolet Carl A. Curling This page is intentionally blank. iii

  15. Generation time, net reproductive rate, and growth in stage-age-structured populations

    DEFF Research Database (Denmark)

    Steiner, Uli; Tuljapurkar, Shripad; Coulson, Tim

    2014-01-01

    examples to show how reproductive timing Tc and level R0 are shaped by stage dynamics (individual trait changes), selection on the trait, and parent-offspring phenotypic correlation. We also show how population structure can affect dispersion in reproduction among ages and stages. These macroscopic...... to age-structured populations. Here we generalize this result to populations structured by stage and age by providing a new, unique measure of reproductive timing (Tc) that, along with net reproductive rate (R0), has a direct mathematical relationship to and approximates growth rate (r). We use simple...

  16. Genetic Diversity and Population Structure in Native Chicken Populations from Myanmar, Thailand and Laos by Using 102 Indels Markers

    Directory of Open Access Journals (Sweden)

    A. A. Maw

    2015-01-01

    Full Text Available The genetic diversity of native chicken populations from Myanmar, Thailand, and Laos was examined by using 102 insertion and/or deletion (indels markers. Most of the indels loci were polymorphic (71% to 96%, and the genetic variability was similar in all populations. The average observed heterozygosities (HO and expected heterozygosities (HE ranged from 0.205 to 0.263 and 0.239 to 0.381, respectively. The coefficients of genetic differentiation (Gst for all cumulated populations was 0.125, and the Thai native chickens showed higher Gst (0.088 than Myanmar (0.041 and Laotian (0.024 populations. The pairwise Fst distances ranged from 0.144 to 0.308 among populations. A neighbor-joining (NJ tree, using Nei’s genetic distance, revealed that Thai and Laotian native chicken populations were genetically close, while Myanmar native chickens were distant from the others. The native chickens from these three countries were thought to be descended from three different origins (K = 3 from STRUCTURE analysis. Genetic admixture was observed in Thai and Laotian native chickens, while admixture was absent in Myanmar native chickens.

  17. Development of genetic diversity, differentiation and structure over 500 years in four ponderosa pine populations.

    Science.gov (United States)

    Lesser, M R; Parchman, T L; Jackson, S T

    2013-05-01

    Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range-margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range-margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500-year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within-population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F(ST) and Jost's D(est)) and diversity within populations (F(IS)) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century. © 2013 Blackwell Publishing Ltd.

  18. Phylogeography and population structure of the grape powdery mildew fungus, Erysiphe necator, from diverse Vitis species

    Directory of Open Access Journals (Sweden)

    Brewer Marin

    2010-09-01

    Full Text Available Abstract Background The grape powdery mildew fungus, Erysiphe necator, was introduced into Europe more than 160 years ago and is now distributed everywhere that grapes are grown. To understand the invasion history of this pathogen we investigated the evolutionary relationships between introduced populations of Europe, Australia and the western United States (US and populations in the eastern US, where E. necator is thought to be native. Additionally, we tested the hypothesis that populations of E. necator in the eastern US are structured based on geography and Vitis host species. Results We sequenced three nuclear gene regions covering 1803 nucleotides from 146 isolates of E. necator collected from the eastern US, Europe, Australia, and the western US. Phylogeographic analyses show that the two genetic groups in Europe represent two separate introductions and that the genetic groups may be derived from eastern US ancestors. Populations from the western US and Europe share haplotypes, suggesting that the western US population was introduced from Europe. Populations in Australia are derived from European populations. Haplotype richness and nucleotide diversity were significantly greater in the eastern US populations than in the introduced populations. Populations within the eastern US are geographically differentiated; however, no structure was detected with respect to host habitat (i.e., wild or cultivated. Populations from muscadine grapes, V. rotundifolia, are genetically distinct from populations from other Vitis host species, yet no differentiation was detected among populations from other Vitis species. Conclusions Multilocus sequencing analysis of the grape powdery mildew fungus is consistent with the hypothesis that populations in Europe, Australia and the western US are derived from two separate introductions and their ancestors were likely from native populations in the eastern US. The invasion history of E. necator follows a pattern

  19. HASIL TANGKAP SAMPINGAN (HTS KAPAL RAWAI TUNA DI SAMUDERA HINDIA YANG BERBASIS DI BENOA

    Directory of Open Access Journals (Sweden)

    Bram Setyadji

    2016-05-01

    Full Text Available Hasil tangkap sampingan (HTS hampir terdapat pada semua jenis perikanan tangkap di Indonesia, termasuk pada perikanan rawai tuna di Samudera Hindia. Kebanyakan jenis HTS merupakan spesies yang tidak diinginkan atau jenis ikan target tapi ukurannya di bawah standar yang diinginkan (yuwana atau ikan muda dan pada kasus tertentu merupakan jenis ikan yang terancam keberadaannya (Endangered species. Penelitian ini bertujuan untuk memberikan informasi tentang komposisi hasil tangkap sampingan, laju pancing dan hubungan antara tuna dengan ikan yang berasosiasi dengannya pada area penangkapan yang sama. Pengamatan dilakukan pada bulan Maret – Juli 2010 dengan mengikuti kegiatan operasi penangkapan 2 kapal rawai tuna komersial yang berbasis di Pelabuhan Benoa. Hasil penelitian menunjukkan terdapat 18 jenis hasil tangkap sampingan yang  didominasi dari family Alepisauridae; ikan naga (Alepisaurus sp.; Gempylidae; ikan gindara (oilfish, dan Dasyatidae; pari lumpur (Dasyatis spp.. Jenis ikan lain adalah ikan paruh panjang (billfish, berbagai jenis cucut dan pari, ikan teleostei, serta penyu lekang. Kebanyakan dari hasil tangkap sampingan merupakan by-product yang mempunyai nilai ekonomis tinggi kecuali jenis ikan naga dan pari lumpur yang merupakan discard/buangan.   By-catch products are mostly available in every kind of capture fisheries in Indonesia including tuna longline fisheries in Indian Ocean. Most of these are unwanted species or juvenile target fish, sometimes endangered species. The research intended to reveal the by-catch from tuna fisheries and its relationship between tuna and its associate in the same fishing ground. Surveillance was conducted on March – July, 2010 by following two commercial tuna longliners vessel based in Port of Benoa. The result showed that there were 18 by-catch species that managed to be retrieved and indentified, family Alepisauridae; lancetfish (Alepisaurus sp.; Gempylidae; oilfish (Ruvettus pretiosus, and

  20. Amphibian population genetics in agricultural landscapes: does viniculture drive the population structuring of the European common frog (Rana temporaria?

    Directory of Open Access Journals (Sweden)

    Patrick P. Lenhardt

    2017-07-01

    Full Text Available Amphibian populations have been declining globally over the past decades. The intensification of agriculture, habitat loss, fragmentation of populations and toxic substances in the environment are considered as driving factors for this decline. Today, about 50% of the area of Germany is used for agriculture and is inhabited by a diverse variety of 20 amphibian species. Of these, 19 are exhibiting declining populations. Due to the protection status of native amphibian species, it is important to evaluate the effect of land use and associated stressors (such as road mortality and pesticide toxicity on the genetic population structure of amphibians in agricultural landscapes. We investigated the effects of viniculture on the genetic differentiation of European common frog (Rana temporaria populations in Southern Palatinate (Germany. We analyzed microsatellite data of ten loci from ten breeding pond populations located within viniculture landscape and in the adjacent forest block and compared these results with a previously developed landscape permeability model. We tested for significant correlation of genetic population differentiation and landscape elements, including land use as well as roads and their associated traffic intensity, to explain the genetic structure in the study area. Genetic differentiation among forest populations was significantly lower (median pairwise FST = 0.0041 at 5.39 km to 0.0159 at 9.40 km distance than between viniculture populations (median pairwise FST = 0.0215 at 2.34 km to 0.0987 at 2.39 km distance. Our analyses rejected isolation by distance based on roads and associated traffic intensity as the sole explanation of the genetic differentiation and suggest that the viniculture landscape has to be considered as a limiting barrier for R. temporaria migration, partially confirming the isolation of breeding ponds predicted by the landscape permeability model. Therefore, arable land may act as a sink habitat

  1. Experimental design and estimation of growth rate distributions in size-structured shrimp populations

    International Nuclear Information System (INIS)

    Banks, H T; Davis, Jimena L; Ernstberger, Stacey L; Hu, Shuhua; Artimovich, Elena; Dhar, Arun K

    2009-01-01

    We discuss inverse problem results for problems involving the estimation of probability distributions using aggregate data for growth in populations. We begin with a mathematical model describing variability in the early growth process of size-structured shrimp populations and discuss a computational methodology for the design of experiments to validate the model and estimate the growth-rate distributions in shrimp populations. Parameter-estimation findings using experimental data from experiments so designed for shrimp populations cultivated at Advanced BioNutrition Corporation are presented, illustrating the usefulness of mathematical and statistical modeling in understanding the uncertainty in the growth dynamics of such populations

  2. Genetic diversity and population structure of leafy kale and Brassica rupestris Raf. in south Italy

    DEFF Research Database (Denmark)

    Maggioni, Lorenzo; von Bothmer, Roland; Poulsen, Gert

    2014-01-01

    Local varieties of leafy kales (Brassica oleracea L.) are grown in home gardens in Calabria and Sicily for self-consumption, in the same area where the wild relative Brassica rupestris Raf. also grows. With the use of AFLP markers, comparisons were made of the genetic diversity and population...... structure of ten wild and 22 cultivated populations, as well as of a hybrid population and of four commercial cultivars of different B. oleracea crops. The level of genetic diversity was higher in leafy kales than in wild populations and this diversity was mainly distributed within populations. Wild...... populations remained distinct from cultivated material. Additionally, most wild populations were distinctively isolated from each other. On the other hand, it was not possible to molecularly distinguish even geographically distant leafy kale populations from each other or from different B. oleracea crops...

  3. Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

    Science.gov (United States)

    Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

    2016-04-01

    Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-based approaches suffer from a lack of statistical rigor, model-based approaches entail assumptions of prior conditions such as that the subpopulations are at Hardy-Weinberg equilibria. Here we present a distance-based approach for inference about population structure using genetic data by defining population structure using network theory terminology and methods. A network is constructed from a pairwise genetic-similarity matrix of all sampled individuals. The community partition, a partition of a network to dense subgraphs, is equated with population structure, a partition of the population to genetically related groups. Community-detection algorithms are used to partition the network into communities, interpreted as a partition of the population to subpopulations. The statistical significance of the structure can be estimated by using permutation tests to evaluate the significance of the partition's modularity, a network theory measure indicating the quality of community partitions. To further characterize population structure, a new measure of the strength of association (SA) for an individual to its assigned community is presented. The strength of association distribution (SAD) of the communities is analyzed to provide additional population structure characteristics, such as the relative amount of gene flow experienced by the different subpopulations and identification of hybrid individuals. Human genetic data and simulations are used to demonstrate the applicability of the analyses. The approach presented here provides a novel, computationally efficient model-free method for inference about population structure that does not entail assumption of

  4. Genetic structure of lake whitefish, Coregonus clupeaformis, populations in the northern main basin of Lake Huron

    Science.gov (United States)

    Stott, Wendylee; Ebener, Mark P.; Mohr, Lloyd; Schaeffer, Jeff; Roseman, Edward F.; Harford, William J.; Johnson, James E.; Fietsch, Cherie-Lee

    2012-01-01

    Genetic analysis of spawning lake whitefish (Coregonus clupeaformis) from six sites in the main basin of Lake Huron was conducted to determine population structure. Samples from fisheryindependent assessment surveys in the northwest main basin were analyzed to determine the relative contributions of lake whitefish genetic populations. Genetic population structure was identified using data from seven microsatellite DNA loci. One population was identified at Manitoulin Island, one to two were observed in the east-central main basin (Fishing Island and Douglas Point), and one to two populations were found in the northwest (Thunder Bay and Duncan Bay). The genetic identity of collections from Duncan Bay and Thunder Bay was not consistent among methods used to analyze population structure. Low genetic distances suggested that they comprised one population, but genic differences indicated that they may constitute separate populations. Simulated data indicated that the genetic origins of samples from a mixed-fishery could be accurately identified, but accuracy could be improved by incorporating additional microsatellite loci. Mixture analysis and individual assignment tests performed on mixed-stock samples collected from the western main basin suggested that genetic populations from the east-central main basin contributed less than those from the western main basin and that the proportional contribution of each baseline population was similar in each assessment sample. Analysis of additional microsatellite DNA loci may be useful to help improve the precision of the estimates, thus increasing our ability to manage and protect this valuable resource.

  5. Population genetic structure of the common warthog (Phacochoerus africanus) in Uganda: evidence for a strong philopatry among warthogs and social structure breakdown in a disturbed population

    DEFF Research Database (Denmark)

    Muwanka, V.B.; Nyakaana, S.; Siegismund, Hans Redlef

    2007-01-01

    populations from five localities in Uganda are genetically structured using both mitochondrial control region sequence and microsatellite allele length variation. Four of the localities (Queen Elizabeth, Murchison Falls, Lake Mburo and Kidepo Valley) are national parks with relatively good wildlife protection...

  6. Mercury in tunas and blue marlin in the North Pacific Ocean.

    Science.gov (United States)

    Drevnick, Paul E; Brooks, Barbara A

    2017-05-01

    Models and data from the North Pacific Ocean indicate that mercury concentrations in water and biota are increasing in response to (global or hemispheric) anthropogenic mercury releases. In the present study, we provide an updated record of mercury in yellowfin tuna (Thunnus albacares) caught near Hawaii that confirms an earlier conclusion that mercury concentrations in these fish are increasing at a rate similar to that observed in waters shallower than 1000 m. We also compiled and reanalyzed data from bigeye tuna (Thunnus obesus) and blue marlin (Makaira nigricans) caught near Hawaii in the 1970s and 2000s. Increases in mercury concentrations in bigeye tuna are consistent with the trend found in yellowfin tuna, in both timing and magnitude. The data available for blue marlin do not allow for a fair comparison among years, because mercury concentrations differ between sexes for this species, and sex was identified (or reported) in only 3 of 7 studies. Also, mercury concentrations in blue marlin may be insensitive to modest changes in mercury exposure, because this species appears to have the ability to detoxify mercury. The North Pacific Ocean is a region of both relatively high rates of atmospheric mercury deposition and capture fisheries production. Other data sets that allow temporal comparisons in mercury concentrations, such as pacific cod (Gadus macrocephalus) in Alaskan waters and albacore tuna (Thunnus alalunga) off the US Pacific coast, should be explored further, to aid in understanding human health and ecological risks and to develop additional baseline knowledge for assessing changes in a region expected to respond strongly to reductions in anthropogenic mercury emissions. Environ Toxicol Chem 2017;36:1365-1374. © 2017 SETAC. © 2017 SETAC.

