WorldWideScience

Sample records for delineating breeding populations

  1. Waterfowl breeding population survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Waterfowl breeding population surveys have been completed annually on the Arctic Coastal Plain of Alaska since 1986. Methods for the 2011 Arctic Coastal Plain...

  2. Waterfowl breeding population survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Waterfowl breeding population surveys have been completed annually on the Arctic Coastal Plain of Alaska since 1986. Methods for the 2010 Arctic Coastal Plain...

  3. Waterfowl Breeding Population and Habitat Survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The Waterfowl Breeding Population and Habitat Survey was initiated experimentally in 1947 and became operational in 1955. It is conducted cooperatively by the U.S....

  4. Western Ontario: Waterfowl breeding population survey: 1986

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1986. The primary purpose of the survey is to provide...

  5. Waterfowl breeding population survey: Southern Saskatchewan: 2000

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for southern Saskatchewan during 2000. The primary purpose of the survey is to provide...

  6. Waterfowl breeding population survey: Southern Manitoba: 1983

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for southern Manitoba during 1983. The primary purpose of the survey is to provide...

  7. Waterfowl breeding population survey for Montana: 1993

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Montana during 1993. The primary purpose of the survey is to provide information on...

  8. Waterfowl breeding population survey for Montana: 1998

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Montana during 1998. The primary purpose of the survey is to provide information on...

  9. Waterfowl breeding population survey: Southern Saskatchewan: 1983

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for southern Saskatchewan during 1983. The primary purpose of the survey is to provide...

  10. Central Quebec: Waterfowl breeding population survey: 2000

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Central Quebec during 2000. The primary purpose of the survey is to provide...

  11. Western Ontario: Waterfowl breeding population survey: 1989

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1989. The primary purpose of the survey is to provide...

  12. Western Ontario: Waterfowl breeding population survey: 1995

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1995. The primary purpose of the survey is to provide...

  13. Western Ontario: Waterfowl breeding population survey: 1993

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1993. The primary purpose of the survey is to provide...

  14. Western Ontario: Waterfowl breeding population survey: 1994

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1994. The primary purpose of the survey is to provide...

  15. Western Ontario: Waterfowl breeding population survey: 1996

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1996. The primary purpose of the survey is to provide...

  16. Western Ontario: Waterfowl breeding population survey: 1987

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1987. The primary purpose of the survey is to provide...

  17. Western Ontario: Waterfowl breeding population survey: 1992

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1992. The primary purpose of the survey is to provide...

  18. Western Ontario: Waterfowl breeding population survey: 1990

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1990. The primary purpose of the survey is to provide...

  19. Western Ontario: Waterfowl breeding population survey: 1997

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1997. The primary purpose of the survey is to provide...

  20. Western Ontario: Waterfowl breeding population survey: 1988

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1988. The primary purpose of the survey is to provide...

  1. Four Square Mile Survey breeding population report for 2001

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Production report of Four Square Mile Survey breeding population estimates for 13 species of ducks. Data includes summaries of breeding population estimates...

  2. Population viability analysis on domestic horse breeds (Equus caballus)

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia; Bach, Lars; Loeschcke, Volker

    2009-01-01

    In this study, we performed a population viability analysis on 3 domestic horse breeds (Equus caballus) of Danish origin, namely, the Frederiksborg, the Knabstrupper, and the Jutland breeds. Because of their small population sizes, these breeds are considered endangered. The Vortex software...... available. The results of this analysis accord with other studies on the Prezwalski horse, indicating robustness in the parameter sensitivity for horses....

  3. Genomic prediction across dairy cattle populations and breeds

    DEFF Research Database (Denmark)

    Zhou, Lei

    Genomic prediction is successful in single breed genetic evaluation. However, there is no achievement in acoress breed prediction until now. This thesis investigated genomic prediction across populations and breeds using Chinese Holsterin, Nordic Holstein, Norwgian Red, and Nordic Red. Nordic Red...

  4. The ascent of cat breeds: genetic evaluations of breeds and worldwide random-bred populations.

    Science.gov (United States)

    Lipinski, Monika J; Froenicke, Lutz; Baysac, Kathleen C; Billings, Nicholas C; Leutenegger, Christian M; Levy, Alon M; Longeri, Maria; Niini, Tirri; Ozpinar, Haydar; Slater, Margaret R; Pedersen, Niels C; Lyons, Leslie A

    2008-01-01

    The diaspora of the modern cat was traced with microsatellite markers from the presumed site of domestication to distant regions of the world. Genetic data were derived from over 1100 individuals, representing 17 random-bred populations from five continents and 22 breeds. The Mediterranean was reconfirmed to be the probable site of domestication. Genetic diversity has remained broad throughout the world, with distinct genetic clustering in the Mediterranean basin, Europe/America, Asia and Africa. However, Asian cats appeared to have separated early and expanded in relative isolation. Most breeds were derived from indigenous cats of their purported regions of origin. However, the Persian and Japanese bobtail were more aligned with European/American than with Mediterranean basin or Asian clusters. Three recently derived breeds were not distinct from their parental breeds of origin. Pure breeding was associated with a loss of genetic diversity; however, this loss did not correlate with breed popularity or age.

  5. Studies on breeding schemes in a closed pig population

    NARCIS (Netherlands)

    Roo, de G.

    1988-01-01

    Size of a population in genetic terms is a function of number of male and female individuals used for breeding over a generation. A breed can be small because of a small total number of individuals but also because of a small number of individuals of one sex. According to this definition,

  6. Maine & the Maritimes: Waterfowl breeding population survey: 2000

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Maine and the Maritimes during 2000. The primary purpose of the survey is to provide...

  7. Waterfowl breeding population survey: Southern Alberta: May 1991

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for southern Alberta during 1991. The primary purpose of the survey is to provide...

  8. Waterfowl breeding population survey: Southern and central Alberta: May 1995

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for southern and central Alberta during 1995. The primary purpose of the survey is to...

  9. Western and Central Ontario: Waterfowl breeding population survey: 2000

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Western and Central Ontario during 2000. The primary purpose of the survey is to...

  10. Waterfowl breeding population survey for Montana: May 1981

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Montana during 1981. The primary purpose of the survey is to provide information on...

  11. Genetic analysis in the Collaborative Cross breeding population.

    Science.gov (United States)

    Philip, Vivek M; Sokoloff, Greta; Ackert-Bicknell, Cheryl L; Striz, Martin; Branstetter, Lisa; Beckmann, Melissa A; Spence, Jason S; Jackson, Barbara L; Galloway, Leslie D; Barker, Paul; Wymore, Ann M; Hunsicker, Patricia R; Durtschi, David C; Shaw, Ginger S; Shinpock, Sarah; Manly, Kenneth F; Miller, Darla R; Donohue, Kevin D; Culiat, Cymbeline T; Churchill, Gary A; Lariviere, William R; Palmer, Abraham A; O'Hara, Bruce F; Voy, Brynn H; Chesler, Elissa J

    2011-08-01

    Genetic reference populations in model organisms are critical resources for systems genetic analysis of disease related phenotypes. The breeding history of these inbred panels may influence detectable allelic and phenotypic diversity. The existing panel of common inbred strains reflects historical selection biases, and existing recombinant inbred panels have low allelic diversity. All such populations may be subject to consequences of inbreeding depression. The Collaborative Cross (CC) is a mouse reference population with high allelic diversity that is being constructed using a randomized breeding design that systematically outcrosses eight founder strains, followed by inbreeding to obtain new recombinant inbred strains. Five of the eight founders are common laboratory strains, and three are wild-derived. Since its inception, the partially inbred CC has been characterized for physiological, morphological, and behavioral traits. The construction of this population provided a unique opportunity to observe phenotypic variation as new allelic combinations arose through intercrossing and inbreeding to create new stable genetic combinations. Processes including inbreeding depression and its impact on allelic and phenotypic diversity were assessed. Phenotypic variation in the CC breeding population exceeds that of existing mouse genetic reference populations due to both high founder genetic diversity and novel epistatic combinations. However, some focal evidence of allele purging was detected including a suggestive QTL for litter size in a location of changing allele frequency. Despite these inescapable pressures, high diversity and precision for genetic mapping remain. These results demonstrate the potential of the CC population once completed and highlight implications for development of related populations.

  12. Population dynamics of mallards breeding in eastern Washington

    Science.gov (United States)

    Dugger, Bruce D.; Coluccy, John M.; Dugger, Katie M.; Fox, Trevor T.; Kraege, Donald K.; Petrie, Mark J.

    2016-01-01

    Variation in regional population trends for mallards breeding in the western United States indicates that additional research into factors that influence demographics could contribute to management and understanding the population demographics of mallards across North America. We estimated breeding incidence and adult female, nest, and brood survival in eastern Washington in 2006 and 2007 by monitoring female mallards with radio telemetry and tested how those parameters were influenced by study year (2006 vs. 2007), landscape type (agricultural vs. natural), and age (second year [SY] vs. after second year [ASY]). We also investigated the effects of female body condition and capture date on breeding incidence, and nest initiation date and hatch date on nest and brood survival, respectively. We included population parameters in a stage-based demographic model and conducted a perturbation analysis to identify which vital rates were most influential on population growth rate (λ). Adult female survival was best modeled with a constant weekly survival rate (0.994, SE = 0.003). Breeding incidence differed between years and was higher for birds in better body condition. Nest survival was higher for ASY females (0.276, SE = 0.118) than SY females (0.066, SE = 0.052), and higher on publicly managed lands (0.383, SE = 0.212) than agricultural (0.114, SE = 0.058) landscapes. Brood survival was best modeled with a constant rate for the 7-week monitoring period (0.50, SE = 0.155). The single variable having the greatest influence on λ was non-breeding season survival, but the combination of parameters from the breeding grounds explained a greater percent of the variance in λ. Mallard population growth rate was most sensitive to changes in non-breeding survival, nest success, brood survival, and breeding incidence. Future management decisions should focus on activities that improve these vital rates if managers want to increase the production of

  13. Population genetic structure in the Holstein breed in Brazil.

    Science.gov (United States)

    Magalhães Araújo da Silva, Mário Henrique; Malhado, Carlos Henrique Mendes; Costa, José Lauro; Cobuci, Jaime Araujo; Costa, Claudio Napolis; Carneiro, Paulo Luiz Souza

    2016-02-01

    We evaluated the population genetic structure of the Holstein breed in Brazil through pedigree analysis with the aim of supporting genetic management of extant herds. We used data from genealogical records of 204,511 animals in farms from south and southeast Brazil. Pedigree records between 1943 and 2005 were divided into seven periods of 8 years to estimate the effective population size (N e ). N e varied during the study periods, ranging from 0.19 to 3016.25. There was an increase in the percentage of inbred animals over time, from 0.18 to 5.0 %. However, this figure may be an underestimate due to the low completeness of pedigree, primarily related to paternal pedigree. The effective number of founders (fe) was 473 animals and ancestors (fa) was 471. The genetic contribution of 260 ancestors (founders or not) accounted for 50 % of the genetic variability in the population. The average relatedness coefficient (AR) and inbreeding coefficient indicate that the Holstein breed in Brazil is being effectively managed, despite a moderate founder effect and the low number of animals that are responsible for the population variance.

  14. Genetic diversity and population structure of indigenous chicken breeds in South China

    Directory of Open Access Journals (Sweden)

    Xunhe HUANG,Jinfeng ZHANG,Danlin HE,Xiquan ZHANG,Fusheng ZHONG,Weina LI,Qingmei ZHENG,Jiebo CHEN,Bingwang DU

    2016-06-01

    Full Text Available A total of 587 individuals from 12 indigenous chicken breeds from South China and two commercial breeds were genotyped for 26 microsatellites to investigate the genetic diversity and population structure. All microsatellites were found to be polymorphic. The number of alleles per locus ranged from 5 to 36, with an average of 12.10 ± 7.00 (SE. All breeds, except White Recessive Rock, had high allelic polymorphism (>0.5. Higher genetic diversity was revealed in the indigenous chicken breeds rather than in the commercial breeds. Potential introgression from the commercial breeds into the indigenous chickens was also detected. The population structure of these indigenous chicken breeds could be explained by their geographical distribution, which suggested the presence of independent history of breed formation. Data generated in this study will provide valuable information to the conservation for indigenous chicken breeds in future.

  15. Population parameters to compare dog breeds : differences between five Dutch purebred populations

    NARCIS (Netherlands)

    Nielen, A.L.J.; Beek, van der S.; Ubbink, G.J.; Knol, B.W.

    2001-01-01

    Differences in five purebred dog populations born in 1994 in the Netherlands were evaluated using different parameters. Numerically, the Golden Retriever was the largest breed (840 litters of 234 sires) and the Kooiker Dog (101 litters of 41 sires) the smallest. The litter per sire ratio was largest

  16. Population parameters to compare dog breeds : differences between five Dutch purebred populations

    NARCIS (Netherlands)

    Nielen, A.L.J.; Beek, van der S.; Ubbink, G.J.; Knol, B.W.

    2001-01-01

    Differences in five purebred dog populations born in 1994 in the Netherlands were evaluated using different parameters. Numerically, the Golden Retriever was the largest breed (840 litters of 234 sires) and the Kooiker Dog (101 litters of 41 sires) the smallest. The litter per sire ratio was largest

  17. Viability of the Alaskan breeding population of Steller’s eiders

    Science.gov (United States)

    Dunham, Kylee; Grand, James B.

    2016-10-11

    The U.S. Fish and Wildlife Service is tasked with setting objective and measurable criteria for delisting species or populations listed under the Endangered Species Act. Determining the acceptable threshold for extinction risk for any species or population is a challenging task, particularly when facing marked uncertainty. The Alaskan breeding population of Steller’s eiders (Polysticta stelleri) was listed as threatened under the Endangered Species Act in 1997 because of a perceived decline in abundance throughout their nesting range and geographic isolation from the Russian breeding population. Previous genetic studies and modeling efforts, however, suggest that there may be dispersal from the Russian breeding population. Additionally, evidence exists of population level nonbreeding events. Research was conducted to estimate population viability of the Alaskan breeding population of Steller’s eiders, using both an open and closed model of population process for this threatened population. Projections under a closed population model suggest this population has a 100 percent probability of extinction within 42 years. Projections under an open population model suggest that with immigration there is no probability of permanent extinction. Because of random immigration process and nonbreeding behavior, however, it is likely that this population will continue to be present in low and highly variable numbers on the breeding grounds in Alaska. Monitoring the winter population, which includes both Russian and Alaskan breeding birds, may offer a more comprehensive indication of population viability.

  18. Phylogeny, genetic relationships and population structure of five Italian local chicken breeds

    Directory of Open Access Journals (Sweden)

    Simone Ceccobelli

    2013-09-01

    Full Text Available Number and population size of local chicken breeds in Italy is considered to be critical. Molecular data can be used to provide reliable insight into the diversity of chicken breeds. The first aim of this study was to investigate the maternal genetic origin of five Italian local chicken breeds (Ancona, Livorno, Modenese, Romagnola and Valdarnese bianca based on mitochondrial DNA (mtDNA information. Secondly, the extent of the genetic diversity, population structure and the genetic relationships among these chicken populations, by using 27 microsatellite markers, were assessed. To achieve these targets, a 506 bp fragment of the D-loop region was sequenced in 50 chickens of the five breeds. Eighteen variable sites were observed which defined 12 haplotypes. They were assigned to three clades and two maternal lineages. Results indicated that 90% of the haplotypes are related to clade E, which has been described to originate from the Indian subcontinent. For the microsatellite analysis, 137 individual blood samples from the five Italian breeds were included. A total of 147 alleles were detected at 27 microsatellite loci. The five Italian breeds showed a slightly higher degree of inbreeding (FIS=0.08 than the commercial populations that served as reference. Structure analysis showed a separation of the Italian breeds from the reference populations. A further sub-clustering allowed discriminating among the five different Italian breeds. This research provides insight into population structure, relatedness and variability of the five studied breeds.

  19. Breeding phenology in Rana temporaria. Local variation is due to pond temperature and population size.

    Science.gov (United States)

    Loman, Jon

    2016-09-01

    Frog breeding phenology in temperate zones is usually compared to progress of spring temperatures at a regional scale. However, local populations may differ substantially in phenology. To understand this, local climate and other aspects must be studied. In this study, breeding phenology of the common frog, Rana temporaria, in a set of ponds in southern Sweden is analyzed. There was within year a variation of up to 3 weeks in start of breeding among local populations. Water temperature was measured in the ponds, and breeding tended to be earlier in warmer ponds (surprise!). Breeding was also earlier in ponds with a large breeding congregation. Alternative reasons for these patterns are suggested and discussed. There was a large residual variation. The common frog has a wide range of acceptable wintering sites, and I hypothesize that the particular choice by a local population may explain part of this residual variation.

  20. 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

  1. A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment

    Science.gov (United States)

    2010-01-01

    Background Technological advances have lead to the rapid increase in availability of single nucleotide polymorphisms (SNPs) in a range of organisms, and there is a general optimism that SNPs will become the marker of choice for a range of evolutionary applications. Here, comparisons between 300 polymorphic SNPs and 14 short tandem repeats (STRs) were conducted on a data set consisting of approximately 500 Atlantic salmon arranged in 10 samples/populations. Results Global FST ranged from 0.033-0.115 and -0.002-0.316 for the 14 STR and 300 SNP loci respectively. Global FST was similar among 28 linkage groups when averaging data from mapped SNPs. With the exception of selecting a panel of SNPs taking the locus displaying the highest global FST for each of the 28 linkage groups, which inflated estimation of genetic differentiation among the samples, inferred genetic relationships were highly similar between SNP and STR data sets and variants thereof. The best 15 SNPs (30 alleles) gave a similar level of self-assignment to the best 4 STR loci (83 alleles), however, addition of further STR loci did not lead to a notable increase assignment whereas addition of up to 100 SNP loci increased assignment. Conclusion Whilst the optimal combinations of SNPs identified in this study are linked to the samples from which they were selected, this study demonstrates that identification of highly informative SNP loci from larger panels will provide researchers with a powerful approach to delineate genetic relationships at the individual and population levels. PMID:20051144

  2. Genetic diversity and population structure of 20 North European cattle breeds

    DEFF Research Database (Denmark)

    kantanen, J; Olsaker, Ingrid; Holm, Lars-Erik

    2000-01-01

    , allelic diversity has been reduced in several breeds, which was explained by limited effective population sizes over the course of man-directed breed development and demographic bottlenecks of indigenous breeds. A tree showing genetic relationships between breeds was constructed from a matrix of random......Blood samples were collected from 743 animals from 15 indigenous, 2 old imported, and 3 commercial North European cattle breeds. The samples were analyzed for 11 erythrocyte antigen systems, 8 proteins, and 10 microsatellites, and used to assess inter- and intrabreed genetic variation and genetic...... population structures. The microsatellites BoLA-DRBP1 and CSSM66 were nonneutral markers according to the Ewens-Watterson test, suggesting some kind of selection imposed on these loci. North European cattle breeds displayed generally similar levels of multilocus heterozygosity and allelic diversity. However...

  3. Dusky Canada goose breeding population survey, May 16 1989

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Dusky Canada goose breeding ground surveys were initiated on the Copper River Delta near Cordova, Alaska during the 1970's by the Waterfowl Division of the Alaska...

  4. Dusky Canada goose breeding population survey, May 18 1990

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Dusky Canada goose breeding ground surveys were initiated on the Copper River Delta near Cordova, Alaska during the 1970's by the Waterfowl Division of the Alaska...

  5. Population and breeding success of Red-headed Vulture Sarcogyps ...

    African Journals Online (AJOL)

    Campbell Murn

    Periodic monitoring of each identified nest was done to determine breeding success ... Historical reports indicate Red- headed Vultures .... 24. 217. 241. Table 2: Age composition of Red-headed and Egyptian Vultures based on highest count.

  6. Analysis of genetic diversity and population structure of Chinese yak breeds (Bos grunniens) using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    Guixiang Zhang; Weisheng Chen; Ming Xue; Zhigang Wang; Hong Chang; Xu Han; Xinjun Liao; Donglei Wang

    2008-01-01

    Nine Chinese yak breeds (Maiwa,Tianzhu White,Qinghai Plateau,Sibu,Zhongdian,Pall,Tibetan High Mountain,Jiulong,and Xin-jiang) and Gayal were analyzed by means of 16 microsatellite markers to determine the level of genetic variation within populations,genetic relationship between populations,and population structure for each breed.A total of 206 microsatellite alleles were observed.Mean F-statistics (0.056) for 9 yak breeds indicated that 94.4% of the genetic variation was observed within yak breeds and 5.6% of the genetic variation existed amongst breeds.The Neighbor-Joining phylogenetic free was constructed based on Nei's standard genetic dis-tances and two clusters were obtained.The Gayal separated from the yaks far away and formed one cluster and 9 yak breeds were grouped together.The analysis of population structure for 9 yak breeds and the Gayal showed that they resulted in four clusters; one clus-ter includes yaks from Tibet Autonomous Region and Qinghai Province,one cluster combines Zhongdian,Maiwa,and Tianzhu White,and Jiulong and Xinjiang come into the third cluster.Pali was mainly in the first cluster (90%),Jiulong was mainly in the second cluster (87.1%),Zhongdian was primarily in the third cluster (83%),and the other yak breeds were distributed in two to three clusters.The Gayal was positively left in the fourth cluster (99.3%).

  7. Nest-site selection, territory quality and breeding performance in a Blue Tit Cyanistes caeruleus population

    Science.gov (United States)

    Maícas, Ramón; Muriel, Jaime; Bonillo, Juan Carlos; Fernández Haeger, Juan

    2012-02-01

    Patterns of territory selection and sources of variation for reproductive performance in a Blue Tit Cyanistes caeruleus population breeding in nest-boxes during years 2007 and 2008 in a holm oak forest are analyzed. Territory selection has been assessed as a function of two fixed effect factors: territory location (peripheral vs. interior in the nestbox patch) and nestbox type (entrance hole: 26 mm vs. 32 mm). Breeding density was independent of these factors. Pairs nesting in periphery nest-boxes and in small-holed nestboxes owned territories bigger than those nesting in interior and large-holed nestboxes, respectively. The breeding traits studied were laying date, clutch size, hatching success, fledgling success and breeding success. Egg laying was earlier in periphery territories and small-holed nestboxes. Between-year variation was a factor significantly affecting to all breeding traits. Clutch size declines in late clutches. Hatching success was higher in territories with more tree density. Although egg laying started earlier in some territories, the mean breeding success was similar in all of them. However, territories with the greatest contribution of individuals to the population were those with small-holed nestboxes. Breeding success in successful pairs had a tendency to be higher in pairs with late clutches and in those nesting in interior territories with large-holed nestboxes. Both decreased breeding success and total breeding failure were much more important in the second breeding year than in the first one. The high breeding density of Blue Tit, favored by the experimental design of nestbox plot, did not suggest significant variation between territories in terms of breeding success achieved. Implications for nestbox management are discussed.

  8. Genealogical analyses in open populations: the case of three Arab-derived Spanish horse breeds.

    Science.gov (United States)

    Cervantes, I; Gutiérrez, J P; Molina, A; Goyache, F; Valera, M

    2009-10-01

    This research assesses the genetic composition of three Arab-derived Spanish horse breeds as an example to highlight the major shortcomings related to genealogical analyses in open populations and to propose approaches useful to deal with this task. The studbooks of three Spanish Arab (SA)-derived horse breeds, Spanish Anglo-Arab (dAA), Hispano-Arab (dHA) and Spanish Sport Horse (dSSH) and those of their parental breeds SA, Spanish Purebred (SPB) and Thoroughbred (TB), totalling 211 754 individuals, were available. The genealogies of the dAA, dHA and dSSH were analysed not only using the corresponding studbook (breed exclusive dataset) but also including the genealogies of the founders from parental breeds (completed dataset). Coancestry analyses revealed that the present SA-derived populations share more genes with the Arab than with the other parental breeds. Effective population size was computed by accounting for migration rates to obtain an equivalent closed-population effective size ((eq)N(e)) of 39.2 for the dAA, 56.3 for dHA and 114.1 for dSSH. The essayed methodologies were useful for characterising populations involving migration. The consequences of the management of the analysed breeds are discussed. The results emphasize the need to include the complete genealogies of the individuals to attain reliable genealogical parameters.

  9. Population-Wide Failure to Breed in the Clark's Nutcracker (Nucifraga columbiana.

    Directory of Open Access Journals (Sweden)

    Taza D Schaming

    Full Text Available In highly variable environments, conditions can be so stressful in some years that entire populations forgo reproduction in favor of higher likelihood of surviving to breed in future years. In two out of five years, Clark's nutcrackers (Nucifraga Columbiana in the Greater Yellowstone Ecosystem exhibited population-wide failure to breed. Clark's nutcrackers at the study site experienced substantial interannual differences in food availability and weather conditions, and the two nonbreeding years corresponded with low whitebark pine (Pinus albicaulis cone crops the previous autumn (≤ an average of 8 ± 2 cones per tree versus ≥ an average of 20 ± 2 cones per tree during breeding years and high snowpack in early spring (≥ 61.2 ± 5.5 cm versus ≤ 51.9 ± 4.4 cm during breeding years. The average adult body condition index during the breeding season was significantly lower in 2011 (-1.5 ± 1.1, a nonbreeding year, as compared to 2012 (6.2 ± 2.0, a breeding year. The environmental cues available to the birds prior to breeding, specifically availability of cached whitebark pine seeds, may have allowed them to predict that breeding conditions would be poor, leading to the decision to skip breeding. Alternatively, the Clark's nutcrackers may have had such low body energy stores that they chose not to or were unable to breed. Breeding plasticity would allow Clark's nutcrackers to exploit an unpredictable environment. However, if large-scale mortality of whitebark pines is leading to an increase in the number of nonbreeding years, there could be serious population-level and ecosystem-wide consequences.

  10. Experimental waterfowl breeding population survey Maine, the Maritime provinces, and Central Quebec: 1997

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Maine, the Maritime provinces, and Central Quebec during 1997. The primary purpose of...

  11. 1992: Northern Alberta, northeastern British Columbia, and the Northwest Territories: Waterfowl breeding population survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for northern Alberta, northeastern British Columbia, and the Northwest Territories during...

  12. 1995: Northern Alberta, northeastern British Columbia, and the Northwest Territories: Waterfowl breeding population survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for northern Alberta, northeastern British Columbia, and the Northwest Territories during...

  13. 1990 waterfowl breeding population survey for South Dakota and North Dakota

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for North and South Dakota during 1990. The primary purpose of the survey is to provide...

  14. Waterfowl breeding population survey: Ontario, Quebec, and New York: May 1996

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Ontario, Quebec, and New York during 1996. The primary purpose of the survey is to...

  15. Alaska-Yukon waterfowl breeding population survey: May 16 to June 14, 1991

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Alaska-Yukon during 1991. The primary purpose of the survey is to provide information...

  16. Plan for Establishment of a Breeding Canada Goose Population on the Montezuma National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report outlines a plan on how to implement a program for the establishment of a breeding Canada Goose population on the Montezuma National Wildlife Refuge. It...

  17. Population age composition, breeding biology and notes on the wolverine in Alaska and Yukon Territory

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report describes the population age, composition, breeding biology and notes on the wolverine in Alaska and the Yukon territory. Life history, physical...

  18. Waterfowl breeding population survey: Northern Saskatchewan, northern Manitoba and western Ontario: May-June 1959

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for northern Saskatchewan, northern Manitoba, and western Ontario during 1959. The...

  19. Pilot study: Waterfowl breeding population survey: Ontario, Quebec, and New York: May 1995

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Ontario, Quebec, and New York during 1995. The primary purpose of the survey is to...

  20. Southern Ontario, Quebec, and New York: Waterfowl breeding population survey: 2000

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Southern Ontario, Quebec, and New York during 2000. The primary purpose of the survey...

  1. Waterfowl breeding population survey: New York, Eastern Ontario, and Southern Quebec: 1999

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for New York, Eastern Ontario, and Southern Quebec during 1999. The primary purpose of...

  2. Selecting Sole: breeding programs for natural - mating populations

    NARCIS (Netherlands)

    Blonk, R.J.W.

    2010-01-01

    The aim of this thesis was to design a breeding program for increased productivity of farmed common sole, Solea solea, 1) using natural mating in groups to obtain offspring and 2) using present farm infrastructures as much as possible. Parental allocation with DNA marker data on offspring from

  3. Extent of linkage disequilibrium and effective population size in four South African Sanga cattle breeds

    Directory of Open Access Journals (Sweden)

    Sithembile Olga Makina

    2015-12-01

    Full Text Available Knowledge on the extent of linkage disequilibrium (LD in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies. This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne for four Sanga cattle breeds in South Africa including the Afrikaner (n=44, Nguni (n=54, Drakensberger (n=47 and Bonsmara breeds (n=46, using Angus (n=31 and Holstein (n=29 as reference populations. We found that moderate LD extends up to inter-marker distances of 40-60 kb in Angus (0.21 and Holstein (0.21 and up to 100 kb in Afrikaner (0.20. This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2 ≥ 0.20 would require about 30,000 -50,000 SNPs. However, r2 ≥ 0.20 extended only up to 10-20 kb in the Nguni and Drakensberger and 20-40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for genome-wide association studies in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne=95 (Nguni, Ne=87 (Drakensberger, Ne=77 (Bonsmara and Ne=41 (Afrikaner. Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.

  4. Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed

    Directory of Open Access Journals (Sweden)

    Jurado Juan J

    2009-09-01

    Full Text Available Abstract Background Assessing genetic biodiversity and population structure of minor breeds through the information provided by neutral molecular markers, allows determination of their extinction risk and to design strategies for their management and conservation. Analysis of microsatellite loci is known to be highly informative in the reconstruction of the historical processes underlying the evolution and differentiation of animal populations. Guadarrama goat is a threatened Spanish breed which actual census (2008 consists of 3057 females and 203 males distributed in 22 populations more or less isolated. The aim of this work is to study the genetic status of this breed through the analysis of molecular data from 10 microsatellites typed in historic and actual live animals. Results The mean expected heterozygosity across loci within populations ranged from 0.62 to 0.77. Genetic differentiation measures were moderate, with a mean FST of 0.074, GST of 0.081 and RST of 0.085. Percentages of variation among and within populations were 7.5 and 92.5, respectively. Bayesian clustering analyses pointed out a population subdivision in 16 clusters, however, no correlation between geographical distances and genetic differences was found. Management factors such as the limited exchange of animals between farmers (estimated gene flow Nm = 3.08 mostly due to sanitary and social constraints could be the major causes affecting Guadarrama goat population subdivision. Conclusion Genetic diversity measures revealed a good status of biodiversity in the Guadarrama goat breed. Since diseases are the first cause affecting the census in this breed, population subdivision would be an advantage for its conservation. However, to maintain private alleles present at low frequencies in such small populations minimizing the inbreeding rate, it would necessitate some mating designs of animals carrying such alleles among populations. The systematic use of molecular markers will

  5. Microsatellite based genetic diversity and population structure of the endangered Spanish Guadarrama goat breed

    Science.gov (United States)

    Serrano, Magdalena; Calvo, Jorge H; Martínez, Marta; Marcos-Carcavilla, Ane; Cuevas, Javier; González, Carmen; Jurado, Juan J; de Tejada, Paloma Díez

    2009-01-01

    Background Assessing genetic biodiversity and population structure of minor breeds through the information provided by neutral molecular markers, allows determination of their extinction risk and to design strategies for their management and conservation. Analysis of microsatellite loci is known to be highly informative in the reconstruction of the historical processes underlying the evolution and differentiation of animal populations. Guadarrama goat is a threatened Spanish breed which actual census (2008) consists of 3057 females and 203 males distributed in 22 populations more or less isolated. The aim of this work is to study the genetic status of this breed through the analysis of molecular data from 10 microsatellites typed in historic and actual live animals. Results The mean expected heterozygosity across loci within populations ranged from 0.62 to 0.77. Genetic differentiation measures were moderate, with a mean FST of 0.074, GST of 0.081 and RST of 0.085. Percentages of variation among and within populations were 7.5 and 92.5, respectively. Bayesian clustering analyses pointed out a population subdivision in 16 clusters, however, no correlation between geographical distances and genetic differences was found. Management factors such as the limited exchange of animals between farmers (estimated gene flow Nm = 3.08) mostly due to sanitary and social constraints could be the major causes affecting Guadarrama goat population subdivision. Conclusion Genetic diversity measures revealed a good status of biodiversity in the Guadarrama goat breed. Since diseases are the first cause affecting the census in this breed, population subdivision would be an advantage for its conservation. However, to maintain private alleles present at low frequencies in such small populations minimizing the inbreeding rate, it would necessitate some mating designs of animals carrying such alleles among populations. The systematic use of molecular markers will facilitate the

  6. Agriculture modifies the seasonal decline of breeding success in a tropical wild bird population

    Science.gov (United States)

    Cartwright, Samantha J; Nicoll, Malcolm A C; Jones, Carl G; Tatayah, Vikash; Norris, Ken

    2014-01-01

    Habitat conversion for agriculture is a major driver of biodiversity loss, but our understanding of the demographic processes involved remains poor. We typically investigate the impacts of agriculture in isolation even though populations are likely to experience multiple, concurrent changes in the environment (e.g. land and climate change). Drivers of environmental change may interact to affect demography, but the mechanisms have yet to be explored fully in wild populations. Here, we investigate the mechanisms linking agricultural land use with breeding success using long-term data for the formerly Critically Endangered Mauritius kestrel Falco punctatus, a tropical forest specialist that also occupies agricultural habitats. We specifically focused on the relationship between breeding success, agriculture and the timing of breeding because the latter is sensitive to changes in climatic conditions (spring rainfall) and enables us to explore the interactive effects of different (land and climate) drivers of environmental change. Breeding success, measured as egg survival to fledging, declines seasonally in this population, but we found that the rate of this decline became increasingly rapid as the area of agriculture around a nest site increased. If the relationship between breeding success and agriculture was used in isolation to estimate the demographic impact of agriculture, it would significantly under-estimate breeding success in dry (early) springs and over-estimate breeding success in wet (late) springs. Analysis of prey delivered to nests suggests that the relationship between breeding success and agriculture might be due, in part, to spatial variation in the availability of native, arboreal geckos. Synthesis and applications. Agriculture modifies the seasonal decline in breeding success in this population. As springs are becoming wetter in our study area and since the kestrels breed later in wetter springs, the impact of agriculture on breeding success will

  7. Agriculture modifies the seasonal decline of breeding success in a tropical wild bird population.

    Science.gov (United States)

    Cartwright, Samantha J; Nicoll, Malcolm A C; Jones, Carl G; Tatayah, Vikash; Norris, Ken

    2014-10-01

    Habitat conversion for agriculture is a major driver of biodiversity loss, but our understanding of the demographic processes involved remains poor. We typically investigate the impacts of agriculture in isolation even though populations are likely to experience multiple, concurrent changes in the environment (e.g. land and climate change). Drivers of environmental change may interact to affect demography, but the mechanisms have yet to be explored fully in wild populations.Here, we investigate the mechanisms linking agricultural land use with breeding success using long-term data for the formerly Critically Endangered Mauritius kestrel Falco punctatus, a tropical forest specialist that also occupies agricultural habitats. We specifically focused on the relationship between breeding success, agriculture and the timing of breeding because the latter is sensitive to changes in climatic conditions (spring rainfall) and enables us to explore the interactive effects of different (land and climate) drivers of environmental change.Breeding success, measured as egg survival to fledging, declines seasonally in this population, but we found that the rate of this decline became increasingly rapid as the area of agriculture around a nest site increased. If the relationship between breeding success and agriculture was used in isolation to estimate the demographic impact of agriculture, it would significantly under-estimate breeding success in dry (early) springs and over-estimate breeding success in wet (late) springs.Analysis of prey delivered to nests suggests that the relationship between breeding success and agriculture might be due, in part, to spatial variation in the availability of native, arboreal geckos.Synthesis and applications. Agriculture modifies the seasonal decline in breeding success in this population. As springs are becoming wetter in our study area and since the kestrels breed later in wetter springs, the impact of agriculture on breeding success will

  8. Efficacy of population structure analysis with breeding populations and inbred lines.

    Science.gov (United States)

    Viana, José Marcelo Soriano; Valente, Mágno Sávio Ferreira; Fonseca E Silva, Fabyano; Mundim, Gabriel Borges; Paes, Geísa Pinheiro

    2013-09-01

    The objective was to assess by simulation the efficacy of population structure analysis in plant breeding. Twelve populations and 300 inbred lines were simulated and genotyped using 100 microsatellite loci. The experimental material included populations with and without admixture, ancestry relationship and linkage disequilibrium, and with distinct levels of genetic differentiation and effective sizes. The analyses were performed using Structure software and employed all available models. For all the group number (K) tested, for both populations and inbred lines, the admixture model with correlated allelic frequencies provided the highest value for the logarithm of the marginal likelihood. Fitting appropriate model and using adequate sample size for individuals and markers, Structure was effective in identifying the correct population structure, migrants and individuals with genome from distinct populations. The linkage model did not result in an improvement in clustering relative to the admixture model with correlated allelic frequencies. The inclusion of prior information did not change the results; for some K values the analyses showed slight higher values of the marginal likelihood. The reduction in the number of individuals and markers negatively affected the results. There was a high variation in the most probable K value between the evaluated methods.

  9. Breeding value estimation in the Hungarian Sport Horse population.

    Science.gov (United States)

    Posta, János; Komlósi, István; Mihók, Sándor

    2009-07-01

    The aims of this study were to estimate phenotypic and genetic parameters for a range of traits in Hungarian Sport Horses, and to compare several methods of estimating breeding value (BV) in this breed. The analyses were based on the Hungarian Sport Horse Studbook, results of self-performance tests (SPTs) and show-jumping competition results. An SPT comprises subjective judgement of conformation traits, movement analysis traits and free-jumping performance, assessed via ordinal scores. Genetic parameters of SPTs were estimated with an animal model. Different measurements of the competition performance were compared using the same repeatability model. Estimates of BV for sport were made with random regression models using a first-order Legendre polynomial. Heritability was found to increase and permanent environmental variance to decrease continuously with age. BVs can be estimated at different ages and from these a composite BV index can be computed. It is possible to weight BVs for the specific age of a horse.