  7. Tuna Species Substitution in the Spanish Commercial Chain: A Knock-On Effect.

    Directory of Open Access Journals (Sweden)

    Ana Gordoa

    Full Text Available Intentional mislabelling of seafood is a widespread problem, particularly with high-value species like tuna. In this study we examine tuna mislabelling, deliberate species substitution, types of substitution and its impact on prices. The survey covered the commercial chain, from Merca-Barna to fishmongers and restaurants in the Spanish Autonomous Community of Catalonia. To understand the geographic extent of the problem we also sampled Merca-Madrid, Europe's biggest fish market, and Merca-Málaga for its proximity to the bluefin tuna migratory route and trap fishery. Monthly surveys were carried out over one year. The results showed a high deficiency in labelling: 75% of points of sale and 83% of restaurants did not specify the species, and in those cases the name of the species had to be asked. A total of 375 samples were analysed genetically, the largest dataset gathered in Europe so far. The identified species were Thunnus albacares, Thunnus thynnus and Thunnus obesus. Species substitution began at suppliers, with 40% of observed cases, increasing to 58% at fishmongers and 62% at restaurants. The substitution was mainly on bluefin tuna (T. thynnus, 73% of cases. At restaurants, only during the bluefin fishing season, we observed a decrease of Bluefin tuna substitution and an increase of reverse substitution revealing some illegal fishing. The effect of species substitution on species prices was relevant: T. obesus increased its price by around €12 kg-1 when it was sold as bluefin. In view of the deficiency of labelling, the abuse of generic names and the lack of the bluefin catch document, we conclude that the Spanish regulations are ineffective, highlighting the need for policy execution, and the urgent need for information campaigns to Spanish consumers.

  8. Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers.

    Science.gov (United States)

    Filippi, Carla V; Aguirre, Natalia; Rivas, Juan G; Zubrzycki, Jeremias; Puebla, Andrea; Cordes, Diego; Moreno, Maria V; Fusari, Corina M; Alvarez, Daniel; Heinz, Ruth A; Hopp, Horacio E; Paniego, Norma B; Lia, Veronica V

    2015-02-13

    Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity incomplete. In this study, 42 microsatellite loci and 384 single nucleotide polymorphisms (SNPs) were used to characterize the first association mapping population used for quantitative trait loci mapping in sunflower, along with a selection of allied open-pollinated and composite populations from the germplasm bank of the National Institute of Agricultural Technology of Argentina. The ability of different kinds of markers to assess genetic diversity and population structure was also evaluated. The analysis of polymorphism in the set of sunflower accessions studied here showed that both the microsatellites and SNP markers were informative for germplasm characterization, although to different extents. In general, the estimates of genetic variability were moderate. The average genetic diversity, as quantified by the expected heterozygosity, was 0.52 for SSR loci and 0.29 for SNPs. Within SSR markers, those derived from non-coding regions were able to capture higher levels of diversity than EST-SSR. A significant correlation was found between SSR and SNP- based genetic distances among accessions. Bayesian and multivariate methods were used to infer population structure. Evidence for the existence of three different genetic groups was found consistently across data sets (i.e., SSR, SNP and SSR + SNP), with the maintainer/restorer status being the most prevalent characteristic associated with group delimitation. The present study constitutes the first report comparing the performance of SSR and SNP markers for population genetics analysis in cultivated sunflower. We show that the SSR and SNP panels examined here, either used separately or in conjunction, allowed consistent

  9. Assessment of DNA quality in processed tuna muscle tissues

    Directory of Open Access Journals (Sweden)

    Zora Piskatá

    2016-06-01

    Full Text Available Authentication of tuna fish products is necessary to assure consumers of accurate labelling of food products. The quality of species specific DNA crucially affects the efficiency of amplification during the subsequent PCR. The problem in DNA detection in canned products lies in the possibility of the fragmentation of DNA during the processing technologies and the use of ingredients (oil, salt, spice, that may inhibit the PCR reaction. In this study three DNA extraction methods were compared: DNeasy Blood and Tissue Kit, DNeasy mericon Food Kit and Chemagic DNA tissue 10 Kit. The quantity and quality of DNA were evaluated by measuring DNA concentration and ratios A260/A280. Several parameters were estimated: the effect of whole and mechanically treated muscle, sterilization procedure used in canned process (high temperature in combination with high pressure and addition of raw materials. The highest DNA concentrations were observed in non-processed muscle that is not influenced by the sterilization process. Canned whole muscle demonstrated lower DNA yield, and furthermore, the mechanical treatment (canned ground resulted in lower values of DNA concentration that was registered by using all three types of DNA extraction kits. DNeasy mericon Food Kit produced DNA of higher concentration in non-processed sample, Chemagic DNA tissue 10 Kit delivered higher DNA yields than kits DNeasy Blood and Tissue Kit and DNeasy mericon Food Kit in canned samples, although the purity was lower, but still within the range 1.7 - 2.0. DNA was considered to be satisfactorily pure in all three types of samples and using all three types of DNA isolation. In case of the samples enriched of ingredients and treated with sterilization process as whole or ground muscle Chemagic DNA tissue 10 Kit produced in all samples (whole and ground muscle the highest values of DNA concentration, but almost all values of A260/A280 were lower than 1.7. Therefore DNeasy mericon Food Kit

  10. Population dynamics of bowfin in a south Georgia reservoir: latitudinal comparisons of population structure, growth, and mortality

    Science.gov (United States)

    Porter, Nicholas J.; Bonvechio, Timothy F.; McCormick, Joshua L.; Quist, Michael

    2014-01-01

    The objectives of this study were to evaluate the population dynamics of bowfin (Amia calva) in Lake Lindsay Grace, Georgia, and to compare those dynamics to other bowfin populations. Relative abundance of bowfin sampled in 2010 in Lake Lindsay Grace was low and variable (mean±SD; 2.7±4.7 fish per hour of electrofishing). Total length (TL) of bowfin collected in Lake Lindsay Grace varied from 233–683 mm. Age of bowfin in Lake Lindsay Grace varied from 0–5 yr. Total annual mortality (A) was estimated at 68%. Both sexes appeared to be fully mature by age 2 with gonadosomatic index values above 8 for females and close to 1 for males. The majority of females were older, longer, and heavier than males. Bowfin in Lake Lindsay Grace had fast growth up to age 4 and higher total annual mortality than the other populations examined in this study. A chi-square test indicated that size structure of bowfin from Lake Lindsay Grace was different than those of a Louisiana population and two bowfin populations from the upper Mississippi River. To further assess bowfin size structure, we proposed standard length (i.e., TL) categories: stock (200 mm, 8 inches), quality (350 mm, 14 inches), preferred (460 mm, 18 inches), memorable (560 mm, 22, inches), and trophy (710 mm, 28 inches). Because our knowledge of bowfin ecology is limited, additional understanding of bowfin population dynamics provides important insight that can be used in management of bowfin across their distribution.

  11. [Genetic structure, subdivision, and population differentiation in Stankewiczii pine Pinus stankewiczii (Sukacz.) Fomin from Mountain Crimea].

    Science.gov (United States)

    Korshikov, I I; Gorlova, E M

    2006-06-01

    In order to analyze the genetic structure, subdivision and differentiation within and between two small isolated populations of the Crimea relict endemic, Pinus stankewiczii (Sukacz.) Fomin, electrophoretic analysis of the isozyme variation at nine enzymatic systems was carried out using 183 oldest trees. It was demonstrated that in populations of P. stankewiczii, 80% of the genes were in polymorphic state. Each tree was heterozygous at 19.1% loci, and at 21.6% loci in artificial 50-year-old plantation. The genetic structure of two populations was less differentiated (DN = 0.006), compared to their individual localities (DN = 0.008-0.009). Within-population subdivision of the diffusely dispersed populations was higher (FST-GST = 1.8-2.0%) than that of the populations themselves (0.8%).

  12. Dynamics of a physiologically structured population in a time-varying environment

    DEFF Research Database (Denmark)

    Heilmann, Irene Louise Torpe; Starke, Jens; Andersen, Ken Haste

    2016-01-01

    Physiologically structured population models have become a valuable tool to model the dynamics of populations. In a stationary environment such models can exhibit equilibrium solutions as well as periodic solutions. However, for many organisms the environment is not stationary, but varies more...... or less regularly. In order to understand the interaction between an external environmental forcing and the internal dynamics in a population, we examine the response of a physiologically structured population model to a periodic variation in the food resource. We explore the addition of forcing in two...... cases: (A) where the population dynamics is in equilibrium in a stationary environment, and (B) where the population dynamics exhibits a periodic solution in a stationary environment. When forcing is applied in case A, the solutions are mainly periodic. In case B the forcing signal interacts...

  13. Genetic variability and population structure of Plasmodium falciparum parasite populations from different malaria ecological regions of Kenya.

    Science.gov (United States)

    Ingasia, Luicer A; Cheruiyot, Jelagat; Okoth, Sheila Akinyi; Andagalu, Ben; Kamau, Edwin

    2016-04-01

    Transmission intensity, movement of human and vector hosts, biogeographical features, and malaria control measures are some of the important factors that determine Plasmodium falciparum parasite genetic variability and population structure. Kenya has different malaria ecologies which might require different disease intervention methods. Refined parasite population genetic studies are critical for informing malaria control and elimination strategies. This study describes the genetic diversity and population structure of P. falciparum parasites from the different malaria ecological zones in Kenya. Twelve multi-locus microsatellite (MS) loci previously described were genotyped in 225 P. falciparum isolates collected between 2012 and 2013 from five sites; three in lowland endemic regions (Kisumu, Kombewa, and Malindi) and two in highland, epidemic regions (Kisii and Kericho). Parasites from the lowland endemic and highland epidemic regions of western Kenya had high genetic diversity compared to coastal lowland endemic region of Kenya [Malindi]. The Kenyan parasites had a mean genetic differentiation index (FST) of 0.072 (p=0.011). The multi-locus genetic analysis of the 12 MS revealed all the parasites had unique haplotypes. Significant linkage disequilibrium (LD) was observed in all the five parasite populations. Kisumu had the most significant index of association values (0.16; pKenya after introduction of the artemether-lumefantrine is important in refining the spread of drug resistant strains and malaria transmission for more effective control and eventual elimination of malaria in Kenya. Copyright © 2015. Published by Elsevier B.V.

  14. An individual-based model of skipjack tuna (Katsuwonus pelamis) movement in the tropical Pacific ocean

    Science.gov (United States)

    Scutt Phillips, Joe; Sen Gupta, Alex; Senina, Inna; van Sebille, Erik; Lange, Michael; Lehodey, Patrick; Hampton, John; Nicol, Simon

    2018-05-01

    The distribution of marine species is often modeled using Eulerian approaches, in which changes to population density or abundance are calculated at fixed locations in space. Conversely, Lagrangian, or individual-based, models simulate the movement of individual particles moving in continuous space, with broader-scale patterns such as distribution being an emergent property of many, potentially adaptive, individuals. These models offer advantages in examining dynamics across spatiotemporal scales and making comparisons with observations from individual-scale data. Here, we introduce and describe such a model, the Individual-based Kinesis, Advection and Movement of Ocean ANimAls model (Ikamoana), which we use to replicate the movement processes of an existing Eulerian model for marine predators (the Spatial Ecosystem and Population Dynamics Model, SEAPODYM). Ikamoana simulates the movement of either individual or groups of animals by physical ocean currents, habitat-dependent stochastic movements (kinesis), and taxis movements representing active searching behaviours. Applying our model to Pacific skipjack tuna (Katsuwonus pelamis), we show that it accurately replicates the evolution of density distribution simulated by SEAPODYM with low time-mean error and a spatial correlation of density that exceeds 0.96 at all times. We demonstrate how the Lagrangian approach permits easy tracking of individuals' trajectories for examining connectivity between different regions, and show how the model can provide independent estimates of transfer rates between commonly used assessment regions. In particular, we find that retention rates in most assessment regions are considerably smaller (up to a factor of 2) than those estimated by this population of skipjack's primary assessment model. Moreover, these rates are sensitive to ocean state (e.g. El Nino vs La Nina) and so assuming fixed transfer rates between regions may lead to spurious stock estimates. A novel feature of the

  15. Population structure of giraffes is affected by management in the Great Rift Valley, Kenya.

    Directory of Open Access Journals (Sweden)

    Zoe Muller

    Full Text Available Giraffe populations in East Africa have declined in the past thirty years yet there has been limited research on this species. This study had four objectives: i to provide a baseline population assessment for the two largest populations of Rothschild's giraffes in Kenya, ii to assess whether there are differences in population structure between the two enclosed populations, iii to assess the potential and possible implications of different management practices on enclosed giraffe populations to inform future decision-making, and iv to add to the availability of information available about giraffes in the wild. I used individual identification to assess the size and structure of the two populations; in Soysambu Conservancy between May 2010 and January 2011, I identified 77 giraffes; in Lake Nakuru National Park between May 2011 and January 2012, I identified 89. Population structure differed significantly between the two sites; Soysambu Conservancy contained a high percentage of juveniles (34% and subadults (29% compared to Lake Nakuru NP, which contained fewer juveniles (5% and subadults (15%. During the time of this study Soysambu Conservancy contained no lions while Lake Nakuru NP contained a high density of lions (30 lions per 100km2. Lions are the main predator of giraffes, and preferential predation on juvenile giraffes has previously been identified in Lake Nakuru NP. My results suggest that high lion density in Lake Nakuru NP may have influenced the structure of the giraffe population by removing juveniles and, consequently, may affect future population growth. I suggest that wildlife managers consider lion densities alongside breeding plans for Endangered species, since the presence of lions appears to influence the population structure of giraffes in enclosed habitats.

  16. Population structure of giraffes is affected by management in the Great Rift Valley, Kenya.

    Science.gov (United States)

    Muller, Zoe

    2018-01-01

    Giraffe populations in East Africa have declined in the past thirty years yet there has been limited research on this species. This study had four objectives: i) to provide a baseline population assessment for the two largest populations of Rothschild's giraffes in Kenya, ii) to assess whether there are differences in population structure between the two enclosed populations, iii) to assess the potential and possible implications of different management practices on enclosed giraffe populations to inform future decision-making, and iv) to add to the availability of information available about giraffes in the wild. I used individual identification to assess the size and structure of the two populations; in Soysambu Conservancy between May 2010 and January 2011, I identified 77 giraffes; in Lake Nakuru National Park between May 2011 and January 2012, I identified 89. Population structure differed significantly between the two sites; Soysambu Conservancy contained a high percentage of juveniles (34%) and subadults (29%) compared to Lake Nakuru NP, which contained fewer juveniles (5%) and subadults (15%). During the time of this study Soysambu Conservancy contained no lions while Lake Nakuru NP contained a high density of lions (30 lions per 100km2). Lions are the main predator of giraffes, and preferential predation on juvenile giraffes has previously been identified in Lake Nakuru NP. My results suggest that high lion density in Lake Nakuru NP may have influenced the structure of the giraffe population by removing juveniles and, consequently, may affect future population growth. I suggest that wildlife managers consider lion densities alongside breeding plans for Endangered species, since the presence of lions appears to influence the population structure of giraffes in enclosed habitats.

  17. Population structure of Cylindrocladium parasiticum infecting peanuts (Arachis hypogaea) in Georgia, USA

    NARCIS (Netherlands)

    Wright, L.P.; Davis, A.J.; Wingfield, B.D.; Crous, P.W.; Brenneman, T.; Wingfield, M.J.

    2010-01-01

    Cylindrocladium parasiticum is an important pathogen of peanut (Arachis hypogaea) causing the disease Cylindrocladium black rot. The genetic structure of this haploid pathogen was determined for populations associated with peanut in Georgia, USA. Ten polymorphic microsatellite markers were used to

  18. SWFSC/MMTD/AK: Structure of Populations, Level of Abundance, and Status of Humpbacks (SPLASH) 2004

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This project was part of a larger international project (SPLASH) designed to estimate the abundance and determine the population structure for humpback whales...

  19. Genetic structure of Leptopilina boulardi populations from different climatic zones of Iran

    NARCIS (Netherlands)

    Seyahooei, M.A.; van Alphen, J.J.M.; Kraaijeveld, K.

    2011-01-01

    Background The genetic structure of populations can be influenced by geographic isolation (including physical distance) and ecology. We examined these effects in Leptopilina boulardi, a parasitoid of Drosophila of African origin and widely distributed over temperate and (sub) tropical climates.

  20. Using Population Matrix Modeling to Predict AEGIS Fire Controlmen Community Structure

    National Research Council Canada - National Science Library

    McKeon, Thomas J

    2007-01-01

    .... A Population Matrix with Markov properties was used to develop the AEGIS FC aging model. The goal of this model was to provide an accurate predication of the future AEGIS FC community structure based upon variables...

  1. Ontogenetic niche shifts and evolutionary branching in size-structured populations

    NARCIS (Netherlands)

    Claessen, D.; Dieckmann, U.

    2002-01-01

    There are many examples of size-structured populations where individuals sequentially exploit several niches in the course of their life history. Efficient exploitation of such ontogenetic niches generally requires specific morphological adaptations. Here, we study the evolutionary implications of

  2. Phylogeography, population structure and evolution of coral-eating butterflyfishes (Family Chaetodontidae, genus Chaetodon , subgenus Corallochaetodon )

    KAUST Repository

    Waldrop, Ellen; Hobbs, Jean-Paul A.; Randall, John E.; DiBattista, Joseph; Rocha, Luiz A.; Kosaki, Randall K.; Berumen, Michael L.; Bowen, Brian W.

    2016-01-01

    This study compares the phylogeography, population structure and evolution of four butterflyfish species in the Chaetodon subgenus Corallochaetodon, with two widespread species (Indian Ocean – C. trifasciatus and Pacific Ocean – C. lunulatus

  3. Estimation of age structure of fish populations from length-frequency data

    International Nuclear Information System (INIS)

    Kumar, K.D.; Adams, S.M.

    1977-01-01

    A probability model is presented to determine the age structure of a fish population from length-frequency data. It is shown that when the age-length key is available, maximum-likelihood estimates of the age structure can be obtained. When the key is not available, approximate estimates of the age structure can be obtained. The model is used for determination of the age structure of populations of channel catfish and white crappie. Practical applications of the model to impact assessment are discussed

  4. CONTRIBUTIONS OF SEXUAL AND ASEXUAL REPRODUCTION TO POPULATION STRUCTURE IN THE CLONAL SOFT CORAL, ALCYONIUM RUDYI.

    Science.gov (United States)

    McFadden, Catherine S

    1997-02-01

    Numerous studies of population structure in sessile clonal marine invertebrates have demonstrated low genotypic diversity and nonequilibrium genotype frequencies within local populations that are monopolized by relatively few, highly replicated genets. All of the species studied to date produce planktonic sexual propagules capable of dispersing long distances; despite local genotypic disequilibria, populations are often panmictic over large geographic areas. The population structure paradigm these species represent may not be typical of the majority of clonal invertebrate groups, however, which are believed to produce highly philopatric sexual propagules. I used allozyme variation to examine the population structure of the temperate soft coral, Alcyonium rudyi, a typical clonal species whose sexually produced larvae and asexually produced ramets both have very low dispersal capabilities. Like other clonal plants and invertebrates, the local population dynamics of A. rudyi are dominated by asexual reproduction, and recruitment of new sexually produced genets occurs infrequently. As expected from its philopatric larval stage, estimates of genetic differentiation among populations of A. rudyi were highly significant at all spatial scales examined (mean θ = 0.300 among 20 populations spanning a 1100-km range), suggesting that genetic exchange seldom occurs among populations separated by as little as a few hundred meters. Mapping of multilocus allozyme genotypes within a dense aggregation of A. rudyi ramets confirmed that dispersal of asexual propagules is also very limited: members of the same genet usually remain within invertebrates, populations of A. rudyi do not appear to be dominated by a few widespread genets: estimates of genotypic diversity (G o ) within 20 geographically distinct populations did not differ from expectations for outcrossing, sexual populations. Despite theoretical suggestions that philopatric dispersal combined with typically small effective

  5. Genetic Structure and Gene Flows within Horses: A Genealogical Study at the French Population Scale

    OpenAIRE

    Pirault, Pauline; Danvy, Sophy; Verrier, Etienne; Leroy, Gr?goire

    2013-01-01

    Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species FIT of 1.37%...

  6. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zong

    Full Text Available Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777. According to the coefficient of genetic differentiation (Fst = 0.1215, genetic variation within the populations (87.85% were remarkably higher than among populations (12.15%. The average gene flow (Nm = 1.8080 significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080 among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km among populations (r = 0.419, P = 0.005, suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic

  7. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    Science.gov (United States)

    Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

    2015-01-01

    Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These

  8. Geographic patterns of genetic variation and population structure in Pinus aristata, Rocky Mountain bristlecone pine

    Science.gov (United States)

    Anna W. Schoettle; Betsy A. Goodrich; Valerie Hipkins; Christopher Richards; Julie Kray

    2012-01-01

    Pinus aristata Engelm., Rocky Mountain bristlecone pine, has a narrow core geographic and elevational distribution, occurs in disjunct populations, and is threatened by rapid climate change, white pine blister rust, and bark beetles. Knowledge of genetic diversity and population structure will help guide gene conservation strategies for this species. Sixteen sites...

  9. Strong population genetic structure and larval dispersal capability of the burrowing ghost shrimp (Neotrypaea californiensis)

    Science.gov (United States)

    The burrowing ghost shrimp, Neotrypaea californiensis, is a vital member of the estuarine benthic community. Dense populations of shrimp are found in the major estuaries of Washington and Oregon. Our study determines the genetic structure of shrimp populations in order to gain ...

  10. Introgression from cultivated rice alters genetic structures of wild relative populations: implications for in situ conservation

    Science.gov (United States)

    Jin, Xin; Chen, Yu; Liu, Ping; Li, Chen; Cai, Xingxing; Rong, Jun

    2018-01-01

    Abstract Maintaining genetic integrity is essential for in situ and ex situ conservation of crop wild relative (CWR) species. However, introgression of crop alleles into CWR species/populations may change their genetic structure and diversity, resulting in more invasive weeds or, in contrast, the extinction of endangered populations. To determine crop-wild introgression and its consequences, we examined the genetic structure and diversity of six wild rice (Oryza rufipogon) populations under in situ conservation in China. Thirty-four simple sequence repeat (SSR) and 34 insertion/deletion markers were used to genotype the wild rice populations and two sets of rice cultivars (O. sativa), corresponding to the two types of molecular markers. Shared alleles and STRUCTURE analyses suggested a variable level of crop-wild introgression and admixture. Principal coordinates and cluster analyses indicated differentiation of wild rice populations, which was associated with the spatial distances to cultivated rice fields. The level of overall genetic diversity was comparable between wild rice populations and rice cultivars, but a great number of wild-specific alleles was detected in the wild populations. We conclude based on the results that crop-wild introgression can considerably alter the pattern of genetic structure and relationships of CWR populations. Appropriate measures should be taken for effective in situ conservation of CWR species under the scenario of crop-wild introgression. PMID:29308123

  11. Comparison of genetic population structure of the large blue butterflies Maculinea nausithous and M. teleius

    DEFF Research Database (Denmark)

    Figurny-Puchalska, Edyta; Gadeberg, Rebekka M.E.; Boomsma, Jacobus Jan

    2000-01-01

    We investigated the genetic population structure of two rare myrmecophilous lycaenid butterflies, Maculinea nausithous and M. teleius, which often live sympatrically and have similar biology. In Europe, both species occur in highly fragmented populations and are vulnerable to local extinction. Th...

  12. Molecular genetic diversity and genetic structure of Vietnamese indigenous pig populations

    DEFF Research Database (Denmark)

    Pham, L. D.; Do, Duy Ngoc; Nam, L. Q.

    2014-01-01

    The study characterized genetic diversity and genetic structure of five indigenous pig populations (Ha Lang, Muong Te, Mong Cai, Lung and Lung Pu), two wild pig populations (Vietnamese and Thai wild pigs) and an exotic pig breed (Yorkshire) using FAO/ISAG recommended 16 microsatellite markers...

  13. Nesting habits influence population genetic structure of a bee living in anthropogenic disturbance.

    Science.gov (United States)

    Vickruck, J L; Richards, M H

    2017-05-01

    While most organisms are negatively affected by anthropogenic disturbance, a few species thrive in landscapes altered by humans. Typically, native bees are negatively impacted by anthropogenic environmental change, including habitat alteration and climate change. Here, we investigate the population structure of the eastern carpenter bee Xylocopa virginica, a generalist pollinator with a broad geographic range spanning eastern North America. Eastern carpenter bees now nest almost exclusively in artificial wooden structures, linking their geographic distribution and population structure to human activities and disturbance. To investigate the population structure of these bees, we sampled females from 16 different populations from across their range. Nine species-specific microsatellite loci showed that almost all populations are genetically distinct, but with high levels of genetic diversity and low levels of inbreeding overall. Broadly speaking, populations clustered into three distinct genetic groups: a northern group, a western group and a core group. The northern group had low effective population sizes, decreased genetic variability and the highest levels of inbreeding in the data set, suggesting that carpenter bees may be expanding their range northward. The western group was genetically distinct, but lacked signals of a recent range expansion. Climatic data showed that summer and winter temperatures explained a significant amount of the genetic differentiation seen among populations, while precipitation did not. Our results indicate that X. virginica may be one of the rare 'anthrophilic' species that thrive in the face of anthropogenic disturbance. © 2017 John Wiley & Sons Ltd.

  14. Population Structure of Acanthaster Planci on the Reef Flat at the Southern Part of Bunaken Island

    OpenAIRE

    Napitupulu, Patritia; Tioho, Hanny; Windarto, Agung

    2013-01-01

    The information on population structure of Acanthaster planci in Bunaken National Park (BNP) is urgent to be presented in order to be considered in decision making especially on coral reef management in BNP. The objectives of this study was to examine the population structure of A. planci, represented by the diameter and weight, number of arms, while the density, distribution and types of coral predation by reef animals in the Southern part of Bunaken Island also observed. Data were collect...

  15. Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean

    OpenAIRE

    Allers, Elke; Wright, Jody J; Konwar, Kishori M; Howes, Charles G; Beneze, Erica; Hallam, Steven J; Sullivan, Matthew B

    2012-01-01

    Marine Group A (MGA) is a candidate phylum of Bacteria that is ubiquitous and abundant in the ocean. Despite being prevalent, the structural and functional properties of MGA populations remain poorly constrained. Here, we quantified MGA diversity and population structure in relation to nutrients and O2 concentrations in the oxygen minimum zone (OMZ) of the Northeast subarctic Pacific Ocean using a combination of catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and ...

  16. Genetic diversity and structure analysis based on hordein protein polymorphism in barley landrace populations from jordan

    International Nuclear Information System (INIS)

    Baloch, A.W.; Ali, M.; Baloch, A.M.; Mangan, B.U.N.; Song, W

    2014-01-01

    Jordan is unanimously considered to be one of the centers of genetic diversity for barley, where wild and landraces of barley has been grown under different climatic conditions. The genetic diversity and genetic structure based on hordein polymorphism was assessed in 90 different accessions collected from four different sites of Jordan. A-PAGE was used to reveal hordein polymorphism among the genotypes. A total of 29 distinct bands were identified, out of them 9 bands were distinguished for D, 11 for C, and 9 for the B hordein regions. The observed genetic similarity was an exceptionally high between the populations than expected, which is probably due to high gene flow estimated between them. The genetic diversity parameters were not differ largely among the populations, indicating that local selection of a particular site did not play a key role in shaping genetic diversity. Analysis of molecular variance (AMOVA) revealed significant population structure when accessions were structured according to population site. There was 94% of hordein variation resided within the populations and only 8% present among the populations. Both Bayesian and Principale Coordinate Analysis (PCoA) concordantly demonstrated admixture genotypes of the landraces barley populations. Consequently, none of the population found to be clustered separately according to its population site. It is concluded that this approach can be useful to explore the germplasm for genetic diversity but perhaps is not suitable for determining phylogenic relations in barley. (author)

  17. Population genetic structure of the point-head flounder, Cleisthenes herzensteini, in the Northwestern Pacific.

    Science.gov (United States)

    Xiao, Yongshuang; Zhang, Yan; Yanagimoto, Takashi; Li, Jun; Xiao, Zhizhong; Gao, Tianxiang; Xu, Shihong; Ma, Daoyuan

    2011-02-01

    Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. To determine the population genetic structure and the demographic and colonization history of Cleisthenes herzensteini in the Northwestern Pacific, one hundred and twenty-one individuals were sampled from six localities along the coastal regions of Japan and the Yellow Sea of China. Mitochondrial DNA variation was analyzed using DNA sequence data from the 5' end of control region. High levels of haplotype diversity (>0.96) were found for all populations, indicating a high level of genetic diversity. No pattern of isolation by distance was detected among the population differentiation throughout the examined range. Analyses of molecular variance (AMOVA) and the conventional population statistic Fst revealed no significant population genetic structure among populations. According to the exact test of differentiation among populations, the null hypothesis that C. herzensteini within the examined range constituted a non-differential mtDNA gene pool was accepted. The demographic history of C. herzensteini was examined using neutrality test and mismatch distribution analyses and results indicated Pleistocene population expansion (about 94-376 kya) in the species, which was consistent with the inference result of nested clade phylogeographical analysis (NCPA) showing contiguous range expansion for C. herzensteini. The lack of phylogeographical structure for the species may reflect a recent range expansion after the glacial maximum and insufficient time to attain migration-drift equilibrium.