  10. Genetic evaluation of the breeding population of a valuable reforestation conifer Platycladus orientalis (Cupressaceae)

    Science.gov (United States)

    Jin, Yuqing; Ma, Yongpeng; Wang, Shun; Hu, Xian-Ge; Huang, Li-Sha; Li, Yue; Wang, Xiao-Ru; Mao, Jian-Feng

    2016-10-01

    Platycladus orientalis, a widespread conifer with long lifespan and significant adaptability. It is much used in reforestation in north China and commonly planted in central Asia. With the increasing demand for plantation forest in central to north China, breeding programs are progressively established for this species. Efficient use of breeding resources requires good understanding of the genetic value of the founder breeding materials. This study investigated the distribution of genetic variation in 192 elite trees collected for the breeding program for the central range of the species. We developed first set of 27 polymorphic EST-derived SSR loci for the species from transcriptome/genome data. After examination of amplification quality, 10 loci were used to evaluate the genetic variation in the breeding population. We found moderate genetic diversity (average He = 0.348) and low population differentiation (Fst = 0.011). Extensive admixture and no significant geographic population structure characterized this set of collections. Our analyses of the diversity and population structure are important steps toward a long-term sustainable deployment of the species and provide valuable genetic information for conservation and breeding applications.

  11. Comparative morphology among northern populations of breeding Cooper's Hawks

    Science.gov (United States)

    Rosenfield, Robert N.; Rosenfield, Laura J.; Bielefeldt, John; Murphy, Robert K.; Stewart, Andrew C.; Stout, William E.; Driscoll, Timothy G.; Bozek, Michael A.

    2010-01-01

    Few studies at a broad geographical scale have characterized intraspecific variation in morphology of woodland hawks in the genus Accipiter. From 1999 to 2007 we investigated morphological variation in large samples of live Cooper's Hawks (A. cooperii) nesting in four study areas: coniferous woodland around Victoria, British Columbia, Canada, isolated deciduous woodlands in short-grass prairies of northwestern North Dakota, towns and rural deciduous woodlands along the border of North Dakota and Minnesota, and urban and rural mixed deciduous and coniferous landscapes of Wisconsin. These sites span 2660 km across the northern part of the species' breeding range. We measured body mass (i.e., size), wing chord, tail length, tarsus diameter, hallux length, and culmen length of breeding adults, finding significant and clinal variation in body mass (or size). The smallest and most similar-sized birds occurred in British Columbia and western North Dakota, larger birds along the border between North Dakota and Minnesota, and the largest birds in Wisconsin. Several other characters varied significantly when mass was used as a covariate. Variation by study site in mean indices of sexual size dimorphism was negligible and not significant. We speculate that the morphological differences we found, in part, are the result of geographic isolation, where diets, migratory behavior, and structural characteristics of nesting habitats vary across landscape types.

  12. Population dynamics in a long-lived seabird: I. Impact of breeding activity on survival and breeding probability in unbanded king penguins.

    Science.gov (United States)

    Le Bohec, Céline; Gauthier-Clerc, Michel; Grémillet, David; Pradel, Roger; Béchet, Arnaud; Gendner, Jean-Paul; Le Maho, Yvon

    2007-11-01

    Understanding the trade-off between current reproductive effort, future survival and future breeding attempts is crucial for demographic analyses and life history studies. We investigated this trade-off in a population of king penguins (Aptenodytes patagonicus) marked individually with transponders using multistate capture-recapture models. This colonial seabird species has a low annual proportion of non-breeders (13%), despite a breeding cycle which lasts over 1 year. To draw inferences about the consequences of non-breeding, we tested for an effect of reproductive activity on survival and on the probability of subsequent breeding. We found that birds non-breeding in year t show the same survival rate as breeders (two-states analysis: breeding and non-breeding). However, breeders had a lower probability of breeding again the following year. This negative phenotypic correlation suggests the existence of reproductive costs affecting future breeding probability, but it might also be strengthened by late arrival for courtship in year t. A three-state analysis including breeding success revealed that failed breeders in year t have a lower probability to reproduce successfully in year t + 1 than non-breeders in year t, providing some evidence for the existence of reproductive costs. Moreover, successful breeders showed higher survival probability. This positive phenotypic correlation between current reproduction and subsequent survival supports the hypothesis of an heterogeneity in individual quality. Males breeding in year t had a lower probability to breed again in year t + 1 than females, suggesting higher reproductive costs for this sex. Such additional costs might be due to higher male parental investment in the final phase of chick-rearing, which also delays the arrival of males in year t + 1, and decreases their breeding probability. Our study is the first to explore the breeding biology and the demography of penguins without the disturbance of flipper-bands.

  13. GENEALOGICAL DECOMPOSITION OF THE EFFECTIVE POPULATION SIZE: A CASE STUDY ON CROATIAN AUTOCHTHONOUS CATTLE BREEDS

    Directory of Open Access Journals (Sweden)

    Martin Reljanović

    2015-09-01

    Full Text Available Effective population size (Ne is one of the most important tools used to assess genetic diversity for conservation purposes. Using pedigree data of three Croatian autochthonous cattle breeds (Buša, Istrian and Slavonian Syrmian Podolian the effective maternal (NeF, paternal (NeM and combined maternal-paternal (NeFM population size was estimated. Additionally, we estimated the effective population size based on the census population sex ratio (Nes, the effective population size from the individual increase in inbreeding (NeFi and the effective population size from individual increase in coancestry (NeCi. We compared these sizes with the values obtained for 20 additional cattle populations, as well as with the newly calculated NeFM. The effective population sizes calculated for three autochthonous breeds were consistently the lowest in amongst all the considered cattle breeds. Utilisation of extremely small numbers of breeding males is the main reason for the observed reduction in the effective population size. The decomposition of effective population size into maternal and paternal components is shown to be an informative parameter in detecting the reduction of the effective population size as a consequence of unequal sex contribution. Still, the impact of the pedigree depth and completeness on the NeF, NeM and NeFM estimation remain to be analysed. A large deviation between Nes and all other methods of Ne estimation was observed and it is our recommendation that breeders and stakeholders should consider using alternative methods of Ne estimation when planning breeding programmes as well as in the determination of the endangered status of animal populations.

  14. Genetic variability of Appaloosa horses: a study of a closed breeding population from Argentina

    Directory of Open Access Journals (Sweden)

    Claudia Malena CORBI-BOTTO,Sebastian Andres SADABA,Elina Ines FRANCISCO,Paula Belen KALEMKERIAN,Juan Pedro LIRON,Egle Etel VILLEGAS-CASTAGNASSO,Guillermo GIOVAMBATTISTA,Pilar PERAL-GARCIA,Silvina DIAZ

    2014-09-01

    Full Text Available The genetic diversity and structure of 72 Appaloosa horses belonging to a closed breeding population from an ecological reserve in Buenos Aires, Argentina, was investigated using eight microsatellite markers from the International Society for Animal Genetics panel. Our data showed that this Appaloosa horse population had an elevated degree of genetic diversity (He= 0.746 and did not present a significant increase of homozygous individuals (FIS~0. However, the short tandem repeats, AHT5, ASB2, HTG10 and VHL20, were not in Hardy–Weinberg equilibrium (P-value<0.05. Genetic relationships between this population and other well known horse breeds showed that Appaloosa horses from Argentina could have had their origin in the horses of the Nez Perce's people in Idaho while other Appaloosa horses may have had influences from Andalusian and Lusitano breeds. This closed breeding population conserves an important degree of Appaloosa genetic diversity and notwithstanding its particular breeding characteristics, represents a valuable genetic resource for conservation.

  15. Seasonal and population variation in male testosterone levels in breeding orange-crowned warblers (Vermivora celata).

    Science.gov (United States)

    Horton, Brent M; Yoon, Jongmin; Ghalambor, Cameron K; Moore, Ignacio T; Scott Sillett, T

    2010-09-15

    Comparative hormone studies can reveal how physiology underlies life history variation. Here, we examined seasonal variation in plasma testosterone concentration between populations of male orange-crowned warblers (Vermivora celata) breeding in Fairbanks, Alaska (V. c. celata) and on Santa Catalina Island, California (V. c. sordida). These populations face different ecological constraints and exhibit different life histories. Alaska birds have a short breeding season, low annual adult survival, and high reproductive rates. In contrast, Catalina Island birds exhibit high adult survival and low reproductive rates despite having a long breeding season. We examined seasonal variation in male testosterone concentrations as a potential mechanism underlying differences in male reproductive strategies between populations. From 2006 to 2008, we sampled males during the pre-incubation, incubation, and nestling stages. Alaska males exhibited a seasonal testosterone pattern typical of northern passerines: testosterone levels were high during pre-incubation and declined during incubation to low levels during nestling provisioning. Testosterone concentrations in Catalina Island males, however, did not vary consistently with breeding stage, remained elevated throughout the breeding season, and were higher than in Alaska males during the nestling stage. We hypothesize that in Alaska, where short seasons and high adult mortality limit breeding opportunities, the seasonal testosterone pattern facilitates high mating effort prior to incubation, but high parental investment during the nestling stage. On Catalina Island, elevated testosterone levels may reflect the extended mating opportunities and high population density facing males in this population. Our results suggest that population variation in seasonal testosterone patterns in orange-crowned warblers may be a function of differences in life history strategy and the social environment.

  16. Estimation of genomic breeding values for residual feed intake in a multibreed cattle population.

    Science.gov (United States)

    Khansefid, M; Pryce, J E; Bolormaa, S; Miller, S P; Wang, Z; Li, C; Goddard, M E

    2014-08-01

    Residual feed intake (RFI) is a measure of the efficiency of animals in feed utilization. The accuracies of GEBV for RFI could be improved by increasing the size of the reference population. Combining RFI records of different breeds is a way to do that. The aims of this study were to 1) develop a method for calculating GEBV in a multibreed population and 2) improve the accuracies of GEBV by using SNP associated with RFI. An alternative method for calculating accuracies of GEBV using genomic BLUP (GBLUP) equations is also described and compared to cross-validation tests. The dataset included RFI records and 606,096 SNP genotypes for 5,614 Bos taurus animals including 842 Holstein heifers and 2,009 Australian and 2,763 Canadian beef cattle. A range of models were tested for combining genotype and phenotype information from different breeds and the best model included an overall effect of each SNP, an effect of each SNP specific to a breed, and a small residual polygenic effect defined by the pedigree. In this model, the Holsteins and some Angus cattle were combined into 1 "breed class" because they were the only cattle measured for RFI at an early age (6-9 mo of age) and were fed a similar diet. The average empirical accuracy (0.31), estimated by calculating the correlation between GEBV and actual phenotypes divided by the square root of estimated heritability in 5-fold cross-validation tests, was near to that expected using the GBLUP equations (0.34). The average empirical and expected accuracies were 0.30 and 0.31, respectively, when the GEBV were estimated for each breed separately. Therefore, the across-breed reference population increased the accuracy of GEBV slightly, although the gain was greater for breeds with smaller number of individuals in the reference population (0.08 in Murray Grey and 0.11 in Hereford for empirical accuracy). In a second approach, SNP that were significantly (P < 0.001) associated with RFI in the beef cattle genomewide association

  17. Genetic diversity of the Mexican Lidia bovine breed and its divergence from the Spanish population.

    Science.gov (United States)

    Eusebi, P G; Cortés, O; Dunner, S; Cañón, J

    2017-08-01

    Lidia bovine breed exists since the XIV century in the Iberian Peninsula. These animals were initially produced for meat but some, showing an aggressive behaviour which difficulted their management, were used to participate in popular traditional and social events. A specialization of the breed giving rise to the original Lidia population is documented in Spain since mid-XVIII century. Following the same tradition than in the Spanish population, Mexico used aggressive animals at the beginning of the XX century until two families of breeders started importing Lidia breed bovines from Spain with the aim of specializing their production. Each family (Llaguno and González) followed different breeding managements, and currently, most of the Lidia Mexican population derives from the Llaguno line. Although genetic structure and diversity of the Spanish population have been studied (using autosomal microsatellite markers, Y chromosome DNA markers and mitochondrial DNA sequences), the Mexican population is not analysed. The aim of the study was to assess both the genetic structure and diversity of the Mexican Lidia breed and its relationship with the original Spanish population using the same molecular tools. A total of 306 animals belonging to 20 breeders issued from both existing Mexican families were genotyped, and the genetic information was compared to the previously existing Spanish information. Slightly higher levels of genetic diversity in Mexican population were found when comparing to the Spanish population, and the variability among populations accounted for differences within them showing mean values of 0.18 and 0.12, respectively. Animals from the Mexican breeders, belonging to each of the two families, clustered together, and there was little evidence of admixture with the Spanish population. The analysis of Y chromosome diversity showed a high frequency of the H6 haplotype in the Mexican population, whereas this haplotype is rare in the Spanish, which is

  18. Breeding site heterogeneity reduces variability in frog recruitment and population dynamics

    Science.gov (United States)

    McCaffery, Rebecca M.; Eby, Lisa A.; Maxell, Bryce A.; Corn, Paul Stephen

    2013-01-01

    Environmental stochasticity can have profound effects on the dynamics and viability of wild populations, and habitat heterogeneity provides one mechanism by which populations may be buffered against the negative effects of environmental fluctuations. Heterogeneity in breeding pond hydroperiod across the landscape may allow amphibian populations to persist despite variable interannual precipitation. We examined recruitment dynamics over 10 yr in a high-elevation Columbia spotted frog (Rana luteiventris) population that breeds in ponds with a variety of hydroperiods. We combined these data with matrix population models to quantify the consequences of heterogeneity in pond hydroperiod on net recruitment (i.e. number of metamorphs produced) and population growth rates. We compared our heterogeneous system to hypothetical homogeneous environments with only ephemeral ponds, only semi-permanent ponds, and only permanent ponds. We also examined the effects of breeding pond habitat loss on population growth rates. Most eggs were laid in permanent ponds each year, but survival to metamorphosis was highest in the semi-permanent ponds. Recruitment success varied by both year and pond type. Net recruitment and stochastic population growth rate were highest under a scenario with homogeneous semi-permanent ponds, but variability in recruitment was lowest in the scenario with the observed heterogeneity in hydroperiods. Loss of pond habitat decreased population growth rate, with greater decreases associated with loss of permanent and semi-permanent habitat. The presence of a diversity of pond hydroperiods on the landscape will influence population dynamics, including reducing variability in recruitment in an uncertain climatic future.

  19. Does breeding population trajectory and age of nesting females influence disparate nestling sex ratios in two populations of Cooper's hawks?

    Science.gov (United States)

    Rosenfield, Robert N; Stout, William E; Giovanni, Matthew D; Levine, Noah H; Cava, Jenna A; Hardin, Madeline G; Haynes, Taylor G

    2015-09-01

    Offspring sex ratios at the termination of parental care should theoretically be skewed toward the less expensive sex, which in most avian species would be females, the smaller gender. Among birds, however, raptors offer an unusual dynamic because they exhibit reversed size dimorphism with females being larger than males. And thus theory would predict a preponderance of male offspring. Results for raptors and birds in general have been varied although population-level estimates of sex ratios in avian offspring are generally at unity. Adaptive adjustment of sex ratios in avian offspring is difficult to predict perhaps in part due to a lack of life-history details and short-term investigations that cannot account for precision or repeatability of sex ratios across time. We conducted a novel comparative study of sex ratios in nestling Cooper's hawks (Accipiter cooperii) in two study populations across breeding generations during 11 years in Wisconsin, 2001-2011. One breeding population recently colonized metropolitan Milwaukee and exhibited rapidly increasing population growth, while the ex-Milwaukee breeding population was stable. Following life-history trade-off theory and our prediction regarding this socially monogamous species in which reversed sexual size dimorphism is extreme, first-time breeding one-year-old, second-year females in both study populations produced a preponderance of the smaller and cheaper sex, males, whereas ASY (after-second-year), ≥2-year-old females in Milwaukee produced a nestling sex ratio near unity and predictably therefore a greater proportion of females compared to ASY females in ex-Milwaukee who produced a preponderance of males. Adjustment of sex ratios in both study populations occurred at conception. Life histories and selective pressures related to breeding population trajectory in two age cohorts of nesting female Cooper's hawk likely vary, and it is possible that these differences influenced the sex ratios we documented for

  20. Breeding bird populations and habitat associations within the Savannah River Site (SRS).

    Energy Technology Data Exchange (ETDEWEB)

    Gauthreaux, Sidney, A.; Steven J. Wagner.

    2005-06-29

    Gauthreaux, Sidney, A., and Steven J. Wagner. 2005. Breeding bird populations and habitat associations within the Savannah River Site (SRS). Final Report. USDA Forest Service, Savannah River, Aiken, SC. 48 pp. Abstract: During the 1970's and 1980's a dramatic decline occurred in the populations of Neotropical migratory birds, species that breed in North America and winter south of the border in Central and South America and in the Caribbean. In 1991 an international initiative was mounted by U. S. governmental land management agencies, nongovernmental conservation agencies, and the academic and lay ornithological communities to understand the decline of Neotropical migratory birds in the Americas. In cooperation with the USDA Forest Service - Savannah River (FS - SR) we began 1992 a project directed to monitoring population densities of breeding birds using the Breeding Bird Census (BBC) methodology in selected habitats within the Savannah River Site SRS. In addition we related point count data on the occurrence of breeding Neotropical migrants and other bird species to the habitat data gathered by the Forest Inventory and Analysis (FIA) program of the USDA Forest Service and data on habitat treatments within forest stands.

  1. Breeding common bean populations for traits using selection index

    Directory of Open Access Journals (Sweden)

    Dayane Cristina Lima

    2015-02-01

    Full Text Available A common bean (Phaseolus vulgarisL. cultivar must combine desirable genotypes for several traits in order to be accepted by producers and consumers. This study aimed to evaluate selection efficiency when segregating bean populations for traits, by means of a selection index, in order to obtain superior progenies for traits considered. A total of 16 populations from the F4 and F5generations were evaluated in 2011 and 2012, respectively. The traits evaluated were plant architecture, plant disease, grain type and yield. Using standard scores (Z, the sum of the four traits (∑Z was obtained and, based on this information, the best populations were identified. The evaluation of selection effectiveness was performed on 31 progenies from each population. The 496 progenies plus eight controls were evaluated in the F5:6and F5:7 generations for the same traits in July and November 2012, respectively. The selection, using the index based on the sum of standardized variables (∑Z, was efficient for identifying populations with superior progenies for all the traits considered.

  2. Genetic diversity of a New Zealand multi-breed sheep population and composite breeds' history revealed by a high-density SNP chip.

    Science.gov (United States)

    Brito, Luiz F; McEwan, John C; Miller, Stephen P; Pickering, Natalie K; Bain, Wendy E; Dodds, Ken G; Schenkel, Flávio S; Clarke, Shannon M

    2017-03-14

    Knowledge about the genetic diversity of a population is a crucial parameter for the implementation of successful genomic selection and conservation of genetic resources. The aim of this research was to establish the scientific basis for the implementation of genomic selection in a composite Terminal sheep breeding scheme by providing consolidated linkage disequilibrium (LD) measures across SNP markers, estimating consistency of gametic phase between breed-groups, and assessing genetic diversity measures, such as effective population size (Ne), and population structure parameters, using a large number of animals (n = 14,845) genotyped with a high density SNP chip (606,006 markers). Information generated in this research will be useful for optimizing molecular breeding values predictions and managing the available genetic resources. Overall, as expected, levels of pairwise LD decreased with increasing distance between SNP pairs. The mean LD r(2) between adjacent SNP was 0.26 ± 0.10. The most recent effective population size for all animals (687) and separately per breed-groups: Primera (974), Lamb Supreme (380), Texel (227) and Dual-Purpose (125) was quite variable. The genotyped animals were outbred or had an average low level of inbreeding. Consistency of gametic phase was higher than 0.94 for all breed pairs at the average distance between SNP on the chip (~4.74 kb). Moreover, there was not a clear separation between the breed-groups based on principal component analysis, suggesting that a mixed-breed training population for calculation of molecular breeding values would be beneficial. This study reports, for the first time, estimates of linkage disequilibrium, genetic diversity and population structure parameters from a genome-wide perspective in New Zealand Terminal Sire composite sheep breeds. The levels of linkage disequilibrium indicate that genomic selection could be implemented with the high density SNP panel. The moderate to high consistency of

  3. A population genetic database of cat breeds developed in coordination with a domestic cat STR multiplex.

    Science.gov (United States)

    Menotti-Raymond, Marilyn; David, Victor A; Weir, Bruce S; O'Brien, Stephen J

    2012-05-01

    A simple tandem repeat (STR) PCR-based typing system developed for the genetic individualization of domestic cat samples has been used to generate a population genetic database of domestic cat breeds. A panel of 10 tetranucleotide STR loci and a gender-identifying sequence tagged site (STS) were co-amplified in genomic DNA of 1043 individuals representing 38 cat breeds. The STR panel exhibits relatively high heterozygosity in cat breeds, with an average 10-locus heterozygosity of 0.71, which represents an average of 38 breed-specific heterozygosities for the 10-member panel. When the entire set of breed individuals was analyzed as a single population, a heterozygosity of 0.87 was observed. Heterozygosities obtained for the 10 loci range from 0.72 to 0.96. The power for genetic individualization of domestic cat samples of the multiplex is high, with a probability of match (p(m)) of 6.2E-14, using a conservative θ = 0.05.

  4. Microsatellite diversity delineates genetic relationships of Shia and Sunni Muslim populations of Uttar Pradesh, India.

    Science.gov (United States)

    Eaaswarkhanth, Muthukrishnan; Dubey, Bhawna; Ramakodi Meganathan, Poorlin; Noor, Sabahat; Haque, Ikramul

    2009-08-01

    In this study we characterize the genetic diversity and relationships between the Shia and Sunni Muslim populations of North India and geographically targeted neighboring and global populations. We examined a number of parameters of population genetic and forensic interest based on the allele frequencies from 15 autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D19S433, VWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818, and FGA). All the studied loci were consistent with Hardy-Weinberg equilibrium, except loci D18S51 and FGA for both Muslim populations, even after applying the Bonferroni correction. The combined power of exclusion and combined power of discrimination values for all 15 STR loci were 0.9999 and >0.99999, respectively, in both Muslim populations. Gene diversity values ranged from 0.6784 (TPOX) to 0.9027 (FGA) for Shia Muslims and from 0.7152 (CSF1PO) to 0.9120 (D18S51) for Sunni Muslims. The observed heterozygosity (H(o)) ranged from 0.5833 (D18S51) to 0.8595 (VWA) in Shia Muslims and from 0.6818 (CSF1PO) to 0.8333 (D21S11) in Sunni Muslims and was lower than the expected heterozygosity (H(e)) for 11 out of the 15 STRs typed. We analyzed the genetic affinities of the Shia and Sunni Muslim populations with their geographically closest neighboring North Indian, Middle Eastern, East Asian, and European populations using distance-based methods, including neighbor-joining trees and multidimensional scaling. In addition, we estimated the genetic contribution of the putative parental populations included in the analysis to the Shia and Sunni Muslim gene pool using admixture analysis. Although we observed a certain degree of genetic contribution from Iran to both Muslim populations, the results of the phylogenetic analyses based on autosomal STRs suggest genetic relatedness with some of the geographically closest neighboring Hindu religious populations.

  5. Evolution of genetic variation for selected traits in successive breeding populations of maritime pine.

    Science.gov (United States)

    Bouffier, L; Raffin, A; Kremer, A

    2008-08-01

    Directional selection impacts a trait distribution by shifting its mean and reducing its variance. The change of variance is of major importance as the response to selection in subsequent generations is highly dependent of the genetic variability available in the population. In this contribution, evolution of genetic variation was investigated through the first breeding populations of the French maritime pine (Pinus pinaster Ait.) breeding program. We considered three populations: P0 (the forest where plus trees were initially selected), G0 (the plus tree population) and G1 (the population composed of trees selected in the progenies of G0). Analyses focused on the following selected traits: total height (H), girth at 1.30 m (D) and stem deviation to verticality (S). More than 150,000 trees from 25 tests of three distinct populations were studied with an individual genetic model. Accurate genetic parameters were obtained by taking all relationships between trees into account. For H and D, we found a strong decrease of the genetic variation from P0 to G0 corresponding to the initial selection of plus trees, which constitutes the base population of the breeding program. Then, despite the second step of selection applied, no appreciable evolution arose from comparisons between G0 and G1 for these traits. For S, the evolution is less significant as phenotypic variation slightly increased, possibly due to changes of silvicultural practices.

  6. Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers.

    Science.gov (United States)

    Edea, Zewdu; Dadi, Hailu; Kim, Sang-Wook; Dessie, Tadelle; Lee, Taeheon; Kim, Heebal; Kim, Jong-Joo; Kim, Kwan-Suk

    2013-01-01

    In total, 166 individuals from five indigenous Ethiopian cattle populations - Ambo (n = 27), Borana (n = 35), Arsi (n = 30), Horro (n = 36), and Danakil (n = 38) - were genotyped for 8773 single nucleotide polymorphism (SNP) markers to assess genetic diversity, population structure, and relationships. As a representative of taurine breeds, Hanwoo cattle (n = 40) were also included in the study for reference. Among Ethiopian cattle populations, the proportion of SNPs with minor allele frequencies (MAFs) ≥0.05 ranged from 81.63% in Borana to 85.30% in Ambo, with a mean of 83.96% across all populations. The Hanwoo breed showed the highest proportion of polymorphism, with MAFs ≥0.05, accounting for 95.21% of total SNPs. The mean expected heterozygosity varied from 0.370 in Danakil to 0.410 in Hanwoo. The mean genetic differentiation (F ST; 1%) in Ethiopian cattle revealed that within individual variation accounted for approximately 99% of the total genetic variation. As expected, F ST and Reynold genetic distance were greatest between Hanwoo and Ethiopian cattle populations, with average values of 17.62 and 18.50, respectively. The first and second principal components explained approximately 78.33% of the total variation and supported the clustering of the populations according to their historical origins. At K = 2 and 3, a considerable source of variation among cattle is the clustering of the populations into Hanwoo (taurine) and Ethiopian cattle populations. The low estimate of genetic differentiation (F ST) among Ethiopian cattle populations indicated that differentiation among these populations is low, possibly owing to a common historical origin and high gene flow. Genetic distance, phylogenic tree, principal component analysis, and population structure analyses clearly differentiated the cattle population according to their historical origins, and confirmed that Ethiopian cattle populations are genetically distinct from the Hanwoo breed.

  7. Analysis of genetic distribution and population genetic structure of the MyoD gene in 10 pig breeds

    Institute of Scientific and Technical Information of China (English)

    Li ZHU; Xuewei LI; Surong SHUAI; Mingzhou LI; Fangqiong LI; Lei CHEN

    2008-01-01

    Restriction fragment length polymorphism (RFLP) data was applied to analyze the distribution of the MyoD gene in 10 pig breeds and pig breed crosses.The population genetic information about genetic distribution,variation,and heterozygosity of the MyoD gene in different breed populations were analyzed.Based on the allele frequency,genetic distance and evolution distance among each breed populations were calculated and Unweighted Pair Group Method with Arithmetic mean (UPGMA) phylogenetic tree was gained based on the evolution distances between populations.The results indicated that the distribution of the MyoD genotype kept in Hardy-Weinberg equilibrium in most tested groups but not in Duroc (D) and Duroc × (Landrance × Yorkshire)(DLY) population.Generally,the genetic diversity of the MyoD gene was abundant and these tested breed populations had high genetic variations.The evolution of the MyoD gene was under natural selection pressure.On the phylogenetic tree,10 pig breeds were divided into 4 clusters.The first cluster consisted of four breeds developed from Landrace.The second cluster was two indigenous Chinese pig breeds.The third cluster was three breeds developed from Duroc.The fourth cluster was a Tibetan pig breed.The constitution of the topology of the phylogenetic tree was consistent with the breeding history of each pig breed.From this experiment,we can conclude that some RFLP data obtained from functional gene can be used in the genetic deviation research between some closely related species or between different populations in certain species.

  8. Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Hanwoo breeds using SNP markers

    Directory of Open Access Journals (Sweden)

    Zewdu eEdea

    2013-03-01

    Full Text Available In total, 166 individuals from 5 indigenous Ethiopian cattle populations—Ambo (n = 27, Borana (n = 35, Arsi (n = 30, Horro (n = 36, and Danakil (n = 38—were genotyped for 8773 single nucleotide polymorphism (SNP markers to assess genetic diversity, population structure, and relationships. As a representative of taurine breeds, Hanwoo cattle (n = 40 were also included in the study for reference. Among Ethiopian cattle populations, the proportion of SNPs with minor allele frequencies (MAFs ≥ 0.05 ranged from 81.63% in Borana to 85.30% in Ambo, with a mean of 83.96% across all populations. The Hanwoo breed showed the highest proportion of polymorphism, with MAFs ≥ 0.05, accounting for 95.21% of total SNPs. The mean expected heterozygosity varied from 0.370 in Danakil to 0.410 in Hanwoo. The mean genetic differentiation (FST (1% in Ethiopian cattle revealed that within-individual variation accounted for approximately 99% of the total genetic variation. As expected, FST and Reynold genetic distance were greatest between Hanwoo and Ethiopian cattle populations, with average values of 17.62 and 18.50, respectively. The first and second principal components explained approximately 78.33% of the total variation and supported the clustering of the populations according to their historical origins. At K = 2 and 3, a considerable source of variation among cattle is the clustering of the populations into Hanwoo (taurine and Ethiopian cattle populations. The low estimate of genetic differentiation (FST among Ethiopian cattle populations indicated that differentiation among these populations is low, possibly owing to a common historical origin and high gene flow. Genetic distance, phylogenic tree, PCA, and population structure analyses clearly differentiated the cattle population according to their historical origins, and confirmed that Ethiopian cattle populations are genetically distinct from the Hanwoo breed

  9. Variance estimation between different body measurements at the males population from Romanian Mioritic Shepherd Dog breed

    Directory of Open Access Journals (Sweden)

    Dorel Dronca

    2015-05-01

    Full Text Available Romanian Mioritic Shepherd Dog, was selected from a natural population breed in Carpathian Mountains. The aim of this paper was to estimate variance at 12 body measurements using 26 males from Romanian Mioritic Shepherd Dog breed. The animals were registered with the Romanian Mioritic Association Club from Romania. The statistical data showed that there is a large variance for body length and tail length, a middle variance for the croup width and thorax width and a small variance for height at withers, height at middle of back, height at croup, height at the base of the tail, depth of thorax, thoracic perimeter, elbow height and height of the hock. We recommend of breeders dogs from this breed to take account in genetic improvement programs, of values presented in this paper.

  10. Crop Breeding for Low Input Agriculture: A Sustainable Response to Feed a Growing World Population

    Directory of Open Access Journals (Sweden)

    Vagner A. Benedito

    2011-10-01

    Full Text Available World population is projected to reach its maximum (~10 billion people by the year 2050. This 45% increase of the current world population (approaching seven billion people will boost the demand for food and raw materials. However, we live in a historical moment when supply of phosphate, water, and oil are at their peaks. Modern agriculture is fundamentally based on varieties bred for high performance under high input systems (fertilizers, water, oil, pesticides, which generally do not perform well under low-input situations. We propose a shift of research goals and plant breeding objectives from high-performance agriculture at high-energy input to those with an improved rationalization between yield and energy input. Crop breeding programs that are more focused on nutrient economy and local environmental fitness will help reduce energy demands for crop production while still providing adequate amounts of high quality food as global resources decline and population is projected to increase.

  11. Molecular study on human tuberculosis in three geographically distinct and time delineated populations from ancient Egypt.

    Science.gov (United States)

    Zink, A R; Grabner, W; Reischl, U; Wolf, H; Nerlich, A G

    2003-04-01

    We describe the molecular identification of human tuberculosis (TB) from vertebral bone tissue samples from three different populations of ancient Egypt. The specimens were obtained from the predynastic to early dynastic necropolis of Abydos (7 individuals, c. 3500-2650 B.C.), from a Middle Kingdom to Second Intermediate Period tomb of the necropolis of Thebes-West (37. c. 2100-1550 B.C.) and from five further Theban tombs used in the New Kingdom and the Late Period (39, c. 1450-500 B.C.). A total of 18 cases tested positive for the presence of ancient DNA (aDNA) of the M. tuberculosis complex. Out of the 9 cases with typical macromorphological signs of tuberculous spondylitis, 6 were positive for mycobacterial aDNA (66.7%). Of 24 cases with non-specific pathological alterations, 5 provided a positive result (20.8%). In 50 cases of normally appearing vertebral bones 7 tested positive (14.0%). There were only minor differences in the frequencies between the three populations. These data strongly support the notion that tuberculosis was present and prevalent in ancient Egypt since very early periods of this civilization. The unexpectedly high rate of mycobacterial aDNA in normal bone samples is presumably due to a pre- to perimortal systemic spread of the bacteria and indicates a generalized infection by M. tuberculosis.

  12. Transcript analysis in two alfalfa salt tolerance selected breeding populations relative to a non-tolerant population.

    Science.gov (United States)

    Gruber, M Y; Xia, J; Yu, M; Steppuhn, H; Wall, K; Messer, D; Sharpe, A G; Acharya, S N; Wishart, D S; Johnson, D; Miller, D R; Taheri, A

    2017-02-01

    With the growing limitations on arable land, alfalfa (a widely cultivated, low-input forage) is now being selected to extend cultivation into saline lands for low-cost biofeedstock purposes. Here, minerals and transcriptome profiles were compared between two new salinity-tolerant North American alfalfa breeding populations and a more salinity-sensitive western Canadian alfalfa population grown under hydroponic saline conditions. All three populations accumulated two-fold higher sodium in roots than shoots as a function of increased electrical conductivity. At least 50% of differentially expressed genes (p population growing under high salinity, while expression remained unchanged in the saline-tolerant populations. In particular, most reduction in transcript levels in the salt-sensitive population was observed in genes specifying cell wall structural components, lipids, secondary metabolism, auxin and ethylene hormones, development, transport, signalling, heat shock, proteolysis, pathogenesis-response, abiotic stress, RNA processing, and protein metabolism. Transcript diversity for transcription factors, protein modification, and protein degradation genes was also more strongly affected in salt-tolerant CW064027 than in salt-tolerant Bridgeview and salt-sensitive Rangelander, while both saline-tolerant populations showed more substantial up-regulation in redox-related genes and B-ZIP transcripts. The report highlights the first use of bulked genotypes as replicated samples to compare the transcriptomes of obligate out-cross breeding populations in alfalfa.

  13. Estimation of the genetic diversity in tetraploid alfalfa populations based on RAPD markers for breeding purposes.

    Science.gov (United States)

    Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan

    2011-01-01

    Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon's information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

  14. Current range of the eastern population of Painted Bunting (Passerina ciris). Part 1: Breeding

    Science.gov (United States)

    Sykes, P.W.; Holzman, S.

    2005-01-01

    This paper presents the current breeding range of Painted Bunting (Passerina ciris) in a series of maps and a narrative, in particular that of the eastern population, which is restricted to the states of North Carolina, South Carolina, Georgia, and Florida. Some conservation measures are recommended to protect this population. In light of the extensive habitat loss in the Outer Coastal Plain of these states, which comprise the areas of the population's greatest density, it is imperative that a consortium of diverse interests work together to provide sufficient habitats for this colorful native songbird.

  15. Molecular genetic studies and delineation of the oculocutaneous albinism phenotype in the Pakistani population

    Directory of Open Access Journals (Sweden)

    Jaworek Thomas J

    2012-06-01

    Full Text Available Abstract Background Oculocutaneous albinism (OCA is caused by a group of genetically heterogeneous inherited defects that result in the loss of pigmentation in the eyes, skin and hair. Mutations in the TYR, OCA2, TYRP1 and SLC45A2 genes have been shown to cause isolated OCA. No comprehensive analysis has been conducted to study the spectrum of OCA alleles prevailing in Pakistani albino populations. Methods We enrolled 40 large Pakistani families and screened them for OCA genes and a candidate gene, SLC24A5. Protein function effects were evaluated using in silico prediction algorithms and ex vivo studies in human melanocytes. The effects of splice-site mutations were determined using an exon-trapping assay. Results Screening of the TYR gene revealed four known (p.Arg299His, p.Pro406Leu, p.Gly419Arg, p.Arg278* and three novel mutations (p.Pro21Leu, p.Cys35Arg, p.Tyr411His in ten families. Ex vivo studies revealed the retention of an EGFP-tagged mutant (p.Pro21Leu, p.Cys35Arg or p.Tyr411His tyrosinase in the endoplasmic reticulum (ER at 37°C, but a significant fraction of p.Cys35Arg and p.Tyr411His left the ER in cells grown at a permissive temperature (31°C. Three novel (p.Asp486Tyr, p.Leu527Arg, c.1045-15 T > G and two known mutations (p.Pro743Leu, p.Ala787Thr of OCA2 were found in fourteen families. Exon-trapping assays with a construct containing a novel c.1045-15 T > G mutation revealed an error in splicing. No mutation in TYRP1, SLC45A2, and SLC24A5 was found in the remaining 16 families. Clinical evaluation of the families segregating either TYR or OCA2 mutations showed nystagmus, photophobia, and loss of pigmentation in the skin or hair follicles. Most of the affected individuals had grayish-blue colored eyes. Conclusions Our results show that ten and fourteen families harbored mutations in the TYR and OCA2 genes, respectively. Our findings, along with the results of previous studies, indicate that the p.Cys35Arg, p.Arg278

  16. Density-mediated carry-over effects explain variation in breeding output across time in a seasonal population.

    Science.gov (United States)

    Betini, Gustavo S; Griswold, Cortland K; Norris, D Ryan

    2013-10-23

    In seasonal environments, where density dependence can operate throughout the annual cycle, vital rates are typically considered to be a function of the number of individuals at the beginning of each season. However, variation in density in the previous season could also cause surviving individuals to be in poor physiological condition, which could carry over to influence individual success in the following season. We examine this hypothesis using replicated populations of Drosophila melanogaster, the common fruitfly, over 23 non-overlapping generations with distinct breeding and non-breeding seasons. We found that the density at the beginning of the non-breeding season negatively affected the fresh weight of individuals that survived the non-breeding season and resulted in a 25% decrease in per capita breeding output among those that survived to the next season to breed. At the population level, per capita breeding output was best explained by a model that incorporated density at the beginning of the previous non-breeding season (carry-over effect, COE) and density at the beginning of the breeding season. Our results support the idea that density-mediated COEs are critical for understanding population dynamics in seasonal environments.

  17. Cross-Breeding Is Inevitable to Conserve the Highly Inbred Population of Puffin Hunter: The Norwegian Lundehund

    Science.gov (United States)

    Daverdin, Marc; Helfjord, Turid; Berg, Peer

    2017-01-01

    The Norwegian Lundehund is a highly endangered native dog breed. Low fertility and high frequency predisposition to intestinal disorder imply inbreeding depression. We assessed the genetic diversity of the Lundehund population from pedigree data and evaluated the potential of optimal contribution selection and cross-breeding in the long-term management of the Lundehund population. The current Norwegian Lundehund population is highly inbred and has lost 38.8% of the genetic diversity in the base population. Effective population size estimates varied between 13 and 82 depending on the method used. Optimal contribution selection alone facilitates no improvement in the current situation in the Lundehund due to the extremely high relatedness of the whole population. Addition of (replacement with) 10 breeding candidates of foreign breed to 30 Lundehund breeders reduced the parental additive genetic relationship by 40–42% (48–53%). Immediate actions are needed to increase the genetic diversity in the current Lundehund population. The only option to secure the conservation of this rare breed is to introduce individuals from foreign breeds as breeding candidates. PMID:28107382

  18. Diversity and effective population size of four horse breeds from microsatellite DNA markers in South-Central Mexico

    Directory of Open Access Journals (Sweden)

    J. F. Vázquez-Armijo

    2017-06-01

    Full Text Available The South-Central region of Mexico has experienced a sizeable introduction of purebred horses for recreational aims. A study was designed to assess effective population sizes and genetic diversity and to verify the genetic integrity of four horse breeds. Using a 12-microsatellite panel, Quarter Horse, Azteca, Thoroughbred and Creole (CRL horses were sampled and analysed for diversity and genetic structure. Genetic diversity parameters showed high numbers of heterozygous horses but small effective population sizes in all breeds. Population structure results suggested some degree of admixture of CRL with the other reference breeds. The highly informative microsatellite panel allowed the verification of diversity in introduced horse populations and the confirmation of small effective population sizes, which suggests a risk for future breed integrity.

  19. Abundance and phenology patterns of two pond-breeding salamanders determine species interactions in natural populations.

    Science.gov (United States)

    Anderson, Thomas L; Hocking, Daniel J; Conner, Christopher A; Earl, Julia E; Harper, Elizabeth B; Osbourn, Michael S; Peterman, William E; Rittenhouse, Tracy A G; Semlitsch, Raymond D

    2015-03-01

    Phenology often determines the outcome of interspecific interactions, where early-arriving species often dominate interactions over those arriving later. The effects of phenology on species interactions are especially pronounced in aquatic systems, but the evidence is largely derived from experimental studies. We examined whether differences in breeding phenology between two pond-breeding salamanders (Ambystoma annulatum and A. maculatum) affected metamorph recruitment and demographic traits within natural populations, with the expectation that the fall-breeding A. annulatum would negatively affect the spring-breeding A. maculatum. We monitored populations of each species at five ponds over 4 years using drift fences. Metamorph abundance and survival of A. annulatum were affected by intra- and interspecific processes, whereas metamorph size and date of emigration were primarily influenced by intraspecific effects. Metamorph abundance, snout-vent length, date of emigration and survival for A. maculatum were all predicted by combinations of intra- and interspecific effects, but often showed negative relationships with A. annulatum metamorph traits and abundance. Size and date of metamorphosis were strongly correlated within each species, but in opposite patterns (negative for A. annulatum and positive for A. maculatum), suggesting that the two species use alternative strategies to enhance terrestrial survival and that these factors may influence their interactions. Our results match predictions from experimental studies that suggest recruitment is influenced by intra- and interspecific processes which are determined by phenological differences between species. Incorporating spatiotemporal variability when modeling population dynamics is necessary to understand the importance of phenology in species interactions, especially as shifts in phenology occur under climate change.

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

    Science.gov (United States)

    Boligon, A A; Long, N; Albuquerque, L G; Weigel, K A; Gianola, D; Rosa, G J M

    2012-12-01

    Genomewide marker information can improve the reliability of breeding value predictions for young selection candidates in genomic selection. However, the cost of genotyping limits its use to elite animals, and how such selective genotyping affects predictive ability of genomic selection models is an open question. We performed a simulation study to evaluate the quality of breeding value predictions for selection candidates based on different selective genotyping strategies in a population undergoing selection. The genome consisted of 10 chromosomes of 100 cM each. After 5,000 generations of random mating with a population size of 100 (50 males and 50 females), generation G(0) (reference population) was produced via a full factorial mating between the 50 males and 50 females from generation 5,000. Different levels of selection intensities (animals with the largest yield deviation value) in G(0) or random sampling (no selection) were used to produce offspring of G(0) generation (G(1)). Five genotyping strategies were used to choose 500 animals in G(0) to be genotyped: 1) Random: randomly selected animals, 2) Top: animals with largest yield deviation values, 3) Bottom: animals with lowest yield deviations values, 4) Extreme: animals with the 250 largest and the 250 lowest yield deviations values, and 5) Less Related: less genetically related animals. The number of individuals in G(0) and G(1) was fixed at 2,500 each, and different levels of heritability were considered (0.10, 0.25, and 0.50). Additionally, all 5 selective genotyping strategies (Random, Top, Bottom, Extreme, and Less Related) were applied to an indicator trait in generation G(0,) and the results were evaluated for the target trait in generation G(1), with the genetic correlation between the 2 traits set to 0.50. The 5 genotyping strategies applied to individuals in G(0) (reference population) were compared in terms of their ability to predict the genetic values of the animals in G(1) (selection

  1. Heirloom tomato cultivars and local populations as sources of genetic variability for breeding

    Directory of Open Access Journals (Sweden)

    Glogovac Svetlana

    2010-01-01

    Full Text Available Five local tomato populations and fourteen heirloom cultivars were analyzed in this study. The analyzed genotypes represent a part of tomato collection of Institute of Field and Vegetable Crops in Novi Sad. The following fruit and plant traits were analyzed: growth type, fruit color, fruit shape index, fruit weight, number of locules and dry matter content. Cluster analysis was performed so as to group the analyzed genotypes by homology and divergence. The aim of this article was to determine the importance of heirloom cultivars and local populations as sources of genetic variability in tomato breeding process.

  2. Breeding biology and success of a reintroduced population of the critically endangered Puaiohi (Myadestes palmeri)

    Science.gov (United States)

    Tweed, E.J.; Foster, J.T.; Woodworth, B.L.; Monahan, W.B.; Kellerman, J.L.; Lieberman, A.

    2006-01-01

    The ultimate success of reintroduction programs for endangered species depends on the ability of reintroduced animals to breed in the wild. We studied the nesting success and breeding biology of a reintroduced population of Puaiohi (Myadestes palmeri) on the island of Kaua'i, Hawaii. Thirty-four captive-bred Puaiohi were released into the Alaka'i Swamp in 1999-2001 and monitored using radiotelemetry. Ten females and two males paired with wild and other released birds, including one polygynous trio. From March to September, 31 nests were built. Mean clutch size was 2.0 eggs, daily nest survival was 0.97 ?? 0.01 (mean ?? SE) and overall nest success was 0.40 ?? 0.02. We confirmed predation, most probably by rats (Rattus spp.), as the greatest cause of nest failure, occurring at 38% of active nests with known fates, and causing the death of two nesting adult females. Ground-based rodent control proved ineffective at protecting nest attempts. Successful nests fledged an average of 1.4 young each (n = 10), and 85% of fledglings survived at least two weeks. Importantly, breeding behavior and success were comparable to those of wild Puaiohi. This is the first record of breeding in the wild from captive-bred endangered Hawaiian passerines. The ability of captive-bred Puaiohi to survive and breed successfully in the wild bodes well for future releases of this and other endangered passerines, but high predation rates on nests and nesting females highlights the importance of maintaining and restoring safe habitat for recovery. ?? The American Ornithologists' Union, 2006.

  3. Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States

    Institute of Scientific and Technical Information of China (English)

    Hao ZHOU; Gary MUEHLBAUER; Brian STEFFENSON

    2012-01-01

    Cultivated barley is known to have a complex population structure and extensive linkage disequilibrium (LD).To conduct robust association mapping (AM) studies of economically important traits in US barley breeding germplasm,population structure and LD decay were examined in a complete panel of US barley breeding germplasm (3840 lines) genotyped with 3072 single nucleotide polymorphisms (SNPs).Nine subpopulations (sp1-sp9) were identified by the program STRUCTURE and subsequently confirmed by principle component analysis (PCA).Out of the nine subpopulations,seven were very similar to the respective subpopulations identified by Hamblin et al.(2010)which were based on half of the germplasm and half of the SN P markers,but two subpopulations were found to be new.One subpopulation was dominated by six-rowed spring lines from Utah State University (UT) and the other was composed of six-rowed spring lines from multiple breeding programs (USDA-ARS Aberdeen (AB),Busch Agricultural Resources Inc.(BA),UT,and Washington State University (WA)).LD was found to decay across a range from 4.0 to 19.8 cM.This result indicates that the germplasm genotyped with 3072 SNPs would be robust for mapping and possibly identifying the causal polymorphisms contributing to disease resistance and perhaps other traits.

  4. Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds.

    Science.gov (United States)

    Uimari, P; Tapio, M

    2011-03-01

    The extent of linkage disequilibrium (LD) and effective population size in Finnish Landrace and Finnish Yorkshire pig populations were studied using a whole genome SNP panel (Illumina PorcineSNP60 BeadChip) and pedigree data. Genotypic data included 86 Finnish Landrace and 32 Finnish Yorkshire boars. Pedigree data included 608,138 Finnish Landrace 554,237 and Finnish Yorkshire pigs, and on average 15 ancestral generations were known for the reference animals, born in 2005 to 2009. The breeding animals of the 2 populations have been kept separate in the breeding programs. Based on the pedigree data, the current effective population size for Finnish Landrace is 91 and for Finnish Yorkshire 61. Linkage disequilibrium measures (D' and r(2)) were estimated for over 1.5 million pairs of SNP. Average r(2) for SNP 30 kb apart was 0.47 and 0.49 and for SNP 5 Mb apart 0.09 and 0.12 for Finnish Landrace and Finnish Yorkshire, respectively. Average LD (r(2)) between adjacent SNP in the Illumina PorcineSNP60 BeadChip was 0.43 (57% of the adjacent SNP pairs had r(2) > 0.2) for Finnish Landrace and 0.46 (60% of the adjacent SNP pairs had r(2) > 0.2) for Finnish Yorkshire, and average r(2) > 0.2 extended to 1.0 and 1.5 Mb for Finnish Landrace and Finnish Yorkshire, respectively. Effective population size estimates based on the decay of r(2) with distance were similar to those based on the pedigree data: 80 and 55 for Finnish Landrace and Finnish Yorkshire, respectively. Thus, the results indicate that the effective population size of Finnish Yorkshire is smaller than of Finnish Landrace and has a clear effect on the extent of LD. The current effective population size of both breeds is above the recommended minimum of 50 but may get smaller than that in the near future, if no action is taken to balance the inbreeding rate and selection response. Because a moderate level of LD extends over a long distance, selection based on whole genome SNP markers (genomic selection) is expected

  5. Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes

    Directory of Open Access Journals (Sweden)

    Slobodan Katic

    2011-08-01

    Full Text Available Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

  6. Particle backtracking improves breeding subpopulation discrimination and natal-source identification in mixed populations.

    Directory of Open Access Journals (Sweden)

    Michael E Fraker

    Full Text Available We provide a novel method to improve the use of natural tagging approaches for subpopulation discrimination and source-origin identification in aquatic and terrestrial animals with a passive dispersive phase. Our method integrates observed site-referenced biological information on individuals in mixed populations with a particle-tracking model to retrace likely dispersal histories prior to capture (i.e., particle backtracking. To illustrate and test our approach, we focus on western Lake Erie's yellow perch (Perca flavescens population during 2006-2007, using microsatellite DNA and otolith microchemistry from larvae and juveniles as natural tags. Particle backtracking showed that not all larvae collected near a presumed hatching location may have originated there, owing to passive drift during the larval stage that was influenced by strong river- and wind-driven water circulation. Re-assigning larvae to their most probable hatching site (based on probabilistic dispersal trajectories from the particle backtracking model improved the use of genetics and otolith microchemistry to discriminate among local breeding subpopulations. This enhancement, in turn, altered (and likely improved the estimated contributions of each breeding subpopulation to the mixed population of juvenile recruits. Our findings indicate that particle backtracking can complement existing tools used to identify the origin of individuals in mixed populations, especially in flow-dominated systems.

  7. Indicators of genetic erosion in an endangered population: the Alentejana cattle breed in Portugal.

    Science.gov (United States)

    Carolino, N; Gama, L T

    2008-01-01

    A study was conducted to characterize genetic diversity in the Alentejana breed of cattle based on its demographic trends and to investigate the major factors affecting genetic erosion in this breed. Herdbook information collected between 1940 and 2004, including pedigree records on 100,562 animals in 155 herds, was used to estimate demographic parameters. The mean generation intervals were 6.0 +/- 2.4 yr and 6.8 +/- 3.2 yr for sires and dams of calves, respectively. Average inbreeding increased steadily over the period analyzed, with an annual rate of inbreeding of 0.33 +/- 0.004% (P < 0.01) and an effective population size of 23.3. In the reference population (28,531 calves born between 2000 and 2003) the average inbreeding was 8.35 +/- 9.02% and nearly 80% of the calves were inbred, whereas the average relationship among all animals was 0.026 +/- 0.040. Nevertheless, the mean relationship was 0.328 +/- 0.264 and 0.022 +/- 0.026 for animals born in the same and in different herds, respectively. The computed genetic contributions to the reference population resulted in estimates for the effective number of founders, ancestors, founding herds, and herds supplying sires of 121.6, 55.0, 17.1, and 26.9, respectively, the 2 most influential herds and ancestors contributing 24.2 and 15.1%, respectively, of the current genetic pool. Of the 671 founding sires, only 24 Y-chromosomes are currently represented, but 1 sire alone contributes nearly 60% of this representation, such that the effective number of Y-chromosomes is only 2.73. The observed inbreeding per herd was, on average, 0.053 +/- 0.071 lower than expected from the relationship among the generation of parents of calves in the reference population, indicating that producers have followed breeding strategies that have kept inbreeding at lower levels than anticipated with random selection and mating. When compared with other cattle breeds, Alentejana has some of the highest levels of mean inbreeding and annual rate

  8. Applications of population genetics to animal breeding, from wright, fisher and lush to genomic prediction.

    Science.gov (United States)

    Hill, William G

    2014-01-01

    Although animal breeding was practiced long before the science of genetics and the relevant disciplines of population and quantitative genetics were known, breeding programs have mainly relied on simply selecting and mating the best individuals on their own or relatives' performance. This is based on sound quantitative genetic principles, developed and expounded by Lush, who attributed much of his understanding to Wright, and formalized in Fisher's infinitesimal model. Analysis at the level of individual loci and gene frequency distributions has had relatively little impact. Now with access to genomic data, a revolution in which molecular information is being used to enhance response with "genomic selection" is occurring. The predictions of breeding value still utilize multiple loci throughout the genome and, indeed, are largely compatible with additive and specifically infinitesimal model assumptions. I discuss some of the history and genetic issues as applied to the science of livestock improvement, which has had and continues to have major spin-offs into ideas and applications in other areas.

  9. Introduction of quinolone resistant Escherichia coli to Swedish broiler population by imported breeding animals.

    Science.gov (United States)

    Börjesson, Stefan; Guillard, Thomas; Landén, Annica; Bengtsson, Björn; Nilsson, Oskar

    2016-10-15

    During recent years a rapid increase of quinolone resistant Escherichia coli have been noted in the Swedish broiler population, despite the lack of a known selective pressure. The current study wanted to investigate if imported breeding birds could be a source for the quinolone resistant E. coli. The occurrence of quinolone resistant E. coli was investigated, using selective cultivation with nalidixic acid, in grand-parent birds on arrival to Sweden and their progeny. In addition, sampling in hatcheries and empty cleaned poultry houses was performed. Clonality of isolates was investigated using a 10-loci multiple-locus variable number tandem repeat analysis (MLVA). To identify the genetic basis for the resistance isolates were also analysed for occurrence of plasmid-mediated quinolone resistance (PMQR) determinants and characterization of chromosomal mutations. E. coli resistant to nalidixic acid occurred in grandparent birds imported to Sweden for breeding purposes. Four predominant MLVA types were identified in isolates from grandparent birds, parent birds and broilers. However, resistant E. coli with identical MLVA patterns were also present in hatcheries and poultry houses suggesting that the environment plays a role in the occurrence. Nalidixic acid resistance was due to a mutation in the gyrA gene and no PMQR could be identified. The occurrence of identical clones in all levels of the production pyramid points to that quinolone resistant E. coli can be introduced through imported breeding birds and spread by vertical transmission to all levels of the broiler production pyramid.

  10. Applications of Population Genetics to Animal Breeding, from Wright, Fisher and Lush to Genomic Prediction

    Science.gov (United States)

    Hill, William G.

    2014-01-01

    Although animal breeding was practiced long before the science of genetics and the relevant disciplines of population and quantitative genetics were known, breeding programs have mainly relied on simply selecting and mating the best individuals on their own or relatives’ performance. This is based on sound quantitative genetic principles, developed and expounded by Lush, who attributed much of his understanding to Wright, and formalized in Fisher’s infinitesimal model. Analysis at the level of individual loci and gene frequency distributions has had relatively little impact. Now with access to genomic data, a revolution in which molecular information is being used to enhance response with “genomic selection” is occurring. The predictions of breeding value still utilize multiple loci throughout the genome and, indeed, are largely compatible with additive and specifically infinitesimal model assumptions. I discuss some of the history and genetic issues as applied to the science of livestock improvement, which has had and continues to have major spin-offs into ideas and applications in other areas. PMID:24395822

  11. Territory occupancy and breeding success of Peregrine Falcons Falco peregrinus at various stages of population recovery

    Science.gov (United States)

    McGrady, Michael J.; Hines, James; Rollie, Chris; Smith, George D.; Morton, Elise R.; Moore, Jennifer F.; Mearns, Richard M.; Newton, Ian; Murillo-Garcia, Oscar E.; Oli, Madan K.

    2017-01-01

    Organochlorine pesticides disrupted reproduction and killed many raptorial birds, and contributed to population declines during the 1940s to 1970s. We sought to discern whether and to what extent territory occupancy and breeding success changed from the pesticide era to recent years in a resident population of Peregrine Falcons Falco peregrinus in southern Scotland using long-term (1964–2015) field data and multi-state, multi-season occupancy models. Peregrine territories that were occupied with successful reproduction in one year were much more likely to be occupied and experience reproductive success in the following year, compared with those that were unoccupied or occupied by unsuccessful breeders in the previous year. Probability of territory occupancy differed between territories in the eastern and western parts of the study area, and varied over time. The probability of occupancy of territories that were unoccupied and those that were occupied with successful reproduction during the previous breeding season generally increased over time, whereas the probability of occupancy of territories that were occupied after failed reproduction decreased. The probability of reproductive success (conditional on occupancy) in territories that were occupied during the previous breeding season increased over time. Specifically, for territories that had been successful in the previous year, the probability of occupancy as well as reproductive success increased steadily over time; these probabilities were substantially higher in recent years than earlier, when the population was still exposed to direct or residual effects of organochlorine pesticides. These results are consistent with the hypothesis that progressive reduction, followed by a complete ban, in the use of organochlorine pesticides improved reproductive success of Peregrines in southern Scotland. Differences in the temporal pattern of probability of reproductive success between south-eastern and south

  12. Wood duck population trends from the North American Breeding Bird Survey

    Science.gov (United States)

    Sauer, J.R.; Droege, S.; Fredrickson, Leigh H.; Burger, George V.; Havera, Stephen P.; Graber, David A.; Kirby, Ronald E.; Taylor, T. Scott

    1990-01-01

    The North American Breeding Bird Survey (BBS) has been conducted yearly since 1966, and can be used to describe relative population density and trends of birds in North America north of Mexico. Wood ducks (Air sponsa) are difficult to survey using conventional waterfowl monitoring techniques, but a large portion of their range is surveyed by the BBS. Wood ducks are detected at low densities on many BBS routes, and population trends can be estimated for most regions. Populations have been increasing throughout North America since 1966, but statistically significant increases generally occurred only in the early (1966-78) part of the period. Roadside survey methodology used in the BBS has limitations that make it inefficient as a survey technique for wood ducks, and we recommend using modified methodologies that specifically survey wood duck habitat.

  13. Long-term population dynamics of breeding bird species in the German Wadden Sea area

    Science.gov (United States)

    Vauk, Gottfried; Prüter, Johannes; Hartwig, Eike

    1989-09-01

    For no other group of organisms in coastal areas are there so exact and long-term data available as there are for seabirds. Since the beginning of the 20th century, documentation of population size, especially for species breeding in colonies from the groups gulls, terns and auks, is almost complete. These species act as bio-indicators, and data on fluctuations in their population size are useful as they reflect changes in the state of the marine ecosystem. The population development of some of these seabird species (Herring Gull, Guillemot, Common, Arctic and Sandwich Tern) from the German North Sea coast, which primarily feed on fish, is given. Common to all these species is an exponential increase in numbers in recent years (1970 1985). Possible causes for this development, e.g. pressure from enemies or competitors, availability of breeding places, anthropogenic stress and mortality factors, as well as the direct and indirect anthropogenic-influenced changes in the trophic system due to the increasing eutrophication of coastal waters, are evaluated. Signs of a collapse in the stocks of seabrids resulting from environmental pollution are discussed. Consequences resulting from the ecosystem changes, such as reduction of nutrient discharge into the North Sea and the expansion of biological monitoring, are described.

  14. Genomic predictions based on a joint reference population for the Nordic Red cattle breeds.

    Science.gov (United States)

    Zhou, L; Heringstad, B; Su, G; Guldbrandtsen, B; Meuwissen, T H E; Svendsen, M; Grove, H; Nielsen, U S; Lund, M S

    2014-07-01

    The main aim of this study was to compare accuracies of imputation and genomic predictions based on single and joint reference populations for Norwegian Red (NRF) and a composite breed (DFS) consisting of Danish Red, Finnish Ayrshire, and Swedish Red. The single nucleotide polymorphism (SNP) data for NRF consisted of 2 data sets: one including 25,000 markers (NRF25K) and the other including 50,000 markers (NRF50K). The NRF25K data set had 2,572 bulls, and the NRF50K data set had 1,128 bulls. Four hundred forty-two bulls were genotyped in both data sets (double-genotyped bulls). The DFS data set (DSF50K) included 50,000 markers of 13,472 individuals, of which around 4,700 were progeny-tested bulls. The NRF25K data set was imputed to 50,000 density using the software Beagle. The average error rate for the imputation of NRF25K decreased slightly from 0.023 to 0.021, and the correlation between observed and imputed genotypes changed from 0.935 to 0.936 when comparing the NRF50K reference and the NRF50K-DFS50K joint reference imputations. A genomic BLUP (GBLUP) model and a Bayesian 4-component mixture model were used to predict genomic breeding values for the NRF and DFS bulls based on the single and joint NRF and DFS reference populations. In the multiple population predictions, accuracies of genomic breeding values increased for the 3 production traits (milk, fat, and protein yields) for both NRF and DFS. Accuracies increased by 6 and 1.3 percentage points, on average, for the NRF and DFS bulls, respectively, using the GBLUP model, and by 9.3 and 1.3 percentage points, on average, using the Bayesian 4-component mixture model. However, accuracies for health or reproduction traits did not increase from the multiple population predictions. Among the 3 DFS populations, Swedish Red gained most in accuracies from the multiple population predictions, presumably because Swedish Red has a closer genetic relationship with NRF than Danish Red and Finnish Ayrshire. The Bayesian 4

  15. Microsatellite based genetic structure of regional transboundary Istrian sheep breed populations in Croatia and Slovenia

    Directory of Open Access Journals (Sweden)

    Beatriz Gutierrez-Gil

    2015-02-01

    Full Text Available Istrian dairy sheep is a local breed essential for the identity and development of the Northern- Adriatic karstic region through high-quality products, primarily the hard sheep artisanal cheese. Border changes fragmented the initial Istrian dairy sheep population in three genetically isolated sub-populations in Italy (1000 animals, Slovenia (1150 animals and Croatia (2500 animals. Due to the drastic reduction of their population sizes and fragmentation, the populations in Croatia and Slovenia are included in governmentally supported conservation programs. The initial subpopulation in Italy was restored after near extinction with stock from Slovenia, and is used today in meat production. The aim of this study was to provide an initial understanding of the current genetic structure and distribution of the genetic variability that exists in Istrian sheep by analysing individuals sampled in two regional groups of Istrian sheep from Croatia and Slovenia. Cres island sheep and Lika pramenka sheep were used as out-groups for comparison. Genetic differentiation was analysed using factorial correspondence analysis and structure clustering over 26 microsatellite loci for a total of 104 sheep belonging to three breeds from Croatia and Slovenia. Factorial correspondence analysis and clustering-based structure analysis both showed three distinct populations: Lika pramenka sheep, Cres island sheep and Istrian sheep. We did not find a marked genetic divergence of the regional groups of Istrian sheep. Istrian sheep regional group from Slovenia showed lower genetic variability compared to the one from Croatia. Variability and structure information obtained in this study considered alongside with socio-cultural-contexts and economic goals for the Istrian sheep reared in Croatia and Slovenia indicate that the cross-border exchange of genetic material of animals carrying private alleles among populations would maintain these alleles at low frequencies and minimize

  16. Survival differences and the effect of environmental instability on breeding dispersal in an Adelie penguin meta-population.

    Science.gov (United States)

    Dugger, Katie M; Ainley, David G; Lyver, Phil O'B; Barton, Kerry; Ballard, Grant

    2010-07-06

    High survival and breeding philopatry was previously confirmed for the Adélie penguin (Pygoscelis adeliae) during a period of stable environmental conditions. However, movements of breeding adults as a result of an unplanned natural experiment within a four-colony meta-population provided interesting insights into this species' population dynamics. We used multistate mark-recapture models to investigate apparent survival and dispersal of breeding birds in the southwestern Ross Sea during 12 breeding seasons (1996-2007). The natural experiment was facilitated by the temporary grounding of two immense icebergs that (i) erected a veritable fence separating colonies and altering migration routes and (ii) added additional stress by trapping extensive sea ice in the region during 5 of 12 y. Colony size varied by orders of magnitude, allowing investigation of apparent survival and dispersal rates in relation to both environmental conditions and colony size within this meta-population. Apparent survival was lowest for the smallest colony (4,000 pairs) and similar for the medium (45,000 pairs) and large colonies (155,000 pairs), despite increased foraging effort expended by breeders at the largest colony. Dispersal of breeding birds was low (population. Contrary to current thought, breeding penguins are not always philopatric. Rather, stressful conditions can significantly increase dispersal rates.

  17. Canine population structure: assessment and impact of intra-breed stratification on SNP-based association studies.

    Directory of Open Access Journals (Sweden)

    Pascale Quignon

    Full Text Available BACKGROUND: In canine genetics, the impact of population structure on whole genome association studies is typically addressed by sampling approximately equal numbers of cases and controls from dogs of a single breed, usually from the same country or geographic area. However one way to increase the power of genetic studies is to sample individuals of the same breed but from different geographic areas, with the expectation that independent meiotic events will have shortened the presumed ancestral haplotype around the mutation differently. Little is known, however, about genetic variation among dogs of the same breed collected from different geographic regions. METHODOLOGY/PRINCIPAL FINDINGS: In this report, we address the magnitude and impact of genetic diversity among common breeds sampled in the U.S. and Europe. The breeds selected, including the Rottweiler, Bernese mountain dog, flat-coated retriever, and golden retriever, share susceptibility to a class of soft tissue cancers typified by malignant histiocytosis in the Bernese mountain dog. We genotyped 722 SNPs at four unlinked loci (between 95 and 271 per locus on canine chromosome 1 (CFA1. We showed that each population is characterized by distinct genetic diversity that can be correlated with breed history. When the breed studied has a reduced intra-breed diversity, the combination of dogs from international locations does not increase the rate of false positives and potentially increases the power of association studies. However, over-sampling cases from one geographic location is more likely to lead to false positive results in breeds with significant genetic diversity. CONCLUSIONS: These data provide new guidelines for association studies using purebred dogs that take into account population structure.

  18. Demography of a breeding population of whimbrel (Numenius phaeopus) near Churchill, Manitoba, Canada

    Science.gov (United States)

    Perz, Johanna

    I used a GIS raster layer of an area in the Churchill, Manitoba region to investigate the effect of breeding habitat on demography and density of Whimbrel from 2010 through 2013. Program MARK was used to quantify adult and daily nest survival. Apparent annual survival of 0.73 +/- 0.06 SE (95% CI = 0.60-0.83) did not significantly differ between sexes or habitats and was lower than expected based on longevity records and estimates for other large-bodied shorebirds. Nest success, corrected for exposure days, was highly variable, ranging from a low of 3% (95% CI = 0-12%) in 2011 to a high of 71% (95% CI = 54-83%) in 2013. The highest rate of nest survival occurred in the spring with the warmest mean temperature. I developed a generalized linear model (GLM) with a negative-binomial distribution from random plots that were surveyed for abundance to extrapolate a local breeding population size of 410 +/- 230 SE and density of 3.2 birds per square km +/- 1.8 SE. The result of my study suggests that other aspects of habitat not captured by the land cover categories may be more important to population dynamics.

  19. Genetic variability and population structure of Salvia lachnostachys: implications for breeding and conservation programs.

    Science.gov (United States)

    Erbano, Marianna; Schühli, Guilherme Schnell E; Santos, Élide Pereira Dos

    2015-04-08

    The genetic diversity and population structure of Salvia lachnostachys Benth were assessed. Inter Simple Sequence Repeat (ISSR) molecular markers were used to investigate the restricted distribution of S. lachnostachys in Parana State, Brazil. Leaves of 73 individuals representing three populations were collected. DNA was extracted and submitted to PCR-ISSR amplification with nine tested primers. Genetic diversity parameters were evaluated. Our analysis indicated 95.6% polymorphic loci (stress value 0.02) with a 0.79 average Simpson's index. The Nei-Li distance dendrogram and principal component analysis largely recovered the geographical origin of each sample. Four major clusters were recognized representing each collected population. Nei's gene diversity and Shannon's information index were 0.25 and 0.40 respectively. As is typical for outcrossing herbs, the majority of genetic variation occurred at the population level (81.76%). A high gene flow (Nm = 2.48) was observed with a correspondingly low fixation index. These values were generally similar to previous studies on congeneric species. The results of principal coordinate analysis (PCA) and of arithmetic average (UPGMA) were consistent and all three populations appear distinct as in STRUCTURE analysis. In addition, this analysis indicated a majority intrapopulation genetic variation. Despite the human pressure on natural populations our study found high levels of genetic diversity for S. lachnostachys. This was the first molecular assessment for this endemic species with medicinal proprieties and the results can guide for subsequent bioprospection, breeding programs or conservation actions.

  20. Genetic diversity and population structure of 10 Chinese indigenous egg-type duck breeds assessed by microsatellite polymorphism

    Indian Academy of Sciences (India)

    Li Hui-Fang; Song Wei-Tao; Shu Jing-Ting; Chen Kuan-Wei; Zhu Wen-Qi; Han Wei; Xu Wen-Juan

    2010-04-01

    The genetic structure and diversity of 10 Chinese indigenous egg-type duck breeds were investigated using 29 microsatellite markers. The total number of animals examined were 569, on average 57 animals per breed were selected. The microsatellite marker set analysed provided 177 alleles (mean 6.1 alleles per locus, ranging from 3 to 10). All populations showed high levels of heterozygosity with the lowest estimate of 0.539 for the Jinding ducks, and the highest 0.609 observed for Jingjiang partridge ducks. The global heterozygote deficit across all populations ($F_{\\text{IT}}$) amounted to $-0.363$. About 10% of the total genetic variability originated from differences among breeds, with all loci contributing significantly. An unrooted consensus tree was constructed using the NeighborNet tree based on the Reynold’s genetic distance. The structure software was used to assess genetic clustering of these egg-type duck breeds. Clustering analysis provided an accurate representation of the current genetic relations among the breeds. An integrated analysis was undertaken to obtain information on the population dynamics in Chinese indigenous egg-type duck breeds, and to better determine the conservation priorities.

  1. Contributions of Weather and Predation to Reduced Breeding Success in a Threatened Northern Loggerhead Shrike Population

    Directory of Open Access Journals (Sweden)

    Douglas M. Collister

    2007-12-01

    Full Text Available Populations on the periphery of a species' range may experience more severe environmental conditions relative to populations closer to the core of the range. As a consequence, peripheral populations may have lower reproductive success or survival, which may affect their persistence. In this study, we examined the influence of environmental conditions on breeding biology and nest survival in a threatened population of Loggerhead Shrikes (Lanius ludovicianus at the northern limit of the range in southeastern Alberta, Canada, and compared our estimates with those from shrike populations elsewhere in the range. Over the 2-year study in 1992–1993, clutch sizes averaged 6.4 eggs, and most nests were initiated between mid-May and mid-June. Rate of renesting following initial nest failure was 19%, and there were no known cases of double-brooding. Compared with southern populations, rate of renesting was lower and clutch sizes tended to be larger, whereas the length of the nestling and hatchling periods appeared to be similar. Most nest failures were directly associated with nest predators, but weather had a greater direct effect in 1993. Nest survival models indicated higher daily nest survival during warmer temperatures and lower precipitation, which may include direct effects of weather on nestlings as well as indirect effects on predator behavior or food abundance. Daily nest survival varied over the nesting cycle in a curvilinear pattern, with a slight increase through laying, approximately constant survival through incubation, and a decline through the nestling period. Partial brood loss during the nestling stage was high, particularly in 1993, when conditions were cool and wet. Overall, the lower likelihood of renesting, lower nest survival, and higher partial brood loss appeared to depress reproductive output in this population relative to those elsewhere in the range, and may have increased susceptibility to population declines.

  2. Genotypic variation in a breeding population of yellow sweet clover (Melilotus officinalis

    Directory of Open Access Journals (Sweden)

    Kai Luo

    2016-07-01

    Full Text Available Yellow sweet clover is a widely spread legume species that has potential to be used as a forage crop in Western China. However, limited information is available on the genetic variation for herbage yield, key morphological traits and coumarin content. In this study, 40 half sib (HS families of M. officinalis were evaluated for genotypic variation and phenotypic and genotypic correlation for the traits: LS (leaf to stem ratio, SV (spring vigour, LA (leaf area, PH (plant height, DW (herbage dry weight, SD (stem diameter, SN (stem number, Cou (coumarin content, SY (seed yield, across two locations, Yuzhong and Linze, in Western China. There was significant (P<0.05 genotypic variation among the HS families for all traits. There was also significant (P<0.05 genotype-by-environment interaction for the traits DW, PH, SD, SN and SV. The estimates of HS family mean repeatability across two locations ranged from 0.32 for SN to 0.89 for LA. Pattern analysis generated four HS family groups where group 3 consisted of families with above average expression for DW and below average expression for Cou. The breeding population developed by polycrossing the selected HS families within group 3 will provide a significant breeding pool for M. officinalis cultivar development in China.

  3. Selection of mango rosa genotypes in a breeding population using the multivariate-biplot method

    Directory of Open Access Journals (Sweden)

    Maria Clideana Cabral Maia

    Full Text Available ABSTRACT: Mango ( Mangifera indica L. trees stand out among the main fruit trees cultivated in Brazil. The mango rosa fruit is a very popular local variety (landrace, especially because of their superior technological characteristics such as high contents of Vitamin C and soluble solids (SS, as well as attractive taste and color. The objective of this study was to select a breeding population of mango rosa (polyclonal variety; ≥5 individuals that can simultaneously meet the fresh and processed fruit markets, using the multivariate method of principal components and the biplot graphic. The principal components, biplot graphic, and phenotype correlations were obtained using the R (2012 software. Pulp percentage and the pulp, skin, and seed mass variables can be indirectly selected using the smallest fruit diameter, which allowed an easier measurement. The P23R AREA3, P30R AREA3, and P32R AREA3 genotypes are selection candidates due to the presence of alleles, which are important agro-technological traits for mango breeding. This study showed that the biplot analysis is a valuable tool for decision making and visualization of interrelationships between variables and genotypes, facilitating the mango selection process.

  4. Optimization of selection contribution and mate allocations in monoecious tree breeding populations

    Directory of Open Access Journals (Sweden)

    Waldmann Patrik

    2009-11-01

    Full Text Available Abstract Background The combination of optimized contribution dynamic selection and various mating schemes was investigated over seven generations for a typical tree breeding scenario. The allocation of mates was optimized using a simulated annealing algorithm for various object functions including random mating (RM, positive assortative mating (PAM and minimization of pair-wise coancestry between mates (MCM all combined with minimization of variance in family size and coancestry. The present study considered two levels of heritability (0.05 and 0.25, two restrictions on relatedness (group coancestry; 1 and 2% and two maximum permissible numbers of crosses in each generation (100 and 400. The infinitesimal genetic model was used to simulate the genetic architecture of the trait that was the subject of selection. A framework of the long term genetic contribution of ancestors was used to examine the impacts of the mating schemes on population parameters. Results MCM schemes produced on average, an increased rate of genetic gain in the breeding population, although the difference between schemes was small but significant after seven generations (up to 7.1% more than obtained with RM. In addition, MCM reduced the level of inbreeding by as much as 37% compared with RM, although the rate of inbreeding was similar after three generations of selection. PAM schemes yielded levels of genetic gain similar to those produced by RM, but the increase in the level of inbreeding was substantial (up to 43%. Conclusion The main reason why MCM schemes yielded higher genetic gains was the improvement in managing the long term genetic contribution of founders in the population; this was achieved by connecting unrelated families. In addition, the accumulation of inbreeding was reduced by MCM schemes since the variance in long term genetic contributions of founders was smaller than in the other schemes. Consequently, by combining an MCM scheme with an algorithm that

  5. Antral follicles population in heifers and cows of Nelore and Girolando breeds

    Directory of Open Access Journals (Sweden)

    Jair Sábio de Oliveira Junior

    2015-12-01

    Full Text Available The aim of this study was to evaluate ovarian antral follicle populations (OAFP of Nelore and Girolando breed heifers (12–18 months old and cows (24–60 months old. Animals were assigned to four groups: (1 Nelore cows (n = 18, (2 Girolando cows (n = 20, (3 Nelore heifers (n = 7, and (4 Girolando heifers (n = 7. Cows were treated to synchronize follicular wave emergence by implantation of an intravaginal device containing 1.9 g of progesterone, as well as intramuscular administration of 2 mg of estradiol benzoate and 25 mg of dinoprost. This synchronization treatment was administered at a random day of the estrous cycle of each cow, designated D0. Intravaginal devices were removed on D7, and on D11, OAFP counts were performed by transvaginal ovarian ultrasound. For each cow, all follicles ?3 mm in diameter were counted in both ovaries and counts were performed three times at 35-day intervals. Counts were also obtained from heifers, but these animals were not treated for synchronization of follicular wave emergence. Analysis of variance (ANOVA with Tukey’s test and Pearson’s correlation test were used to compare mean OAFPs between counts as well as mean OAFPs between breed and age groups. No differences were observed in mean OAFPs between Nelore and Girolando cows (30.9 vs. 26.7, respectively; P > 0.05 or heifers (16.2 vs. 18.1, respectively; P > 0.05. However, within each breed, there were differences in mean OAFPs between heifers and cows (for Nelore cattle: 16.2 and 30.9, respectively; for Girolando cattle: 18.1 and 26.7, respectively; both P < 0.05. In conclusion, OAFPs were similar between Nelore and Girolando breeds and were influenced by age. Furthermore, we observed a high correlation for individual animals between the mean numbers of follicles counted in both ovaries and total number of follicles counted in either the right or left ovary, indicating that the evaluation of a single ovary is sufficient to estimate the OAFP of an

  6. Autosomal genetic diversity in non-breed horses from eastern Eurasia provides insights into historical population movements.