  18. Population structure of four Thai indigenous chicken breeds.

    Science.gov (United States)

    Mekchay, Supamit; Supakankul, Pantaporn; Assawamakin, Anunchai; Wilantho, Alisa; Chareanchim, Wanwisa; Tongsima, Sissades

    2014-03-27

    In recent years, Thai indigenous chickens have increasingly been bred as an alternative in Thailand poultry market. Due to their popularity, there is a clear need to improve the underlying quality and productivity of these chickens. Studying chicken genetic variation can improve the chicken meat quality as well as conserving rare chicken species. To begin with, a minimal set of molecular markers that can characterize the Thai indigenous chicken breeds is required. Using AFLP-PCR, 30 single nucleotide polymorphisms (SNPs) from Thai indigenous chickens were obtained by DNA sequencing. From these SNPs, we genotyped 465 chickens from 7 chicken breeds, comprising four Thai indigenous chicken breeds--Pradhuhangdum (PD), Luenghangkhao (LK), Dang (DA) and Chee (CH), one wild chicken--the red jungle fowls (RJF), and two commercial chicken breeds--the brown egg layer (BL) and commercial broiler (CB). The chicken genotypes reveal unique genetic structures of the four Thai indigenous chicken breeds. The average expected heterozygosities of PD=0.341, LK=0.357, DA=0.349 and CH=0.373, while the references RJF= 0.327, CB=0.324 and BL= 0.285. The F(ST) values among Thai indigenous chicken breeds vary from 0.051 to 0.096. The F(ST) values between the pairs of Thai indigenous chickens and RJF vary from 0.083 to 0.105 and the FST values between the Thai indigenous chickens and the two commercial chicken breeds vary from 0.116 to 0.221. A neighbour-joining tree of all individual chickens showed that the Thai indigenous chickens were clustered into four groups which were closely related to the wild RJF but far from the commercial breeds. Such commercial breeds were split into two closely groups. Using genetic admixture analysis, we observed that the Thai indigenous chicken breeds are likely to share common ancestors with the RJF, while both commercial chicken breeds share the same admixture pattern. These results indicated that the Thai indigenous chicken breeds may descend from the

  19. Genetic structure of local populations of Lutzomyia longipalpis (Diptera: Psychodidae) in central Colombia.

    Science.gov (United States)

    Munstermann, L E; Morrison, A C; Ferro, C; Pardo, R; Torres, M

    1998-01-01

    Lutzomyia longipalpis (Lutz & Neiva), the sand fly vector of American visceral leishmaniasis in the New World tropics, has a broad but discontinuous geographical distribution from southern Mexico to Argentina. A baseline for population genetic structure and genetic variability for this species was obtained by analyzing 5 local, peridomestic populations at the approximate center of its distribution, the Magdalena River Valley of central Colombia. Three populations of L. longipalpis from El Callejón, a small rural community, were compared with 2 populations from neighboring areas 12 and 25 km distant for genetic variation at 15 isoenzyme loci. The mean heterozygosity ranged from 11 to 16%, with 1.2 to 2.3 alleles detected per locus. Nei's genetic distances among the populations were very low, ranging from 0.001 to 0.007. Gene flow estimates based on FST indicated high levels of gene flow among local L. longipalpis populations, with minimal population substructuring.

  20. Spatial genetic structure in continuous and fragmented populations of Pinus pinaster Aiton.

    Science.gov (United States)

    De-Lucas, A I; González-Martínez, S C; Vendramin, G G; Hidalgo, E; Heuertz, M

    2009-11-01

    Habitat fragmentation, i.e., the reduction of populations into small isolated remnants, is expected to increase spatial genetic structure (SGS) in plant populations through nonrandom mating, lower population densities and potential aggregation of reproductive individuals. We investigated the effects of population size reduction and genetic isolation on SGS in maritime pine (Pinus pinaster Aiton) using a combined experimental and simulation approach. Maritime pine is a wind-pollinated conifer which has a scattered distribution in the Iberian Peninsula as a result of forest fires and habitat fragmentation. Five highly polymorphic nuclear microsatellites were genotyped in a total of 394 individuals from two population pairs from the Iberian Peninsula, formed by one continuous and one fragmented population each. In agreement with predictions, SGS was significant and stronger in fragments (Sp = 0.020 and Sp = 0.026) than in continuous populations, where significant SGS was detected for one population only (Sp = 0.010). Simulations suggested that under fat-tailed dispersal, small population size is a stronger determinant of SGS than genetic isolation, while under normal dispersal, genetic isolation has a stronger effect. SGS was always stronger in real populations than in simulations, except if unrealistically narrow dispersal and/or high variance of reproductive success were modelled (even when accounting for potential overestimation of SGS in real populations as a result of short-distance sampling). This suggests that factors such as nonrandom mating or selection not considered in the simulations were additionally operating on SGS in Iberian maritime pine populations.

  1. Genetic diversity and population structure of Sitodiplosis mosellana in Northern China.

    Directory of Open Access Journals (Sweden)

    Yun Duan

    Full Text Available The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups, broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (F ST = 0.117 between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (F ST = 0.116, Nm = 1.89 than those in the eastern group (F ST = 0.049, Nm = 4.91. Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001. The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.

  2. Genetic diversity and structure of domestic cavy (Cavia porcellus populations from smallholder farms in southern Cameroon

    Directory of Open Access Journals (Sweden)

    Basengere Ayagirwe

    2017-09-01

    Full Text Available Although domestic cavies are widely used in sub-Saharan Africa as a source of meat and income, there are only a few studies of their population structure and genetic relatedness. This seminal study was designed with the main objective to assess the genetic diversity and determine the population structure of cavy populations from Cameroon to guide the development of a cavy improvement program. Sixteen microsatellite markers were used to genotype 109 individuals from five cavy populations (Wouri, Moungo and Nkongsamba in the Littoral region, and Mémé and Fako in the Southwest region of Cameroon. Twelve markers worked in the five populations with a total of 17 alleles identified, with a range of 2.9 to 4.0 alleles per locus. Observed heterozygosity (from 0.022 to 0.277 among populations was lower than expected heterozygosity (from 0.42 to 0.54. Inbreeding rates between individuals of the populations and between individuals in each population were 59.3% and 57.2%, respectively, against a moderate differentiation rate of 4.9%. All the tested loci deviated from Hardy-Weinberg equilibrium, except for locus 3. Genetic distances between populations were small (from 0.008 to 0.277, with a high rate of variability among individuals within each population (54.4%. Three distinct genetic groups were structured. This study has shown that microsatellites are useful for the genetic characterization of cavy populations in Cameroon and that the populations investigated have sufficient genetic diversity that can be used to be deployed as a basis for weight, prolificacy and disease resistance improvement. The genetic of diversity in Southern Cameroon is wide and constitute an opportunity for cavy breeding program.

  3. An agent-based computational model for tuberculosis spreading on age-structured populations

    Science.gov (United States)

    Graciani Rodrigues, C. C.; Espíndola, Aquino L.; Penna, T. J. P.

    2015-06-01

    In this work we present an agent-based computational model to study the spreading of the tuberculosis (TB) disease on age-structured populations. The model proposed is a merge of two previous models: an agent-based computational model for the spreading of tuberculosis and a bit-string model for biological aging. The combination of TB with the population aging, reproduces the coexistence of health states, as seen in real populations. In addition, the universal exponential behavior of mortalities curves is still preserved. Finally, the population distribution as function of age shows the prevalence of TB mostly in elders, for high efficacy treatments.

  4. Population genetic structure of peninsular Malaysia Malay sub-ethnic groups.

    Science.gov (United States)

    Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Zahri, Mohd-Khairi; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi

    2011-04-05

    Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.

  5. Population structure from NOS genes correlates with geographical differences in coronary incidence across Europe.

    Science.gov (United States)

    Carreras-Torres, Robert; Ferran, Albert; Zanetti, Daniela; Esteban, Esther; Varesi, Laurent; Pojskic, Naris; Coia, Valentina; Chaabani, Hassen; Via, Marc; Moral, Pedro

    2016-12-01

    The population analysis of cardiovascular risk and non-risk genetic variation can help to identify adaptive or random demographic processes that shaped coronary incidence variation across geography. In this study, 114 single nucleotide polymorphisms and 17 tandem repeat polymorphisms from Nitric Oxide Synthases (NOS) regions were analyzed in 1686 individuals from 35 populations from Europe, North Africa, and the Middle East. NOS genes encode for key enzymes on nitric oxide availability, which is involved in several cardiovascular processes. These genetic variations were used to test for selection and to infer the population structure of NOS regions. Moreover, we tested whether the variation in the incidence of coronary events and in the levels of classical risk factors in 11 of these European populations could be explained by the population structure estimates. Our results supported, first, the absence of clear signs of selection for NOS genetic variants associated with cardiovascular diseases, and second, the presence of a continuous genetic pattern of variation across European and North African populations without a Mediterranean barrier for gene flow. Finally, population structure estimates from NOS regions are closely correlated with coronary event rates and classical risk parameters (explaining 39-98%) among European populations. Our results reinforce the hypothesis that genetic bases of cardiovascular diseases and associated complex phenotypes could be geographically shaped by random demographic processes. © 2016 Wiley Periodicals, Inc.

  6. Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups

    Science.gov (United States)

    Hatin, Wan Isa; Nur-Shafawati, Ab Rajab; Zahri, Mohd-Khairi; Xu, Shuhua; Jin, Li; Tan, Soon-Guan; Rizman-Idid, Mohammed; Zilfalil, Bin Alwi

    2011-01-01

    Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia. PMID:21483678

  7. The impact of divergence time on the nature of population structure: an example from Iceland.

    Directory of Open Access Journals (Sweden)

    Alkes L Price

    2009-06-01

    Full Text Available The Icelandic population has been sampled in many disease association studies, providing a strong motivation to understand the structure of this population and its ramifications for disease gene mapping. Previous work using 40 microsatellites showed that the Icelandic population is relatively homogeneous, but exhibits subtle population structure that can bias disease association statistics. Here, we show that regional geographic ancestries of individuals from Iceland can be distinguished using 292,289 autosomal single-nucleotide polymorphisms (SNPs. We further show that subpopulation differences are due to genetic drift since the settlement of Iceland 1100 years ago, and not to varying contributions from different ancestral populations. A consequence of the recent origin of Icelandic population structure is that allele frequency differences follow a null distribution devoid of outliers, so that the risk of false positive associations due to stratification is minimal. Our results highlight an important distinction between population differences attributable to recent drift and those arising from more ancient divergence, which has implications both for association studies and for efforts to detect natural selection using population differentiation.

  8. The structuring process of the macroparasite community of an experimental population of cichlasoma urophthalmus through time

    Science.gov (United States)

    Vidal-Martinez; Kennedy; Aguirre-Macedo

    1998-09-01

    The structuring process of the macroparasite community of caged Cichlasoma urophthalmus was studied over time using sentinel fish. Three thousand uninfected cichlids were stocked in floating cages introduced into a quarry in which a wild population of the same species was present. Caged and wild cichlids were sampled monthly over 6 and 7 months, respectively. Seventeen macroparasite species were found in the wild C. urophthalmus population, ten of which were detected in the caged population after 6 months. Early infections were by those species that were more frequent and abundant in the wild population, while helminths with a low prevalence and abundance in the wild appeared later in the caged fish population. The results suggested that the structuring process of the macroparasite community of caged C. urophthalmus followed a predictable pattern, in which those species that were most frequent and abundant in the wild were the first to establish in sentinel fish.

  9. Population structure of Tor tor inferred from mitochondrial gene cytochrome b.

    Science.gov (United States)

    Pasi, Komal Shyamakant; Lakra, W S; Bhatt, J P; Goswami, M; Malakar, A Kr

    2013-06-01

    Tor tor, commonly called as Tor mahseer, is a high-valued food and game fish endemic to trans-Himalayan region. Mitochondrial cytochrome b (cyt b) gene region of 967 bp was used to estimate the population structure of T. tor. Three populations of T. tor were collected from Narmada (Hosangabad), Ken (Madla), and Parbati river (Sheopur) in Madhya Pradesh, India. The sequence analysis revealed that the nucleotide diversity (π) was low, ranging from 0.000 to 0.0150. Haplotype diversity (h) ranged from 0.000 to 1.000. The analysis of molecular variance analysis indicated significant genetic divergence among the three populations of T. tor. Neighboring-joining tree also showed that all individuals from three populations clustered into three distinct clades. The data generated by cyt b marker revealed interesting insight about population structure of T. tor, which would serve as baseline data for conservation and management of mahseer fishery.

  10. Population structure, spatial distribution and life-history traits of blacktip reef sharks Carcharhinus melanopterus.

    Science.gov (United States)

    Mourier, J; Mills, S C; Planes, S

    2013-03-01

    During a survey of the population of blacktip reef shark Carcharhinus melanopterus in Moorea (French Polynesia) between 2007 and 2011, population structural characteristics were estimated from 268 individuals. Total length (LT ) ranged from 48 to 139 cm and 48 to 157 cm for males and females, respectively, demonstrating that the average LT of females was larger than that of males. The C. melanopterus population at Moorea showed an apparent spatial sexual segregation with females preferentially frequenting lagoons and males the fore-reefs. Mean growth rate was c. 6 cm year(-1) . Males reached sexual maturity at 111 cm LT . This study reports on the population characteristics of this widespread carcharhinid shark species and makes comparisons with other locations, confirming high geographic variability in the population structure of the species. © 2013 The Authors. Journal of Fish Biology © 2013 The Fisheries Society of the British Isles.