    Science.gov (United States)

    Warmuth, Vera; Manica, Andrea; Eriksson, Anders; Barker, Graeme; Bower, Mim

    2013-02-01

    Many events in the history of eastern Eurasia, including the process of domestication itself, the initial spread of domestic horses and subsequent movements, are believed to have affected the genetic structure of domestic horse populations in this area. We investigated levels of within- and between-population genetic diversity in 'non-breed horses' (working horses sampled in remote areas) from 17 locations in Asia and parts of Eastern Europe, using 26 autosomal microsatellite loci. Non-breed horses have not been subject to the same intensity of artificial selection and closed breeding as have most breed animals and are thus expected to better reflect the population history of domestic horses. Despite geographic distances of between 300 and 7000 km between sampling locations, pairwise F (ST) was very low (range: horses revealed a pattern of isolation by distance and a significant decline in genetic diversity (expected heterozygosity and allelic richness) from east to west, consistent with a westward expansion of horses out of East Asia. Although the timing of this putative expansion is unclear, our results highlight the benefit of studying animals that do not belong to particular breeds when investigating aspects of a population's history. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

  7. Cross-breeding of Different Geological Populations of Scallop, Chlamys farreri

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Wild populations of Chlamys farreri derived from Japan and China are used as parents in a cross-breeding experiment conducted in Zhangzi Island of Liaoning Province in the early May of 2000. Four different first filial genera tions of the crossbreeding, namely JC,CJ,CC and JJ,which represent different cross combinations of the parents,are differentiated from each other in some obse rved quantitative traits including survival rate, hatchery rate and attachment rate, etc. By ANOVA analysis, significant differences in growth rate are found a mong the four populations of the offspring after one year of culturing in Shando ng Province. JJ population shows the fastest growth rate and has shell height of 46.1±0.71(SD)mm in average, whereas the other three populations,CC,CJ and JC,has the shell height of 43.1±0.42mm, 41.5±0.48mm and 37.2 ±0.31mm,resp ectively. No heterosis is detected in the experiment.

  8. Population recovery following decline in an endangered stream-breeding frog (Mixophyes fleayi from subtropical Australia.

    Directory of Open Access Journals (Sweden)

    David Alan Newell

    Full Text Available Amphibians have undergone dramatic declines and extinctions worldwide. Prominent among these have been the stream-breeding frogs in the rainforests of eastern Australia. The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd has been postulated as the primary cause of these declines. We conducted a capture-mark-recapture study over a 7-year period on the endangered Fleay's barred frog (Mixophyes fleayi at two independent streams (30 km apart in order to assess the stability of these populations. This species had undergone a severe decline across its narrow geographic range. Mark-recapture modelling showed that the number of individuals increased 3-10 fold along stream transects over this period. Frog detection probabilities were frequently above 50% but declined as the populations increased. Adult survival was important to overall population persistence in light of low recruitment events, suggesting that longevity may be a key factor in this recovery. One male and female were present in the capture record for >6 years. This study provides an unambiguous example of population recovery in the presence of Bd.

  9. Variation of cats under domestication: genetic assignment of domestic cats to breeds and worldwide random-bred populations.

    Science.gov (United States)

    Kurushima, J D; Lipinski, M J; Gandolfi, B; Froenicke, L; Grahn, J C; Grahn, R A; Lyons, L A

    2013-06-01

    Both cat breeders and the lay public have interests in the origins of their pets, not only in the genetic identity of the purebred individuals, but also in the historical origins of common household cats. The cat fancy is a relatively new institution with over 85% of its 40-50 breeds arising only in the past 75 years, primarily through selection on single-gene aesthetic traits. The short, yet intense cat breed history poses a significant challenge to the development of a genetic marker-based breed identification strategy. Using different breed assignment strategies and methods, 477 cats representing 29 fancy breeds were analysed with 38 short tandem repeats, 148 intergenic and five phenotypic single nucleotide polymorphisms. Results suggest the frequentist method of Paetkau (single nucleotide polymorphisms = 0.78, short tandem repeats = 0.88) surpasses the Bayesian method of Rannala and Mountain (single nucleotide polymorphisms = 0.56, short tandem repeats = 0.83) for accurate assignment of individuals to the correct breed. Additionally, a post-assignment verification step with the five phenotypic single nucleotide polymorphisms accurately identified between 0.31 and 0.58 of the misassigned individuals raising the sensitivity of assignment with the frequentist method to 0.89 and 0.92 for single nucleotide polymorphisms and short tandem repeats respectively. This study provides a novel multistep assignment strategy and suggests that, despite their short breed history and breed family groupings, a majority of cats can be assigned to their proper breed or population of origin, that is, race.

  10. INVESTIGATION OF ALFALFA LOCAL POPULATIONS FOR CREATION OF NEW BREEDING GERMPLAZM

    Directory of Open Access Journals (Sweden)

    Tihomir Čupić

    2008-12-01

    Full Text Available Yield of dry matter and green mass are important factors in selection of fodder crop cultivars. Low genetic gain was achieved during the long time of fodder crops breeding for yield. Therefore we investigated possibility of using local populations of alfalfa for yield increase with direct and indirect selection. Strong and significant influence of genotypes and environments was recorded for all examined traits and their interactions at the level p<0.01. The highest variability was recorded for green mass yield 48.21%; while the lowest variation was for height 13.18%. High share of genotype variance as well as high heritability were recorded in total variance for the traits number of stem and plant height.

  11. Fidelity and breeding probability related to population density and individual quality in black brent geese Branta bernicla nigricans

    Science.gov (United States)

    Sedinger, J.S.; Chelgren, N.D.; Ward, D.H.; Lindberg, M.S.

    2008-01-01

    1. Patterns of temporary emigration (associated with non-breeding) are important components of variation in individual quality. Permanent emigration from the natal area has important implications for both individual fitness and local population dynamics. 2. We estimated both permanent and temporary emigration of black brent geese (Branta bernicla nigricans Lawrence) from the Tutakoke River colony, using observations of marked brent geese on breeding and wintering areas, and recoveries of ringed individuals by hunters. We used the likelihood developed by Lindberg, Kendall, Hines & Anderson 2001 (Combining band recovery data and Pollock's robust design to model temporary and permanent emigration. Biometrics, 57, 273-281) to assess hypotheses and estimate parameters. 3. Temporary emigration (the converse of breeding) varied among age classes up to age 5, and differed between individuals that bred in the previous years vs. those that did not. Consistent with the hypothesis of variation in individual quality, individuals with a higher probability of breeding in one year also had a higher probability of breeding the next year. 4. Natal fidelity of females ranged from 0.70 ?? 0.07-0.96 ?? 0.18 and averaged 0.83. In contrast to Lindberg et al. (1998), we did not detect a relationship between fidelity and local population density. Natal fidelity was negatively correlated with first-year survival, suggesting that competition among individuals of the same age for breeding territories influenced dispersal. Once females nested at the Tutakoke River, colony breeding fidelity was 1.0. 5. Our analyses show substantial variation in individual quality associated with fitness, which other analyses suggest is strongly influenced by early environment. Our analyses also suggest substantial interchange among breeding colonies of brent geese, as first shown by Lindberg et al. (1998).

  12. Genetic Variability and Population Structure of Salvia lachnostachys: Implications for Breeding and Conservation Programs

    Directory of Open Access Journals (Sweden)

    Marianna Erbano

    2015-04-01

    Full Text Available The genetic diversity and population structure of Salvia lachnostachys Benth were assessed. Inter Simple Sequence Repeat (ISSR molecular markers were used to investigate the restricted distribution of S. lachnostachys in Parana State, Brazil. Leaves of 73 individuals representing three populations were collected. DNA was extracted and submitted to PCR-ISSR amplification with nine tested primers. Genetic diversity parameters were evaluated. Our analysis indicated 95.6% polymorphic loci (stress value 0.02 with a 0.79 average Simpson’s index. The Nei-Li distance dendrogram and principal component analysis largely recovered the geographical origin of each sample. Four major clusters were recognized representing each collected population. Nei’s gene diversity and Shannon’s information index were 0.25 and 0.40 respectively. As is typical for outcrossing herbs, the majority of genetic variation occurred at the population level (81.76%. A high gene flow (Nm = 2.48 was observed with a correspondingly low fixation index. These values were generally similar to previous studies on congeneric species. The results of principal coordinate analysis (PCA and of arithmetic average (UPGMA were consistent and all three populations appear distinct as in STRUCTURE analysis. In addition, this analysis indicated a majority intrapopulation genetic variation. Despite the human pressure on natural populations our study found high levels of genetic diversity for S. lachnostachys. This was the first molecular assessment for this endemic species with medicinal proprieties and the results can guide for subsequent bioprospection, breeding programs or conservation actions.

  13. Post-fragmentation population structure in a cooperative breeding Afrotropical cloud forest bird: emergence of a source-sink population network.

    Science.gov (United States)

    Husemann, M; Cousseau, L; Callens, T; Matthysen, E; Vangestel, C; Hallmann, C; Lens, L

    2015-03-01

    The impact of demographic parameters on the genetic population structure and viability of organisms is a long-standing issue in the study of fragmented populations. Demographic and genetic tools are now readily available to estimate census and effective population sizes and migration and gene flow rates with increasing precision. Here we analysed the demography and genetic population structure over a recent 15-year time span in five remnant populations of Cabanis's greenbul (Phyllastrephus cabanisi), a cooperative breeding bird in a severely fragmented cloud forest habitat. Contrary to our expectation, genetic admixture and effective population sizes slightly increased, rather than decreased between our two sampling periods. In spite of small effective population sizes in tiny forest remnants, none of the populations showed evidence of a recent population bottleneck. Approximate Bayesian modelling, however, suggested that differentiation of the populations coincided at least partially with an episode of habitat fragmentation. The ratio of meta-Ne to meta-Nc was relatively low for birds, which is expected for cooperative breeding species, while Ne /Nc ratios strongly varied among local populations. While the overall trend of increasing population sizes and genetic admixture may suggest that Cabanis's greenbuls increasingly cope with fragmentation, the time period over which these trends were documented is rather short relative to the average longevity of tropical species. Furthermore, the critically low Nc in the small forest remnants keep the species prone to demographic and environmental stochasticity, and it remains open if, and to what extent, its cooperative breeding behaviour helps to buffer such effects.

  14. Influence of model specifications on the reliabilities of genomic prediction in a Swedish-Finnish red breed cattle population

    DEFF Research Database (Denmark)

    Rius-Vilarrasa, E; Strandberg, E; Fikse, W F

    2012-01-01

    Using a combined multi-breed reference population, this study explored the influence of model specification and the effect of including a polygenic effect on the reliability of genomic breeding values (DGV and GEBV). The combined reference population consisted of 2986 Swedish Red Breed (SRB...... effects. The influence of the inclusion of a polygenic effect on the reliability of DGV varied across traits and model specifications. Average correlation between DGV with the Mendelian sampling term, across traits, was highest (R =0.25) for the GBLUP model and decreased with increasing proportion...... of markers with large effects. Reliabilities increased when DGV and parent average information were combined in an index. The GBLUP model with the largest gain across traits in the reliability of the index achieved the highest DGV mean reliability. However, the polygenic models showed to be less biased...

  15. Adaptation of Musca domestica L. field population to laboratory breeding causes transcriptional alterations.

    Directory of Open Access Journals (Sweden)

    Dorte H Højland

    Full Text Available BACKGROUND: The housefly, Musca domestica, has developed resistance to most insecticides applied for its control. Expression of genes coding for detoxification enzymes play a role in the response of the housefly when encountered by a xenobiotic. The highest level of constitutive gene expression of nine P450 genes was previously found in a newly-collected susceptible field population in comparison to three insecticide-resistant laboratory strains and a laboratory reference strain. RESULTS: We compared gene expression of five P450s by qPCR as well as global gene expression by RNAseq in the newly-acquired field population (845b in generation F1, F13 and F29 to test how gene expression changes following laboratory adaption. Four (CYP6A1, CYP6A36, CYP6D3, CYP6G4 of five investigated P450 genes adapted to breeding by decreasing expression. CYP6D1 showed higher female expression in F29 than in F1. For males, about half of the genes accessed in the global gene expression were up-regulated in F13 and F29 in comparison with the F1 population. In females, 60% of the genes were up-regulated in F13 in comparison with F1, while 33% were up-regulated in F29. Forty potential P450 genes were identified. In most cases, P450 gene expression was decreased in F13 flies in comparison with F1. Gene expression then increased from F13 to F29 in males and decreased further in females. CONCLUSION: The global gene expression changes massively during adaptation to laboratory breeding. In general, global expression decreased as a result of laboratory adaption in males, while female expression was not unidirectional. Expression of P450 genes was in general down-regulated as a result of laboratory adaption. Expression of hexamerin, coding for a storage protein was increased, while gene expression of genes coding for amylases decreased. This suggests a major impact of the surrounding environment on gene response to xenobiotics and genetic composition of housefly strains.

  16. Survival of Coelaenomenodera lameensis (Coleoptera: Chrysomelidae) in Relation to the Physical Characteristics of Different Oil Palm (Elaeis sp.) Breeding Populations.

    Science.gov (United States)

    Beaudoin-Ollivier, L; Flori, A; Coffi, A; Cros, D; Glitho, I; Nodichao, L

    2015-01-01

    The edibility of different Elaeis sp. breeding populations present in Benin was tested for the leaf miner Coelaenomenodera lameensis Berti (Coleoptera: Chrysomelidae), a major oil palm pest in Africa. Experiments carried out in sleeves revealed the oviposition capacities of females and the mortality rates for the different developmental stages by comparing the populations found on two breeding populations of Elaeis oleifera (HBK) Cortes, four of Elaeis guineensis Jacquin and four (E. guineensis × E. oleifera) × E. guineensis backcrosses. Females laid their eggs similarly on all breeding populations, with a preference for the E. guineensis La Mé origin. The average hatching rate reached 80% for the La Mé origin as opposed to 28% for the Deli origin. The mortality rates for the larval instars were greater on E. oleifera, on certain backcrosses and on the Deli origin of E. guineensis. Development at the second- and third- larval instars was the most affected, with a mortality rate of three to five times greater than that seen on La Mé. Epidermis and cuticle measurements indicated which breeding populations were suitable or unsuitable for the development of C. lameensis. E. guineensis, with its thin epidermis (12 µm) and cuticle (2 µm), proved to be highly susceptible to C. lameensis attacks. On the other hand, E. oleifera, which is very resistant, exhibited a thicker epidermis (17 µm) and cuticle (4 µm). The breeding populations were thus classified according to the positive or negative influence they exerted on the insect's egg laying and feeding. © The Author 2015. Published by Oxford University Press on behalf of the Entomological Society of America.

  17. Breeding Status and Population Trends of Golden Eagles in Northeastern Québec, Canada

    Directory of Open Access Journals (Sweden)

    Junior A. Tremblay

    2012-12-01

    Full Text Available In North America, it is hypothesized that the Golden Eagle's (Aquila chrysaetos eastern population declined during the period 1946-1973 because of organochlorine pesticides and other anthropogenic causes of mortality. Since 1970, upward trends for the species have been observed at most eastern hawkwatches. To determine whether such positive trends can be observed on breeding grounds, Golden Eagle counts were performed to monitor nesting territory occupancy between 1994 and 2007 in the Moisie and Sainte-Marguerite River valleys, northeastern Québec. Aerial surveys were conducted during seven of the 14 years. During this period, the number of known nesting territories in the study area increased from 10 to 20, while the number of pairs rose from six to 14. The increase is attributed mostly to investigators' improved experience in finding nests and to their greater familiarity with the study area, and possibly to the growth of the regional population. Occupancy of nesting territories by pairs was very stable over the years. Annual mean % of laying pairs (or laying rate was 48.0 (SD = 19.9, and productivity (mean number of fledglings per pair was 0.49 (SD = 0.35.

  18. An effective rotational mating scheme for inbreeding reduction in captive populations illustrated by the rare sheep breed

    NARCIS (Netherlands)

    Windig, J.J.; Lansbergen, L.M.T.E.

    2008-01-01

    Within breeds and other captive populations, the risk of high inbreeding rates and loss of diversity can be high within (small) herds or subpopulations. When exchange of animals between different subpopulations is organised according to a rotational mating scheme, inbreeding rates can be restricted.

  19. Integrating Breeding Bird Survey and demographic data to estimate Wood Duck population size in the Atlantic Flyway

    Science.gov (United States)

    Zimmerman, Guthrie S.; Sauer, John; Boomer, G. Scott; Devers, Patrick K.; Garrettson, Pamela R.

    2017-01-01

    The U.S. Fish and Wildlife Service (USFWS) uses data from the North American Breeding Bird Survey (BBS) to assist in monitoring and management of some migratory birds. However, BBS analyses provide indices of population change rather than estimates of population size, precluding their use in developing abundance-based objectives and limiting applicability to harvest management. Wood Ducks (Aix sponsa) are important harvested birds in the Atlantic Flyway (AF) that are difficult to detect during aerial surveys because they prefer forested habitat. We integrated Wood Duck count data from a ground-plot survey in the northeastern U.S. with AF-wide BBS, banding, parts collection, and harvest data to derive estimates of population size for the AF. Overlapping results between the smaller-scale intensive ground-plot survey and the BBS in the northeastern U.S. provided a means for scaling BBS indices to the breeding population size estimates. We applied these scaling factors to BBS results for portions of the AF lacking intensive surveys. Banding data provided estimates of annual survival and harvest rates; the latter, when combined with parts-collection data, provided estimates of recruitment. We used the harvest data to estimate fall population size. Our estimates of breeding population size and variability from the integrated population model (N̄ = 0.99 million, SD = 0.04) were similar to estimates of breeding population size based solely on data from the AF ground-plot surveys and the BBS (N̄ = 1.01 million, SD = 0.04) from 1998 to 2015. Integrating BBS data with other data provided reliable population size estimates for Wood Ducks at a scale useful for harvest and habitat management in the AF, and allowed us to derive estimates of important demographic parameters (e.g., seasonal survival rates, sex ratio) that were not directly informed by data.

  20. Structure of Allozymatic Diversity of Ten Temperate and Adapted Exotic Breeding Populations of Maize (Zea mays L.)

    Institute of Scientific and Technical Information of China (English)

    ZHENG Da-hao; YU Yang; WANG Zhen-ping; LI Yan-ru

    2009-01-01

    Ten temperate and adapted exotic breeding populations of maize were studied with electrophoretic techniques. Three isozyme systems coded by nine allozyme loci were used for evaluating the genetic variability within and among populations.The results revealed that 78.57% of allozyme loci were polymorphic. Low allelic variation with a mean number of 1.84 alleles per locus per population was detected. But, these populations still maintained higher level of heterozygosity;moreover, the exotic populations had greater gene diversity than the temperate populations. All the populations were non-panmictic with negative Wright's fixation indexes (-0.091- -0.424). The tropical BS16 was typified by maximum allelic richness, percent of polymorphic loci and heterozygosity. More than 93% of the gene diversity maintained within populations, and the genetic differentiation among populations was low (0.002-0.191). Multivariate analysis demonstrated that the tropical BS29 diverged from other populations in the reverse direction. The temperate BS9 and tropical BS 16 were divergent each other, and highly differentiated from other temperate and tropical populations, consequently, these two populations would be analogically postulated as potential germplasms to establish new heterotic groups for temperate maize breeding programs.

  1. Effective population size, extended linkage disequilibrium and signatures of selection in the rare dog breed lundehund.

    Directory of Open Access Journals (Sweden)

    Sophia Pfahler

    Full Text Available The Lundehund is an old dog breed with remarkable anatomical features including polydactyly in all four limbs and extraordinary flexibility of the spine. We genotyped 28 Lundehund using the canine Illumina high density beadchip to estimate the effective population size (Ne and inbreeding coefficients as well as to identify potential regions of positive selection. The decay of linkage disequilibrium was slow with r2 = 0.95 in 50 kb distance. The last 7-200 generations ago, Ne was at 10-13. An increase of Ne was noted in the very recent generations with a peak value of 19 for Ne at generation 4. The FROH estimated for 50-, 65- and 358-SNP windows were 0.87, 087 and 0.81, respectively. The most likely estimates for FROH after removing identical-by-state segments due to linkage disequilibria were at 0.80-0.81. The extreme loss of heterozygosity has been accumulated through continued inbreeding over 200 generations within a probably closed population with a small effective population size. The mean inbreeding coefficient based on pedigree data for the last 11 generations (FPed = 0.10 was strongly biased downwards due to the unknown coancestry of the founders in this pedigree data. The long-range haplotype test identified regions with genes involved in processes of immunity, olfaction, woundhealing and neuronal development as potential targets of selection. The genes QSOX2, BMPR1B and PRRX2 as well as MYOM1 are candidates for selection on the Lundehund characteristics small body size, increased number of digits per paw and extraordinary mobility, respectively.

  2. Breeding biology and variable mating system of a population of introduced dunnocks (Prunella modularis in New Zealand.

    Directory of Open Access Journals (Sweden)

    Eduardo S A Santos

    Full Text Available Species with variable mating systems provide a unique opportunity to investigate whether females receive direct fitness benefits from additional male partners. The direct benefits provide an obvious explanation for why females would breed polyandrously, in a situation where males clearly do not attain their optimal reproductive success. Evidence for these direct benefits is, however, mixed. Here, we present a detailed study of the breeding biology of the dunnock, Prunella modularis, which inform an investigation into the effects of the social mating system on the reproductive success in a population of dunnocks in Southern New Zealand. We studied 80 different social groups over the course of three breeding seasons. Dunnocks in our population presented a variable mating system, with socially monogamous (45%, socially polyandrous (54% and socially polygynandrous (1% groups being observed in the same breeding season. We did not observe any polygynous social units in our study period although polygyny exists in the population. We found little difference in the numbers of eggs laid, and egg volume between monogamous and polyandrous nests. However, polyandrous groups had better hatching and fledging success than monogamous groups (composite d = 0.385, 95% CI: 0.307 to 0.463. Overall our results support the notion that polyandry is beneficial for females.

  3. Diet specialization in a generalist population: the case of breeding great tits Parus major in the Mediterranean area.

    Science.gov (United States)

    Pagani-Núñez, E; Valls, M; Senar, J C

    2015-11-01

    The analysis of diet specialization provides key information on how different individuals deal with similar food and habitat constraints within populations. Characterizing parental diet specialization at the moment of breeding, and the consistency of these preferences under different levels of effort, may help us to understand why parents exploit alternative resources. We investigated these questions in a species commonly considered a generalist: a breeding population of Mediterranean great tits Parus major. Our aim was to determine whether they are specialists or generalists at the pair level, and the consistency of this behaviour under different levels of effort. Using proportional similarity and mean pairwise overlap indices, we found that parents showed great variability in prey selection between territories. That is, they displayed a small niche overlap. Interestingly, the most specialized breeding pairs showed a tendency to have larger broods. Additionally, we experimentally manipulated brood size and found that parents showed high short-term consistency in their foraging behaviour. They precisely adjusted the number of provisioning trips to the number of nestlings, while they were unable to modify prey proportions or prey size after brood size was changed. We can therefore characterize their foraging strategies as highly consistent. Our results suggest that although the great tit may be considered a generalist at the species or population level, there was a tendency for trophic specialization among breeding pairs. This high inter- and intrapopulation plasticity could account for their great success and wide distribution.

  4. Variation in phenotypic plasticity and selection patterns in blue tit breeding time: between- and within-population comparisons.

    Science.gov (United States)

    Porlier, Melody; Charmantier, Anne; Bourgault, Patrice; Perret, Philippe; Blondel, Jacques; Garant, Dany

    2012-09-01

    1. Phenotypic plasticity, the response of individual phenotypes to their environment, can allow organisms to cope with spatio-temporal variation in environmental conditions. Recent studies have shown that variation exists among individuals in their capacity to adjust their traits to environmental changes and that this individual plasticity can be under strong selection. Yet, little is known on the extent and ultimate causes of variation between populations and individuals in plasticity patterns. 2. In passerines, timing of breeding is a key life-history trait strongly related to fitness and is known to vary with the environment, but few studies have investigated the within-species variation in individual plasticity. 3. Here, we studied between- and within-population variation in breeding time, phenotypic plasticity and selection patterns for this trait in four Mediterranean populations of blue tits (Cyanistes caeruleus) breeding in habitats varying in structure and quality. 4. Although there was no significant warming over the course of the study, we found evidence for earlier onset of breeding in warmer years in all populations, with reduced plasticity in the less predictable environment. In two of four populations, there was significant inter-individual variation in plasticity for laying date. Interestingly, selection for earlier laying date was significant only in populations where there was no inter-individual differences in plasticity. 5. Our results show that generalization of plasticity patterns among populations of the same species might be challenging even at a small spatial scale and that the amount of within-individual variation in phenotypic plasticity may be linked to selective pressures acting on these phenotypic traits.

  5. Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

    Directory of Open Access Journals (Sweden)

    Rangel-Figueiredo Teresa

    2010-06-01

    Full Text Available Abstract Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95. With breed information, 30 cows and three bulls were identified (q > 0.95 that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10 relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P st = 0.028, P > 0.05. Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50 to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions Molecular analyses complemented previous morphological findings to identify 33 animals that

  6. Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

    Science.gov (United States)

    2010-01-01

    Background Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed. Methods 46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA) were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity. Results Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95). With breed information, 30 cows and three bulls were identified (q > 0.95) that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10) relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P 0.05). Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50) to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity. Conclusions Molecular analyses complemented previous morphological findings to identify 33 animals that can be considered remnants of the

  7. Breeding ecology of the southern shrike, Lanius meridionalis, in an agrosystem of south–eastern Spain: the surprisingly excellent breeding success in a declining population

    Energy Technology Data Exchange (ETDEWEB)

    Moreno-Rueda, G.; Abril-Colon, I.; Lopez-Orta, A.; Alvarez-Benito, I.; Castillo-Gomez, C.; Comas, M.; Rivas, J.M.

    2016-07-01

    The southern shrike, Lanius meridionalis, is declining at the Spanish and European level. One cause of this decline could be low reproductive success due to low availability of prey in agricultural environments. To investigate this possibility we analysed the breeding ecology of a population of southern shrike in an agrosystem in Lomas de Padul (SE Spain). Our results suggest the population is declining in this area. However, contrary to expectations, the population showed the highest reproductive success (% nests in which at least one egg produces a fledgling) reported for this species to date (83.3%), with a productivity of 4.04 fledglings per nest. Reproductive success varied throughout the years, ranging from 75% in the worst year to 92.9% in the best year. Similarly, productivity ranged from 3.25 to 5.0 fledglings per nest depending on the year. Other aspects of reproductive biology, such as clutch size, brood size, and nestling diet, were similar to those reported in other studies. Based on these results, we hypothesise that the determinant of population decline acts on the juvenile fraction, drastically reducing the recruitment rate, or affecting the dispersion of adults and recruits. Nevertheless, the exact factor or factors are unknown. This study shows that a high reproductive success does not guarantee good health status of the population. (Author)

  8. Quantitative genetics theory for genomic selection and efficiency of breeding value prediction in open-pollinated populations

    Directory of Open Access Journals (Sweden)

    José Marcelo Soriano Viana

    2016-06-01

    Full Text Available ABSTRACT To date, the quantitative genetics theory for genomic selection has focused mainly on the relationship between marker and additive variances assuming one marker and one quantitative trait locus (QTL. This study extends the quantitative genetics theory to genomic selection in order to prove that prediction of breeding values based on thousands of single nucleotide polymorphisms (SNPs depends on linkage disequilibrium (LD between markers and QTLs, assuming dominance. We also assessed the efficiency of genomic selection in relation to phenotypic selection, assuming mass selection in an open-pollinated population, all QTLs of lower effect, and reduced sample size, based on simulated data. We show that the average effect of a SNP substitution is proportional to LD measure and to average effect of a gene substitution for each QTL that is in LD with the marker. Weighted (by SNP frequencies and unweighted breeding value predictors have the same accuracy. Efficiency of genomic selection in relation to phenotypic selection is inversely proportional to heritability. Accuracy of breeding value prediction is not affected by the dominance degree and the method of analysis, however, it is influenced by LD extent and magnitude of additive variance. The increase in the number of markers asymptotically improved accuracy of breeding value prediction. The decrease in the sample size from 500 to 200 did not reduce considerably accuracy of breeding value prediction.

  9. Chronic lack of breeding by Galápagos Blue-footed Boobies and associated population decline

    Directory of Open Access Journals (Sweden)

    David Anchundia

    2014-06-01

    Full Text Available A survey of Blue-footed Boobies (Sula nebouxii excisa throughout the taxon's range in Galápagos, Ecuador found ~6400 adults, compared to a rough estimate of 20,000 in the 1960s. Few pairs bred in 2011-2013 and almost no birds in juvenile plumage were seen. Long-term data suggest that poor breeding began in 1998. Lack of recruitment over this period would mean that the current population is mostly elderly and experiencing senescent decline in performance. Anthropogenic effects such as introduced predators are unlikely to explain this decline because islands with and without such factors exhibited the same low breeding. The poor reproduction seems to be linked to diet. Previous work indicated that sardine and herring (Clupeidae supported successful breeding, but these fish were mostly absent from the diet during this study, except in the central part of Galápagos, where most breeding attempts during this study occurred. Elsewhere in the eastern Pacific sardine abundance has decreased dramatically by natural processes in the last 15 years, as part of a well-documented and apparently natural cycle. This cyclic change in abundance provides a possible explanation for the recent demographic changes in Blue-footed Boobies in Galápagos. Whether natural or anthropogenic in origin, the implications of senescent decline in breeding ability and survival are dramatic for this genetically distinct icon of biodiversity and ecotourism.

  10. Genetic shift in local rice populations during rice breeding programs in the northern limit of rice cultivation in the world.

    Science.gov (United States)

    Fujino, Kenji; Obara, Mari; Ikegaya, Tomohito; Tamura, Kenichi

    2015-09-01

    The rapid accumulation of pre-existing mutations may play major roles in the establishment and shaping of adaptability for local regions in current rice breeding programs. The cultivated rice, Oryza sativa L., which originated from tropical regions, is now grown worldwide due to the concerted efforts of breeding programs. However, the process of establishing local populations and their origins remain unclear. In the present study, we characterized DNA polymorphisms in the rice variety KITAAKE from Hokkaido, one of the northern limits of rice cultivation in the world. Indel polymorphisms were attributed to transposable element-like insertions, tandem duplications, and non-TE deletions as the original mutation events in the NIPPONBARE and KITAAKE genomes. The allele frequencies of the KITAAKE alleles markedly shifted to the current variety types among the local population from Hokkaido in the last two decades. The KITAAKE alleles widely distributed throughout wild rice and cultivated rice over the world. These have accumulated in the local population from Hokkaido via Japanese landraces as the ancestral population of Hokkaido. These results strongly suggested that combinations of pre-existing mutations played a role in the establishment of adaptability. This approach using the re-sequencing of local varieties in unique environmental conditions will be useful as a genetic resource in plant breeding programs in local regions.

  11. Unravelling the annual cycle in a migratory animal: breeding-season habitat loss drives population declines of monarch butterflies.

    Science.gov (United States)

    Flockhart, D T Tyler; Pichancourt, Jean-Baptiste; Norris, D Ryan; Martin, Tara G

    2015-01-01

    Threats to migratory animals can occur at multiple periods of the annual cycle that are separated by thousands of kilometres and span international borders. Populations of the iconic monarch butterfly (Danaus plexippus) of eastern North America have declined over the last 21 years. Three hypotheses have been posed to explain the decline: habitat loss on the overwintering grounds in Mexico, habitat loss on the breeding grounds in the United States and Canada, and extreme weather events. Our objectives were to assess population viability, determine which life stage, season and geographical region are contributing the most to population dynamics and test the three hypotheses that explain the observed population decline. We developed a spatially structured, stochastic and density-dependent periodic projection matrix model that integrates patterns of migratory connectivity and demographic vital rates across the annual cycle. We used perturbation analysis to determine the sensitivity of population abundance to changes in vital rate among life stages, seasons and geographical regions. Next, we compared the singular effects of each threat to the full model where all factors operate concurrently. Finally, we generated predictions to assess the risk of host plant loss as a result of genetically modified crops on current and future monarch butterfly population size and extinction probability. Our year-round population model predicted population declines of 14% and a quasi-extinction probability (5% within a century. Monarch abundance was more than four times more sensitive to perturbations of vital rates on the breeding grounds than on the wintering grounds. Simulations that considered only forest loss or climate change in Mexico predicted higher population sizes compared to milkweed declines on the breeding grounds. Our model predictions also suggest that mitigating the negative effects of genetically modified crops results in higher population size and lower extinction

  12. Breeding Bird Populations at Selected Sites on Tewaukon National Wildlife Refuge Complex : 2002

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes breeding bird surveys that were conducted on Tewaukon National Wildlife Refuge in June and July of 2002. Eleven study plots were established...

  13. Breeding status, population trends and diets of seabirds in Alaska, 2008

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report is the thirteenth in a series of annual reports summarizing the results of seabird monitoring efforts at breeding colonies on the Alaska Maritime...

  14. Breeding Bird Populations at Selected Sites on Tewaukon National Wildlife Refuge Complex : 2001

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes breeding bird surveys that were conducted on Tewaukon National Wildlife Refuge in June of 2001. Eleven study plots were established and...

  15. Genome-wide association mapping of quantitative traits in a breeding population of sugarcane.

    Science.gov (United States)

    Racedo, Josefina; Gutiérrez, Lucía; Perera, María Francisca; Ostengo, Santiago; Pardo, Esteban Mariano; Cuenya, María Inés; Welin, Bjorn; Castagnaro, Atilio Pedro

    2016-06-24

    Molecular markers associated with relevant agronomic traits could significantly reduce the time and cost involved in developing new sugarcane varieties. Previous sugarcane genome-wide association analyses (GWAS) have found few molecular markers associated with relevant traits at plant-cane stage. The aim of this study was to establish an appropriate GWAS to find molecular markers associated with yield related traits consistent across harvesting seasons in a breeding population. Sugarcane clones were genotyped with DArT (Diversity Array Technology) and TRAP (Target Region Amplified Polymorphism) markers, and evaluated for cane yield (CY) and sugar content (SC) at two locations during three successive crop cycles. GWAS mapping was applied within a novel mixed-model framework accounting for population structure with Principal Component Analysis scores as random component. A total of 43 markers significantly associated with CY in plant-cane, 42 in first ratoon, and 41 in second ratoon were detected. Out of these markers, 20 were associated with CY in 2 years. Additionally, 38 significant associations for SC were detected in plant-cane, 34 in first ratoon, and 47 in second ratoon. For SC, one marker-trait association was found significant for the 3 years of the study, while twelve markers presented association for 2 years. In the multi-QTL model several markers with large allelic substitution effect were found. Sequences of four DArT markers showed high similitude and e-value with coding sequences of Sorghum bicolor, confirming the high gene microlinearity between sorghum and sugarcane. In contrast with other sugarcane GWAS studies reported earlier, the novel methodology to analyze multi-QTLs through successive crop cycles used in the present study allowed us to find several markers associated with relevant traits. Combining existing phenotypic trial data and genotypic DArT and TRAP marker characterizations within a GWAS approach including population structure as

  16. Genome-wide association mapping for yield and other agronomic traits in an elite breeding population of tropical rice (Oryza sativa).

    Science.gov (United States)

    Begum, Hasina; Spindel, Jennifer E; Lalusin, Antonio; Borromeo, Teresita; Gregorio, Glenn; Hernandez, Jose; Virk, Parminder; Collard, Bertrand; McCouch, Susan R

    2015-01-01

    Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

  17. Breed effects and genetic parameter estimates for calving difficulty and birth weight in a multibreed population.

    Science.gov (United States)

    Ahlberg, C M; Kuehn, L A; Thallman, R M; Kachman, S D; Snelling, W M; Spangler, M L

    2016-05-01

    Birth weight (BWT) and calving difficulty (CD) were recorded on 4,579 first-parity females from the Germplasm Evaluation Program at the U.S. Meat Animal Research Center (USMARC). Both traits were analyzed using a bivariate animal model with direct and maternal effects. Calving difficulty was transformed from the USMARC scores to corresponding -scores from the standard normal distribution based on the incidence rate of the USMARC scores. Breed fraction covariates were included to estimate breed differences. Heritability estimates (SE) for BWT direct, CD direct, BWT maternal, and CD maternal were 0.34 (0.10), 0.29 (0.10), 0.15 (0.08), and 0.13 (0.08), respectively. Calving difficulty direct breed effects deviated from Angus ranged from -0.13 to 0.77 and maternal breed effects deviated from Angus ranged from -0.27 to 0.36. Hereford-, Angus-, Gelbvieh-, and Brangus-sired calves would be the least likely to require assistance at birth, whereas Chiangus-, Charolais-, and Limousin-sired calves would be the most likely to require assistance at birth. Maternal breed effects for CD were least for Simmental and Charolais and greatest for Red Angus and Chiangus. Results showed that the diverse biological types of cattle have different effects on both BWT and CD. Furthermore, results provide a mechanism whereby beef cattle producers can compare EBV for CD direct and maternal arising from disjoined and breed-specific genetic evaluations.

  18. Biochemical evaluation of triploid progenies of diploid × tetraploid breeding populations of Camellia for genotypes rich in catechin and caffeine.

    Science.gov (United States)

    Das, Sourabh Kumar; Sabhapondit, Santanu; Ahmed, Giasuddin; Das, Sudripta

    2013-06-01

    To verify the quality of triploid varieties of Camellia tea species at the secondary metabolite level, we tested caffeine and catechin profiles of 97 F(1) segregating progenies in two breeding populations with a common tetraploid parent and diploid parents of two geographic and varietal origins. Catechin and caffeine levels of the triploid progenies were quantified and compared against their diploid parent. Some of the progenies showed better performance than their diploid parent. Most of the progenies of the diploid C. sinensis × tetraploid cross showed heterosis for caffeine and EGCG. Progenies of the C. assamica subsp. lasiocalyx × tetraploid cross showed heterosis for +C, EC, EGC, and TC. The genomic contributions of the diploid parent seem to be the main factor in the variation between the two populations. Our studies showed quantitative enhancement of some of the quality-related parameters in tea, providing a platform to refocus on this classical breeding approach for developing quality cultivars in tea.

  19. The phenology of a rare salamander (Salamandra infraimmaculata in a population breeding under unpredictable ambient conditions: a 25 year study

    Directory of Open Access Journals (Sweden)

    Michael R. Warburg

    2007-11-01

    Full Text Available This is a long-term study (1974-1999 on the phenology of the rare, xeric- inhabiting salamander Salamandra infraimmaculata in a small isolated population during the breeding season near the breeding ponds on Mt. Carmel. This is a fringe area of the genus’ south-easternmost Palaearctic distribution. Salamanders were captured during the 25 year long study. The first years up to the 1980s the total number of salamanders increased but during the last years there seems to have been a decline. Although this could be a phase in normal population cyclic oscillations nevertheless when compared with long-term data on a European Salamandra it does not seem so. The interpretation of the species’ status is dependent on numbers of salamanders captured as well as on the duration of the study. These subjects are reviewed and discussed in this paper.

  20. Presence of persistent organic pollutants in a breeding common tern (Sterna hirundo) population in Ireland.

    Science.gov (United States)

    Acampora, Heidi; White, Philip; Lyashevska, Olga; O'Connor, Ian

    2017-05-01

    Persistent organic pollutants (POPs) are chemical compounds of environmental concern due to their toxic, persistent nature and their ability to bio-accumulate in biological tissue. Seabirds, for often being at the top of the food web, have been used as monitors of environmental pollutants. Adverse effects caused by POPs have been reported in common terns (Sterna hirundo) since the 1970s. Egg shell thinning, embryo and hatchling deformities have been reported for this species. Environmental legislation, such as the Oslo-Paris Convention (OSPAR), has agreed on the monitoring of concentration of POPs in common terns. This study set out to investigate contemporary concentrations of polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides (OCPs) and brominated flame retardants (BFRs) in common terns breeding in Ireland, along with congener profiles. Investigation was conducted in live (n = 15) and dead birds (n = 20) to test for the efficiency of different methodologies using preen oil and feathers versus liver and preen gland. Mean concentrations of POPs followed the order: PCB (36.48 ng/g ww feather) > PAH (30.01 ng/g ww feather) > OCP (13.36 ng/g ww feather) > BFR (1.98 ng/g ww feather) in live birds; and PAH (46.65 ng/g ww preen gland) > PCB (44.11 ng/g ww preen gland) > OCP (15.15 ng/g ww liver) > BFR (5.07 ng/g ww liver) in dead birds. Comparison of contaminant results with toxicity pre-established levels concluded that this population of common terns in Ireland is not at risk of anomalies caused by POPs. However, some levels are higher in comparison to the ones established by OSPAR's EcoQO and must be monitored periodically.

  1. Effect of predictor traits on accuracy of genomic breeding values for feed intake based on a limited cow reference population.

    Science.gov (United States)

    Pszczola, M; Veerkamp, R F; de Haas, Y; Wall, E; Strabel, T; Calus, M P L

    2013-11-01

    pedigree, and 0.63 for CV and 0.61 for PEV in genomic analyses). Recording predictor traits for only the reference population did not increase DMI breeding value accuracy. Recording predictor traits for both reference and evaluated animals significantly increased DMI breeding value accuracy and removed the bias observed when only reference animals had records. The benefit of using genomic instead of pedigree relationships was reduced when more predictor traits were used. Using predictor traits may be an inexpensive way to significantly increase the accuracy and remove the bias of (genomic) breeding values of scarcely recorded traits such as feed intake.

  2. Aspen Delineation - Aspen Delineation Project [ds362

    Data.gov (United States)

    California Department of Resources — The database represents delineations of aspen stands, where aspen assessment data was gathered. Aspen assessment information corresponding to this polygon layer can...

  3. Public availability of a genotyped, segregating population may foster marker assisted breeding (MAB) and quantitative trait loci (QTL) discovery: An example using strawberry

    Science.gov (United States)

    Much of the cost associated with marker discovery for marker assisted breeding (MAB) can be eliminated if a diverse, segregating population is generated, genotyped and made available to the global breeding community. Herein, we present an example of a hybrid, wild-derived family of the octoploid str...

  4. Effects of breeding versus winter habitat loss and fragmentation on the population dynamics of a migratory songbird.

    Science.gov (United States)

    Taylor, Caz M; Stutchbury, Bridget J M

    2016-03-01

    Many migratory species are in decline and understanding these declines is challenging because individuals occupy widely divergent and geographically distant habitats during a single year and therefore populations across the range are interconnected in complex ways. Network modeling has been used to show, theoretically, that shifts in migratory connectivity patterns can occur in response to habitat or climate changes and that habitat loss in one region can affect sub-populations in regions that are not directly connected. Here, we use a network model, parameterized by integrating long-term monitoring data with direct tracking of -100 individuals, to explain population trends in the rapidly declining Wood Thrush (Hylocichla mustelina) and to predict future trends. Our model suggests that species-level declines in Wood Thrush are driven primarily by tropical deforestation in Central America but that protection of breeding habitat in some regions is necessary to prevent shifts in migratory connectivity and to sustain populations in all breeding regions. The model illustrates how shifts in migratory connectivity may lead to unexpected population declines in key regions. We highlight current knowledge gaps that make modeling full life-cycle population demographics in migratory species challenging but also demonstrate that modeling can inform conservation while these gaps are being filled.

  5. Spatial genetic structure of Long-tailed Ducks (Clangula hyemalis) among Alaskan, Canadian, and Russian breeding populations

    Science.gov (United States)

    Wilson, Robert E.; Gust, J R; Petersen, Margaret; Talbot, Sandra

    2016-01-01

    Arctic ecosystems are changing at an unprecedented rate. How Arctic species are able to respond to such environmental change is partially dependent on the connections between local and broadly distributed populations. For species like the Long-tailed Duck (Clangula hyemalis), we have limited telemetry and band-recovery information from which to infer population structure and migratory connectivity; however, genetic analyses can offer additional insights. To examine population structure in the Long-tailed Duck, we characterized variation at mtDNA control region and microsatellite loci among four breeding areas in Alaska, Canada, and Russia. We observed significant differences in the variance of mtDNA haplotype frequencies between the Yukon-Kuskokwim Delta (YKD) and the three Arctic locations (Arctic Coastal Plain in Alaska, eastern Siberia, and central Canadian Arctic). However, like most sea duck genetic assessments, our study found no evidence of population structure based on autosomal microsatellite loci. Long-tailed Ducks use multiple wintering areas where pair formation occurs with some populations using both the Pacific and Atlantic Oceans. This situation provides a greater opportunity for admixture across breeding locales, which would likely homogenize the nuclear genome even in the presence of female philopatry. The observed mtDNA differentiation was largely due to the presence of two divergent clades: (A) a clade showing signs of admixture among all breeding locales and (B) a clade primarily composed of YKD samples. We hypothesize that the pattern of mtDNA differentiation reflects some degree of philopatry to the YKD and isolation of two refugial populations with subsequent expansion and admixture. We recommend additional genetic assessments throughout the circumpolar range of Long-tailed Ducks to further quantify aspects of genetic diversity and migratory connectivity in this species.

  6. Population size, breeding biology and on-land threats of Cape Verde petrel (Pterodroma feae) in Fogo Island, Cape Verde

    Science.gov (United States)

    Zango, Laura; Calabuig, Pascual; Stefan, Laura M.; González-Solís, Jacob

    2017-01-01

    Cape Verde petrel (Pterodroma feae) is currently considered near threatened, but little is known about its population size, breeding biology and on land threats, jeopardizing its management and conservation. To improve this situation, we captured, marked and recaptured (CMR) birds using mist-nets over 10 years; measured and sexed them; monitored up to 14 burrows, deployed GPS devices on breeders and analyzed activity data of geolocators retrieved from breeders in Fogo (Cape Verde). We set cat traps over the colony and investigated their domestic/feral origin by marking domestic cats from a nearby village with transponders, by deploying GPS devices on domestic cats and by performing stable isotope analyses of fur of the trapped and domestic cats. The population of Fogo was estimated to be 293 birds, including immatures (95% CI: 233–254, CMR modelling). Based on geolocator activity data and nest monitoring we determined the breeding phenology of this species and we found biometric differences between sexes. While monitoring breeding performance, we verified a still ongoing cat predation and human harvesting. Overall, data gathered from trapped cats without transponder, cats GPS trips and the distinct isotopic values between domestic and trapped cats suggest cats visiting the colony are of feral origin. GPS tracks from breeders showed birds left and returned to the colony using the sector NE of the islands, where high level of public lights should be avoided specially during the fledging period. Main threats for the Cape Verde petrel in the remaining breeding islands are currently unknown but likely to be similar to Fogo, calling for an urgent assessment of population trends and the control of main threats in all Cape Verde Islands and uplisting its conservation status. PMID:28369105

  7. Multiple Stressors in a Top Predator Seabird: Potential Ecological Consequences of Environmental Contaminants, Population Health and Breeding Conditions.

    Directory of Open Access Journals (Sweden)

    Jan O Bustnes

    Full Text Available Environmental contaminants may have impacts on reproduction and survival in wildlife populations suffering from multiple stressors. This study examined whether adverse effects of persistent organic pollutants (POPs increased with poor population health and breeding conditions in three colonies (60-74°N of great skua (Stercorarius skua in the north-eastern Atlantic (Shetland, Iceland and Bjørnøya [Bear Island]. POPs (organochlorines [OCs] and polybrominated diphenyl ethers [BDEs] were measured in plasma of incubating birds (n = 222, concentrations differing nearly tenfold among colonies: Bjørnøya (2009 > Bjørnøya (2010 > Iceland (2009 > Shetland (2009. Reproductive success (hatching success and chick survival showed that breeding conditions were favourable in Shetland and at Bjørnøya (2010, but were very poor in Iceland and at Bjørnøya (2009. Biomarkers indicated that health was poor in the Shetland population compared to the other populations. Females whose chicks hatched late had high POP concentrations in all colonies except at Bjørnøya (2010, and females losing their eggs at Bjørnøya (2009 tended to have higher concentrations than those hatching. Moreover, there was a negative relationship between female POP concentrations and chick body condition at hatching in Iceland and at Bjørnøya (2010. Supplementary feeding experiments were conducted, and in Iceland where feeding conditions were poor, significant negative relationships were found between female POP concentrations and daily growth-rate in first-hatched chicks of control nests, but not in food supplemented nests. This suggests that negative impacts of POPs were mitigated by improved feeding conditions. For second-chicks, there was a strong negative relationship between the female POP concentrations and growth-rate, but no effects of supplementary feeding. Lowered adult return-rate between breeding seasons with increasing POP loads were found both at Bjørnøya (2009 and

  8. Multiple Stressors in a Top Predator Seabird: Potential Ecological Consequences of Environmental Contaminants, Population Health and Breeding Conditions.

    Science.gov (United States)

    Bustnes, Jan O; Bourgeon, Sophie; Leat, Eliza H K; Magnusdóttir, Ellen; Strøm, Hallvard; Hanssen, Sveinn A; Petersen, Aevar; Olafsdóttir, Kristin; Borgå, Katrine; Gabrielsen, Geir W; Furness, Robert W

    2015-01-01

    Environmental contaminants may have impacts on reproduction and survival in wildlife populations suffering from multiple stressors. This study examined whether adverse effects of persistent organic pollutants (POPs) increased with poor population health and breeding conditions in three colonies (60-74°N) of great skua (Stercorarius skua) in the north-eastern Atlantic (Shetland, Iceland and Bjørnøya [Bear Island]). POPs (organochlorines [OCs] and polybrominated diphenyl ethers [BDEs]) were measured in plasma of incubating birds (n = 222), concentrations differing nearly tenfold among colonies: Bjørnøya (2009) > Bjørnøya (2010) > Iceland (2009) > Shetland (2009). Reproductive success (hatching success and chick survival) showed that breeding conditions were favourable in Shetland and at Bjørnøya (2010), but were very poor in Iceland and at Bjørnøya (2009). Biomarkers indicated that health was poor in the Shetland population compared to the other populations. Females whose chicks hatched late had high POP concentrations in all colonies except at Bjørnøya (2010), and females losing their eggs at Bjørnøya (2009) tended to have higher concentrations than those hatching. Moreover, there was a negative relationship between female POP concentrations and chick body condition at hatching in Iceland and at Bjørnøya (2010). Supplementary feeding experiments were conducted, and in Iceland where feeding conditions were poor, significant negative relationships were found between female POP concentrations and daily growth-rate in first-hatched chicks of control nests, but not in food supplemented nests. This suggests that negative impacts of POPs were mitigated by improved feeding conditions. For second-chicks, there was a strong negative relationship between the female POP concentrations and growth-rate, but no effects of supplementary feeding. Lowered adult return-rate between breeding seasons with increasing POP loads were found both at Bjørnøya (2009) and in

  9. Population ecology of breeding Pacific common eiders on the Yukon-Kuskokwim Delta, Alaska

    Science.gov (United States)

    Wilson, Heather M.; Flint, Paul L.; Powell, Abby N.; Grand, J. Barry; Moral, Christine L.

    2012-01-01

    -years. Study sites with lower sample sizes and more frequent visitations appeared to experience greater observer effects. In general, Pacific common eiders exhibited high spatio-temporal variance in reproductive components. Larger clutch sizes and high nest survival at early initiation dates suggested directional selection favoring early nesting. However, stochastic environmental effects may have precluded response to this apparent selection pressure. Our results suggest that females breeding early in the season have the greatest reproductive value, as these birds lay the largest clutches and have the highest probability of successfully hatching. We developed stochastic, stage-based, matrix population models that incorporated observed spatio-temporal (process) variance and co-variation in vital rates, and projected the stable stage distribution () and population growth rate (λ). We used perturbation analyses to examine the relative influence of changes in vital rates on λ and variance decomposition to assess the proportion of variation in λ explained by process variation in each vital rate. In addition to matrix-based λ, we estimated λ using capture–recapture approaches, and log-linear regression. We found the stable age distribution for Pacific common eiders was weighted heavily towards experienced adult females (≥4 yr of age), and all calculations of λ indicated that the YKD population was stable to slightly increasing (λmatrix = 1.02, CI: 1.00–1.04); λreverse-capture–recapture = 1.05, CI: 0.99–1.11; λlog-linear = 1.04, CI: 0.98–1.10). Perturbation analyses suggested the population would respond most dramatically to changes in adult female survival (relative influence of adult survival was 1.5 times that of fecundity), whereas retrospective variation in λ was primarily explained by fecundity parameters (60%), particularly duckling survival (42%). Among components of fecundity, sensitivities were highest for duckling survival, suggesti

  10. Effects of habitat change along Breeding Bird Survey routes in the central Appalachians on Cerulean Warbler population

    Science.gov (United States)

    McElhone, P.; Wood, P.W.; Dawson, D.

    2007-01-01

    The cerulean warbler (Dendroica cerulea) is one of the highest priority bird species in the eastern United States because populations have declined 4.3% annually during 1966?2005 based on Breeding Bird Survey (BBS) data. Habitat loss and fragmentation due to land use changes is thought to be one of the major factors contributing to the decline. BBS routes, the primary source for monitoring bird population trends, include 50 sampling stops every 0.8 km. Although data from BBS routes are extrapolated to determine regional trends in bird populations, it is important to understand the effects of habitat changes at the stop-level along BBS routes. Route-level analysis of habitat changes may mask important changes that are occurring at a smaller scale particularly for the cerulean warbler which displays several micro-scale habitat preferences. We are examining cerulean warbler habitat and population changes in its core breeding range of the Ohio Hills and Cumberland Plateau physiographic regions. We quantified land cover changes within 300 m of BBS routes in the core cerulean warbler breeding range of Ohio, West Virginia, and Kentucky by digitizing aerial photographs from two time periods: the 1980s and 2004. We also quantified land cover changes within 300 m of BBS routes with the National Land Cover Dataset (NLCD) from 1992 and 2001. The hand-digitized aerial photos will be compared with the NLCD to determine how similar the two methods are in quantifying land cover changes. We then compared stop-level land cover changes with stop level changes in cerulean warbler detections within the same time periods along the BBS routes. This will allow for a more detailed analysis of how well habitat changes along BBS routes reflect the changes in cerulean warbler populations.

  11. Breeding without breeding: is a complete pedigree necessary for efficient breeding?

    Directory of Open Access Journals (Sweden)

    Yousry A El-Kassaby

    Full Text Available Complete pedigree information is a prerequisite for modern breeding and the ranking of parents and offspring for selection and deployment decisions. DNA fingerprinting and pedigree reconstruction can substitute for artificial matings, by allowing parentage delineation of naturally produced offspring. Here, we report on the efficacy of a breeding concept called "Breeding without Breeding" (BwB that circumvents artificial matings, focusing instead on a subset of randomly sampled, maternally known but paternally unknown offspring to delineate their paternal parentage. We then generate the information needed to rank those offspring and their paternal parents, using a combination of complete (full-sib: FS and incomplete (half-sib: HS analyses of the constructed pedigrees. Using a random sample of wind-pollinated offspring from 15 females (seed donors, growing in a 41-parent western larch population, BwB is evaluated and compared to two commonly used testing methods that rely on either incomplete (maternal half-sib, open-pollinated: OP or complete (FS pedigree designs. BwB produced results superior to those from the incomplete design and virtually identical to those from the complete pedigree methods. The combined use of complete and incomplete pedigree information permitted evaluating all parents, both maternal and paternal, as well as all offspring, a result that could not have been accomplished with either the OP or FS methods alone. We also discuss the optimum experimental setting, in terms of the proportion of fingerprinted offspring, the size of the assembled maternal and paternal half-sib families, the role of external gene flow, and selfing, as well as the number of parents that could be realistically tested with BwB.

  12. Breeding system and reproductive skew in a highly polygynous ant population

    DEFF Research Database (Denmark)

    Haag-Liautard, C.; Pedersen, Jes Søe; Ovaskainen, O.

    2008-01-01

     Factors affecting relatedness among nest members in ant colonies with high queen number are still poorly understood. In order to identify the major determinants of nest kin structure, we conducted a detailed analysis of the breeding system of the ant Formica exsecta. We estimated the number...

  13. Breeding programs for indigenous chicken in Ethiopia : analysis of diversity in production systems and chicken populations

    NARCIS (Netherlands)

    Dana, N.M.

    2011-01-01

    The aim of this research was to generate information required to establish a sustainable breeding program for improving the productivity of locally adapted chickens to enhance the livelihood of rural farmers in Ethiopia. The first step was to characterize village poultry production environments and

  14. Post-breeding population dynamics indicate upslope molt-migration by Wilson's Warblers

    Science.gov (United States)

    Andrew K. Wiegardt; Daniel C. Barton; Jared D. Wolfe

    2017-01-01

    Molt is an energetically costly process, and songbirds (Order Passeriformes) exhibit a diversity of strategies to maximize their survival and reproductive success while meeting the energetic demands of the annual prebasic molt. Nearctic-Neotropic migrants in western North America commonly exhibit one of three strategies: (1) remain in breeding areas to molt, (2)...

  15. Mapping quantitative trait loci in plant breeding populations : Use of parental haplotype sharing

    NARCIS (Netherlands)

    Jansen, Ritsert C.; Jannink, Jean-Luc; Beavis, William D.

    2003-01-01

    Applied breeding programs evaluate large numbers of progeny derived from multiple related crosses for a wide range of agronomic traits and for tens to hundreds of molecular markers. This study was conducted to determine how these phenotypic and genetic data could be used for routinely mapping quanti

  16. Open-nucleus breeding strategies compared with population-wide positive assortative mating: I. Equal distribution of testing efforts.

    Science.gov (United States)

    Lstibůrek, M; Mullin, T J; Lindgren, D; Rosvall, O

    2004-10-01

    Positive assortative mating (PAM) can enhance the additive genetic variance in a breeding population(BP). This increases the potential for gains in the production population (PP, selected subset of the BP) for recurrent selection programs in forest trees. The assortment of mates can be either: (1) by individual tree rank across the whole BP (PAM), or (2) trees of similar rank can be merged into larger hierarchical groups and then mated randomly within group ("open"-nucleus breeding,NB). The objective of this study was to compare PAM and NB in quantitative terms. The NB simulation model assumed two tiers (nucleus, main) with unrestricted migration between the tiers. Clonal tests were used to predict breeding values and test resources per mate were kept constant for all mates. Both gain and diversity were combined into a single selection criterion, "group-merit selection." Alternatives were compared over five breeding cycles by considering genetic gain and diversity in a selected PP established in a seed orchard. The assortment of mates in both alternatives enhanced additive variance and increased the additive effect in the BP, leading to additional gain in the PP. Gains generated under PAM always exceeded gains under NB. Thus, the main message from this study is that PAM in both the short- and long-term results in more gain at any target level of diversity in the PP (the breeder's target) than is achieved by the NB alternative. The optimum size of the nucleus varies with the desired level of seed orchard diversity. At lower target diversity, smaller nucleus sizes are favorable, while larger sizes result in more gain when seed orchard diversity is considered more important.

  17. Breeding-season sympatry facilitates genetic exchange among allopatric wintering populations of Northern Pintails in Japan and California

    Science.gov (United States)

    Flint, P.L.; Ozaki, K.; Pearce, J.M.; Guzzetti, B.; Higuchi, H.; Fleskes, J.P.; Shimada, T.; Derksen, D.V.

    2009-01-01

    The global redistribution of pathogens, such as highly pathogenic avian influenza, has renewed interest in the connectivity of continental populations of birds. Populations of the Northern Pintail (Anas acuta) wintering in Japan and California are considered separate from a management perspective. We used data from band recoveries and population genetics to assess the degree of biological independence of these wintering populations. Distributions of recoveries in Russia of Northern Pintails originally banded during winter in North America overlapped with distributions of Northern Pintails banded during winter in Japan. Thus these allopatric wintering populations are partially sympatric during the breeding season. The primary areas of overlap were along the Chukotka and Kamchatka peninsulas in Russia. Furthermore, band recoveries demonstrated dispersal of individuals between wintering populations both from North America to Japan and vice versa. Genetic analyses of samples from both wintering populations showed little evidence of population differentiation. The combination of banding and genetic markers demonstrates that these two continental populations are linked by low levels of dispersal as well as likely interbreeding in eastern Russia. Although the levels of dispersal are inconsequential for population dynamics, the combination of dispersal and interbreeding represents a viable pathway for exchange of genes, diseases, and/or parasites. ?? The Cooper Ornithological Society 2009.

  18. Effects of weather on the abundance and distribution on populations of 103 breeding bird species across the United States

    Science.gov (United States)

    Allstadt, A. J.; Gorzo, J.; Bateman, B. L.; Heglund, P. J.; Pidgeon, A. M.; Thogmartin, W.; Vavrus, S. J.; Radeloff, V.

    2016-12-01

    Often, fewer birds are often observed in an area experiencing extreme weather, as local populations tend to leave an area (via out-migration or concentration in refugia) or experience a change in population size (via mortality or reduced fecundity). Further, weather patterns are often coherent over large areas so unsuitable weather may threaten large portions of an entire species range simultaneously. However, beyond a few iconic irruptive species, rarely have studies applied both the necessary scale and sensitivity required to assess avian population responses over entire species range. Here, we examined the effects of pre-breeding season weather on the distribution and abundances of 103 North American bird species from the late 1966-2010 using observed abundance records from the Breeding Bird Survey. We compared abundances with measures of drought and temperature over each species' range, and with three atmospheric teleconnections that describe large-scale circulation patterns influencing conditions on the ground. More than 90% of the species responded to at least one of our five weather variables. Grassland bird species tended to be most responsive to weather conditions and forest birds the least, though we found relations among all habitat types. For most species, the response was movement rather than large effects on the overall population size. Maps of these responses indicate that concentration and out-migration are both common strategies for coping with challenging weather conditions across a species range. The dynamic distribution of many bird species makes clear the need to account for temporal variability in conservation planning, as areas that are less important for a species' breeding success in most years may be very important in years with abnormal weather conditions.

  19. Combined analysis of roadside and off-road breeding bird survey data to assess population change in Alaska

    Science.gov (United States)

    Handel, Colleen M.; Sauer, John

    2017-01-01

    Management interest in North American birds has increasingly focused on species that breed in Alaska, USA, and Canada, where habitats are changing rapidly in response to climatic and anthropogenic factors. We used a series of hierarchical models to estimate rates of population change in 2 forested Bird Conservation Regions (BCRs) in Alaska based on data from the roadside North American Breeding Bird Survey (BBS) and the Alaska Landbird Monitoring Survey, which samples off-road areas on public resource lands. We estimated long-term (1993–2015) population trends for 84 bird species from the BBS and short-term (2003–2015) trends for 31 species from both surveys. Among the 84 species with long-term estimates, 11 had positive trends and 17 had negative trends in 1 or both BCRs; negative trends were primarily found among aerial insectivores and wetland-associated species, confirming range-wide negative continental trends for many of these birds. Three species with negative trends in the contiguous United States and southern Canada had positive trends in Alaska, suggesting different population dynamics at the northern edges of their ranges. Regional population trends within Alaska differed for several species, particularly those represented by different subspecies in the 2 BCRs, which are separated by rugged, glaciated mountain ranges. Analysis of the roadside and off-road data in a joint hierarchical model with shared parameters resulted in improved precision of trend estimates and suggested a roadside-related difference in underlying population trends for several species, particularly within the Northwestern Interior Forest BCR. The combined analysis highlights the importance of considering population structure, physiographic barriers, and spatial heterogeneity in habitat change when assessing patterns of population change across a landscape as broad as Alaska. Combined analysis of roadside and off-road survey data in a hierarchical framework may be particularly

  20. Genetic and morphological divergence among Cooper's Hawk (Accipiter cooperii) populations breeding in north-central and western North America

    Science.gov (United States)

    Sonsthagen, Sarah A.; Rosenfield, Robert N.; Bielefeldt, John; Murphy, Robert K.; Stewart, Andrew C.; Stout, William C.; Driscoll, Timothy G.; Bozek, Michael A.; Sloss, Brian L.; Talbot, Sandra L.

    2012-01-01

    Cooper's Hawk (Accipiter cooperii) populations breeding in the northern portion of the species' range exhibit variation in morphological traits that conforms to predictions based on differences in prey size, tree stand density, and migratory behavior. We examined genetic structure and gene flow and compared divergence at morphological traits (PST) and genetic markers (FST) to elucidate mechanisms (selection or genetic drift) that promote morphological diversification among Cooper's Hawk populations. Cooper's Hawks appear to conform to the genetic pattern of an east-west divide. Populations in British Columbia are genetically differentiated from north-central populations (Wisconsin, Minnesota, and North Dakota; pairwise microsatellite FST= 0.031-0.050; mitochondrial DNA ΦST = 0.177-0.204), which suggests that Cooper's Hawks were restricted to at least two Pleistocene glacial refugia. The strength of the Rocky Mountains—Great Plains area as a barrier to dispersal is further supported by restricted gene-flow rates between British Columbia and other sampled breeding populations. Divergence in morphological traits (PST) was also observed across study areas, but with British Columbia and North Dakota differentiated from Wisconsin and Minnesota, a pattern not predicted on the basis of FST and ΦST interpopulation estimates. Comparison of PSTand FSTestimates suggests that heterogeneous selection may be acting on Cooper's Hawks in the northern portion of their distribution, which is consistent with hypotheses that variation in prey mass and migratory behavior among populations may be influencing overall body size and wing chord. We were unable to distinguish between the effects of genetic drift and selection on tail length in the study populations.

  1. Simulating range-wide population and breeding habitat dynamics for an endangered woodland warbler in the face of uncertainty

    Science.gov (United States)

    Adam Duarte,; Hatfield, Jeffrey; Todd M. Swannack,; Michael R. J. Forstner,; M. Clay Green,; Floyd W. Weckerly,

    2015-01-01

    Population viability analyses provide a quantitative approach that seeks to predict the possible future status of a species of interest under different scenarios and, therefore, can be important components of large-scale species’ conservation programs. We created a model and simulated range-wide population and breeding habitat dynamics for an endangered woodland warbler, the golden-cheeked warbler (Setophaga chrysoparia). Habitat-transition probabilities were estimated across the warbler's breeding range by combining National Land Cover Database imagery with multistate modeling. Using these estimates, along with recently published demographic estimates, we examined if the species can remain viable into the future given the current conditions. Lastly, we evaluated if protecting a greater amount of habitat would increase the number of warblers that can be supported in the future by systematically increasing the amount of protected habitat and comparing the estimated terminal carrying capacity at the end of 50 years of simulated habitat change. The estimated habitat-transition probabilities supported the hypothesis that habitat transitions are unidirectional, whereby habitat is more likely to diminish than regenerate. The model results indicated population viability could be achieved under current conditions, depending on dispersal. However, there is considerable uncertainty associated with the population projections due to parametric uncertainty. Model results suggested that increasing the amount of protected lands would have a substantial impact on terminal carrying capacities at the end of a 50-year simulation. Notably, this study identifies the need for collecting the data required to estimate demographic parameters in relation to changes in habitat metrics and population density in multiple regions, and highlights the importance of establishing a common definition of what constitutes protected habitat, what management goals are suitable within those protected

  2. Estimation of genealogical coancestry in plant species using a pedigree reconstruction algorithm and application to an oil palm breeding population.

    Science.gov (United States)

    Cros, David; Sánchez, Leopoldo; Cochard, Benoit; Samper, Patrick; Denis, Marie; Bouvet, Jean-Marc; Fernández, Jesús

    2014-04-01

    Explicit pedigree reconstruction by simulated annealing gave reliable estimates of genealogical coancestry in plant species, especially when selfing rate was lower than 0.6, using a realistic number of markers. Genealogical coancestry information is crucial in plant breeding to estimate genetic parameters and breeding values. The approach of Fernández and Toro (Mol Ecol 15:1657-1667, 2006) to estimate genealogical coancestries from molecular data through pedigree reconstruction was limited to species with separate sexes. In this study it was extended to plants, allowing hermaphroditism and monoecy, with possible selfing. Moreover, some improvements were made to take previous knowledge on the population demographic history into account. The new method was validated using simulated and real datasets. Simulations showed that accuracy of estimates was high with 30 microsatellites, with the best results obtained for selfing rates below 0.6. In these conditions, the root mean square error (RMSE) between the true and estimated genealogical coancestry was small (0.9) and a low RMSE (pedigree data were scarce. The estimated genealogical coancestries were highly correlated (>0.9) with the molecular coancestries using 100 markers. Reconstructed pedigrees were used to estimate effective population sizes. In conclusion, this method gave reliable genealogical coancestry estimates. The strategy was implemented in the software MOLCOANC 3.0.

  3. A Study of the Effects of Gas Well Compressor Noise on Breeding Bird Populations of the Rattlesnake Canyon Habitat Management Area, San Juan County, New Mexico

    Energy Technology Data Exchange (ETDEWEB)

    LaGory, K.E.; Chang, Young-Soo; Chun, K.C.; Reeves, T.; Liebich, R.; Smith, K.

    2001-06-04

    This report, conducted from May through July 2000, addressed the potential effect of compressor noise on breeding birds in gas-production areas administered by the FFO, specifically in the Rattlesnake Canyon Habitat Management Area northeast of Farmington, New Mexico. The study was designed to quantify and characterize noise output from these compressors and to determine if compressor noise affected bird populations in adjacent habitat during the breeding season.

  4. Modelling the sensitivity of colonially breeding marine birds to oil spills: guillemot and kittiwake populations on the Pribilof Islands, Bering Sea.

    OpenAIRE

    Ford, RG; Wiens, JA; Heinemann, D.; HUNT, GL

    1982-01-01

    Applications of the model to populations of Brunnich's guillemot Uria lomvia, common guillemot U. aalge, red-legged kittiwake Rissa brevirostris, and black-legged kittiwake R. tridactyla breeding on the Pribilof Islands suggest that guillemot mortality is greatest following perturbations located in shallow inshore areas about the breeding islands, while kittiwakes are less severely affected by localized perturbations but are sensitive to spills occurring over a wider area about the islands. M...

  5. Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis.

    Science.gov (United States)

    Malhado, Carlos Henrique Mendes; Malhado, Ana Claudia Mendes; Carneiro, Paulo Luiz Souza; Ramos, Alcides Amorim; Ambrosini, Diego Pagung; Pala, Akin

    2012-12-01

    The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability in the Murrah dairy breed of water buffalo (Bubalus bubalis) in Brazil. Pedigree analysis was performed on 5,061 animals born between 1972 and 2002. The effective number of founders (fe) was 60, representing 6.32 % of the potential number of founders. The effective number of ancestors (fa) was 36 and the genetic contribution of the 17 most influent ancestors explained 50 % of the genetic variability in the population. The ratio fe/fa (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.66. Completeness level for the whole pedigree was 76.8, 49.2, 27.7, and 12.8 % for, respectively, the first, second, third, and fourth known parental generations. The average inbreeding values for the whole analyzed pedigree and for inbreed animals were, respectively, 1.28 and 7.64 %. The average relatedness coefficient between individuals of the population was estimated to be 2.05 %-the highest individual coefficient was 10.31 %. The actual inbreeding and average relatedness coefficient are probably higher than estimated due to low levels of pedigree completeness. Moreover, the inbreeding coefficient increased with the addition of each generation to the pedigree, indicating that incomplete pedigrees tend to underestimate the level of inbreeding. Introduction of new sires with the lowest possible average relatedness coefficient and the use of appropriate mating strategies are recommended to keep inbreeding at acceptable levels and increase the genetic variability in this economically important species, which has relatively low numbers compared to other commercial cattle breeds. The inclusion of additional parameters, such as effective number of founders, effective number of ancestors, and fe/fa ratio, provides better resolution as compared to the inclusion of inbreeding coefficient and may help

  6. Breeding without Breeding: Is a Complete Pedigree Necessary for Efficient Breeding?

    Science.gov (United States)

    El-Kassaby, Yousry A.; Cappa, Eduardo P.; Liewlaksaneeyanawin, Cherdsak; Klápště, Jaroslav; Lstibůrek, Milan

    2011-01-01

    Complete pedigree information is a prerequisite for modern breeding and the ranking of parents and offspring for selection and deployment decisions. DNA fingerprinting and pedigree reconstruction can substitute for artificial matings, by allowing parentage delineation of naturally produced offspring. Here, we report on the efficacy of a breeding concept called “Breeding without Breeding” (BwB) that circumvents artificial matings, focusing instead on a subset of randomly sampled, maternally known but paternally unknown offspring to delineate their paternal parentage. We then generate the information needed to rank those offspring and their paternal parents, using a combination of complete (full-sib: FS) and incomplete (half-sib: HS) analyses of the constructed pedigrees. Using a random sample of wind-pollinated offspring from 15 females (seed donors), growing in a 41-parent western larch population, BwB is evaluated and compared to two commonly used testing methods that rely on either incomplete (maternal half-sib, open-pollinated: OP) or complete (FS) pedigree designs. BwB produced results superior to those from the incomplete design and virtually identical to those from the complete pedigree methods. The combined use of complete and incomplete pedigree information permitted evaluating all parents, both maternal and paternal, as well as all offspring, a result that could not have been accomplished with either the OP or FS methods alone. We also discuss the optimum experimental setting, in terms of the proportion of fingerprinted offspring, the size of the assembled maternal and paternal half-sib families, the role of external gene flow, and selfing, as well as the number of parents that could be realistically tested with BwB. PMID:21991342

  7. The breeding systems of diploid and neoautotetraploid clones of Acacia mangium Willd. in a synthetic sympatric population in Vietnam.

    Science.gov (United States)

    Griffin, A R; Vuong, T D; Vaillancourt, R E; Harbard, J L; Harwood, C E; Nghiem, C Q; Thinh, H H

    2012-12-01

    Colchicine-induced neoautotetraploid genotypes of Acacia mangium were cloned and planted in mixture with a set of diploid clones in an orchard in southern Vietnam. Following good general flowering, open-pollinated seed was collected from trees of both cytotypes and microsatellite markers were used to determine the breeding system as characterised by the proportion of outcrosses in young seedling progeny. As predicted from the literature, the progeny of diploid clones were predominantly outcrossed (t(m) = 0.97). In contrast, the progeny of the tetraploid clones were almost entirely selfs (t(m) = 0.02; 3 of 161 seedlings assayed were tetraploid outcrosses and there were no triploids). Segregation at loci heterozygous in the tetraploid mothers followed expected ratios, indicating sexual reproduction rather than apomixis. Post-zygotic factors are primarily responsible for divergence of the breeding systems. Commonly, less than 1 % of Acacia flowers mature as a pod, and after mixed pollination, diploid outcrossed seed normally develops at the expense of selfs. Selfs of the tetraploid trees appear to express less genetic load and have a higher probability of maturing. However, this does not fully explain the observed deficiency of outcross tetraploid progeny. Presumably, there are cytogenetic reasons which remain to be investigated. In nature, selfing would increase the probability of establishment of neotetraploids irrespective of cytotype frequency in the population. Breeders need to review their open-pollinated breeding and seed production strategies. It remains to be seen whether this is an ephemeral problem, with strong fertility selection restoring potential for outcrossing over generations.

  8. Connectivity patterns and key non–breeding areas of white–throated bluethroat (Luscinia svecica European populations

    Directory of Open Access Journals (Sweden)

    Arizaga, J.