  11. Population Structure and Gene Flow of the Yellow Anaconda (Eunectes notaeus) in Northern Argentina

    Science.gov (United States)

    McCartney-Melstad, Evan; Waller, Tomás; Micucci, Patricio A.; Barros, Mariano; Draque, Juan; Amato, George; Mendez, Martin

    2012-01-01

    Yellow anacondas (Eunectes notaeus) are large, semiaquatic boid snakes found in wetland systems in South America. These snakes are commercially harvested under a sustainable management plan in Argentina, so information regarding population structuring can be helpful for determination of management units. We evaluated genetic structure and migration using partial sequences from the mitochondrial control region and mitochondrial genes cyt-b and ND4 for 183 samples collected within northern Argentina. A group of landscape features and environmental variables including several treatments of temperature and precipitation were explored as potential drivers of observed genetic patterns. We found significant population structure between most putative population comparisons and bidirectional but asymmetric migration in several cases. The configuration of rivers and wetlands was found to be significantly associated with yellow anaconda population structure (IBD), and important for gene flow, although genetic distances were not significantly correlated with the environmental variables used here. More in-depth analyses of environmental data may be needed to fully understand the importance of environmental conditions on population structure and migration. These analyses indicate that our putative populations are demographically distinct and should be treated as such in Argentina's management plan for the harvesting of yellow anacondas. PMID:22675425

  12. Polygyny and strong genetic structuring within an isolated population of the wood ant Formica rufa

    Directory of Open Access Journals (Sweden)

    Wouter Dekoninck

    2014-12-01

    Full Text Available Social structuring of populations within some Formica species exhibits considerable variation going from monodomous and monogynous populations to polydomous, polygynous populations. The wood ant species Formica rufa appears to be mainly monodomous and monogynous throughout most of its distribution area in central and northern Europe. Only occasionally it was mentioned that F. rufa can have both polygynous and monogynous colonies in the same geographical region. We studied an isolated polydomous F. rufa population in a deciduous mixed forest in the north-west of Belgium. The level of polydomy within the colonies varied from monodomous to 11 nests per colony. Our genetic analysis of eight variable microsatellites suggest an oligo- to polygynous structure for at least the major part of the sampled nests. Relatedness amongst nest mate workers varies considerable within the population and colonies but confirms in general a polygynous structure. Additionally high genetic diversity (e.g. up to 8 out of 11 alleles per nest for the most variable locus and high within nest genetic variance (93% indicate that multiple queens contribute to the gene pool of workers of the same nest. Moreover significant genetic structuring among colonies indicates that gene flow between colonies is restricted and that exchange of workers between colonies is very limited. Finally we explain how possible factors as budding and the absence of Serviformica can explain the differences in genetic structure within this polygynous F. rufa population.

  13. Distribution and population structure of North Atlantic harbour seals (Phoca vitulina

    Directory of Open Access Journals (Sweden)

    Liselotte Andersen

    2010-09-01

    Full Text Available A review of the known geographical distribution and current knowledge on the genetic population structure of harbour seals (Phoca vitulina in the North Atlantic is presented. Based on a synthesis of the results fromfive different studies of neutral geneticmarkers (mtDNAand nuclear microsatellites, mainly twelve genetically distinct populations were identified in the North Atlantic: USA/Canada, Iceland, west coast of Norway, Ireland-Scotland, English east coast, Channel area, Wadden Sea, Limfjord, Skagerrak, Kattegat, West Baltic, and East Baltic. Most of the studies addressed the population structure at the regional level, while only a few addressed the structuring at a local level, i.e. within countries. Due to the limited number of studies conducted, the identified population units were considered preliminary andmore detailed, local studieswould probably reveal structuring on a finer scale. The choice of genetic markers, their properties, resolution in time and applicability in population structure studies is shortly discussed and compared to ecological methods used to delineate populations.

  14. Influence of physical damage and freezing on histamine concentration and microbiological quality of yellowfin tuna during processing

    Directory of Open Access Journals (Sweden)

    Gonzalo García-Tapia

    2013-09-01

    Full Text Available Yellowfin tuna has a high level of free histidine in their muscle, which can lead to histamine formation by microorganisms if temperature abuse occurs during handling and further processing. The objective of this study was to measure levels of histamine in damaged and undamaged thawed muscle to determine the effect of physical damage on the microbial count and histamine formation during the initial steps of canning processing and to isolate and identify the main histamine-forming microorganisms present in the flesh of yellowfin tuna. Total mesophilic and psicrophilic microorganisms were determined using the standard plate method. The presence of histamine-forming microorganisms was determined in a modified Niven's agar. Strains were further identified using the API 20E kit for enterobacteriaceae and Gram-negative bacilli. Physically damaged tuna did not show higher microbiological contamination than that of undamaged muscle tuna. The most active histamine-forming microorganism present in tuna flesh was Morganella morganii. Other decarboxylating microorganisms present were Enterobacter agglomerans and Enterobacter cloacae. Physical damage of tune during catching and handling did not increase the level of histamine or the amount of microorganisms present in tuna meat during frozen transportation, but they showed a higher risk of histamine-forming microorganism growth during processing.

  15. Influences of oceanographic features on the distribution and abundance of yellowfin tuna, Thunnus albacares, larvae in the Gulf of Mexico

    Science.gov (United States)

    Cornic, M.; Rooker, J. R.

    2016-02-01

    Summer ichthyoplankton surveys were conducted in the northern Gulf of Mexico (NGoM) from 2007-2010 to characterize patterns of distribution and abundance of yellowfin tuna (Thunnus albacares) larvae in this region. Yellowfin tuna larvae were moderately abundant representing 9% of the overall Thunnus larvae collected (18765) and had a percent occurrence ranging from 13 to 57% among surveys. Interannual variations were detected with highest mean densities observed in 2009 (2.2 larvae per 1000m3) and the lowest mean densities observed in 2008 (0.7 larvae per 1000 m3). Generalized additive models were used to investigate the influence of oceanographic conditions on abundance of yellowfin tuna larvae. Increased densities were associated with high sea surface temperatures, positive sea surface heights, and intermediate salinities, revealing that these physicochemical conditions may be favorable for yellowfin tuna larvae. These results indicate that the NGoM is an important spawning and/or nursery habitat for yellowfin tuna and suggest that mesoscale features and physicochemical characteristics of water masses may impact distribution and abundance of yellowfin tuna larvae in the NGoM.

  16. Are Consumers Willing to Pay More for Sustainable Products? A Study of Eco-Labeled Tuna Steak

    Directory of Open Access Journals (Sweden)

    Guzhen Zhou

    2016-05-01

    Full Text Available A high demand for seafood leads to overfishing, harms the long-term health of seafood stocks, and threatens environmental sustainability in oceans. Sustainability certification is one of the major sustainability movements and is known as eco-labeling. For instance, in the tuna industry, leading tuna brands have committed to protecting sea turtles by allowing the tracing of the source of their tuna “from catch to can.” This paper relies on an Internet survey on consumers from Kentucky conducted in July 2010. The survey investigates household-level tuna steak (sashimi grade consumption and examines consumer preferences for eco-labeling (“Certified Turtle Safe” (CTS in this study while mimicking individuals’ seafood procurement processes. A random parameter logit model is utilized, and willingness-to-pay measures are calculated based on model estimation results. It was found that respondents on average preferred turtle-safe-labeled tuna steak and were likely to pay more for it; however, they were less likely to purchase wild-caught species, and insignificant results were found for pre-frozen. Moreover, significant heterogeneities were found across individuals regarding tuna steak purchases. The findings indicate evidence of public support for environmental friendliness, particularly with regard to eco-labeling.

  17. Genetic diversity and population structure of Plasmodium falciparum in Thailand, a low transmission country.

    Science.gov (United States)

    Pumpaibool, Tepanata; Arnathau, Céline; Durand, Patrick; Kanchanakhan, Naowarat; Siripoon, Napaporn; Suegorn, Aree; Sitthi-Amorn, Chitr; Renaud, François; Harnyuttanakorn, Pongchai

    2009-07-14

    The population structure of the causative agents of human malaria, Plasmodium sp., including the most serious agent Plasmodium falciparum, depends on the local epidemiological and demographic situations, such as the incidence of infected people, the vector transmission intensity and migration of inhabitants (i.e. exchange between sites). Analysing the structure of P. falciparum populations at a large scale, such as continents, or with markers that are subject to non-neutral selection, can lead to a masking and misunderstanding of the effective process of transmission. Thus, knowledge of the genetic structure and organization of P. falciparum populations in a particular area with neutral genetic markers is needed to understand which epidemiological factors should be targeted for disease control. Limited reports are available on the population genetic diversity and structure of P. falciparum in Thailand, and this is of particular concern at the Thai-Myanmar and Thai-Cambodian borders, where there is a reported high resistance to anti-malarial drugs, for example mefloquine, with little understanding of its potential gene flow. The diversity and genetic differentiation of P. falciparum populations were analysed using 12 polymorphic apparently neutral microsatellite loci distributed on eight of the 14 different chromosomes. Samples were collected from seven provinces in the western, eastern and southern parts of Thailand. A strong difference in the nuclear genetic structure was observed between most of the assayed populations. The genetic diversity was comparable to the intermediate level observed in low P. falciparum transmission areas (average HS = 0.65 +/- 0.17), where the lowest is observed in South America and the highest in Africa. However, uniquely the Yala province, had only a single multilocus genotype present in all samples, leading to a strong geographic differentiation when compared to the other Thai populations during this study. Comparison of the genetic

  18. Population genetic structure of Rhizoctonia solani AG 3-PT from potatoes in South Africa.

    Science.gov (United States)

    Muzhinji, Norman; Woodhall, James W; Truter, Mariette; van der Waals, Jacquie E

    2016-05-01

    Rhizoctonia solani AG 3-PT is an important potato pathogen causing significant yield and quality losses in potato production. However, little is known about the levels of genetic diversity and structure of this pathogen in South Africa. A total of 114 R. solani AG 3-PT isolates collected from four geographic regions were analysed for genetic diversity and structure using eight microsatellite loci. Microsatellite analysis found high intra-population genetic diversity, population differentiation and evidence of recombination. A total of 78 multilocus genotypes were identified with few shared among populations. Low levels of clonality (13-39 %) and high levels of population differentiation were observed among populations. Most of the loci were in Hardy-Weinberg equilibrium and all four populations showed evidence of a mixed reproductive mode of both clonality and recombination. The PCoA clustering method revealed genetically distinct geographic populations of R. solani AG 3-PT in South Africa. This study showed that populations of R. solani AG 3-PT in South Africa are genetically differentiated and disease management strategies should be applied accordingly. This is the first study of the population genetics of R. solani AG 3-PT in South Africa and results may help to develop knowledge-based disease management strategies. Copyright © 2016 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  19. Population Structure and Dispersal Patterns within and between Atlantic and Mediterranean Populations of a Large-Range Pelagic Seabird

    Science.gov (United States)

    Genovart, Meritxell; Thibault, Jean-Claude; Igual, José Manuel; Bauzà-Ribot, Maria del Mar; Rabouam, Corinne; Bretagnolle, Vincent

    2013-01-01

    Dispersal is critically linked to the demographic and evolutionary trajectories of populations, but in most seabird species it may be difficult to estimate. Using molecular tools, we explored population structure and the spatial dispersal pattern of a highly pelagic but philopatric seabird, the Cory's shearwater Calonectris diomedea. Microsatellite fragments were analysed from samples collected across almost the entire breeding range of the species. To help disentangle the taxonomic status of the two subspecies described, the Atlantic form C. d. borealis and the Mediterranean form C. d. diomedea, we analysed genetic divergence between subspecies and quantified both historical and recent migration rates between the Mediterranean and Atlantic basins. We also searched for evidence of isolation by distance (IBD) and addressed spatial patterns of gene flow. We found a low genetic structure in the Mediterranean basin. Conversely, strong genetic differentiation appeared in the Atlantic basin. Even if the species was mostly philopatric (97%), results suggest recent dispersal between basins, especially from the Atlantic to the Mediterranean (aprox. 10% of migrants/generation across the last two generations). Long-term gene flow analyses also suggested an historical exchange between basins (about 70 breeders/generation). Spatial analysis of genetic variation indicates that distance is not the main factor in shaping genetic structure in this species. Given our results we recommend gathering more data before concluded whether these taxa should be treated as two species or subspecies. PMID:23950986

  20. Determination of the sterile release rate for stopping growing age-structured populations

    International Nuclear Information System (INIS)

    Barclay, Hugh John

    2016-01-01

    A freely-growing age-structured population was modelled for growth and control by sterile male releases. Equilibrium populations yield critical sterile male release rates that would hold the population at equilibrium. It is shown here that these rates may be different from the release rates required to stop a growing population and bring it to an equilibrium. A computer simulation was constructed of this population and a parameter sensitivity analysis graphed the effects on the required sterile male release rate of fertility, mating delay in adult females, net juvenile survivorship, three adult survivorship curves, the time spent in the juvenile stages, and total life span. The adult survivorship curves had the greatest effect on the required sterile release rate for population elimination. The required release rate was also determined for Ceratitis capitata (Wiedemann) using survivorship and fertility data from a laboratory strain. The concepts of over-flooding ratio and release ratio were discussed and quantified for the cases above. (author)

  1. Population genetic structure of urban malaria vector Anopheles stephensi in India.

    Science.gov (United States)

    Sharma, Richa; Sharma, Arvind; Kumar, Ashwani; Dube, Madhulika; Gakhar, S K

    2016-04-01

    Malaria is a major public health problem in India because climatic condition and geography of India provide an ideal environment for development of malaria vector. Anopheles stephensi is a major urban malaria vector in India and its control has been hampered by insecticide resistance. In present study population genetic structure of A. stephensi is analyzed at macro geographic level using 13 microsatellite markers. Significantly high genetic differentiation was found in all studied populations with differentiation values (FST) ranging from 0.0398 to 0.1808. The geographic distance was found to be playing a major role in genetic differentiation between different populations. Overall three genetic pools were observed and population of central India was found to be coexisting in two genetic pools. High effective population size (Ne) was found in all the studied populations. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. SINTESIS FOSFOLIPID MENGANDUNG ASAM LEMAK w-3 DARI FOSFOLIPID KEDELAI DAN MINYAK KAYA ASAM LEMAK w-3 DARI HASIL SAMPING PENGALENGAN TUNA

    Directory of Open Access Journals (Sweden)

    Teti Estiasih

    2013-03-01

    Full Text Available Synthesis of Phospholipid Containing w-3 Fatty Acids from Soy Phospholipidsand Fish Oil Enriched with w-3 Fatty Acids from Tuna Canning Processing Teti Estiasih, Moch. Nur, Jaya Mahar Maligan, Satrio Maulana ABSTRAK Keunggulan fosfolipid dapat ditingkatkan dengan menggabungkan asam lemak w-3, terutama EPA (eicosapentaenoicacid, C20:5w-3 dan DHA (docosahexaenoic acid, C22:6w-3, pada struktur fosfolipid sehingga diperoleh fosfolipidterstruktur. Strukturisasi fosfolipid kedelai komersial dilakukan dengan cara mengganti asam lemak dari fosfolipidkedelai dengan asam lemak w-3 dari minyak kaya asam lemak w-3 dari hasil samping pengalengan tuna. Sintesisfosfolipid terstruktur dilakukan secara asidolisis enzimatis dengan menggunakan lipase dari R. miehei. Faktor yangdikaji pada proses sintesis ini adalah konsentrasi enzim dan lama sintesis. Tingkat inkorporasi EPA dan DHA padastruktur fosfolipid dipengaruhi oleh konsentrasi enzim. Pada konsentrasi enzim yang rendah, peningkatan lama reaksisetelah tingkat inkoporasi optimum tercapai cenderung menyebabkan penurunan tingkat inkorporasi EPA+DHA. Padakonsentrasi enzim yang tinggi, lama reaksi tampaknya tidak mempengaruhi tingkat inkorporasi. Tingkat inkorporasiDHA lebih tinggi dari EPA sehingga fosfolipid terstruktur yang dihasilkan sangat sesuai digunakan untuk produk panganyang memerlukan kadar DHA tinggi. Ada preferensi inkorporasi EPA+DHA pada fosfatidiletanolamin dibandingkanjenis fosfolipid yang lain.Kata kunci: Fosfolipid terstruktur, asam lemak w-3, EPA, DHA, asidolisis enzimatis ABSTRACT The superiority of soy phospholipids could be obtained by incorporation of w-3 fatty acids into phospholipids structure,especially EPA (eicosapentaenoic acid, C20:5w-3 and DHA docosahexaenoic acid, C22:6w-3. Structurization ofcommercial soy phospholipids was conducted by replacement of natural fatty acids in soy phospholipids by w-3 fattyacids from w-3 fatty acids enriched Þ sh oil from tuna canning processing

  3. Detection of pelagic habitat hotspots for skipjack tuna in the Gulf of Bone-Flores Sea, southwestern Coral Triangle tuna, Indonesia.