    2013-01-01

    Full Text Available Using ring recovery data from the EURING databank, the aims of this study were: (1 to identify the chief migration and wintering areas of white–throated bluethroat European subspecies, L. s. namnetum, L. s. cyanecula and L. s. azuricollis, (2 to evaluate the degree of connectivity between breeding and non–breeding regions and determine the migration patterns of each subspecies, and (3 to evaluate whether recovery data are sufficient to answer the previous questions adequately. Most of the recoveries were obtained during the autumn migration period (n = 155, 68.9%, followed by winter (n = 49, 21.8% and spring (n = 21, 9.3%. For L. s. azuricollis, we did not find any ring recoveries at more than 100 km in autumn or spring, and there were none at all in winter. All analyses thus relate to L. s. cyanecula and L. s. namnetum. Both subspecies move across a NE–SW axis from their breeding to their wintering areas within the circum–Mediterranean region, mainly in Iberia, following population–specific parallel migration routes. L. s. namnetum mainly uses the Atlantic coastal marshes from France to south–western Iberia, where the chief wintering areas are found. L. s. cyanecula, however, uses both Atlantic and Mediterranean wetlands in autumn, but only those in the Mediterranean in spring, thus giving rise to a loop–migration pattern. Telescopic migration was demonstrated for L. s. cyanecula. Recovery data were insufficient to identify in detail the entire wintering range for all white–throated bluethroat European populations. Technologies such as the use of geolocators will play a relevant role in this scenario

  9. Conditional Viral Tract Tracing Delineates the Projections of the Distinct Kisspeptin Neuron Populations to Gonadotropin-Releasing Hormone (GnRH) Neurons in the Mouse.

    Science.gov (United States)

    Yip, Siew Hoong; Boehm, Ulrich; Herbison, Allan E; Campbell, Rebecca E

    2015-07-01

    Kisspeptin neurons play an essential role in the regulation of fertility through direct regulation of the GnRH neurons. However, the relative contributions of the two functionally distinct kisspeptin neuron subpopulations to this critical regulation are not fully understood. Here we analyzed the specific projection patterns of kisspeptin neurons originating from either the rostral periventricular nucleus of the third ventricle (RP3V) or the arcuate nucleus (ARN) using a cell-specific, viral-mediated tract-tracing approach. We stereotaxically injected a Cre-dependent recombinant adenovirus encoding farnesylated enhanced green fluorescent protein into the ARN or RP3V of adult male and female mice expressing Cre recombinase in kisspeptin neurons. Fibers from ARN kisspeptin neurons projected widely; however, we did not find any evidence for direct contact with GnRH neuron somata or proximal dendrites in either sex. In contrast, we identified RP3V kisspeptin fibers in close contact with GnRH neuron somata and dendrites in both sexes. Fibers originating from both the RP3V and ARN were observed in close contact with distal GnRH neuron processes in the ARN and in the lateral and internal aspects of the median eminence. Furthermore, GnRH nerve terminals were found in close contact with the proximal dendrites of ARN kisspeptin neurons in the ARN, and ARN kisspeptin fibers were found contacting RP3V kisspeptin neurons in both sexes. Together these data delineate selective zones of kisspeptin neuron inputs to GnRH neurons and demonstrate complex interconnections between the distinct kisspeptin populations and GnRH neurons.

  10. Scale Breeding of Tree Shrews and the Establishment of Breeding Population%树鼩规模化繁殖及繁殖群的建立

    Institute of Scientific and Technical Information of China (English)

    江勤芳; 匡德宣; 仝品芬; 孙晓梅; 代解杰

    2011-01-01

    目的 对野生来源树鼩的繁殖性能及仔树鼩的哺育方法进行了研究,探索出一套经济实用、规模化的繁殖方法,取代以往依靠人工喂养的方式.方法 提供适合的饲养管理环境和条件,完全由母树鼩主动自然哺育新生树鼩,观察统计怀孕率、产仔数、成活率、仔树鼩生长情况.结果 2010年通过120对繁殖群,成功离乳354只F1代仔树鼩,自然繁殖成活率为90.76%.目前已建立野生来源树鼩繁殖群150对,F1代繁殖群40对,为建立达到标准要求的树鼩种群奠定了基础.结论 该方法的树鼩繁殖率和成活率较高,成本低且操作简单,为树鼩实验动物化应提倡的一种方法.%Objective Observation the reproductive features of wide original tree shrews. Exploring an optimum method that is economical, practical and on a large scale to raising tree shrews baby. Instead of artificial feeding which were reported previously. Method Provided suitable environment and conditions for feeding and management, entirely breast feeding and care by mother tree shrews. More data were collected and statistics from the pregnancy rate , each litter size , survival rate and observation the growth of young tree shrews. Results In 2010,354 tree shrews offspring have been successfully weaned from 120 couples and the survival rate of natural reproduction was 90. 76 percent. Now breeding population had been established with 150 couples of wild original tree shrews and 40 couples of Fl generation, which have laid the foundation for reaching standard requirements. Conclusion This method was one of higher reproductive and survival rate, low cost and simple to operate, it should be promoted to scale produce the tree shrews as laboratory animals.

  11. High rabbit abundance proves detrimental to the population growth rate in European rabbit (Oryctolagus cuniculus L. extensive breeding enclosures

    Directory of Open Access Journals (Sweden)

    L. Ruiz-Aizpurua

    2014-09-01

    Full Text Available The European rabbit (Oryctolagus cuniculus L. is a key prey species in Mediterranean ecosystems that has declined in its natural ranges as a result of diseases and loss of habitat. This situation has led to the production of wild rabbits in enclosures in which they can acclimate and breed. The efficiency of these enclosures as extensive breeding systems is defined by their population growth rate (PGR. The aim of this study is to analyse the effect of rabbit abundance on the PGR. This has been done by creating general linear models to explain autumn and spring PGR with the use of rabbit abundance estimates, enclosure size, aerial predation and previous PGR as possible explanatory variables. Rabbit abundance and enclosure size negatively affected the autumn PGR, while only rabbit abundance affected the spring PGR in the best-fit models. It is suggested that maintaining rabbit densities at fewer than 30 rabbits per hectare might help to optimise the efficiency inside enclosures.

  12. Comparison of breeding value prediction for two traits in a Nellore-Angus crossbred population using different Bayesian modeling methodologies

    Directory of Open Access Journals (Sweden)

    Lauren L. Hulsman Hanna

    2014-12-01

    Full Text Available The objectives of this study were to 1 compare four models for breeding value prediction using genomic or pedigree information and 2 evaluate the impact of fixed effects that account for family structure. Comparisons were made in a Nellore-Angus population comprising F2, F3 and half-siblings to embryo transfer F2 calves with records for overall temperament at weaning (TEMP; n = 769 and Warner-Bratzler shear force (WBSF; n = 387. After quality control, there were 34,913 whole genome SNP markers remaining. Bayesian methods employed were BayesB ( π = 0.995 or 0.997 for WBSF or TEMP, respectively and BayesC (π = 0 and π, where π is the ideal proportion of markers not included. Direct genomic values (DGV from single trait Bayesian analyses were compared to conventional pedigree-based animal model breeding values. Numerically, BayesC procedures (using π had the highest accuracy of all models for WBSF and TEMP ( ρgg = 0.843 and 0.923, respectively, but BayesB had the least bias (regression of performance on prediction closest to 1, βy,x = 2.886 and 1.755, respectively. Accounting for family structure decreased accuracy and increased bias in prediction of DGV indicating a detrimental impact when used in these prediction methods that simultaneously fit many markers.

  13. Population Densities of Birds Breeding in Urbanized Habitats in the Grabiszyn District in the City of Wrocław

    Directory of Open Access Journals (Sweden)

    Kopij Grzegorz

    2014-11-01

    Full Text Available Studies were carried out in 2010 by mean of simplified version of the mapping method. The study area (395 ha was located close to the city centre. It comprised a mosaic of urbanized habitats, with a clear dominance of green areas, such as parks (41.1 ha, gardens, cemeteries and tree clumps. A total of 48 breeding bird species were recorded in the whole study area. The most common (<25 pairs/100 ha were Passer domesticus, Passer montanus, Sturnus vulgaris, Parus caeruleus, Parus major, Apus apus and Columba livia. Numerous (7-15 pairs/100 ha were also the following species: Columba palumbus, Turdus pilaris, Sylvia atricapilla, Serinus serinus, Turdus merula and Pica pica. Insectivorous birds were the most common birds constituting 63.3%, and granivorous -32.6% of all pairs recorded. Most birds nested in tree holes (39.3%, in/on buildings (30.2% and in trees/shrubs (25.6%. Distribution of breeding pairs of 23 bird species was presented on maps. Population trends for 17 species were documented. Rapid increase in numbers of Turdus pilaris, Corvus cornix and Phoenicurus phoenicurus and decrease of Pica pica were recorded.

  14. Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress.

    Science.gov (United States)

    Fernández, Jesús; Toro, Miguel Á; Sonesson, Anna K; Villanueva, Beatriz

    2014-01-01

    The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in the initial founders. Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and, therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during 10 generations of phenotypic selection applied in the subsequent breeding program.

  15. Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress

    Directory of Open Access Journals (Sweden)

    Jesús eFernández

    2014-11-01

    Full Text Available The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in those initial founders. Traditionally base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during ten generations of phenotypic selection applied in the subsequent breeding program.

  16. Recurrent Selection and Participatory Plant Breeding for Improvement of Two Organic Open-Pollinated Sweet Corn (Zea mays L. Populations

    Directory of Open Access Journals (Sweden)

    Adrienne C. Shelton

    2015-04-01

    Full Text Available Organic growers face unique challenges when raising sweet corn, and benefit from varieties that maintain high eating quality, germinate consistently, deter insect pests, and resist diseases. Genotype by environment rank changes can occur in the performance of cultivars grown on conventional and organic farms, yet few varieties have been bred specifically for organic systems. The objective of this experiment was to evaluate the changes made to open-pollinated sweet corn populations using recurrent selection and a participatory plant breeding (PPB methodology. From 2008 to 2011, four cycles of two open-pollinated (OP sweet corn populations were selected on a certified organic farm in Minnesota using a modified ear-to-row recurrent selection scheme. Selections were made in collaboration with an organic farmer, with selection criteria based on traits identified by the farmer. In 2012 and 2013, the population cycles were evaluated in a randomized complete block design in two certified organic locations in Wisconsin, with multiple replications in each environment. Significant linear trends were found among cycles of selection for quantitative and qualitative traits, suggesting the changes were due to recurrent selection and PPB methodology for these populations. However, further improvement is necessary to satisfy the requirements for a useful cultivar for organic growers.

  17. Avian response to timber harvesting applied experimentally to manage Cerulean Warbler breeding populations

    Science.gov (United States)

    Sheehan, James; Wood, Petra Bohall; Buehler, David A.; Keyser, Patrick D.; Larkin, Jeffrey L.; Rodewald, Amanda D.; Wigley, T. Bently; Boves, Than J.; George, Gregory A.; Bakermans, Marja H.; Beachy, Tiffany A.; Evans, Andrea; McDermott, Molly E.; Newell, Felicity L.; Perkins, Kelly A.; White, Matthew

    2014-01-01

    Timber harvesting has been proposed as a management tool to enhance breeding habitat for the Cerulean Warbler (Setophaga cerulea), a declining Neotropical–Nearctic migratory songbird that nests in the canopy of mature eastern deciduous forests. To evaluate how this single-species management focus might fit within an ecologically based management approach for multiple forest birds, we performed a manipulative experiment using four treatments (three intensities of timber harvests and an unharvested control) at each of seven study areas within the core Cerulean Warbler breeding range. We collected pre-harvest (one year) and post-harvest (four years) data on the territory density of Cerulean Warblers and six additional focal species, avian community relative abundance, and several key habitat variables. We evaluated the avian and habitat responses across the 3–32 m2 ha−1 residual basal area (RBA) range of the treatments. Cerulean Warbler territory density peaked with medium RBA (∼16 m2 ha−1). In contrast, territory densities of the other focal species were negatively related to RBA (e.g., Hooded Warbler [Setophaga citrina]), were positively related to RBA (e.g., Ovenbird [Seiurus aurocapilla]), or were not sensitive to this measure (Scarlet Tanager [Piranga olivacea]). Some species (e.g., Hooded Warbler) increased with time post-treatment and were likely tied to a developing understory, whereas declines (e.g., Ovenbird) were immediate. Relative abundance responses of additional species were consistent with the territory density responses of the focal species. Across the RBA gradient, greatest separation in the avian community was between early successional forest species (e.g., Yellow-breasted Chat [Icteria virens]) and closed-canopy mature forest species (e.g., Ovenbird), with the Cerulean Warbler and other species located intermediate to these two extremes. Overall, our results suggest that harvests within 10–20 m2 ha−1 RBA yield the largest

  18. Climate and habitat interact to shape the thermal reaction norms of breeding phenology across lizard populations.

    Science.gov (United States)

    Rutschmann, Alexis; Miles, Donald B; Le Galliard, Jean-François; Richard, Murielle; Moulherat, Sylvain; Sinervo, Barry; Clobert, Jean

    2016-03-01

    Substantial plastic variation in phenology in response to environmental heterogeneity through time in the same population has been uncovered in many species. However, our understanding of differences in reaction norms of phenology among populations from a given species remains limited. As the plasticity of phenological traits is often influenced by local thermal conditions, we expect local temperature to generate variation in the reaction norms between populations. Here, we explored temporal variation in parturition date across 11 populations of the common lizard (Zootoca vivipara) from four mountain chains as a function of air temperatures during mid-gestation. We characterized among-population variation to assess how local weather conditions (mean and variance of ambient temperatures during mid-gestation) and habitat openness (an index of anthropogenic disturbance) influence the thermal reaction norms of the parturition date. Our results provide evidence of interactive effects of anthropogenic disturbance and thermal conditions, with earlier parturition dates in warmer years on average especially in closed habitats. Variation in the reaction norms for parturition date was correlated with mean local thermal conditions at a broad geographical scale. However, populations exposed to variable thermal conditions had flatter thermal reaction norms. Assessing whether environmental heterogeneity drives differentiation among reaction norms is crucial to estimate the capacity of different populations to contend with projected climatic and anthropogenic challenges.

  19. Human and animal Trypanosomes in Cote d'Ivoire form a single breeding population.

    Directory of Open Access Journals (Sweden)

    Paul Capewell

    Full Text Available BACKGROUND: Trypanosoma brucei is the causative agent of African Sleeping Sickness in humans and contributes to the related veterinary disease, Nagana. T. brucei is segregated into three subspecies based on host specificity, geography and pathology. T. b. brucei is limited to animals (excluding some primates throughout sub-Saharan Africa and is non-infective to humans due to trypanolytic factors found in human serum. T. b. gambiense and T. b. rhodesiense are human infective sub-species. T. b. gambiense is the more prevalent human, causing over 97% of human cases. Study of T. b. gambiense is complicated in that there are two distinct groups delineated by genetics and phenotype. The relationships between the two groups and local T. b. brucei are unclear and may have a bearing on the evolution of the human infectivity traits. METHODOLOGY/PRINCIPAL FINDINGS: A collection of sympatric T. brucei isolates from Côte d'Ivoire, consisting of T. b. brucei and both groups of T. b. gambiense have previously been categorized by isoenzymes, RFLPs and Blood Incubation Infectivity Tests. These samples were further characterized using the group 1 specific marker, TgSGP, and seven microsatellites. The relationships between the T. b. brucei and T. b. gambiense isolates were determined using principal components analysis, neighbor-joining phylogenetics, STRUCTURE, FST, Hardy-Weinberg equilibrium and linkage disequilibrium. CONCLUSIONS/SIGNIFICANCE: Group 1 T. b. gambiense form a clonal genetic group, distinct from group 2 and T. b. brucei, whereas group 2 T. b. gambiense are genetically indistinguishable from local T. b. brucei. There is strong evidence for mating within and between group 2 T. b. gambiense and T. b. brucei. We found no evidence to support the hypothesis that group 2 T. b. gambiense are hybrids of group 1 and T. b. brucei, suggesting that human infectivity has evolved independently in groups 1 and 2 T. b. gambiense.

  20. A Mathematical Model for Singly-Peaked Population Processes from Breeding to Extinction

    CERN Document Server

    Huzimura, R; Huzimura, Ryoitiro; Matsuyama, Toyoki

    1999-01-01

    When a small number of individuals of organism of single species is confined in a closed space with limited amount of indispensable resources, their breading may start initially under suitable conditions, and after peaking, the population should go extinct as the resources are exhausted. Assuming that the carrying capacity of the environment is a function of resource amount, a mathematical model describing such pattern of population change is obtained. An application of this model to typical population records, that of deer herds by Scheffer (1951) and O'Roke and Hamerstrome (1948), yields estimations of the initial amount of indispensable food and its availability or nutritional efficiency which were previously unspecified.

  1. Analysis of Breeding Systems, Ploidy, and the Role of Hexaploids in Three Hypericum perforatum L. Populations

    Science.gov (United States)

    Hexaploid seeds are produced by predominantly tetraploid populations of Hypericum perforatum, but the fate of hexaploid seedlings and their reproductive behavior have not been closely examined. We used flow cytometry to analyze single seeds and individual plant samples of three accessions of H. per...

  2. Long term demographic monitoring of wader populations in non-breeding areas

    NARCIS (Netherlands)

    Robinson, Robert A.; Clark, Nigel A.; Lanctot, Richard; Nebel, Silke; Harrington, Brian; Clark, Jacquie A.; Gill, Jennifer A.; Meltofte, Hans; Rogers, Danny I.; Rogers, Ken G.; Ens, Bruno J.; Reynolds, Christopher M.; Ward, Robin M.; Piersma, Theunis; Atkinson, Philip W.

    2005-01-01

    Understanding numeric changes in wader populations requires knowledge of the demographic parameters underlying such changes, i.e. survival and recruitment. Data from long-term monitoring programmes are crucial for obtaining these parameters. Following discussions held at a workshop on demographic mo

  3. Annual recapture and survival rates of two non-breeding adult populations of Roseate Terns Stema dougallii captured on the Great Barrier Reef, Australia, and estimates of their population sizes

    Science.gov (United States)

    O'Neill, P.; Minton, C.D.T.; Nisbet, I.C.T.; Hines, J.E.

    2008-01-01

    Capture-recapture data from two disparate breeding populations of Roseate Terns (Sterna dougallii) captured together as non-breeding individuals from 2002 to 2007 in the southern Great Barrier Reef. Australia were analyzed for both survival rate and recapture rate. The average annual survival rate for the birds from the Asian population (S. d. bangsi) (0.901) is higher than that of the other population of unknown breeding origin (0.819). There was large variability in survival in both populations among years, but the average survival rate of 0.85 is similar to estimates for the same species in North America. The Cormack-Jolly-Seber models used in program MARK to estimate survival rates also produced estimated of recapture probabilities and population sizes. These estimates of population size were 29,000 for S. D. bangsi and 8,300 for the study area and much larger than the documented numbers in the likely breeding areas, suggesting that many breeding sites are currently unknown.

  4. Comparison of Model Predictions and Laboratory Observations of Transgene Frequencies in Continuously-Breeding Mosquito Populations.

    Science.gov (United States)

    Valerio, Laura; North, Ace; Collins, C Matilda; Mumford, John D; Facchinelli, Luca; Spaccapelo, Roberta; Benedict, Mark Q

    2016-09-22

    The persistence of transgenes in the environment is a consideration in risk assessments of transgenic organisms. Combining mathematical models that predict the frequency of transgenes and experimental demonstrations can validate the model predictions, or can detect significant biological deviations that were neither apparent nor included as model parameters. In order to assess the correlation between predictions and observations, models were constructed to estimate the frequency of a transgene causing male sexual sterility in simulated populations of a malaria mosquito Anopheles gambiae that were seeded with transgenic females at various proportions. Concurrently, overlapping-generation laboratory populations similar to those being modeled were initialized with various starting transgene proportions, and the subsequent proportions of transgenic individuals in populations were determined weekly until the transgene disappeared. The specific transgene being tested contained a homing endonuclease gene expressed in testes, I-PpoI, that cleaves the ribosomal DNA and results in complete male sexual sterility with no effect on female fertility. The transgene was observed to disappear more rapidly than the model predicted in all cases. The period before ovipositions that contained no transgenic progeny ranged from as little as three weeks after cage initiation to as long as 11 weeks.

  5. Breeding matters: Natal experience influences population state-dependent host acceptance by an eruptive insect herbivore

    Science.gov (United States)

    2017-01-01

    Eruptive forest insects are highly influential agents of change in forest ecosystems, and their effects have increased with recent climate change. State-dependent life histories contribute significantly to the population dynamics of eruptive forest insect herbivores; however, the proximate mechanisms by which these species shift between states is poorly understood. Laboratory bioassays were conducted using the mountain pine beetle (Dendroctonus ponderosae) to determine the effect of maternal host selection on offspring host preferences, as they apply to population state-dependent behaviors. Female mountain pine beetles exhibited state-dependent preference for artificial host material amended with monoterpenes in the absence of other cues, such that individuals reared in high-density epidemic-state simulations rejected low monoterpene conditions, while low-density endemic-state beetles accepted low monoterpene conditions. State-specific behavior in offspring was dependent on rearing conditions, as a function of maternal host selection, and these effects were observed within one generation. Density-dependent host selection behaviors exhibited by female mountain pine beetle offspring is reinforced by context-dependent maternal effects arising from parental host selection, and in situ exposure to conspecifics. These results demonstrate potential proximate mechanisms that control population dynamics in eruptive forest insects, and will allow for more accurate predictions of continued impact and spread of these species. PMID:28207862

  6. Comparison of Model Predictions and Laboratory Observations of Transgene Frequencies in Continuously-Breeding Mosquito Populations

    Directory of Open Access Journals (Sweden)

    Laura Valerio

    2016-09-01

    Full Text Available The persistence of transgenes in the environment is a consideration in risk assessments of transgenic organisms. Combining mathematical models that predict the frequency of transgenes and experimental demonstrations can validate the model predictions, or can detect significant biological deviations that were neither apparent nor included as model parameters. In order to assess the correlation between predictions and observations, models were constructed to estimate the frequency of a transgene causing male sexual sterility in simulated populations of a malaria mosquito Anopheles gambiae that were seeded with transgenic females at various proportions. Concurrently, overlapping-generation laboratory populations similar to those being modeled were initialized with various starting transgene proportions, and the subsequent proportions of transgenic individuals in populations were determined weekly until the transgene disappeared. The specific transgene being tested contained a homing endonuclease gene expressed in testes, I-PpoI, that cleaves the ribosomal DNA and results in complete male sexual sterility with no effect on female fertility. The transgene was observed to disappear more rapidly than the model predicted in all cases. The period before ovipositions that contained no transgenic progeny ranged from as little as three weeks after cage initiation to as long as 11 weeks.

  7. Are life history events of a northern breeding population of Cooper's Hawks influenced by changing climate?

    Science.gov (United States)

    Rosenfield, Robert N; Hardin, Madeline G; Bielefeldt, John; Keyel, Edward R

    2017-01-01

    Numerous studies have demonstrated earlier timing of spring migration and egg-laying in small passerines, but documentation of such responses to recent climate change in the life histories of higher trophic feeding birds such as raptors is relatively scarce. Raptors may be particularly susceptible to possible adverse effects of climate change due to their longer generation turnover times and lower reproductive capacity, which could lead to population declines because of an inability to match reproductive timing with optimal brood rearing conditions. Conversely adaptively favorable outcomes due to the influence of changing climate may occur. In general, birds that seasonally nest earlier typically have higher reproductive output compared to conspecifics that nest later in the season. Given the strong seasonal decline in reproductive output, and the heritability of nesting phenology, it is possible that nesting seasons would (adaptively) advance over time. Recent climate warming may release prior ecological constraints on birds that depend on food availability at the time of egg production, as do various raptors including Cooper's Hawks (Accipiter cooperii). Under this scenario, productivity, especially clutch size, might increase because it is likely that this reproductive demographic may be the most immediate response to the earlier seasonal presence of food resources. We demonstrated a statistically significant shift of about 4-5 days to an earlier timing of egg-hatching in spring across 36 years during 1980-2015 for a partially migratory population of Cooper's Hawks in Wisconsin, United States, which is consistent with a recent study that showed that Cooper's Hawks had advanced their timing of spring migration during 1979-2012. Both studies occurred in the Great Lakes region, an area that compared to global averages is experiencing earlier and increased warming particularly in the spring in Wisconsin. The nesting period did not lengthen. We suggest that the

  8. Genetic map of the common bean using a breeding population derived from the Mesoamerican gene pool

    Directory of Open Access Journals (Sweden)

    Luciana Gomes Ferreira

    2010-01-01

    Full Text Available The mapping population consisted of 94 F2 generation plants derived from a cross between the CNFC 7812and CNFC 8056 lines, with different protein contents, 24% and 19% respectively. Seven hundred and fifty-two molecularmarkers were tested among the parents and four individuals from the segregant population. A total of 101 loci were used todevelop the genetic map. The polymorphism rate was 8.3% and 23.2% for the microsatellite and RAPD markers, respectively.The sizes of the linkage groups ranged from 6.7 to 139.0 cM , presenting a mean of 49.4 ± 36.8. The map length was 840.7cM and the mean group length was 45.9 cM. The average distance between the framework loci was 16.1 cM. This map wascompared with international reference bean maps and results were discussed. The construction of the genetic map fromparents of the same center of origin and the commercial grain type were discussed.

  9. Abundance, distribution and trend of the lesser spotted eagle (Aquila pomarina breeding population in Slovakia

    Directory of Open Access Journals (Sweden)

    Dravecký Miroslav

    2015-06-01

    Full Text Available Odhad pocetnosti hniezdnej populácie orla kriklavého na Slovensku bol publikovaný v rokoch 1955-2002. V tejto štúdii odhadujeme pocetnost hniezdnej populácie orla kriklavého k rokom 1997 a 2014. K roku 1997 bol odhadnutý celkový pocet 762 párov. V roku 2002 bol publikovaný odhad pocetnosti k roku 2000 vo výške 800-900 párov. K roku 2014 odhadujeme pocetnost hniezdnej populácie orla kriklavého na Slovensku na 600-800 párov a klesajúci trend vývoja populácie v rokoch 2000-2013 priemerne -23%. Náš odhad je podložený výsledkami extrapolácie údajov, získaných v rokoch 2011-2013 z ôsmich vybraných chránených vtácích území v rámci riešenia projektu LIFE09 NAT/SK/000396 „Ochrana orla kriklavého na Slovensku“. Pri štatistickej analýze pocetnosti, hustôt a trendov pre celý areál hniezdneho rozšírenia druhu na Slovensku sme vychádzali zo sumarizovaných poctov hniezdnych párov, ich hustôt a trendov vo vybraných územiach a z ich stratifikácie podla výsledkov ANOVA a zhlukovej analýzy. Pre 8 chránených vtácích území vcelku (n = 8 i v clenení podla kvadrátov Databanky Fauny Slovenska (n = 119 sme vypocítali intervalové odhady stredných hodnôt poctu párov (prosté i vážené aritmetické priemery a mediány. Ich sumarizáciou pri postupnom zväcšovaní vzorky (n = 8, 9, 11a 12 a extrapoláciou na celý areál hniezdneho rozšírenia druhu na Slovensku (ca 28 935 km2 sa výsledné odhady stredných hodnôt stabilizovali na úrovni 670 (aritmetický priemer s 95%LCL = 507 a 95%UCL = 834 resp. 765 (medián s 95%LCL = 393 a 95%UCL = 841 hniezdnych párov. Ako najspolahlivejší odhad pocetnosti hniezdnej populácie orla kriklavého na Slovensku k roku 2014 vychádza medián 765 párov v 95 %-nom intervale spolahlivosti od 393 do 841 párov a s medzikvartilovým rozpätím od 418 do 835 párov. Odhadujeme 23 %-ný pokles celoslovenskej populácie v rokoch 2000-2013, co predstavuje mierny

  10. Recovery of native genetic background in admixed populations using haplotypes, phenotypes, and pedigree information--using Cika cattle as a case breed.

    Science.gov (United States)

    Simčič, Mojca; Smetko, Anamarija; Sölkner, Johann; Seichter, Doris; Gorjanc, Gregor; Kompan, Dragomir; Medugorac, Ivica

    2015-01-01

    The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had

  11. Genetic evaluation of the total hip score of four populous breeds of dog, as recorded by the New Zealand Veterinary Association Hip Dysplasia Scheme (1991-2011).

    Science.gov (United States)

    Soo, M; Sneddon, N W; Lopez-Villalobos, N; Worth, A J

    2015-03-01

    To use estimated breeding value (EBV) analysis to investigate the genetic trend of the total hip score (to assess canine hip dysplasia) in four populous breeds of dogs using the records from the New Zealand Veterinary Association (NZVA) Canine Hip Dysplasia Scheme database (1991 to 2011). Estimates of heritability and EBV for the NZVA total hip score of individual dogs from the German Shepherd, Labrador Retriever, Golden Retriever and Rottweiler breeds were obtained using restricted maximum likelihood procedures with a within-breed linear animal model. The model included the fixed effects of gender, birth year, birth season, age at scoring and the random effect of animal. The pedigree file included animals recorded between 1990 and 2011. A total of 2,983 NZVA hip score records, from a pedigree of 3,172 animals, were available for genetic evaluation. Genetic trends of the NZVA total hip score were calculated as the regression coefficient of the EBV (weighted by reliabilities) on year of birth. The estimates of heritability for hip score were 0.32 (SE 0.08) in German Shepherd, 0.37 (SE 0.08) in Labrador Retriever, 0.29 (SE 0.08) in Golden Retriever and 0.52 (SE 0.18) in Rottweiler breeds. Genetic trend analysis revealed that only the German Shepherd breed exhibited a genetic trend towards better hip conformation over time, with a decline of 0.13 (SE 0.04) NZVA total hip score units per year (phip score for the remaining three breeds were not significantly different from zero (p>0.1). Despite moderate heritability of the NZVA total hip score, there has not been substantial improvement of this trait for the four breeds analysed in the study period. Greater improvement in reducing the prevalence of canine hip dysplasia may be possible if screening were to be compulsory as a requirement for registration of pedigree breeding stock, greater selection pressure were to be applied and selection of breeding stock made on the basis on an individual's EBV rather than the NZVA

  12. Genome Wide Screening of Candidate Genes for Improving Piglet Birth Weight Using High and Low Estimated Breeding Value Populations

    Science.gov (United States)

    Zhang, Lifan; Zhou, Xiang; Michal, Jennifer J.; Ding, Bo; Li, Rui; Jiang, Zhihua

    2014-01-01

    Birth weight is an economically important trait in pig production because it directly impacts piglet growth and survival rate. In the present study, we performed a genome wide survey of candidate genes and pathways associated with individual birth weight (IBW) using the Illumina PorcineSNP60 BeadChip on 24 high (HEBV) and 24 low estimated breeding value (LEBV) animals. These animals were selected from a reference population of 522 individuals produced by three sires and six dam lines, which were crossbreds with multiple breeds. After quality-control, 43,257 SNPs (single nucleotide polymorphisms), including 42,243 autosomal SNPs and 1,014 SNPs on chromosome X, were used in the data analysis. A total of 27 differentially selected regions (DSRs), including 1 on Sus scrofa chromosome 1 (SSC1), 1 on SSC4, 2 on SSC5, 4 on SSC6, 2 on SSC7, 5 on SSC8, 3 on SSC9, 1 on SSC14, 3 on SSC18, and 5 on SSCX, were identified to show the genome wide separations between the HEBV and LEBV groups for IBW in piglets. A DSR with the most number of significant SNPs (including 7 top 0.1% and 31 top 5% SNPs) was located on SSC6, while another DSR with the largest genetic differences in FST was found on SSC18. These regions harbor known functionally important genes involved in growth and development, such as TNFRSF9 (tumor necrosis factor receptor superfamily member 9), CA6 (carbonic anhydrase VI) and MDFIC (MyoD family inhibitor domain containing). A DSR rich in imprinting genes appeared on SSC9, which included PEG10 (paternally expressed 10), SGCE (sarcoglycan, epsilon), PPP1R9A (protein phosphatase 1, regulatory subunit 9A) and ASB4 (ankyrin repeat and SOCS box containing 4). More importantly, our present study provided evidence to support six quantitative trait loci (QTL) regions for pig birth weight, six QTL regions for average birth weight (ABW) and three QTL regions for litter birth weight (LBW) reported previously by other groups. Furthermore, gene ontology analysis with 183 genes

  13. The Effects of Both Recent and Long-Term Selection and Genetic Drift Are Readily Evident in North American Barley Breeding Populations

    Directory of Open Access Journals (Sweden)

    Ana M. Poets

    2016-03-01

    Full Text Available Barley was introduced to North America ∼400 yr ago but adaptation to modern production environments is more recent. Comparisons of allele frequencies among growth habits and spike (inflorescence types in North America indicate that significant genetic differentiation has accumulated in a relatively short evolutionary time span. Allele frequency differentiation is greatest among barley with two-row vs. six-row spikes, followed by spring vs. winter growth habit. Large changes in allele frequency among breeding programs suggest a major contribution of genetic drift and linked selection on genetic variation. Despite this, comparisons of 3613 modern North American cultivated barley breeding lines that differ for spike-type and growth habit permit the discovery of 142 single nucleotide polymorphism (SNP outliers putatively linked to targets of selection. For example, SNPs within the Cbf4, Ppd-H1, and Vrn-H1 loci, which have previously been associated with agronomically adaptive phenotypes, are identified as outliers. Analysis of extended haplotype sharing identifies genomic regions shared within and among breeding populations, suggestive of a number of genomic regions subject to recent selection. Finally, we are able to identify recent bouts of gene flow between breeding populations that could point to the sharing of agronomically adaptive variation. These results are supported by pedigrees and breeders’ understanding of germplasm sharing.

  14. Effects of sea ice on breeding numbers and clutch size of a high arctic population of the common eider Somateria mollissima

    Science.gov (United States)

    Mehlum, Fridtjof

    2012-04-01

    The breeding performance of high-arctic bird populations shows large inter-annual variation that may be attributed to environmental variability, such as the timing of snow melt and break-up of the landfast sea ice that surrounds breeding colonies on islands and along coasts. In the Kongsfjorden area (79°N) on Svalbard, the number of breeding pairs and the average egg clutch size vary considerably among years. In this study, data on breeding performance are presented from 15 years in the period 1981-2000. The results showed that early break-up of sea ice in Kongsfjorden resulted in larger numbers of nests and larger average clutch sizes than late break-up. Also, individual islands with early break-up of sea ice in a particular year had more nests and larger clutch sizes compared to other islands surrounded by sea ice during a longer period in spring. Thus, the inter-annual variation in the break-up of sea ice in the fjord has considerable implications for the inter-annual variability of recruitment to the population. The results indicate that the effects of global warming on changes in the sea ice melting regime in coastal regions are important for the reproductive output of island-nesting eiders.

  15. Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers.

    Science.gov (United States)

    Wang, Hui; Khera, Pawan; Huang, Bingyan; Yuan, Mei; Katam, Ramesh; Zhuang, Weijian; Harris-Shultz, Karen; Moore, Kim M; Culbreath, Albert K; Zhang, Xinyou; Varshney, Rajeev K; Xie, Lianhui; Guo, Baozhu

    2016-05-01

    Cultivated peanut is grown worldwide as rich-source of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat (SSR) markers and to assess the genetic diversity and population structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene diversity and polymorphic information content (PIC) were 0.480 and 0.429, respectively. Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US, China and India was 0.363, 0.489 and 0.47 with an average PIC of 0.323, 0.43 and 0.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations (P1, P2), which was consistent with the dendrogram based on genetic distance (G1, G2) and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies.

  16. Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers

    Institute of Scientific and Technical Information of China (English)

    Hui Wang; Xinyou Zhang; Rajeev K. Varshney; Lianhui Xie; Baozhu Guo; Pawan Khera; Bingyan Huang; Mei Yuan; Ramesh Katam; Weijian Zhuang; Karen Harris-Shultz; Kim M. Moore; Albert K. Culbreath

    2016-01-01

    Cultivated peanut is grown worldwide as rich-source of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat (SSR) markers and to assess the genetic diversity and population structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene diversity and polymorphic information content (PIC) were 0.480 and 0.429, respectively. Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US, China and India was 0.363, 0.489 and 0.47 with an average PIC of 0.323, 0.43 and 0.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations (P1, P2), which was consistent with the dendro-gram based on genetic distance (G1, G2) and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies.

  17. Identification of Putative Wintering Areas and Ecological Determinants of Population Dynamics of Common House-Martin (Delichon urbicum and Common Swift (Apus apus Breeding in Northern Italy

    Directory of Open Access Journals (Sweden)

    Roberto Ambrosini

    2011-06-01

    Full Text Available To identify the causes of population decline in migratory birds, researchers must determine the relative influence of environmental changes on population dynamics while the birds are on breeding grounds, wintering grounds, and en route between the two. This is problematic when the wintering areas of specific populations are unknown. Here, we first identified the putative wintering areas of Common House-Martin (Delichon urbicum and Common Swift (Apus apus populations breeding in northern Italy as those areas, within the wintering ranges of these species, where the winter Normalized Difference Vegetation Index (NDVI, which may affect winter survival, best predicted annual variation in population indices observed in the breeding grounds in 1992-2009. In these analyses, we controlled for the potentially confounding effects of rainfall in the breeding grounds during the previous year, which may affect reproductive success; the North Atlantic Oscillation Index (NAO, which may account for climatic conditions faced by birds during migration; and the linear and squared term of year, which account for nonlinear population trends. The areas thus identified ranged from Guinea to Nigeria for the Common House-Martin, and were located in southern Ghana for the Common Swift. We then regressed annual population indices on mean NDVI values in the putative wintering areas and on the other variables, and used Bayesian model averaging (BMA and hierarchical partitioning (HP of variance to assess their relative contribution to population dynamics. We re-ran all the analyses using NDVI values at different spatial scales, and consistently found that our population of Common House-Martin was primarily affected by spring rainfall (43%-47.7% explained variance and NDVI (24%-26.9%, while the Common Swift population was primarily affected by the NDVI (22.7%-34.8%. Although these results must be further validated, currently they are the only hypotheses about the wintering

  18. Morpho-Productive Characterization of Some Tzurcana Breed Populations, White Variety, Bred in Some Zones of Transylvania

    Directory of Open Access Journals (Sweden)

    Stelian Vasile Dărăban

    2011-10-01

    Full Text Available The Tzurcana breed, a rustic breed with mixed morpho-productive character, named for good “the queen of mountains”, constitutes the main ovine breed exploited in Romania, being almost 90% from the total ovine livestock bred and exploited in our country. It presents great biodiversity both as color varieties and also as ecotype, the most spread one being white variety and for that reason in this article we propose to present a study on white variety bred in farms from Bistriţa-Năsăud, Cluj, Satu Mare and Sălaj Counties. In the morpho-productive characterization we followed aspects concerning the body development and some body sizes, the wool production, the lambs’ number and milk production. In abstract, we refer to the body weight and we can say that comparing with the breed standard, in which in females it is between 35.00 and 45.00 kg, in our analyzed livestock this parameter varied between 57.12 and 66.00 kg, and in males was surpassed the standard with over 25 kg. This fact shows a tenacious work for breed massiveness increasing and other analyzed features improvement comparatively to the breed standard.