    Science.gov (United States)

    Zainuddin, Mukti; Farhum, Aisjah; Safruddin, Safruddin; Selamat, Muhammad Banda; Sudirman, Sudirman; Nurdin, Nurjannah; Syamsuddin, Mega; Ridwan, Muhammad; Saitoh, Sei-Ichi

    2017-01-01

    Using remote sensing of sea surface temperature (SST), sea surface height anomaly (SSHA) and chlorophyll-a (Chl-a) together with catch data, we investigated the detection and persistence of important pelagic habitat hotspots for skipjack tuna in the Gulf of Bone-Flores Sea, Indonesia. We analyzed the data for the period between the northwest and southeast monsoon 2007-2011. A pelagic hotspot index was constructed from a model of multi-spectrum satellite-based oceanographic data in relation to skipjack fishing performance. Results showed that skipjack catch per unit efforts (CPUEs) increased significantly in areas of highest pelagic hotspot indices. The distribution and dynamics of habitat hotspots were detected by the synoptic measurements of SST, SSHA and Chl-a ranging from 29.5° to 31.5°C, from 2.5 to 12.5 cm and from 0.15 to 0.35 mg m-3, respectively. Total area of hotspots consistently peaked in May. Validation of skipjack CPUE predicted by our model against observed data from 2012 was highly significant. The key pelagic habitat corresponded with the Chl-a front, which could be related to the areas of relatively high prey abundance (enhanced feeding opportunity) for skipjack. We found that the area and persistence of the potential skipjack habitat hotspots for the 5 years were clearly identified by the 0.2 mg m-3 Chl-a isopleth, suggesting that the Chl-a front provides a key oceanographic indicator for global understanding on skipjack tuna habitat hotspots in the western tropical Pacific Ocean, especially within Coral Triangle tuna.

  4. Genetic structure and diversity of three Colombian southwest afrodescendent populations using 8 STR's

    International Nuclear Information System (INIS)

    Guauque Olarte, Sandra; Fuentes Pardo, Angela Patricia; Cardenas Henao, Heiber; Barreto, Guillermo

    2010-01-01

    To estimate the diversity, structure and genetic flow in three Colombian southwest afrodescendent populations (Buenaventura, Mulalo y Tumaco), the alleles revealed by 8 autosomal STR's were analyzed in 78 no-related individuals, by the use of PCR and comparison with specific allelic ladders for every system resolved by polyacrylamide gel (8%). the results were compared with 2 Amerindian populations (Awa-Kuaikier and Coyaima) and 2 mixed Colombian populations (Valle del Cauca and Cauca). For the afrodescendent and Amerindian populations was found moderate diversity (h between 0.768±0.414 and 0.796±0.424), in contrast, the mixed population showed higher rates (>0.803), which is probably caused by mixing with Amerindians, that also can explain the high endogamy seen in mixed populations. The AMOVA exhibited moderate genetic structure between the afrodescendent populations (FST= 0.098; p<0.05), but higher between the three ethnical groups compared (FST=0.26723; p<0.05). The closer genetics distances are in favor of Tumaco and Buenaventura, supported for the migration rate found (34.298), which was the same inside of Amerindian and mixed populations. Maybe, because Mulalo is a closed isolated population, its differences in front others afrodescendent populations are explained. The neighbor-joining tree showed nearest relations among Amerindian and mixed populations, furthermore, the ancestral character for the afrodescendents. That sustains the idea of genetic flow maintained between the 3 ethnical groups, principally between Amerindian and mixed populations, supported because the genetic differences, migration rates and Amerindian matrilineality reported in the literature

  5. Effects of the North Atlantic Oscillation on Spanish catches of albacore, Thunnus alalunga, and yellowfin tuna, Thunnus albacares, in the North–east Atlantic Ocean

    Energy Technology Data Exchange (ETDEWEB)

    Rubio, C.J.; MacIas, D.; Camiñas, J.A.; Fernandez, I.L.; Baez, J.C.

    2016-07-01

    Tuna are highly migratory pelagic species (HMPS) with great importance in commercial fishing. Several authors have highlighted the effect of climatic oscillations such as the NAO (North Atlantic Oscillation) on HMPS. This paper analyzes the effects of the NAO on two HMPS: albacore, Thunnus alalunga, and yellowfin tuna, Thunnus albacares. Fishing data from the Spanish fleet operating in the North Atlantic area were obtained from the International Commission for the Conservation of Atlantic Tunas (ICCAT) database. The results show a positive correlation between the NAO index and the Catch per Unit Effort (CPUE) for both albacore and yellowfin tuna, depicting a potential effect on their capturability. (Author)

  6. Kin groups and trait groups: population structure and epidemic disease selection.

    Science.gov (United States)

    Fix, A G

    1984-10-01

    A Monte Carlo simulation based on the population structure of a small-scale human population, the Semai Senoi of Malaysia, has been developed to study the combined effects of group, kin, and individual selection. The population structure resembles D.S. Wilson's structured deme model in that local breeding populations (Semai settlements) are subdivided into trait groups (hamlets) that may be kin-structured and are not themselves demes. Additionally, settlement breeding populations are connected by two-dimensional stepping-stone migration approaching 30% per generation. Group and kin-structured group selection occur among hamlets the survivors of which then disperse to breed within the settlement population. Genetic drift is modeled by the process of hamlet formation; individual selection as a deterministic process, and stepping-stone migration as either random or kin-structured migrant groups. The mechanism for group selection is epidemics of infectious disease that can wipe out small hamlets particularly if most adults become sick and social life collapses. Genetic resistance to a disease is an individual attribute; however, hamlet groups with several resistant adults are less likely to disintegrate and experience high social mortality. A specific human gene, hemoglobin E, which confers resistance to malaria, is studied as an example of the process. The results of the simulations show that high genetic variance among hamlet groups may be generated by moderate degrees of kin-structuring. This strong microdifferentiation provides the potential for group selection. The effect of group selection in this case is rapid increase in gene frequencies among the total set of populations. In fact, group selection in concert with individual selection produced a faster rate of gene frequency increase among a set of 25 populations than the rate within a single unstructured population subject to deterministic individual selection. Such rapid evolution with plausible rates of

  7. Genetic population structure accounts for contemporary ecogeographic patterns in tropic and subtropic-dwelling humans.

    Science.gov (United States)

    Hruschka, Daniel J; Hadley, Craig; Brewis, Alexandra A; Stojanowski, Christopher M

    2015-01-01

    Contemporary human populations conform to ecogeographic predictions that animals will become more compact in cooler climates and less compact in warmer ones. However, it remains unclear to what extent this pattern reflects plastic responses to current environments or genetic differences among populations. Analyzing anthropometric surveys of 232,684 children and adults from across 80 ethnolinguistic groups in sub-Saharan Africa, Asia and the Americas, we confirm that body surface-to-volume correlates with contemporary temperature at magnitudes found in more latitudinally diverse samples (Adj. R2 = 0.14-0.28). However, far more variation in body surface-to-volume is attributable to genetic population structure (Adj. R2 = 0.50-0.74). Moreover, genetic population structure accounts for nearly all of the observed relationship between contemporary temperature and body surface-to-volume among children and adults. Indeed, after controlling for population structure, contemporary temperature accounts for no more than 4% of the variance in body form in these groups. This effect of genetic affinity on body form is also independent of other ecological variables, such as dominant mode of subsistence and household wealth per capita. These findings suggest that the observed fit of human body surface-to-volume with current climate in this sample reflects relatively large effects of existing genetic population structure of contemporary humans compared to plastic response to current environments.

  8. Genetic population structure accounts for contemporary ecogeographic patterns in tropic and subtropic-dwelling humans.

    Directory of Open Access Journals (Sweden)

    Daniel J Hruschka

    Full Text Available Contemporary human populations conform to ecogeographic predictions that animals will become more compact in cooler climates and less compact in warmer ones. However, it remains unclear to what extent this pattern reflects plastic responses to current environments or genetic differences among populations. Analyzing anthropometric surveys of 232,684 children and adults from across 80 ethnolinguistic groups in sub-Saharan Africa, Asia and the Americas, we confirm that body surface-to-volume correlates with contemporary temperature at magnitudes found in more latitudinally diverse samples (Adj. R2 = 0.14-0.28. However, far more variation in body surface-to-volume is attributable to genetic population structure (Adj. R2 = 0.50-0.74. Moreover, genetic population structure accounts for nearly all of the observed relationship between contemporary temperature and body surface-to-volume among children and adults. Indeed, after controlling for population structure, contemporary temperature accounts for no more than 4% of the variance in body form in these groups. This effect of genetic affinity on body form is also independent of other ecological variables, such as dominant mode of subsistence and household wealth per capita. These findings suggest that the observed fit of human body surface-to-volume with current climate in this sample reflects relatively large effects of existing genetic population structure of contemporary humans compared to plastic response to current environments.

  9. Population size structure indices and growth standards for Salmo (trutta trutta Linnaeus, 1758 in Central Italy

    Directory of Open Access Journals (Sweden)

    Pedicillo G.

    2010-10-01

    Full Text Available The purpose of this study was to provide reference data on the growth and population structure of brown trout Salmo (trutta trutta Linnaeus, in Central Italy. Standards for growth (percentiles and a standard growth model were developed from the von Bertalanffy growth model by using length-at-age data obtained from 122 sampling sites in the River Tiber basin. Length-frequency indices provide a numeric estimation for deviations of the population structure from a balanced population. We adapted the traditional North American Relative Stock Density (RSD and Proportional Stock Density (PSD indices to brown trout populations in Central Italy by means of two methods. In the first method, the benchmarks of length categories were established by using percentages applied to the largest individual in the dataset. In the second method, asymptotic length and size at maturity were used to define the length categories for index calculation. Both methods were tested on length-frequency data from 263 sampling sites in the River Tiber basin. The results showed that the PSD calculated by the first method provided a better insight into the population structures of brown trout. These results provide tools that will help ichthyologists and fish managers to compare the growth and population structure of brown trout throughout Central Italy.

  10. Structure and genetic diversity of natural Brazilian pepper populations (Schinus terebinthifolius Raddi).

    Science.gov (United States)

    Álvares-Carvalho, S V; Duarte, J F; Santos, T C; Santos, R M; Silva-Mann, R; Carvalho, D

    2016-06-17

    In the face of a possible loss of genetic diversity in plants due the environmental changes, actions to ensure the genetic variability are an urgent necessity. The extraction of Brazilian pepper fruits is a cause of concern because it results in the lack of seeds in soil, hindering its distribution in space and time. It is important to address this concern and explore the species, used by riparian communities and agro-factories without considering the need for keeping the seeds for natural seed banks and for species sustainability. The objective of this study was to evaluate the structure and the genetic diversity in natural Brazilian pepper populations (Schinus terebinthifolius Raddi). Twenty-two alleles in 223 individuals were identified from eight forest remnants located in the states of Minas Gerais, Espírito Santo, and Sergipe. All populations presented loci in Hardy-Weinberg equilibrium deviation. Four populations presented six combinations of loci in linkage disequilibrium. Six exclusive alleles were detected in four populations. Analysis of molecular variance showed the absence of diversity between regions and that between the populations (GST) was 41%. Genetic diversity was structured in seven clusters (ΔK7). Brazilian pepper populations were not structured in a pattern of isolation by distance and present genetic bottleneck. The populations São Mateus, Canastra, Barbacena, and Ilha das Flores were identified as management units and may support conservation projects, ecological restoration and in implementation of management plans for Brazilian pepper in the State of Sergipe.

  11. A Large Plasmodium vivax Reservoir and Little Population Structure in the South Pacific.

    Directory of Open Access Journals (Sweden)

    Cristian Koepfli

    Full Text Available The importance of Plasmodium vivax in malaria elimination is increasingly being recognized, yet little is known about its population size and population genetic structure in the South Pacific, an area that is the focus of intensified malaria control.We have genotyped 13 microsatellite markers in 295 P. vivax isolates from four geographically distinct sites in Papua New Guinea (PNG and one site from Solomon Islands, representing different transmission intensities.Diversity was very high with expected heterozygosity values ranging from 0.62 to 0.98 for the different markers. Effective population size was high (12'872 to 19'533 per site. In PNG population structuring was limited with moderate levels of genetic differentiation. F ST values (adjusted for high diversity of markers were 0.14-0.15. Slightly higher levels were observed between PNG populations and Solomon Islands (F ST = 0.16.Low levels of population structure despite geographical barriers to transmission are in sharp contrast to results from regions of low P. vivax endemicity. Prior to intensification of malaria control programs in the study area, parasite diversity and effective population size remained high.

  12. Genetic structure of Plasmodium falciparum populations across the Honduras-Nicaragua border.

    Science.gov (United States)

    Larrañaga, Nerea; Mejía, Rosa E; Hormaza, José I; Montoya, Alberto; Soto, Aida; Fontecha, Gustavo A

    2013-10-04

    The Caribbean coast of Central America remains an area of malaria transmission caused by Plasmodium falciparum despite the fact that morbidity has been reduced in recent years. Parasite populations in that region show interesting characteristics such as chloroquine susceptibility and low mortality rates. Genetic structure and diversity of P. falciparum populations in the Honduras-Nicaragua border were analysed in this study. Seven neutral microsatellite loci were analysed in 110 P. falciparum isolates from endemic areas of Honduras (n = 77) and Nicaragua (n = 33), mostly from the border region called the Moskitia. Several analyses concerning the genetic diversity, linkage disequilibrium, population structure, molecular variance, and haplotype clustering were conducted. There was a low level of genetic diversity in P. falciparum populations from Honduras and Nicaragua. Expected heterozigosity (H(e)) results were similarly low for both populations. A moderate differentiation was revealed by the F(ST) index between both populations, and two putative clusters were defined through a structure analysis. The main cluster grouped most of samples from Honduras and Nicaragua, while the second cluster was smaller and included all the samples from the Siuna community in Nicaragua. This result could partially explain the stronger linkage disequilibrium (LD) in the parasite population from that country. These findings are congruent with the decreasing rates of malaria endemicity in Central America.

  13. CULTURAL MEMORY OF VICTORY OF LAS TUNAS CITY' LODGES FROM 1930 TO 1945 / MEMORIA CULTURAL DE LAS LOGIAS DE VICTORIA DE LAS TUNAS 1930-1945

    OpenAIRE

    Milena Medina Pérez

    2012-01-01

    The cultural memory of the lodges of Victoria de Las Tunas (1930-1945), it constitutes the topic of the present investigation. The thematic of the lodges has been approached for studious and investigating, not alone of the town but of several parts of the world. Still when these studies exist, the related with the cultural memory of the lodges of the territory, is in the pages of the documents of the time that which leaves to the light starting from this investigation, to show yesterday's Tun...

  14. Population structure and genetic diversity of the parasite Trichomonas vaginalis in Bristol, UK.

    Science.gov (United States)

    Hawksworth, Joseph; Levy, Max; Smale, Chloe; Cheung, Dean; Whittle, Alice; Longhurst, Denise; Muir, Peter; Gibson, Wendy

    2015-08-01

    The protozoan parasite Trichomonas vaginalis is the causative agent of trichomoniasis, an extremely common, but non-life-threatening, sexually-transmitted disease throughout the world. Recent population genetics studies of T. vaginalis have detected high genetic diversity and revealed a two-type population structure, associated with phenotypic differences in sensitivity to metronidazole, the drug commonly used for treatment, and presence of T. vaginalis virus. There is currently a lack of data on UK isolates; most isolates examined to date are from the US. Here we used a recently described system for multilocus sequence typing (MLST) of T. vaginalis to study diversity of clinical isolates from Bristol, UK. We used MLST to characterise 23 clinical isolates of T. vaginalis collected from female patients during 2013. Seven housekeeping genes were PCR-amplified for each isolate and sequenced. The concatenated sequences were then compared with data from other MLST-characterised isolates available from http://tvaginalis.mlst.net/ to analyse the population structure and construct phylogenetic trees. Among the 23 isolates from the Bristol population of T. vaginalis, we found 23 polymorphic nucleotide sites, 25 different alleles and 19 sequence types (genotypes). Most isolates had a unique genotype, in agreement with the high levels of heterogeneity observed elsewhere in the world. A two-type population structure was evident from population genetic analysis and phylogenetic reconstruction split the isolates into two major clades. Tests for recombination in the Bristol population of T. vaginalis gave conflicting results, suggesting overall a clonal pattern of reproduction. We conclude that the Bristol population of T. vaginalis parasites conforms to the two-type population structure found in most other regions of the world. We found the MLST scheme to be an efficient genotyping method. The online MLST database provides a useful repository and resource that will prove

  15. Constructing stage-structured matrix population models from life tables: comparison of methods

    Directory of Open Access Journals (Sweden)

    Masami Fujiwara

    2017-10-01

    Full Text Available A matrix population model is a convenient tool for summarizing per capita survival and reproduction rates (collectively vital rates of a population and can be used for calculating an asymptotic finite population growth rate (λ and generation time. These two pieces of information can be used for determining the status of a threatened species. The use of stage-structured population models has increased in recent years, and the vital rates in such models are often estimated using a life table analysis. However, potential bias introduced when converting age-structured vital rates estimated from a life table into parameters for a stage-structured population model has not been assessed comprehensively. The objective of this study was to investigate the performance of methods for such conversions using simulated life histories of organisms. The underlying models incorporate various types of life history and true population growth rates of varying levels. The performance was measured by comparing differences in λ and the generation time calculated using the Euler-Lotka equation, age-structured population matrices, and several stage-structured population matrices that were obtained by applying different conversion methods. The results show that the discretization of age introduces only small bias in λ or generation time. Similarly, assuming a fixed age of maturation at the mean age of maturation does not introduce much bias. However, aggregating age-specific survival rates into a stage-specific survival rate and estimating a stage-transition rate can introduce substantial bias depending on the organism’s life history type and the true values of λ. In order to aggregate survival rates, the use of the weighted arithmetic mean was the most robust method for estimating λ. Here, the weights are given by survivorship curve after discounting with λ. To estimate a stage-transition rate, matching the proportion of individuals transitioning, with λ used

  16. Genetic structure in two northern muriqui populations (Brachyteles hypoxanthus, Primates, Atelidae as inferred from fecal DNA

    Directory of Open Access Journals (Sweden)

    Valéria Fagundes

    2008-01-01

    Full Text Available We assessed the genetic diversity of two northern muriqui (Brachyteles hypoxanthus Primata, Atelidae populations, the Feliciano Miguel Abdala population (FMA, n = 108 in the Brazilian state of Minas Gerais (19°44' S, 41°49' W and the Santa Maria de Jetibá population (SMJ, n = 18 in the Brazilian state of Espírito Santo (20°01' S, 40°44' W. Fecal DNA was isolated and PCR-RFLP analysis used to analyze 2160 bp of mitochondrial DNA, made up of an 820 bp segment of the gene cytochrome c oxidase subunit 2 (cox2, EC 1.9.3.1, an 880 bp segment of the gene cytochrome b (cytb, EC 1.10.2.2 and 460 bp of the hypervariable segment of the mtDNA control region (HVRI. The cox2 and cytb sequences were monomorphic within and between populations whereas the HVRI revealed three different population exclusive haplotypes, one unique to the SMJ population and two, present at similar frequencies, in the FMA population. Overall haplotype diversity (h = 0.609 and nucleotide diversity (pi = 0.181 were high but reduced within populations. The populations were genetically structured with a high fixation index (F ST = 0.725, possibly due to historical subdivision. These findings have conservation implications because they seem to indicate that the populations are distinct management units.

  17. Spatial genetic structure within populations and management implications of the South American species Acacia aroma (Fabaceae).

    Science.gov (United States)

    Pometti, Carolina; Bessega, Cecilia; Cialdella, Ana; Ewens, Mauricio; Saidman, Beatriz; Vilardi, Juan

    2018-01-01

    The identification of factors that structure intraspecific diversity is of particular interest for biological conservation and restoration ecology. All rangelands in Argentina are currently experiencing some form of deterioration or desertification. Acacia aroma is a multipurpose species widely distributed throughout this country. In this study, we used the AFLP technique to study genetic diversity, population genetic structure, and fine-scale spatial genetic structure in 170 individuals belonging to 6 natural Argentinean populations. With 401 loci, the mean heterozygosity (HE = 0.2) and the mean percentage of polymorphic loci (PPL = 62.1%) coefficients indicated that the genetic variation is relatively high in A. aroma. The analysis with STRUCTURE showed that the number of clusters (K) was 3. With Geneland analysis, the number of clusters was K = 4, sharing the same grouping as STRUCTURE but dividing one population into two groups. When studying SGS, significant structure was detected in 3 of 6 populations. The neighbourhood size in these populations ranged from 15.2 to 64.3 individuals. The estimated gene dispersal distance depended on the effective population density and disturbance level and ranged from 45 to 864 m. The combined results suggest that a sampling strategy, which aims to maintain a considerable part of the variability contained in natural populations sampled here, would include at least 3 units defined by the clusters analyses that exhibit particular genetic properties. Moreover, the current SGS analysis suggests that within the wider management units/provinces, seed collection from A. aroma should target trees separated by a minimum distance of 50 m but preferably 150 m to reduce genetic relatedness among seeds from different trees.

  18. Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure.

    Science.gov (United States)

    Bohmann, Kristine; Gopalakrishnan, Shyam; Nielsen, Martin; Nielsen, Luisa Dos Santos Bay; Jones, Gareth; Streicker, Daniel G; Gilbert, M Thomas P

    2018-04-19

    Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co-amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat, we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing populations of common vampire bats impact human, livestock and wildlife health in Latin America through transmission of pathogens, such as lethal rabies viruses. Techniques to determine large-scale variation in vampire bat diet and bat population structure would empower locality- and species-specific projections of disease transmission risks. However, previously used methods are not cost-effective and efficient for large-scale applications. Using bloodmeal and faecal samples from common vampire bats from coastal, Andean and Amazonian regions of Peru, we showcase metabarcoding as a scalable tool to assess vampire bat population structure and feeding preferences. Dietary metabarcoding was highly effective, detecting vertebrate prey in 93.2% of the samples. Bats predominantly preyed on domestic animals, but fed on tapirs at one Amazonian site. In addition, we identified arthropods in 9.3% of samples, likely reflecting consumption of ectoparasites. Using the same data, we document mitochondrial geographic population structure in the common vampire bat in Peru. Such simultaneous inference of vampire bat diet and population structure can enable new insights into the interplay between vampire bat ecology and disease transmission risks. Importantly, the methodology can be incorporated into metabarcoding diet studies of other animals to couple information on diet and population structure. © 2018 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

  19. Distance, dams and drift: What structures populations of an endangered, benthic stream fish?

    Science.gov (United States)

    Roberts, James H.; Angermeier, Paul; Hallerman, Eric M.

    2013-01-01

    Spatial population structure plays an important role in species persistence, evolution and conservation. Benthic stream fishes are diverse and frequently imperilled, yet the determinants and spatial scaling of their population structure are understudied. We investigated the range-wide population genetic structure of Roanoke logperch (Percina rex), an endangered, benthic stream fish of the eastern United States. Fish were sampled from 35 sites and analysed at 11 microsatellite DNA loci. Clustering models were used to sort individuals into genetically cohesive groups and thereby estimate the spatial scaling of population structure. We then used Bayesian generalized linear mixed models (BGLMMs) to test alternative hypotheses about the environmental factors most responsible for generating structure, as measured by the differentiation statistic FST. Clustering models delineated seven discrete populations, whose boundaries coincided with agents of fragmentation, including hydroelectric dams and tailwaters. In the absence of hydrological barriers, gene flow was extensive throughout catchments, whereas there was no evidence for contemporary dispersal between catchments across barriers. In the best-supported BGLMM, FST was positively related to the spatial distance and degree of hydrological alteration between sites and negatively related to genetic diversity within sites. Whereas the effect of tailwaters was equivocal, dams strongly influenced differentiation: the effect of a dam on FST was comparable to that of a between-site distance of over 1200 km of unimpounded river. Overall, the effect of distance-mediated dispersal was negligible compared to the combined effects of fragmentation and genetic drift. The contemporary population structure of P. rex comprises a few geographically extensive ‘islands’ that are fragmented by hydroelectric projects. This information clarifies the importance of a catchment-scale perspective on conserving the species and

  20. Characterization of Population Genetic Structure of red swamp crayfish, Procambarus clarkii, in China.

    Science.gov (United States)

    Yi, Shaokui; Li, Yanhe; Shi, Linlin; Zhang, Long; Li, Qingbin; Chen, Jing

    2018-04-03

    The red swamp crayfish (Procambarus clarkii) is one of the most economically important farmed aquatic species in China. However, it is also a famous invasive species in the world. This invasive species was dispersed most via human activities including intentional or unintentional carry in China. Thus, P. clarkii naturally distributed in China provides us a desirable mode to investigate the genetic structure of an invasive species dispersed mainly by human-mediated factors. To reveal the impact of human-mediated dispersal on genetic structure of P. clarkii in China, a total of 22,043 genome-wide SNPs were obtained from approximately 7.4 billion raw reads using 2b-RAD technique in this study. An evident pattern of population genetic structure and the asymmetrical migrational rates between different regions were observed with 22 populations based on these SNPs. This study provide a better understanding of the population genetic structure and demographic history of P. clarkii populations in China, inferring that anthropogenic factors (aquaculture or by accident) and ecological factors (e.g., complicated topography and climatic environment), as well as its special biological traits could account for the current population structure pattern and dispersal history of P. clarkii.

  1. Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries.

    Science.gov (United States)

    Uren, Caitlin; Kim, Minju; Martin, Alicia R; Bobo, Dean; Gignoux, Christopher R; van Helden, Paul D; Möller, Marlo; Hoal, Eileen G; Henn, Brenna M

    2016-09-01

    Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa. Copyright © 2016 by the Genetics Society of America.

  2. Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations.

    Science.gov (United States)

    Wang, Yuchen; Lu, Dongsheng; Chung, Yeun-Jun; Xu, Shuhua

    2018-01-01

    Han Chinese, Japanese and Korean, the three major ethnic groups of East Asia, share many similarities in appearance, language and culture etc., but their genetic relationships, divergence times and subsequent genetic exchanges have not been well studied. We conducted a genome-wide study and evaluated the population structure of 182 Han Chinese, 90 Japanese and 100 Korean individuals, together with the data of 630 individuals representing 8 populations wordwide. Our analyses revealed that Han Chinese, Japanese and Korean populations have distinct genetic makeup and can be well distinguished based on either the genome wide data or a panel of ancestry informative markers (AIMs). Their genetic structure corresponds well to their geographical distributions, indicating geographical isolation played a critical role in driving population differentiation in East Asia. The most recent common ancestor of the three populations was dated back to 3000 ~ 3600 years ago. Our analyses also revealed substantial admixture within the three populations which occurred subsequent to initial splits, and distinct gene introgression from surrounding populations, of which northern ancestral component is dominant. These estimations and findings facilitate to understanding population history and mechanism of human genetic diversity in East Asia, and have implications for both evolutionary and medical studies.