  19. Post–breeding movements and migration patterns of western populations of common quail (Coturnix coturnix: from knowledge to hunting management

    Directory of Open Access Journals (Sweden)

    Rodríguez–Teijeiro, J. D.

    2012-01-01

    Full Text Available We investigated the patterns of post–breeding movements of the common quail (Coturnix coturnix in the Iberian peninsula with the aim of describing its migratory phenology and some physiological features of individuals. This information is needed to adjust hunting seasons in an optimal way. We worked with two data–sets: a captures made in a non–breeding site (Garraf from August to October in 2009 and 2010; b post–breeding recoveries of individuals ringed in Europe and recaptured in Spain between 1933 and 2005. The results showed that post–breeding movements in Garraf occur in two waves: a first wave that occurs around 10 VIII and is mainly composed of non–sexually active yearlings that do not correspond physiologically to migrants, and a second much more intense wave, which occurs around 17 IX and is mainly composed of non–sexually active migrant yearlings. The hunting season in Spain takes place mainly during the first wave, preserving the passage of migrant individuals from Spain and other European countries. Information on the post–breeding movements in other Spanish regions and other European countries where the common quail is a popular game species would improve timing between the hunting season and migration by providing more precise recommendations for hunting management.

  20. Factors affecting the accuracy of genomic selection for growth and wood quality traits in an advanced-breeding population of black spruce (Picea mariana).

    Science.gov (United States)

    Lenz, Patrick R N; Beaulieu, Jean; Mansfield, Shawn D; Clément, Sébastien; Desponts, Mireille; Bousquet, Jean

    2017-04-28

    Genomic selection (GS) uses information from genomic signatures consisting of thousands of genetic markers to predict complex traits. As such, GS represents a promising approach to accelerate tree breeding, which is especially relevant for the genetic improvement of boreal conifers characterized by long breeding cycles. In the present study, we tested GS in an advanced-breeding population of the boreal black spruce (Picea mariana [Mill.] BSP) for growth and wood quality traits, and concurrently examined factors affecting GS model accuracy. The study relied on 734 25-year-old trees belonging to 34 full-sib families derived from 27 parents and that were established on two contrasting sites. Genomic profiles were obtained from 4993 Single Nucleotide Polymorphisms (SNPs) representative of as many gene loci distributed among the 12 linkage groups common to spruce. GS models were obtained for four growth and wood traits. Validation using independent sets of trees showed that GS model accuracy was high, related to trait heritability and equivalent to that of conventional pedigree-based models. In forward selection, gains per unit of time were three times higher with the GS approach than with conventional selection. In addition, models were also accurate across sites, indicating little genotype-by-environment interaction in the area investigated. Using information from half-sibs instead of full-sibs led to a significant reduction in model accuracy, indicating that the inclusion of relatedness in the model contributed to its higher accuracies. About 500 to 1000 markers were sufficient to obtain GS model accuracy almost equivalent to that obtained with all markers, whether they were well spread across the genome or from a single linkage group, further confirming the implication of relatedness and potential long-range linkage disequilibrium (LD) in the high accuracy estimates obtained. Only slightly higher model accuracy was obtained when using marker subsets that were

  1. Genetic diversity and population genetic analysis of bovine MHC class II DRB3.2 locus in three Bos indicus cattle breeds of Southern India.

    Science.gov (United States)

    Das, D N; Sri Hari, V G; Hatkar, D N; Rengarajan, K; Saravanan, R; Suryanarayana, V V S; Murthy, L K

    2012-12-01

    The present study was performed to evaluate the genetic polymorphism of BoLA-DRB3.2 locus in Malnad Gidda, Hallikar and Ongole South Indian Bos indicus cattle breeds, employing the PCR-RFLP technique. In Malnad Gidda population, 37 BoLA-DRB3.2 alleles were detected, including one novel allele DRB3*2503 (GenBank: HM031389) that was observed in the frequency of 1.87%. In Hallikar and Ongole populations, 29 and 21 BoLA-DRB3.2 alleles were identified, respectively. The frequencies of the most common BoLA-DRB3.2 alleles (with allele frequency > 5%), in Malnad Gidda population, were DRB3.2*15 (10.30%), DRB3*5702 (9.35%), DRB3.2*16 (8.41%), DRB3.2*23 (7.01%) and DRB3.2*09 (5.61%). In Hallikar population, the most common alleles were DRB3.2*11 (13.00%), DRB3.2*44 (11.60%), DRB3.2*31 (10.30%), DRB3.2*28 (5.48%) and DRB3.2*51 (5.48%). The most common alleles in Ongole population were DRB3.2*15 (22.50%), DRB3.2*06 (20.00%), DRB3.2*13 (13.30%), DRB3.2*12 (9.17%) and DRB3.2*23 (7.50%). A high degree of heterozygosity observed in Malnad Gidda (H(O) = 0.934, H(E) = 0.955), Hallikar (H(O) = 0.931, H(E) = 0.943) and Ongole (H(O) = 0.800, H(E) = 0.878) populations, along with F(IS) values close to F(IS) zero (Malnad Gidda: F(IS) = 0.0221, Hallikar: F(IS) = 0.0127 and Ongole: F(IS) = 0.0903), yielded nonsignificant P-values with respect to Hardy-Weinberg equilibrium probabilities revealing, no perceptible inbreeding, greater genetic diversity and characteristic population structure being preserved in the three studied cattle populations. The phylogenetic tree constructed based on the frequencies of BoLA-DRB3.2 alleles observed in 10 Bos indicus and Bos taurus cattle breeds revealed distinct clustering of specific Bos indicus cattle breeds, along with unique genetic differentiation observed among them. The results of this study demonstrated that the BoLA-DRB3.2 is a highly polymorphic locus, with significant breed-specific genetic diversities being present amongst the three studied

  2. Aedes albopictus (Diptera: Culicidae) population size survey in the 2007 Chikungunya outbreak area in Italy. I. Characterization of breeding sites and evaluation of sampling methodologies.

    Science.gov (United States)

    Carrieri, M; Angelini, P; Venturelli, C; Maccagnani, B; Bellini, R

    2011-11-01

    The population of Aedes albopictus (Skuse) (Diptera: Culicidae) was measured in four towns in northern Italy by means of Stegomyia indices (house index: percentage of houses with at least one active breeding site; container index: percentage of containers with larvae; and Breteau index: number of active breeding sites per premises), pupae per premises index (PPI), pupae per hectare index (PHI), and ovitrap monitoring. A detailed investigation on types and number of productive or potential larval habitats in the inspected premises was performed. Catch basins were the most productive breeding sites in both private and public areas. The influence of the premises maintenance and premises shading indices (PMI and PSI) on the population indices and the correlations between the latter and egg density were assessed. The highest PPI was found in badly maintained premises, most times combined with shady coverage. Stegomyia indices and PPI were well correlated with each other, but not with the PHI, which also included the pupae collected in public areas. We obtained a highly positive correlation (R = 0.86) between the PHI and weekly mean egg density estimated 7-14 d after inspection of the premises. The number of females per hectare, calculated using the Focks model, was correlated with the mean egg density of the week after sampling (R = 0.79), and we propose that ovitrap monitoring can be used to evaluate the efficiency of the control activities or to determine a mean egg density threshold for epidemic risk evaluation.

  3. A global population redistribution in a migrant shorebird detected with continent-wide qualitative breeding survey data

    NARCIS (Netherlands)

    Rakhimberdiev, E.; Verkuil, Y.I.; Saveliev, A.A.; Vaisanen, R.A.; Karagicheva, J.; Soloviev, M.Y.; Tomkovich, P.S.; Piersma, T.

    2011-01-01

    Aim Over the last two decades, thousands of northward migrating ruffs (Philomachus pugnax) have disappeared from western European staging sites. These migratory ruffs were partly temperate breeding birds, but most individuals head towards the Eurasian Arctic tundras where 95% of the global populati

  4. Effect of imputing markers from a low-density chip on the reliability of genomic breeding values in Holstein populations

    DEFF Research Database (Denmark)

    Dassonneville, R; Brøndum, Rasmus Froberg; Druet, T

    2011-01-01

    The purpose of this study was to investigate the imputation error and loss of reliability of direct genomic values (DGV) or genomically enhanced breeding values (GEBV) when using genotypes imputed from a 3,000-marker single nucleotide polymorphism (SNP) panel to a 50,000-marker SNP panel. Data co...

  5. Scrapie prevalence in sheep of susceptible genotype is declining in a population subject to breeding for resistance

    NARCIS (Netherlands)

    Hagenaars, T.H.J.; Melchior, M.B.; Bossers, A.; Davidse, A.; Engel, B.; Zijderveld, van F.G.

    2010-01-01

    Background - Susceptibility of sheep to scrapie infection is known to be modulated by the PrP genotype of the animal. In the Netherlands an ambitious scrapie control programme was started in 1998, based on genetic selection of animals for breeding. From 2002 onwards EU regulations required intensive

  6. Optimizing Training Population Size and Genotyping Strategy for Genomic Prediction Using Association Study Results and Pedigree Information. A Case of Study in Advanced Wheat Breeding Lines

    Science.gov (United States)

    Jahoor, Ahmed; Orabi, Jihad; Andersen, Jeppe R.; Janss, Luc L.; Jensen, Just

    2017-01-01

    Wheat breeding programs generate a large amount of variation which cannot be completely explored because of limited phenotyping throughput. Genomic prediction (GP) has been proposed as a new tool which provides breeding values estimations without the need of phenotyping all the material produced but only a subset of it named training population (TP). However, genotyping of all the accessions under analysis is needed and, therefore, optimizing TP dimension and genotyping strategy is pivotal to implement GP in commercial breeding schemes. Here, we explored the optimum TP size and we integrated pedigree records and genome wide association studies (GWAS) results to optimize the genotyping strategy. A total of 988 advanced wheat breeding lines were genotyped with the Illumina 15K SNPs wheat chip and phenotyped across several years and locations for yield, lodging, and starch content. Cross-validation using the largest possible TP size and all the SNPs available after editing (~11k), yielded predictive abilities (rGP) ranging between 0.5–0.6. In order to explore the Training population size, rGP were computed using progressively smaller TP. These exercises showed that TP of around 700 lines were enough to yield the highest observed rGP. Moreover, rGP were calculated by randomly reducing the SNPs number. This showed that around 1K markers were enough to reach the highest observed rGP. GWAS was used to identify markers associated with the traits analyzed. A GWAS-based selection of SNPs resulted in increased rGP when compared with random selection and few hundreds SNPs were sufficient to obtain the highest observed rGP. For each of these scenarios, advantages of adding the pedigree information were shown. Our results indicate that moderate TP sizes were enough to yield high rGP and that pedigree information and GWAS results can be used to greatly optimize the genotyping strategy. PMID:28081208

  7. Differences between populations of Spinturnix myoti (Acari: Mesostigmata) in breeding and non-breeding colonies of Myotis myotis (Chiroptera) in central Europe: the effect of roost type.

    Science.gov (United States)

    Postawa, Tomasz; Szubert-Kruszyńska, Agnieszka; Ferenc, Hanna

    2014-12-01

    We studied variations in the abundance of parasitic spinturnicid mites in relation to the gender, age and body condition of bats living in different habitats. Populations of Spinturnix myoti Kolenati, 1856 (Acari: Spinturnicidae), an ectoparasite of the bat Myotis myotis (Borkhausen) (Mammalia: Chiroptera), were investigated in two types of roosts differing in microclimatic conditions: caves (low temperature and high humidity) and attics (high temperature and low humidity). Our data suggest that bats from cave nursery colonies harbour more parasites than those from attic colonies, irrespective of host sex or age. In underground colonies, adult females and their young differ in the mean abundance of parasites, whereas no such differences were found in attic colonies. Non-lactating females from underground roosts and lactating females from attic colonies had similar parasite loads, were lower than those of adult lactating females from caves. A negative correlation between the host body condition index and parasite load was found only in the most infected sex/age group of bats. In spite of significant differences in parasite load, the mean abundance of particular life stages of mites seems to be independent of the type of roost occupied by the host, its sex or age. However, in attic colonies the number of female deutonymphs was twice that of male deutonymphs, whereas in cave colonies the proportions of the sexes were similar. We suggest that the microclimate of the host's roosts may influence ectoparasite abundance through pressure on the sex ratio in the nymphal stages of mites.

  8. Patterns of molecular genetic variation among cat breeds.

    Science.gov (United States)

    Menotti-Raymond, Marilyn; David, Victor A; Pflueger, Solveig M; Lindblad-Toh, Kerstin; Wade, Claire M; O'Brien, Stephen J; Johnson, Warren E

    2008-01-01

    Genetic variation in cat breeds was assessed utilizing a panel of short tandem repeat (STR) loci genotyped in 38 cat breeds and 284 single-nucleotide polymorphisms (SNPs) genotyped in 24 breeds. Population structure in cat breeds generally reflects their recent ancestry and absence of strong breed barriers between some breeds. There is a wide range in the robustness of population definition, from breeds demonstrating high definition to breeds with as little as a third of their genetic variation partitioning into a single population. Utilizing the STRUCTURE algorithm, there was no clear demarcation of the number of population subdivisions; 16 breeds could not be resolved into independent populations, the consequence of outcrossing in established breeds to recently developed breeds with common ancestry. These 16 breeds were divided into 6 populations. Ninety-six percent of cats in a sample set of 1040 were correctly assigned to their classified breed or breed group/population. Average breed STR heterozygosities ranged from moderate (0.53; Havana, Korat) to high (0.85; Norwegian Forest Cat, Manx). Most of the variation in cat breeds was observed within a breed population (83.7%), versus 16.3% of the variation observed between populations. The hierarchical relationships of cat breeds is poorly defined as demonstrated by phylogenetic trees generated from both STR and SNP data, though phylogeographic grouping of breeds derived completely or in part from Southeast Asian ancestors was apparent.

  9. Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    Science.gov (United States)

    Spindel, Jennifer; Begum, Hasina; Akdemir, Deniz; Virk, Parminder; Collard, Bertrand; Redoña, Edilberto; Atlin, Gary; Jannink, Jean-Luc; McCouch, Susan R

    2015-02-01

    Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  10. Genomic selection and association mapping in rice (Oryza sativa: effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines.

    Directory of Open Access Journals (Sweden)

    Jennifer Spindel

    2015-02-01

    Full Text Available Genomic Selection (GS is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

  11. Variance estimation between different body measurements at the females population from Romanian Mioritic Shepherd Dog breed, to develop a genetic improvement program

    Directory of Open Access Journals (Sweden)

    Dorel Dronca

    2016-05-01

    Full Text Available Romanian Mioritic Shepherd Dog, was selected from a natural population breed in Carpathian Mountains. The aim of this paper was to estimate variance at 12 body measurements using 23 females from Romanian Mioritic Shepherd Dog breed. The animals were registered with the Romanian Mioritic Association Club from Romania. In order to develop a genetic improvement program at this effective of 23 females from Romanian Sheperd Dog breed, found in evidence of Romanian Mioritic Association Club from Romania, should be considered the following conclusions on variance those 12 characters studied in this paper, respectively, there is a large variance for the height at the middle back, the height at the croup, the height at the base of the tail, the width of the croup, the length of the tail, the depth of the thorax, the thorax perimeter, the height of the elbow and  for the height at the withers, the body length and the height at the hocks, the variance is middle.

  12. Recruitment in a Colorado population of big brown bats: Breeding probabilities, litter size, and first-year survival

    Science.gov (United States)

    O'Shea, T.J.; Ellison, L.E.; Neubaum, D.J.; Neubaum, M.A.; Reynolds, C.A.; Bowen, R.A.

    2010-01-01

    We used markrecapture estimation techniques and radiography to test hypotheses about 3 important aspects of recruitment in big brown bats (Eptesicus fuscus) in Fort Collins, Colorado: adult breeding probabilities, litter size, and 1st-year survival of young. We marked 2,968 females with passive integrated transponder (PIT) tags at multiple sites during 2001-2005 and based our assessments on direct recaptures (breeding probabilities) and passive detection with automated PIT tag readers (1st-year survival). We interpreted our data in relation to hypotheses regarding demographic influences of bat age, roost, and effects of years with unusual environmental conditions: extreme drought (2002) and arrival of a West Nile virus epizootic (2003). Conditional breeding probabilities at 6 roosts sampled in 2002-2005 were estimated as 0.64 (95% confidence interval [95% CI] = 0.530.73) in 1-year-old females, but were consistently high (95% CI = 0.940.96) and did not vary by roost, year, or prior year breeding status in older adults. Mean litter size was 1.11 (95% CI = 1.051.17), based on examination of 112 pregnant females by radiography. Litter size was not higher in older or larger females and was similar to results of other studies in western North America despite wide variation in latitude. First-year survival was estimated as 0.67 (95% CI = 0.610.73) for weaned females at 5 maternity roosts over 5 consecutive years, was lower than adult survival (0.79; 95% CI = 0.770.81), and varied by roost. Based on model selection criteria, strong evidence exists for complex roost and year effects on 1st-year survival. First-year survival was lowest in bats born during the drought year. Juvenile females that did not return to roosts as 1-year-olds had lower body condition indices in late summer of their natal year than those known to survive. ?? 2009 American Society of Mammalogists.

  13. Combining site occupancy, breeding population sizes and reproductive success to calculate time-averaged reproductive output of different habitat types: an application to Tricolored Blackbirds.

    Directory of Open Access Journals (Sweden)

    Marcel Holyoak

    Full Text Available In metapopulations in which habitat patches vary in quality and occupancy it can be complicated to calculate the net time-averaged contribution to reproduction of particular populations. Surprisingly, few indices have been proposed for this purpose. We combined occupancy, abundance, frequency of occurrence, and reproductive success to determine the net value of different sites through time and applied this method to a bird of conservation concern. The Tricolored Blackbird (Agelaius tricolor has experienced large population declines, is the most colonial songbird in North America, is largely confined to California, and breeds itinerantly in multiple habitat types. It has had chronically low reproductive success in recent years. Although young produced per nest have previously been compared across habitats, no study has simultaneously considered site occupancy and reproductive success. Combining occupancy, abundance, frequency of occurrence, reproductive success and nest failure rate we found that that large colonies in grain fields fail frequently because of nest destruction due to harvest prior to fledging. Consequently, net time-averaged reproductive output is low compared to colonies in non-native Himalayan blackberry or thistles, and native stinging nettles. Cattail marshes have intermediate reproductive output, but their reproductive output might be improved by active management. Harvest of grain-field colonies necessitates either promoting delay of harvest or creating alternative, more secure nesting habitats. Stinging nettle and marsh colonies offer the main potential sources for restoration or native habitat creation. From 2005-2011 breeding site occupancy declined 3x faster than new breeding colonies were formed, indicating a rapid decline in occupancy. Total abundance showed a similar decline. Causes of variation in the value for reproduction of nesting substrates and factors behind continuing population declines merit urgent

  14. PRINCIPLES OF ANIMAL BREEDING

    Directory of Open Access Journals (Sweden)

    Sonja Jovanovac

    2014-06-01

    Full Text Available University textbook Principles of Animal Breeding is intended for students of agriculture and veterinary medicine. The material is the adapted curricula of undergraduate and graduate level studies in the framework of which the modules Principles of animal breeding as well as Basics of genetics and selection of animals attended are listened. The textbook contains 14 chapters and a glossary of terms. Its concept enables combining fundamental and modern knowledge in the breeding and selection of animals based on balanced and quality manner. The textbook material can be divided into several thematic sections. The first one relates to the classical notions of domestic animals breeding such as the history of breeding, domestication, breed, hereditary and non-hereditary variability and description of general and production traits. The second section focuses on the basic concepts in population and quantitative genetics, as well as biometrics. The third unit is dedicated to the principles of selection and domestic animals improving. The fourth unit relates to the current concepts and objectives of the molecular markers use in domestic animals selection and breeding. The above material has been submitted to the Croatian universities, but so far it has not been published as a textbook. The Ministry of Science, Education and Sports of Republic of Croatia approved financial support for the textbook publication.

  15. [MspI-POLYMORPHISM IN FOURTH INTRON OF THE GROWTH HORMONE GENE IN CHICKEN POPULATIONS OF DIFFERENT BREEDS. ANALYSIS OF THE CAUSES OF ADDITIONAL RESTRICTION PATTERN ORIGIN].

    Science.gov (United States)

    Kulibaba, R A; Yurko, P S; Liashenkon, Y V

    2015-01-01

    The MspI-polymorphism in the fourth intron of the growth hormone gene in populations of White Plymouth Rock, Poltava Clay, Rhode Island Red and Borkovskaya Barvistaya chicken breeds was studied. It is shown that in all examined chicken populations the growth hormone gene is polymorphic. It was found that the presence of "additional" phenotype (restriction pattern) is not associated with duplication of the growth hormone gene. The possibility of formation of heteroduplex DNA of two different types in the course of amplification of heterozygous samples B/C, containing the site 'CCGG', which leads to formation the additional DNA fragment which do not contain the site 'CCGG', was described. The nucleotide sequences of alleles A, B, C and "additional" fragment is described. Frequencies of alleles A, B and C in chicken population of White Plymouth Rock breed were 0.56; 0.16 and 0.28; Poltava Clay--0.10; 0.07 and 0.83; Rhode Island Red--0.27; 0.31 and 0.42; Borkovskaya Barvistaya--0.75; 0.08 and 0.17 respectively.

  16. Demographic effects of extreme weather events: snow storms, breeding success, and population growth rate in a long-lived Antarctic seabird.

    Science.gov (United States)

    Descamps, Sébastien; Tarroux, Arnaud; Varpe, Øystein; Yoccoz, Nigel G; Tveraa, Torkild; Lorentsen, Svein-Håkon

    2015-01-01

    Weather extremes are one important element of ongoing climate change, but their impacts are poorly understood because they are, by definition, rare events. If the frequency and severity of extreme weather events increase, there is an urgent need to understand and predict the ecological consequences of such events. In this study, we aimed to quantify the effects of snow storms on nest survival in Antarctic petrels and assess whether snow storms are an important driver of annual breeding success and population growth rate. We used detailed data on daily individual nest survival in a year with frequent and heavy snow storms, and long term data on petrel productivity (i.e., number of chicks produced) at the colony level. Our results indicated that snow storms are an important determinant of nest survival and overall productivity. Snow storm events explained 30% of the daily nest survival within the 2011/2012 season and nearly 30% of the interannual variation in colony productivity in period 1985-2014. Snow storms are a key driver of Antarctic petrel breeding success, and potentially population dynamics. We also found state-dependent effects of snow storms and chicks in poor condition were more likely to die during a snow storm than chicks in good condition. This stresses the importance of considering interactions between individual heterogeneity and extreme weather events to understand both individual and population responses to climate change.

  17. Breeding-assisted genomics.

    Science.gov (United States)

    Poland, Jesse

    2015-04-01

    The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition.

  18. Morphological, molecular and cross-breeding analysis of geographic populations of coconut-mite associated predatory mites identified as Neoseiulus baraki: evidence for cryptic species?

    Science.gov (United States)

    Famah Sourassou, Nazer; Hanna, Rachid; Zannou, Ignace; Breeuwer, Johannes A J; de Moraes, Gilberto; Sabelis, Maurice W

    2012-05-01

    Surveys were conducted in Brazil, Benin and Tanzania to collect predatory mites as candidates for control of the coconut mite Aceria guerreronis Keifer, a serious pest of coconut fruits. At all locations surveyed, one of the most dominant predators on infested coconut fruits was identified as Neoseiulus baraki Athias-Henriot, based on morphological similarity with regard to taxonomically relevant characters. However, scrutiny of our own and published descriptions suggests that consistent morphological differences may exist between the Benin population and those from the other geographic origins. In this study, we combined three methods to assess whether these populations belong to one species or a few distinct, yet closely related species. First, multivariate analysis of 32 morphological characters showed that the Benin population differed from the other three populations. Second, DNA sequence analysis based on the mitochondrial cytochrome oxidase subunit I (COI) showed the same difference between these populations. Third, cross-breeding between populations was unsuccessful in all combinations. These data provide evidence for the existence of cryptic species. Subsequent morphological research showed that the Benin population can be distinguished from the others by a new character (not included in the multivariate analysis), viz. the number of teeth on the fixed digit of the female chelicera.

  19. Effects of flow regimes altered by dams on survival, population declines, and range-wide losses of California river-breeding frogs.

    Science.gov (United States)

    Kupferberg, Sarah J; Palen, Wendy J; Lind, Amy J; Bobzien, Steve; Catenazzi, Alessandro; Drennan, Joe; Power, Mary E

    2012-06-01

    Widespread alteration of natural hydrologic patterns by large dams combined with peak demands for power and water delivery during summer months have resulted in frequent aseasonal flow pulses in rivers of western North America. Native species in these ecosystems have evolved with predictable annual flood-drought cycles; thus, their likelihood of persistence may decrease in response to disruption of the seasonal synchrony between stable low-flow conditions and reproduction. We evaluated whether altered flow regimes affected 2 native frogs in California and Oregon (U.S.A.) at 4 spatial and temporal extents. We examined changes in species distribution over approximately 50 years, current population density in 11 regulated and 16 unregulated rivers, temporal trends in abundance among populations occupying rivers with different hydrologic histories, and within-year patterns of survival relative to seasonal hydrology. The foothill yellow-legged frog (Rana boylii), which breeds only in flowing water, is more likely to be absent downstream of large dams than in free-flowing rivers, and breeding populations are on average 5 times smaller in regulated rivers than in unregulated rivers. Time series data (range = 8 - 19 years) from 5 populations of yellow-legged frogs and 2 populations of California red-legged frogs (R. draytonii) across a gradient of natural to highly artificial timing and magnitude of flooding indicate that variability of flows in spring and summer is strongly correlated with high mortality of early life stages and subsequent decreases in densities of adult females. Flow management that better mimics natural flow timing is likely to promote persistence of these species and others with similar phenology.

  20. Estimating Breeding Values With Molecular Relatedness and Reconstructed Pedigrees in Natural Mating Populations of Common Sole, Solea Solea

    NARCIS (Netherlands)

    Blonk, R.J.W.; Komen, J.; Kamstra, A.; Arendonk, van J.A.M.

    2010-01-01

    Captive populations where natural mating in groups is used to obtain offspring typically yield unbalanced population structures with highly skewed parental contributions and unknown pedigrees. Consequently, for genetic parameter estimation, relationships need to be reconstructed or estimated using D

  1. Trends in the breeding population of Adélie penguins in the Ross Sea, 1981-2012: a coincidence of climate and resource extraction effects.

    Science.gov (United States)

    Lyver, Phil O'B; Barron, Mandy; Barton, Kerry J; Ainley, David G; Pollard, Annie; Gordon, Shulamit; McNeill, Stephen; Ballard, Grant; Wilson, Peter R

    2014-01-01

    Measurements of the size of Adélie penguin (Pygoscelis adeliae) colonies of the southern Ross Sea are among the longest biologic time series in the Antarctic. We present an assessment of recent annual variation and trends in abundance and growth rates of these colonies, adding to the published record not updated for more than two decades. High angle oblique aerial photographic surveys of colonies were acquired and penguins counted for the breeding seasons 1981-2012. In the last four years the numbers of Adélie penguins in the Ross and Beaufort Island colonies (southern Ross Sea metapopulation) reached their highest levels since aerial counts began in 1981. Results indicated that 855,625 pairs of Adélie penguins established breeding territories in the western Ross Sea, with just over a quarter (28%) of those in the southern portion, constituting a semi-isolated metapopulation (three colonies on Ross Island, one on nearby Beaufort Island). The southern population had a negative per capita growth rate of -0.019 during 1981-2000, followed by a positive per capita growth rate of 0.067 for 2001-2012. Colony growth rates for this metapopulation showed striking synchrony through time, indicating that large-scale factors influenced their annual growth. In contrast to the increased colony sizes in the southern population, the patterns of change among colonies of the northern Ross Sea were difficult to characterize. Trends were similar to southern colonies until the mid-1990s, after which the signal was lost owing to significantly reduced frequency of surveys. Both climate factors and recovery of whale populations likely played roles in the trends among southern colonies until 2000, after which depletion of another trophic competitor, the Antarctic toothfish (Dissostichus mawsoni), may explain the sharp increasing trend evident since then.

  2. Trends in the breeding population of Adelie penguins in the Ross Sea, 1981-2012: a coincidence of climate and resource extraction effects.

    Directory of Open Access Journals (Sweden)

    Phil O'B Lyver

    Full Text Available Measurements of the size of Adélie penguin (Pygoscelis adeliae colonies of the southern Ross Sea are among the longest biologic time series in the Antarctic. We present an assessment of recent annual variation and trends in abundance and growth rates of these colonies, adding to the published record not updated for more than two decades. High angle oblique aerial photographic surveys of colonies were acquired and penguins counted for the breeding seasons 1981-2012. In the last four years the numbers of Adélie penguins in the Ross and Beaufort Island colonies (southern Ross Sea metapopulation reached their highest levels since aerial counts began in 1981. Results indicated that 855,625 pairs of Adélie penguins established breeding territories in the western Ross Sea, with just over a quarter (28% of those in the southern portion, constituting a semi-isolated metapopulation (three colonies on Ross Island, one on nearby Beaufort Island. The southern population had a negative per capita growth rate of -0.019 during 1981-2000, followed by a positive per capita growth rate of 0.067 for 2001-2012. Colony growth rates for this metapopulation showed striking synchrony through time, indicating that large-scale factors influenced their annual growth. In contrast to the increased colony sizes in the southern population, the patterns of change among colonies of the northern Ross Sea were difficult to characterize. Trends were similar to southern colonies until the mid-1990s, after which the signal was lost owing to significantly reduced frequency of surveys. Both climate factors and recovery of whale populations likely played roles in the trends among southern colonies until 2000, after which depletion of another trophic competitor, the Antarctic toothfish (Dissostichus mawsoni, may explain the sharp increasing trend evident since then.

  3. Development of a novel sticky trap for container-breeding mosquitoes and evaluation of its sampling properties to monitor urban populations of Aedes albopictus.

    Science.gov (United States)

    Facchinelli, L; Valerio, L; Pombi, M; Reiter, P; Costantini, C; Della Torre, A

    2007-06-01

    Collection methods currently used for large-scale sampling of adult Stegomyia mosquitoes (Diptera: Culicidae) present several operational limitations, which constitute major drawbacks to the epidemiological surveillance of arboviruses, the evaluation of the impact of control strategies, and the surveillance of the spreading of allochthonous species into non-endemic regions. Here, we describe a new sticky trap designed to capture adult container-breeding mosquitoes and to monitor their population dynamics. We tested the sampling properties of the sticky trap in Rome, Italy, where Aedes (Stegomyia) albopictus is common. The results of our observations, and the comparison between sticky trap catches and catches made with the standard oviposition trap, are presented. The sticky trap collected significantly larger numbers of Ae. albopictus females than any other Culicidae species representing >90% of the total catches. A maximum of 83 An. albopictus females was collected in a single week. A high correlation (Pearson correlation coefficient r= 0.96) was found between the number of females and the number of eggs collected by the traps. The functional relationship between the number of eggs and the number of adult females was assessed by major axis regression fitted to log(1 +x)-transformed trap counts as y= 0.065 + 1.695x. Trap samples significantly departed from a random distribution; Taylor's power law was fitted to the trap samples to quantify the degree of aggregation in the catches, returning the equations s(2)= 2.401 m(1.325) for the sticky trap and s(2)= 13.068 m(1.441) for the ovitrap, with s(2) and m denoting the weekly catch variance and mean, respectively, indicating that eggs were significantly more aggregated than mosquitoes (P ovitrap. At low population densities (c. ovitrap was more sensitive at detecting the presence of this species. Overall, our results indicate that our new model of sticky trap can be used to sample Ae. albopictus females in urban

  4. Are population dynamics of shorebirds affected by El Niño/Southern Oscillation (ENSO) while on their non-breeding grounds in Ecuador?

    Science.gov (United States)

    O'Hara, Patrick D.; Haase, Ben J. M.; Elner, Robert W.; Smith, Barry D.; Kenyon, Jamie K.

    2007-08-01

    Declines in avian populations are a global concern, particularly for species that migrate between Arctic-temperate and tropical locations. Long-term population studies offer opportunities to detect and document ecological effects attributable to long-term climatic cycles such as the El Niño/Southern Oscillation (ENSO). In this study, we report possible population-level effects of such climatic cycles on shorebird species that use two non-breeding season sites in Ecuador (Santa Elena peninsula area, near La Libertad). During our 9-year study period (1991/1992-1999/2000), there was a particularly strong ENSO warm phase event during 1997/1998. Population trend data for three species of shorebird, Western Sandpipers ( Calidris mauri), Semipalmated Sandpipers ( C. pusilla), and Least Sandpipers ( C. minutilla), indicated abundances generally declined during the 1990s, but there was an increase in the proportion of first-year birds and their abundance in the years following the 1997/1998 ENSO warm phase. There was some support for variation in apparent survivorship associated with the onset of the ENSO warm phase event in our population models, based on capture-mark-recapture data. Following the 1997/1998 ENSO event onset, individuals for all three species were significantly lighter during the non-breeding season ( F1,3789 = 6.6, p = 0.01). Least-squares mean mass (controlling for size, sex and day of capture) for first-year birds dropped significantly more than for adults following ENSO (first-year mass loss = 0.69 ± 0.12 g; adult mass loss = 0.34 ± 0.11 g, F1,3789 = 5.31, p = 0.021), and least-squares mean mass dropped most during the period when sandpipers prepare for northward migration by gaining mass and moulting into breeding plumage. Least Sandpipers may have declined the most in mean mass following ENSO (0.76 ± 0.19 g), whereas Semipalmated Sandpipers were 0.52 ± 0.12 g lighter, and Western Sandpipers 0.40 ± 0.13 g lighter, but overall variation among

  5. Altitudinal genetic variation among Pinus oocarpa populations in Michoacan, Mexico: implications for seed zoning, conservation, tree breeding and global warming

    Science.gov (United States)

    Cuauhtemoc Saenz-Romero; R. Ricardo Guzman-Reyna; Gerald E. Rehfeldt

    2006-01-01

    Pinus oocarpa has a large natural distribution in the sub-tropical forests of Mexico. Populations, however, are rapidly disappearing particularly in the Michoacan State as native forests are converted to avocado (Persea sp.) orchards.We investigated the patterning of genetic variation among P. oocarpa populations...

  6. Variation in breeding phenology provides insights into drivers of long-term population change in harbour seals.

    Science.gov (United States)

    Cordes, Line S; Thompson, Paul M

    2013-08-07

    Phenological trends provide important indicators of environmental change and population dynamics. However, the use of untested population-level measures can lead to incorrect conclusions about phenological trends, particularly when changes in population structure or density are ignored. We used individual-based estimates of birth date and lactation duration of harbour seals (Phoca vitulina) to investigate energetic consequences of changes in pupping phenology. Using generalized linear mixed models, we first demonstrate annual variation in pupping phenology. Second, we show a negative relationship between lactation duration and the timing of pupping, indicating that females who pup early nurse their pups longer, thereby highlighting lactation duration as a useful proxy of female condition and resource availability. Third, individual-based data were used to derive a population-level proxy that demonstrated an advance in pupping date over the last 25 years, co-incident with a reduction in population abundance that resulted from fisheries-related shootings. These findings demonstrate that phenological studies examining the impacts of climate change on mammal populations must carefully control for changes in population density and highlight how joint investigations of phenological and demographic change provide insights into the drivers of population declines.

  7. Parameters in the estimation of the most suitable F2 population size in conventional maize (Zea mays L. breeding programs

    Directory of Open Access Journals (Sweden)

    Delić Nenad

    2010-01-01

    Full Text Available The objective of the present study was to observe differences among four sizes of the F2 populations (100, 200, 300 and 500 plants on the basis of test-crosses for grain yield according to the average values of the populations, genetic and phenotypic variances, genotypic and phenotypic coefficients of variations and broad-sense heritability. The values of genetic variance did not significantly differ over population sizes according to all possible comparisons, including the comparison of values obtained for the phenotypic variance. Furthermore, the values of broadsense heritability (67.8%-69% did not significantly vary over different F2 population sizes. Genetic variability of the observed progenies, as a principal prerequisite of successful selection, was at the satisfactory level in all population sizes.

  8. Genetic network and breeding patterns of a sicklefin lemon shark (Negaprion acutidens population in the Society Islands, French Polynesia.

    Directory of Open Access Journals (Sweden)

    Johann Mourier

    Full Text Available Human pressures have put many top predator populations at risk of extinction. Recent years have seen alarming declines in sharks worldwide, while their resilience remains poorly understood. Studying the ecology of small populations of marine predators is a priority to better understand their ability to withstand anthropogenic and environmental stressors. In the present study, we monitored a naturally small island population of 40 adult sicklefin lemon sharks in Moorea, French Polynesia over 5 years. We reconstructed the genetic relationships among individuals and determined the population's mating system. The genetic network illustrates that all individuals, except one, are interconnected at least through one first order genetic relationship. While this species developed a clear inbreeding avoidance strategy involving dispersal and migration, the small population size, low number of breeders, and the fragmented environment characterizing these tropical islands, limits its complete effectiveness.

  9. 75 FR 37245 - 2010 Standards for Delineating Metropolitan and Micropolitan Statistical Areas

    Science.gov (United States)

    2010-06-28

    ...(b) is used in a much more limited fashion, only applying that criterion to those potential... estimates. The urbanized areas and urban clusters used in the 2018 update will be those delineated with 2010... delineated urbanized area of at least 50,000 population or a Census Bureau delineated urban cluster of...