  3. A longitudinal genetic survey identifies temporal shifts in the population structure of Dutch house sparrows

    Science.gov (United States)

    Cousseau, L; Husemann, M; Foppen, R; Vangestel, C; Lens, L

    2016-01-01

    Dutch house sparrow (Passer domesticus) densities dropped by nearly 50% since the early 1980s, and similar collapses in population sizes have been reported across Europe. Whether, and to what extent, such relatively recent demographic changes are accompanied by concomitant shifts in the genetic population structure of this species needs further investigation. Therefore, we here explore temporal shifts in genetic diversity, genetic structure and effective sizes of seven Dutch house sparrow populations. To allow the most powerful statistical inference, historical populations were resampled at identical locations and each individual bird was genotyped using nine polymorphic microsatellites. Although the demographic history was not reflected by a reduction in genetic diversity, levels of genetic differentiation increased over time, and the original, panmictic population (inferred from the museum samples) diverged into two distinct genetic clusters. Reductions in census size were supported by a substantial reduction in effective population size, although to a smaller extent. As most studies of contemporary house sparrow populations have been unable to identify genetic signatures of recent population declines, results of this study underpin the importance of longitudinal genetic surveys to unravel cryptic genetic patterns. PMID:27273323

  4. Genetic structure of typical and atypical populations of Candida albicans from Africa.

    Science.gov (United States)

    Forche, A; Schönian, G; Gräser, Y; Vilgalys, R; Mitchell, T G

    1999-11-01

    Atypical isolates of the pathogenic yeast Candida albicans have been reported with increasing frequency. To investigate the origin of a set of atypical isolates and their relationship to typical isolates, we employed a combination of molecular phylogenetic and population genetic analyses using rDNA sequencing, PCR fingerprinting, and analysis of co-dominant DNA nucleotide polymorphisms to characterize the population structure of one typical and two atypical populations of C. albicans from Angola and Madagascar. The extent of clonality and recombination was assessed in each population. The analyses revealed that the structure of all three populations of C. albicans was predominantly clonal but, as in previous studies, there was also evidence for recombination. Allele frequencies differed significantly between the typical and the atypical populations, suggesting very low levels of gene flow between them. However, allele frequencies were quite similar in the two atypical C. albicans populations, suggesting that they are closely related. Phylogenetic analysis of partial sequences encoding the nuclear 26S rDNA demonstrated that all three populations belong to a single monophyletic group, which includes the type strain of C. albicans. Copyright 1999 Academic Press.

  5. Low-temperature transitions in cod and tuna determined by differential scanning calorimetry

    DEFF Research Database (Denmark)

    Jensen, Kristina Nedenskov; Jørgensen, Bo; Nielsen, Jette

    2003-01-01

    Differential scanning calorimetry measurements have revealed different thermal transitions in cod and tuna samples. Transition temperatures detected Lit -11degreesC, -15degreesC and -21degreesC were highly dependent on the annealing temperature. In tuna muscle an additional transition was observed...... at -72degreesC. This transition appeared differently than the thermal events observed at higher temperatures, as it spanned a broad temperature interval of 25degreesC. The transition was comparable to low-temperature glass transitions reported in protein-rich systems. No transition at this low...... temperature was detected in cod samples. The transitions observed at higher temperatures (-11degreesC to -21degreesC) may possibly stein from a glassy matrix containing muscle proteins. However, the presence of a glass transition at - 11degreesC was in disagreement with the low storage stability at -18degrees...

  6. The imprint of anthropogenic CO2 emissions on Atlantic bluefin tuna otoliths

    Science.gov (United States)

    Fraile, Igaratza; Arrizabalaga, Haritz; Groeneveld, Jeroen; Kölling, Martin; Santos, Miguel Neves; Macías, David; Addis, Piero; Dettman, David L.; Karakulak, Saadet; Deguara, Simeon; Rooker, Jay R.

    2016-06-01

    Otoliths of Atlantic bluefin tuna (Thunnus thynnus) collected from the Mediterranean Sea and North Atlantic Ocean were analyzed to evaluate changes in the seawater isotopic composition over time. We report an annual otolith δ13C record that documents the magnitude of the δ13C depletion in the Mediterranean Sea between 1989 and 2010. Atlantic bluefin tuna in our sample (n = 632) ranged from 1 to 22 years, and otolith material corresponding to the first year of life (back-calculated birth year) was used to reconstruct seawater isotopic composition. Otolith δ18O remained relatively stable between 1989 and 2010, whereas a statistically significant decrease in δ13C was detected across the time interval investigated, with a rate of decline of 0.05‰ yr- 1 (- 0.94‰ depletion throughout the recorded period). The depletion in otolith δ13C over time was associated with the oceanic uptake of anthropogenically derived CO2.

  7. Mercury levels of yellowfin tuna (Thunnus albacares) are associated with capture location.

    Science.gov (United States)

    Nicklisch, Sascha C T; Bonito, Lindsay T; Sandin, Stuart; Hamdoun, Amro

    2017-10-01

    Mercury is a toxic compound to which humans are exposed by consumption of fish. Current fish consumption advisories focus on minimizing the risk posed by the species that are most likely to have high levels of mercury. Less accounted for is the variation within species, and the potential role of the geographic origin of a fish in determining its mercury level. Here we surveyed the mercury levels in 117 yellowfin tuna caught from 12 different locations worldwide. Our results indicated significant variation in yellowfin tuna methylmercury load, with levels that ranged from 0.03 to 0.82 μg/g wet weight across individual fish. Mean mercury levels were only weakly associated with fish size (R 2  mercury load, and argue for better traceability of fish to improve the accuracy of exposure risk predictions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Readiness Assessment Towards Smart Manufacturing System for Tuna Processing Industry in Indonesia

    Science.gov (United States)

    Anggrahini, D.; Kurniati, N.; Karningsih, P. D.; Parenreng, S. M.; Syahroni, N.

    2018-04-01

    Marine product processing is one of the top priority clusters in the national development. Tuna, as a kind of deep ocean fishes, has the highest number of production that significantly increased throughout the years. Indonesia government encourages tuna processing industry, which are mostly dominated by small to medium enterprises, to grow continuously. Nowadays, manufacturers are facing substantial challenges in adopting modern system and technology that will lead a significant improvement through the internet of things (IoT). A smart factory transform integrated manufacturing process, in a high speed processing to respond customer needs. It has some positive impacts, such as increasing productivity, reducing set up time, shortening marketing and other support activities, hence the process is being more flexible and efficient. To implement smart manufacturing system, factories should know the readiness at any level of them, technology capability and strategy appropriateness. This exploratory study aims to identify the criterias, and develop an assessment tools to measure the level towards smart factory.

  9. Genetic population structure in an equatorial sparrow: roles for culture and geography.

    Science.gov (United States)

    Danner, J E; Fleischer, R C; Danner, R M; Moore, I T

    2017-06-01

    Female preference for local cultural traits has been proposed as a barrier to breeding among animal populations. As such, several studies have found correlations between male bird song dialects and population genetics over relatively large distances. To investigate whether female choice for local dialects could act as a barrier to breeding between nearby and contiguous populations, we tested whether variation in male song dialects explains genetic structure among eight populations of rufous-collared sparrows (Zonotrichia capensis) in Ecuador. Our study sites lay along a transect, and adjacent study sites were separated by approximately 25 km, an order of magnitude less than previously examined for this and most other species. This transect crossed an Andean ridge and through the Quijos River Valley, both of which may be barriers to gene flow. Using a variance partitioning approach, we show that song dialect is important in explaining population genetics, independent of the geographic variables: distance, the river valley and the Andean Ridge. This result is consistent with the hypothesis that song acts as a barrier to breeding among populations in close proximity. In addition, songs of contiguous populations differed by the same degree or more than between two populations previously shown to exhibit female preference for local dialect, suggesting that birds from these populations would also breed preferentially with locals. As expected, all geographic variables (distance, the river valley and the Andean Ridge) also predicted population genetic structure. Our results have important implications for the understanding whether, and at what spatial scale, culture can affect population divergence. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  10. Gender inequality on the example of socio-demographic structures of Belgrade population

    Directory of Open Access Journals (Sweden)

    Kuburović Ankica

    2007-01-01

    Full Text Available An analysis of demographic characteristics from the gender perspective represents a contribution to enlightening the social relations between female and male population in Belgrade. Gender specificity and explicitness of socio-demographic structures indicate to different positions and statuses of the female and male populations. There are more females than men in the total population of the capital city of Serbia. The sex imbalance of age groups is determined by gender differences in the number of born boys and girls, in migration characteristics and in the level of mortality. The male population is greater in the age group up to 20 years old, while the female population is more numerous among the middle-aged and older generations. Gender differences in marital structure, level of education and economic activities cannot be reduced only to demographic limits. A larger rate of married persons among the males in relation to female population is determined by the different behavior in view of remarriage in case of divorce or death of partner. Women are widowed or divorced more often than men, which can be interpreted as a less favorable position in everyday functioning, especially when the women have small or school-age children, as well as in the case of older women. Gender differences in the level of education of Belgrade population are not exceptionally pronounced and are a consequence of unfavorable positions of older women to a certain degree. Differences in economic activity, among other things, are determined by uneven utilization of female and male work force. The rate of economic activity is greater in the male population, and the coefficient of economic dependency in the female population. The gender difference in the rate of supported persons among the work capable population increases the unfavorable social position of women. The characteristics of socio-demographic structures of female and male population of the city of Belgrade vary

  11. A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau

    Science.gov (United States)

    Peter, Benjamin M.; Basnyat, Buddha; Neupane, Maniraj; Beall, Cynthia M.; Childs, Geoff; Craig, Sienna R.; Novembre, John; Di Rienzo, Anna

    2017-01-01

    Indigenous populations of the Tibetan plateau have attracted much attention for their good performance at extreme high altitude. Most genetic studies of Tibetan adaptations have used genetic variation data at the genome scale, while genetic inferences about their demography and population structure are largely based on uniparental markers. To provide genome-wide information on population structure, we analyzed new and published data of 338 individuals from indigenous populations across the plateau in conjunction with worldwide genetic variation data. We found a clear signal of genetic stratification across the east-west axis within Tibetan samples. Samples from more eastern locations tend to have higher genetic affinity with lowland East Asians, which can be explained by more gene flow from lowland East Asia onto the plateau. Our findings corroborate a previous report of admixture signals in Tibetans, which were based on a subset of the samples analyzed here, but add evidence for isolation by distance in a broader geospatial context. PMID:28448508

  12. The confounding effect of population structure on bayesian skyline plot inferences of demographic history

    DEFF Research Database (Denmark)

    Heller, Rasmus; Chikhi, Lounes; Siegismund, Hans

    2013-01-01

    Many coalescent-based methods aiming to infer the demographic history of populations assume a single, isolated and panmictic population (i.e. a Wright-Fisher model). While this assumption may be reasonable under many conditions, several recent studies have shown that the results can be misleading...... when it is violated. Among the most widely applied demographic inference methods are Bayesian skyline plots (BSPs), which are used across a range of biological fields. Violations of the panmixia assumption are to be expected in many biological systems, but the consequences for skyline plot inferences...... the best scheme for inferring demographic change over a typical time scale. Analyses of data from a structured African buffalo population demonstrate how BSP results can be strengthened by simulations. We recommend that sample selection should be carefully considered in relation to population structure...

  13. Population genetic structure of rare and endangered plants using molecular markers

    Science.gov (United States)

    Raji, Jennifer; Atkinson, Carter T.

    2013-01-01

    This study was initiated to assess the levels of genetic diversity and differentiation in the remaining populations of Phyllostegia stachyoides and Melicope zahlbruckneri in Hawai`i Volcanoes National Park and determine the extent of gene flow to identify genetically distinct individuals or groups for conservation purposes. Thirty-six Amplified Fragment Length Polymorphic (AFLP) primer combinations generated a total of 3,242 polymorphic deoxyribonucleic acid (DNA) fragments in the P. stachyoides population with a percentage of polymorphic bands (PPB) ranging from 39.3 to 65.7% and 2,780 for the M. zahlbruckneri population with a PPB of 18.8 to 64.6%. Population differentiation (Fst) of AFLP loci between subpopulations of P. stachyoides was low (0.043) across populations. Analysis of molecular variance of P. stachyoides showed that 4% of the observed genetic differentiation occurred between populations in different kīpuka and 96% when individuals were pooled from all kīpuka. Moderate genetic diversity was detected within the M. zahlbruckneri population. Bayesian and multivariate analyses both classified the P. stachyoides and M. zahlbruckneri populations into genetic groups with considerable sub-structuring detected in the P. stachyoides population. The proportion of genetic differentiation among populations explained by geographical distance was estimated by Mantel tests. No spatial correlation was found between genetic and geographic distances in both populations. Finally, a moderate but significant gene flow that could be attributed to insect or bird-mediated dispersal of pollen across the different kīpuka was observed. The results of this study highlight the utility of a multi-allelic DNA-based marker in screening a large number of polymorphic loci in small and closely related endangered populations and revealed the presence of genetically unique groups of individuals in both M. zahlbruckneri and P. stachyoides populations. Based on these findings

  14. Transectional heat transfer in thermoregulating bigeye tuna (Thunnus obesus) - a 2D heat flux model.

    Science.gov (United States)

    Boye, Jess; Musyl, Michael; Brill, Richard; Malte, Hans

    2009-11-01

    We developed a 2D heat flux model to elucidate routes and rates of heat transfer within bigeye tuna Thunnus obesus Lowe 1839 in both steady-state and time-dependent settings. In modeling the former situation, we adjusted the efficiencies of heat conservation in the red and the white muscle so as to make the output of the model agree as closely as possible with observed cross-sectional isotherms. In modeling the latter situation, we applied the heat exchanger efficiencies from the steady-state model to predict the distribution of temperature and heat fluxes in bigeye tuna during their extensive daily vertical excursions. The simulations yielded a close match to the data recorded in free-swimming fish and strongly point to the importance of the heat-producing and heat-conserving properties of the white muscle. The best correspondence between model output and observed data was obtained when the countercurrent heat exchangers in the blood flow pathways to the red and white muscle retained 99% and 96% (respectively) of the heat produced in these tissues. Our model confirms that the ability of bigeye tuna to maintain elevated muscle temperatures during their extensive daily vertical movements depends on their ability to rapidly modulate heating and cooling rates. This study shows that the differential cooling and heating rates could be fully accounted for by a mechanism where blood flow to the swimming muscles is either exclusively through the heat exchangers or completely shunted around them, depending on the ambient temperature relative to the body temperature. Our results therefore strongly suggest that such a mechanism is involved in the extensive physiological thermoregulatory abilities of endothermic bigeye tuna.

  15. Improving the safety and quality of raw tuna fillets by x-ray irradiation

    Science.gov (United States)

    In this study, raw tuna fillet (25 g) samples were inoculated by immersing in 0.1% peptone water that contained 108-9 CFU ml-1 of a three-strain mixture of Salmonella enterica for 1 min. The samples were then air dried at 22 oC for 30 min and were packaged separately in sterilized bags prior to X-ra...

  16. EVALUASI IMPLEMENTASI MANAJEMEN BERBASIS SEKOLAH (MBSDI SMK TELEKOMUNIKASI TUNAS HARAPAN KABUPATEN SEMARANG (STUDI TENTANG PEMBELAJARAN PAKEM

    Directory of Open Access Journals (Sweden)

    Prima Widyatmoko

    2015-06-01

    Full Text Available This study aims at evaluating (a the design of implementation of PAKEM learning in SMK Telekomunikasi Tunas Harapan, (b the installation of implementation of PAKEM learning in SMK Telekomunikasi Tunas Harapan, (c the process of implementation of PAKEM learning in SMK Telekomunikasi Tunas Harapan, and (d the product evaluation of implementation of PAKEM learning in SMK Te