  10. Cestode communities in non-breeding populations of four grebe species (Aves: Podicipedidae) from the Bulgarian Black Sea coast.

    Science.gov (United States)

    Vasileva, G P; Georgiev, B B

    1999-09-01

    Cestode communities in Podiceps cristatus, P. grisegena, P. nigricollis and Tachybaptus ruficollis during their migrations and overwintering are studied at the Bulgarian Black Sea coast. The infracommunities exhibit high richness, abundance and dominance, and low diversity and similarity. The component communities have a similar taxonomic structure at the levels higher than species, a small number of core species and a high portion of grebe specialists in the richness and abundance. The comparison with cestode communities in grebes from Canada (Stock & Holmes, 1987) reveals several differences and similarities. The higher richness and abundance of the infracommunities in Canada are explained by the constant conditions of breeding habitats enhancing higher transmission rates. At the component community level, there is a significant difference between the two species lists. The degree of parasite exchange among the grebe species in Bulgaria is lower. Several characters of cestode component communities in grebes do not depend on either historical factors or different habitats. These are the similar patterns of the taxonomic structure at the levels higher than species, almost the same list of generalists, the participation of specialists of anatids, and the leading role of grebe specialists in the structure.

  11. Comparison of molecular breeding values based on within- and across-breed training in beef cattle.

    Science.gov (United States)

    Kachman, Stephen D; Spangler, Matthew L; Bennett, Gary L; Hanford, Kathryn J; Kuehn, Larry A; Snelling, Warren M; Thallman, R Mark; Saatchi, Mahdi; Garrick, Dorian J; Schnabel, Robert D; Taylor, Jeremy F; Pollak, E John

    2013-08-16

    molecular breeding values had similar accuracies. The benefit of adding data from other breeds to a within-breed training population is the ability to produce molecular breeding values that are more robust across breeds and these can be utilized until enough training data has been accumulated to allow for a within-breed training set.

  12. Food Production in Habitats Utilized by the Rocky Mountain Population of Sandhill Cranes during Breeding, Migration, and Wintering.

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This author chose to investigate the Rocky Mountain Population (RMP) of the Sandhill Crane in an effort to provide information that identifies the distribution,...

  13. Population Genetic Structure of the Magnificent Frigatebird Fregata magnificens (Aves, Suliformes) Breeding Colonies in the Western Atlantic Ocean.

    Science.gov (United States)

    Nuss, Andressa; Carlos, Caio J; Moreno, Ignacio B; Fagundes, Nelson J R

    2016-01-01

    The Magnificent Frigatebird Fregata magnificens has a pantropical distribution, nesting on islands along the Atlantic and Pacific coasts. In the Caribbean, there is little genetic structure among colonies; however, the genetic structure among the colonies off Brazil and its relationship with those in the Caribbean are unknown. In this study, we used mtDNA and microsatellite markers to infer population structure and evolutionary history in a sample of F. magnificens individuals collected in Brazil, Grand Connétable (French Guyana), and Barbuda. Virtually all Brazilian individuals had the same mtDNA haplotype. There was no haplotype sharing between Brazil and the Caribbean, though Grand Connétable shared haplotypes with both regions. A Bayesian clustering analysis using microsatellite data found two genetic clusters: one associated with Barbuda and the other with the Brazilian populations. Grand Connétable was more similar to Barbuda but had ancestry from both clusters, corroborating its "intermediate" position. The Caribbean and Grand Connétable populations showed higher genetic diversity and effective population size compared to the Brazilian population. Overall, our results are in good agreement with an effect of marine winds in isolating the Brazilian meta-population.

  14. An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds.

    Directory of Open Access Journals (Sweden)

    Beatriz eGutiérrez-Gil

    2015-05-01

    Full Text Available This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1,049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds and 6 dual-purpose breeds, and four different beef-vs-dairy comparisons, which we subsequently grouped into core selective sweep (CSS regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57% of which were associated with a single-breed (Single-breed CSSs, 134 CSSs (33% were associated with a limited number of breeds (Two-to-four-breed CSSs and 39 CSSs (9% were associated with five or more breeds (Multi-breed CSSs. For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5,183 BioMart-extracted genes linked to dairy and meat production, stature and coat colour traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behaviour, immune response and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as divergence signals, which may be useful in characterising and protecting livestock genetic diversity.

  15. An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds

    Science.gov (United States)

    Gutiérrez-Gil, Beatriz; Arranz, Juan J.; Wiener, Pamela

    2015-01-01

    This review compiles the results of 21 genomic studies of European Bos taurus breeds and thus provides a general picture of the selection signatures in taurine cattle identified by genome-wide selection-mapping scans. By performing a comprehensive summary of the results reported in the literature, we compiled a list of 1049 selection sweeps described across 37 cattle breeds (17 beef breeds, 14 dairy breeds, and 6 dual-purpose breeds), and four different beef-vs.-dairy comparisons, which we subsequently grouped into core selective sweep (CSS) regions, defined as consecutive signals within 1 Mb of each other. We defined a total of 409 CSSs across the 29 bovine autosomes, 232 (57%) of which were associated with a single-breed (Single-breed CSSs), 134 CSSs (33%) were associated with a limited number of breeds (Two-to-Four-breed CSSs) and 39 CSSs (9%) were associated with five or more breeds (Multi-breed CSSs). For each CSS, we performed a candidate gene survey that identified 291 genes within the CSS intervals (from the total list of 5183 BioMart-extracted genes) linked to dairy and meat production, stature, and coat color traits. A complementary functional enrichment analysis of the CSS positional candidates highlighted other genes related to pathways underlying behavior, immune response, and reproductive traits. The Single-breed CSSs revealed an over-representation of genes related to dairy and beef production, this was further supported by over-representation of production-related pathway terms in these regions based on a functional enrichment analysis. Overall, this review provides a comparative map of the selection sweeps reported in European cattle breeds and presents for the first time a characterization of the selection sweeps that are found in individual breeds. Based on their uniqueness, these breed-specific signals could be considered as “divergence signals,” which may be useful in characterizing and protecting livestock genetic diversity. PMID:26029239

  16. Conservation priorities for Ethiopian sheep breeds combining threat status, breed merits and contributions to genetic diversity

    Directory of Open Access Journals (Sweden)

    Windig Jack J

    2008-07-01

    Full Text Available Abstract Prioritizing livestock breeds for conservation needs to incorporate both genetic and non-genetic aspects important for the survival of the breeds. Here, we apply a maximum-utility-strategy to prioritize 14 traditional Ethiopian sheep breeds based on their threat status, contributions to farmer livelihoods (current breed merits and contributions to genetic diversity. Contributions of the breeds to genetic diversity were quantified using Eding's marker-estimated kinship approaches. Non-genetic aspects included threats (e.g. low population size, low preferences by farmers and current merits (economic, ecological and cultural merits. Threat analysis identified eight of the 14 breeds as threatened. Analysis of current merits showed that sub-alpine and arid-lowland breeds contribute most to farmer livelihoods in comparison to other breeds. The highest contribution to the genetic diversity conserved was from the Simien breed. Simien showed high between-breed (low between-breed kinship = 0.04 as well as high within-breed diversity (low within-breed kinship = 0.09 and high HE = 0.73 and allelic richness = 6.83. We combined the results on threat status, current breed merits and contributions to genetic diversity to produce a ranking of the 14 breeds for conservation purposes. Our results balance the trade-offs between conserving breeds as insurance against future uncertainties and current sustainable utilization. The ranking of breeds provides a basis for conservation strategies for Ethiopian sheep and contributes to a regional or global conservation plan.

  17. Accuracies of genomically estimated breeding values from pure-breed and across-breed predictions in Australian beef cattle.

    Science.gov (United States)

    Boerner, Vinzent; Johnston, David J; Tier, Bruce

    2014-10-24

    The major obstacles for the implementation of genomic selection in Australian beef cattle are the variety of breeds and in general, small numbers of genotyped and phenotyped individuals per breed. The Australian Beef Cooperative Research Center (Beef CRC) investigated these issues by deriving genomic prediction equations (PE) from a training set of animals that covers a range of breeds and crosses including Angus, Murray Grey, Shorthorn, Hereford, Brahman, Belmont Red, Santa Gertrudis and Tropical Composite. This paper presents accuracies of genomically estimated breeding values (GEBV) that were calculated from these PE in the commercial pure-breed beef cattle seed stock sector. PE derived by the Beef CRC from multi-breed and pure-breed training populations were applied to genotyped Angus, Limousin and Brahman sires and young animals, but with no pure-breed Limousin in the training population. The accuracy of the resulting GEBV was assessed by their genetic correlation to their phenotypic target trait in a bi-variate REML approach that models GEBV as trait observations. Accuracies of most GEBV for Angus and Brahman were between 0.1 and 0.4, with accuracies for abattoir carcass traits generally greater than for live animal body composition traits and reproduction traits. Estimated accuracies greater than 0.5 were only observed for Brahman abattoir carcass traits and for Angus carcass rib fat. Averaged across traits within breeds, accuracies of GEBV were highest when PE from the pooled across-breed training population were used. However, for the Angus and Brahman breeds the difference in accuracy from using pure-breed PE was small. For the Limousin breed no reasonable results could be achieved for any trait. Although accuracies were generally low compared to published accuracies estimated within breeds, they are in line with those derived in other multi-breed populations. Thus PE developed by the Beef CRC can contribute to the implementation of genomic selection in

  18. Formação e estrutura populacional do eqüino Brasileiro de Hipismo Formation and population structure of the Brasileiro de Hipismo horse breed

    Directory of Open Access Journals (Sweden)

    I.M.G. Dias

    2000-12-01

    Full Text Available Analisaram-se dados do Stud Book Brasileiro do Cavalo de Hipismo, da Associação Brasileira de Criadores do Cavalo de Hipismo (ABCCH, correspondentes a julho de 1977 a setembro de 1998. O arquivo final continha 19.303 eqüinos, 11.508 da raça Brasileira de Hipismo (BH e 7.795 de raças formadoras. Distribuição de freqüência, medidas de tendência central e de dispersão por criador, proprietário, sexo, tipo de registro, estado do nascimento, raça formadora, cruzamento utilizado na formação e coeficiente de endogamia foram estabelecidas para os efetivos da raça BH. Foram também calculados número da geração de cada animal, intervalo de gerações (anos e tamanho efetivo da população (Ne. Vinte raças foram utilizadas na formação do BH, sendo as principais: BH (22,5%, animais sem genealogia conhecida (21,9%, PSI (15,0%, Hanoverana (8,1%, Westfalen (5,2%, Holsteiner (4,8% e Trakehner (4,1%. Registros foram feitos em 14 estados da Federação, 76% deles em São Paulo. Número máximo de gerações encontrado foi de 3,12 (um animal, 59,7% dos animais na geração base e 24,1% na geração 1,5. O intervalo médio de gerações foi de 9,9 anos, 10,4 para garanhões e 9,3 para éguas. O Ne foi de 253 animais e os coeficientes de endogamia observado e esperado foram próximos de zero.Data from Brasileiro de Hipismo Stud Book, collected by the breed Association (ABCCH, from July 1977 to September 1998 were analyzed. Final data set included 19,303 animals, 11,508 Brasileiro de Hipismo (BH and 7,795 of other foundation breeds. Data were analyzed for frequency, central tendency and range of variation according to owner, breeder, sex, type of registration, county and state of birth and foundation breeds. The frequency of crosses using foundation breeds and inbreeding coefficient according to year of birth and sex were estimated. Generation number for each animal, generation interval and effective population size (Ne were calculated. Among

  19. Employing individual measures of baseline glucocorticoids as population-level conservation biomarkers: considering within-individual variation in a breeding passerine

    Science.gov (United States)

    Madliger, Christine L.; Love, Oliver P.

    2016-01-01

    Labile physiological variables, such as stress hormones [i.e. glucocorticoids (GCs)], allow individuals to react to perturbations in their environment and may therefore reflect the effect of disturbances or positive conservation initiatives in advance of population-level demographic measures. Although the application of GCs as conservation biomarkers has been of extensive interest, few studies have explicitly investigated whether baseline GC concentrations respond to disturbances consistently across individuals. However, confirmation of consistent responses is of paramount importance to assessing the ease of use of GCs in natural systems and to making valid interpretations regarding population-level change (or lack of change) in GC concentrations. We investigated whether free-ranging female tree swallows (Tachycineta bicolor) display individually specific changes in baseline glucocorticoid concentrations naturally over the breeding season (from incubation to offspring provisioning) and in response to a manipulation of foraging profitability (representing a decrease in access to food resources). We show that baseline GC concentrations are repeatable within individuals over reproduction in natural conditions. However, in response to a reduction in foraging ability, baseline GC concentrations increase at the population level but are not repeatable within individuals, indicating a high level of within-individual variation. Overall, we suggest that baseline GCs measured on a subset of individuals may not provide a representative indication of responses to environmental change at the population level, and multiple within-individual measures may be necessary to determine the fitness correlates of GC concentrations. Further validation should be completed across a variety of taxa and life-history stages. Moving beyond a traditional cross-sectional approach by incorporating repeated-measures methods will be necessary to assess the suitability of baseline GCs as biomarkers of

  20. The relationship between sea surface temperature and population change of Great Cormorants Phalacrocorax carbo breeding near Disko Bay, Greenland

    DEFF Research Database (Denmark)

    White, C.R.; Boertmann, David; Gremillet, D.

    2011-01-01

    Arctic seas have warmed and sea ice has retreated. This has resulted in range contraction and population declines in some species, but it could potentially be a boon for others. Great Cormorants Phalacrocorax carbo have a partially wettable plumage and seem poorly suited to foraging in Arctic...

  1. Future breeding and foraging sites of a southern edge population of the locally endangered Black Guillemot Cepphus grylle

    NARCIS (Netherlands)

    Buchadas, Ana R.C.; Hof, Anouschka R.

    2017-01-01

    Capsule: One of the southernmost populations of the Black Guillemot Cepphus grylle is currently endangered, and the risk may be exacerbated by climate change. Aims: We evaluated the future vulnerability of the Black Guillemot by predicting the impact of climate change on the geographic distribution

  2. The relationship between sea surface temperature and population change of Great Cormorants Phalacrocorax carbo breeding near Disko Bay, Greenland

    DEFF Research Database (Denmark)

    White, C.R.; Boertmann, David; Gremillet, D.

    2011-01-01

    Arctic seas have warmed and sea ice has retreated. This has resulted in range contraction and population declines in some species, but it could potentially be a boon for others. Great Cormorants Phalacrocorax carbo have a partially wettable plumage and seem poorly suited to foraging in Arctic wat...

  3. Multi-Generational Kinship, Multiple Mating, and Flexible Modes of Parental Care in a Breeding Population of the Veery (Catharus fuscescens), a Trans-Hemispheric Migratory Songbird.

    Science.gov (United States)

    Halley, Matthew R; Heckscher, Christopher M; Kalavacharla, Venugopal

    2016-01-01

    We discovered variable modes of parental care in a breeding population of color-banded Veeries (Catharus fuscescens), a Nearctic-Neotropical migratory songbird, long thought to be socially monogamous, and performed a multi-locus DNA microsatellite analysis to estimate parentage and kinship in a sample of 37 adults and 21 offspring. We detected multiple mating in both sexes, and four modes of parental care that varied in frequency within and between years including multiple male feeders at some nests, and males attending multiple nests in the same season, each with a different female. Unlike other polygynandrous systems, genetic evidence indicates that multi-generational patterns of kinship occur among adult Veeries at our study site, and this was corroborated by the capture of an adult male in 2013 that had been banded as a nestling in 2011 at a nest attended by multiple male feeders. All genotyped adults (n = 37) were related to at least one other bird in the sample at the cousin level or greater (r ≥ 0.125), and 81% were related to at least one other bird at the half-sibling level or greater (r ≥ 0.25, range 0.25-0.60). Although our sample size is small, it appears that the kin structure is maintained by natal philopatry in both sexes, and that Veeries avoid mating with close genetic kin. At nests where all adult feeders were genotyped (n = 9), the male(s) were unrelated to the female (mean r = -0.11 ± 0.15), whereas genetic data suggest close kinship (r = 0.254) between two male co-feeders at the nests of two females in 2011, and among three of four females that were mated to the same polygynous male in 2012. To our knowledge, this is the first evidence of polygynandry occurring among multiple generations of close genetic kin on the breeding ground of a Nearctic-Neotropical migratory songbird.

  4. Multi-Generational Kinship, Multiple Mating, and Flexible Modes of Parental Care in a Breeding Population of the Veery (Catharus fuscescens, a Trans-Hemispheric Migratory Songbird.

    Directory of Open Access Journals (Sweden)

    Matthew R Halley

    Full Text Available We discovered variable modes of parental care in a breeding population of color-banded Veeries (Catharus fuscescens, a Nearctic-Neotropical migratory songbird, long thought to be socially monogamous, and performed a multi-locus DNA microsatellite analysis to estimate parentage and kinship in a sample of 37 adults and 21 offspring. We detected multiple mating in both sexes, and four modes of parental care that varied in frequency within and between years including multiple male feeders at some nests, and males attending multiple nests in the same season, each with a different female. Unlike other polygynandrous systems, genetic evidence indicates that multi-generational patterns of kinship occur among adult Veeries at our study site, and this was corroborated by the capture of an adult male in 2013 that had been banded as a nestling in 2011 at a nest attended by multiple male feeders. All genotyped adults (n = 37 were related to at least one other bird in the sample at the cousin level or greater (r ≥ 0.125, and 81% were related to at least one other bird at the half-sibling level or greater (r ≥ 0.25, range 0.25-0.60. Although our sample size is small, it appears that the kin structure is maintained by natal philopatry in both sexes, and that Veeries avoid mating with close genetic kin. At nests where all adult feeders were genotyped (n = 9, the male(s were unrelated to the female (mean r = -0.11 ± 0.15, whereas genetic data suggest close kinship (r = 0.254 between two male co-feeders at the nests of two females in 2011, and among three of four females that were mated to the same polygynous male in 2012. To our knowledge, this is the first evidence of polygynandry occurring among multiple generations of close genetic kin on the breeding ground of a Nearctic-Neotropical migratory songbird.

  5. Retrospective study of mortality in Asiatic lions (Panthera leo persica) in the European breeding population between 2000 and 2014.

    Science.gov (United States)

    Metz, Olivia; Williams, Jonathan; Nielsen, Rikke Kruse; Masters, Nic

    2017-01-01

    Although the European population of Asiatic lions (Panthera leo persica) has been managed under the European Endangered Species Program (EEP) since 1990, little is known about the health status of the population. This study was designed to characterize mortality for this population through examination of the studbook and other records on 392 Asiatic lions living in the EEP between 2000 and 2014. A total of 270 animals died during the period with 80% of them being under 1 year old. The mortality rate for under 1 year olds was 54%, while the odds of survival of cubs within a litter increased if the dam had had litters previously. Survival to reproductive age was 44%. Post-mortem reports were requested and the cause of death was obtained for 133 animals. Trauma inflicted by a conspecific and lack of care were common causes of death (26% and 22%, respectively) and were also responsible for most of the neonatal mortalities. Congenital defects were responsible for 9% of deaths, although the true prevalence is likely underestimated. A common necropsy protocol for all Asiatic lion collections is needed to facilitate future studies. Zoo Biol. 36:66-73, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  6. Reproduction performances of a synthetic rabbit line and rabbits of of local populations in Algeria, in 2 breeding locations

    Directory of Open Access Journals (Sweden)

    Nacira Zerrouki

    2014-12-01

    Full Text Available The aim of this study was to compare the production of a synthetic line (Syn of rabbits to that of 2 local Algerian populations (W and Loc. The Syn line was obtained from the crossbreeding of a well adapted local population frequently used in Algerian familial farms (Loc with a more productive French strain. The W population is maintained by a public cooperative and is used mainly in Kabylia region; it is called “white” because of its albino phenotype. Rabbits were placed under the same experimental conditions in 2 rabbitries of a state technical institute. In Baba Ali (Algiers, 50 does of each genotype were raised during 2 yr. In Lamtar (Sidi Bel Abbes, 30 does of the Syn line and 30 of Loc population were compared during 16 mo of production. Natural mating was used 10-11 d after parturition. Kits were weaned at 33-35 d. Litter size and litter weights were measured at birth and weaning. In both locations Syn dams were heavier than those of the other genotypes: (3616, 3464 and 3305 g for Syn, W and Loc in Baba Ali, and 3592 and 3173 for Syn and Loc in Lamtar; P<0.001. The observed litter sizes showed a superiority (P<0.001 of the Syn line compared to W and Loc does at birth time (8.76, 6.78 and 6.19 for Syn, W and Loc in Baba Ali, and 8.02 and 5.90 for Syn and Loc in Lamtar and at weaning (6.85, 5.83 and 5.44 for Syn, W and Loc in Baba Ali, and 6.61 and 5.15 for Syn and Loc in Lamtar; P<0.001. Most probably as a consequence of the important difference in litter sizes, average individual weight at weaning was weaker for the synthetic line than for the Loc population: 543 vs. 563 g in Baba Ali and 561 vs. 621 g in Lamtar. For the W population in Baba Ali, the weaning weight was similar to that of the Loc population: 565 vs. 563 g. There were no genotype×season interactions which changed the genotypes ranking, and the Syn line performances were more regular from one season to the other than those of the 2 other genotypes

  7. South-East Asia bovine populations and the Japanese cattle breeds do not harbour the E211K variant of the PRNP

    Directory of Open Access Journals (Sweden)

    George Msalya

    2014-02-01

    Full Text Available An important outcome of intensive worldwide Bovine spongiform encephalopathy (BSE obtained with the surveillance by The National Creutzfeldt-Jakob Disease Surveillance Unit (http://www.cjd.ed.ac.uk/figures. htm, has been the detection of atypical BSE in cattle. The discovery of a prion protein gene (PRNP E211K variant in an atypical BSE case is particularly remarkable because it is analogous to the most common pathogenic mutation in humans (E200K, which causes hereditary Creutzfeldt-Jakob disease (CJD. Knowledge of the distribution and frequency of PRNP E211K variants in cattle populations is critical for understanding and managing atypical BSE. This study was carried out to investigate the prevalence of the E211K variant in the South-East Asia bovine populations and in the Japanese cattle breeds. It was discovered that E211K variant was monomorphic for a G allele and the GG genotype in the 745 animals analyzed in this study. Therefore, neither the Bos indicus nor the Bos taurus animals analyzed are presently known to harbor the 211K variant predicting that the number of carriers for this variant will also be vanishingly low.

  8. 30 CFR 282.22 - Delineation Plan.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 2 2010-07-01 2010-07-01 false Delineation Plan. 282.22 Section 282.22 Mineral... § 282.22 Delineation Plan. All exploration activities shall be conducted in accordance with a Delineation Plan submitted by the lessee and approved by the Director. The Delineation Plan shall describe...

  9. Native Pig and Chicken Breed Database: NPCDB.

    Science.gov (United States)

    Jeong, Hyeon-Soo; Kim, Dae-Won; Chun, Se-Yoon; Sung, Samsun; Kim, Hyeon-Jeong; Cho, Seoae; Kim, Heebal; Oh, Sung-Jong

    2014-10-01

    Indigenous (native) breeds of livestock have higher disease resistance and adaptation to the environment due to high genetic diversity. Even though their extinction rate is accelerated due to the increase of commercial breeds, natural disaster, and civil war, there is a lack of well-established databases for the native breeds. Thus, we constructed the native pig and chicken breed database (NPCDB) which integrates available information on the breeds from around the world. It is a nonprofit public database aimed to provide information on the genetic resources of indigenous pig and chicken breeds for their conservation. The NPCDB (http://npcdb.snu.ac.kr/) provides the phenotypic information and population size of each breed as well as its specific habitat. In addition, it provides information on the distribution of genetic resources across the country. The database will contribute to understanding of the breed's characteristics such as disease resistance and adaptation to environmental changes as well as the conservation of indigenous genetic resources.

  10. Inheritance patterns and identification of microsatellite markers linked to the rice blast resistance in BC2F1 population of rice breeding

    Directory of Open Access Journals (Sweden)

    Gous Miah

    2015-03-01

    Full Text Available The BC2F1 population was derived from a cross between rice variety, MR219 (susceptible to blast and Pongsu Seribu 1 (resistant to blast. The objectives of this research were to know the inheritance pattern of blast resistance and to identify the linked markers associated with blast resistance in BC2F1 population. Sixteen microsatellite markers were found as polymorphic between the parents related to blast resistant genes (Pi-genes. Among the selected blast resistant linked markers, two markers RM6836 and RM8225 showed expected testcross ratio (1:1 for single-gene model in the BC2F1 population with the association between resistant and susceptible progeny. A total of 333-BC2F1 plants were challenged with the most virulent pathotype P7.2 of Magnaporthe oryzae. Chi-square (χ2 analysis for phenotypic segregation in single-gene model showed goodness of fit (P = 0.4463 to the expected segregation ratio (1:1. In marker segregation analysis, two polymorphic markers (RM6836 and RM8225 clearly showed goodness of fit to the expected segregation testcross ratio (1:1 for the single-gene model. The marker RM8225 and RM6836 showed significant R2 values higher than 10 for the trait of the blast lesions degree (BLD. The positions of RM6836 and RM8225 markers on rice chromosome 6 and the distance between these two markers is 0.2 cM. We conclude that single dominant gene control the blast resistance in Pongsu Seribu 1 located on chromosome 6, which is linked to RM8225 and RM6836 microsatellite markers. This information could be useful in marker-assisted selection for blast resistance in rice breeding involving Pongsu Seribu 1.

  11. Assortative mating and fragmentation within dog breeds

    Directory of Open Access Journals (Sweden)

    Hailer Frank

    2008-01-01

    Full Text Available Abstract Background There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Results Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. Conclusion The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic

  12. Assortative mating and fragmentation within dog breeds.

    Science.gov (United States)

    Björnerfeldt, Susanne; Hailer, Frank; Nord, Maria; Vilà, Carles

    2008-01-28

    There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure. The same processes which have

  13. The sub-annual breeding cycle of a tropical seabird.

    Science.gov (United States)

    Reynolds, S James; Martin, Graham R; Dawson, Alistair; Wearn, Colin P; Hughes, B John

    2014-01-01

    Breeding periodicity allows organisms to synchronise breeding attempts with the most favourable ecological conditions under which to raise offspring. For most animal species, ecological conditions vary seasonally and usually impose an annual breeding schedule on their populations; sub-annual breeding schedules will be rare. We use a 16-year dataset of breeding attempts by a tropical seabird, the sooty tern (Onychoprion fuscatus), on Ascension Island to provide new insights about this classical example of a population of sub-annually breeding birds that was first documented in studies 60 years previously on the same island. We confirm that the breeding interval of this population has remained consistently sub-annual. By ringing >17,000 birds and re-capturing a large sample of them at equivalent breeding stages in subsequent seasons, we reveal for the first time that many individual birds also consistently breed sub-annually (i.e. that sub-annual breeding is an individual as well as a population breeding strategy). Ascension Island sooty terns appear to reduce their courtship phase markedly compared with conspecifics breeding elsewhere. Our results provide rare insights into the ecological and physiological drivers of breeding periodicity, indicating that reduction of the annual cycle to just two life-history stages, breeding and moult, is a viable life-history strategy and that moult may determine the minimum time between breeding attempts.

  14. Bee Queen Breeding Methods - Review

    Directory of Open Access Journals (Sweden)

    Silvia Patruica

    2016-05-01

    Full Text Available The biological potential of a bee family is mainly generated by the biological value of the queen. Whether we grow queens widely or just for our own apiaries, we must consider the acquisition of high-quality biological material, and also the creation of optimal feeding and caring conditions, in order to obtain high genetic value queens. Queen breeding technology starts with the setting of hoeing families, nurse families, drone-breeding families – necessary for the pairing of young queens, and also of the families which will provide the bees used to populate the nuclei where the next queens will hatch. The complex of requirements for the breeding of good, high-production queens is sometimes hard to met, under the application of artificial methods. The selection of breeding method must rely on all these requirements and on the beekeeper’s level of training.

  15. Beyond breeding area management

    DEFF Research Database (Denmark)

    Pedersen, Lykke; Thorup, Kasper; Tøttrup, Anders P.

    Every year, billions of songbirds migrate thousands of kilometres between their European breeding grounds and African overwintering area. As migratory birds are dependent on resources at a number of sites varying in both space and time, they are likely to be more vulnerable to environmental change...... technological advances are currently enabling us to track yet smaller songbirds throughout their migration cycle providing valuable insight into the life cycle of individual birds. However, direct tracking of migratory birds has so far mainly been conducted on single populations and our understanding of entire...... and provide important information for conservation management of migratory birds....

  16. Sport horses : breeding specialist from a single breeding programme?

    NARCIS (Netherlands)

    Rovere, G.A.

    2016-01-01

    Summary The general goal of this thesis was to provide information useful for the breeding programme of the Royal Dutch Warmblood Studbook (KWPN) in relation with the ongoing specialisation of the population. Data provided by KWPN consisted of records from studbook-first inspection,

  17. Southwestern Willow Flycatcher Breeding Site and Territory Summary - 2007

    Science.gov (United States)

    Durst, Scott L.; Sogge, Mark K.; Stump, Shay D.; Walker, Hira A.; Kus, Barbara E.; Sferra, Susan J.

    2008-01-01

    The Southwestern willow flycatcher (Empidonax traillii extimus; hereafter references to willow flycatcher and flycatcher refer to E.t. extimus, except where specifically noted) is an endangered bird that breeds only in dense riparian habitats in parts of six Southwestern states (Arizona, New Mexico, southern California, extreme southern Nevada, southern Utah, and southwestern Colorado). Since 1993, hundreds of Southwestern willow flycatcher surveys have been conducted each year, and many new flycatcher breeding sites located. This document synthesizes the most current information available on all known Southwestern willow flycatcher breeding sites. This rangewide data synthesis was designed to meet two objectives: (1) identify all known Southwestern willow flycatcher breeding sites and (2) assemble data to estimate population size, location, habitat, and other information for all breeding sites, for as many years as possible, from 1993 through 2007. This report provides data summaries in terms of the number of flycatcher sites and the number of territories. When interpreting and using this information, it must be kept in mind that a 'site' is a geographic location where one or more willow flycatchers establishes a territory. Sites with unpaired territorial males are considered breeding sites, even if no nesting attempts were documented. A site is often a discrete patch of riparian habitat but may also be a cluster of riparian patches; there is no standardized definition for site, and its use varies within and among states. For example, five occupied habitat patches along a 10-km stretch of river might be considered five different sites in one state but only a single site in another state. This lack of standardization makes comparisons based on site numbers problematic. Researchers for this report generally deferred to statewide summary documents or to local managers and researchers when delineating a site for inclusion in the database. However, to avoid inflating

  18. California Least Tern Breeding Survey 1995 Season

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Sterna antillarum browni) nested at 37 sites along the coast of California. This 7% decrease in breeding population size from 1994 brings to an end the trend since...

  19. Final Performance Report : Snowy Plover Breeding Distribution

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Surveys of breeding populations and nesting habitat of the snowy plover were conducted from January to August, 1989 along the Gulf Coast of Florida and Alabama....

  20. Waterfowl breeding pair survey: Southern Alberta: 1981

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for southern Alberta during 1981. The primary purpose of the survey is to provide...

  1. Aspen Delineation - Inyo National Forest [ds366

    Data.gov (United States)

    California Department of Resources — The database represents delineations of known aspen stands where aspen assessments were collected in the Inyo National Forest, Inyo County, California. The Inyo...

  2. The use of clones in dairy cattle breeding.

    NARCIS (Netherlands)

    Boer, de I.J.M.

    1994-01-01

    The aim of this thesis was to determine a breeding scheme that optimally uses large scale production of genetically identical individuals (clones) in dairy cattle. Such a breeding scheme should optimize the continuous genetic improvement of the breeding population (genetic response), and the selecti

  3. Evolution, plant breeding and biodiversity

    Directory of Open Access Journals (Sweden)

    Salvatore Ceccarelli

    2011-11-01

    Full Text Available This paper deals with changes in biodiversity during the course of evolution, plant domestication and plant breeding. It shows than man has had a strong influence on the progressive decrease of biodiversity, unconscious at first and deliberate in modern times. The decrease in biodiversity in the agricultures of the North causes a severe threat to food security and is in contrasts with the conservation of biodiversity which is part of the culture of several populations in the South. The concluding section of the paper shows that man could have guided evolution in a different way and shows an example of participatory plant breeding, a type of breeding which is done in collaboration with farmers and is based on selection for specific adaptation. Even though participatory plant breeding has been practiced for only about 20 years and by relatively few groups, the effects on both biodiversity and crop production are impressive. Eventually the paper shows how participatory plant breeding can be developed into ‘evolutionary plant breeding’ to cope in a dynamic way with climate changes.

  4. Emperor penguins breeding on iceshelves.

    Science.gov (United States)

    Fretwell, Peter T; Trathan, Phil N; Wienecke, Barbara; Kooyman, Gerald L

    2014-01-01

    We describe a new breeding behaviour discovered in emperor penguins; utilizing satellite and aerial-survey observations four emperor penguin breeding colonies have been recorded as existing on ice-shelves. Emperors have previously been considered as a sea-ice obligate species, with 44 of the 46 colonies located on sea-ice (the other two small colonies are on land). Of the colonies found on ice-shelves, two are newly discovered, and these have been recorded on shelves every season that they have been observed, the other two have been recorded both on ice-shelves and sea-ice in different breeding seasons. We conduct two analyses; the first using synthetic aperture radar data to assess why the largest of the four colonies, for which we have most data, locates sometimes on the shelf and sometimes on the sea-ice, and find that in years where the sea-ice forms late, the colony relocates onto the ice-shelf. The second analysis uses a number of environmental variables to test the habitat marginality of all emperor penguin breeding sites. We find that three of the four colonies reported in this study are in the most northerly, warmest conditions where sea-ice is often sub-optimal. The emperor penguin's reliance on sea-ice as a breeding platform coupled with recent concerns over changed sea-ice patterns consequent on regional warming, has led to their designation as "near threatened" in the IUCN red list. Current climate models predict that future loss of sea-ice around the Antarctic coastline will negatively impact emperor numbers; recent estimates suggest a halving of the population by 2052. The discovery of this new breeding behaviour at marginal sites could mitigate some of the consequences of sea-ice loss; potential benefits and whether these are permanent or temporary need to be considered and understood before further attempts are made to predict the population trajectory of this iconic species.

  5. Breeding performance in the Italian chicken breed Mericanel della Brianza

    Directory of Open Access Journals (Sweden)

    Silvia Cerolini

    Full Text Available In Italy, 90 local avian breeds were described; the majority (61% were classified as extinct and only 8.9% as still widely spread. Therefore, efforts for conservation of Italian avian breeds are urgently required. The aim of this study was to record the breeding performance of the Italian breed Mericanel della Brianza to multiply a small population, in order to develop a conservation programme. Fourteen females and eight males were available at the beginning of the reproductive season in 2009 and organised into eight families (1 male/1-2 females kept in floor pens. Birds received a photoperiod of 14L:10D and were fed ad libitum. Breeding performance was recorded from March to June. Egg production and egg weight were recorded daily; eggs were set every two weeks and fertility, embryo mortality and hatchability were recorded. Mean egg production was 37% and mean egg weight was 34±3.49 g. High fertility values from 94% to 87% were recorded in the first three settings and the overall mean fertility value was 81.6%. Overall hatchability was only 49.6% owing to a high proportion of dead embryos. Embryo mortality occurred mainly between days 2 and 7 of incubation and during hatching. The highest hatchability values were recorded in settings 1 and 2, 69% and 60% respectively, and a large decrease was found in the subsequent settings. Marked variations in egg production, fertility, hatchability and embryo mortality were found among families. The present results represent the basic know ledge of reproductive parameters necessary to improve the reproductive efficiency of the breed within a conservation plan.

  6. Breeding performance in the Italian chicken breed Mericanel della Brianza

    Directory of Open Access Journals (Sweden)

    Stefano P. Marelli

    2010-11-01

    Full Text Available In Italy, 90 local avian breeds were described, the majority (61% were classified extinct and only 8.9 % still diffused. Therefore, efforts for conservation of Italian avian breeds are urgently required. The aim of this study was to record the breeding performance of the Italian breed Mericanel della Brianza and multiply a small population, in order to develop a conservation program. Fourteen females and 8 males were available at the beginning of the reproductive season in 2009 and organized in 8 families (1 male/1-2 females kept in floor pens. Birds received a photoperiod of 14L:10D and fed ad libitum. Breeding performance was recorded from March to June. Egg production and egg weight were recorded daily; eggs were set every 2 weeks and fertility, embryo mortality and hatchability were recorded. Mean egg production was 37% and mean egg weight was 34±3.49 g. High fertility values were recorded in the first three settings, from 94 to 87%, and the overall mean fertility value was 81.6%. Overall hatchability was only 49.6% due to a high proportion of dead embryos. Embryo mortality occurred mainly between day 2 and 7 of incubation and during hatch. Highest hatchability values were recorded in setting 1 and 2, 69 and 60% respectively, and a great decrease was found in the following settings. Great variations in egg production, fertility, hatchability and embryo mortality were found among families. The present results are the basic knowledge on reproductive parameters necessary to improve the reproductive efficiency of the breed within a conservation plan.

  7. Breeding schemes in reindeer husbandry

    Directory of Open Access Journals (Sweden)

    Lars Rönnegård

    2003-04-01

    Full Text Available The objective of the paper was to investigate annual genetic gain from selection (G, and the influence of selection on the inbreeding effective population size (Ne, for different possible breeding schemes within a reindeer herding district. The breeding schemes were analysed for different proportions of the population within a herding district included in the selection programme. Two different breeding schemes were analysed: an open nucleus scheme where males mix and mate between owner flocks, and a closed nucleus scheme where the males in non-selected owner flocks are culled to maximise G in the whole population. The theory of expected long-term genetic contributions was used and maternal effects were included in the analyses. Realistic parameter values were used for the population, modelled with 5000 reindeer in the population and a sex ratio of 14 adult females per male. The standard deviation of calf weights was 4.1 kg. Four different situations were explored and the results showed: 1. When the population was randomly culled, Ne equalled 2400. 2. When the whole population was selected on calf weights, Ne equalled 1700 and the total annual genetic gain (direct + maternal in calf weight was 0.42 kg. 3. For the open nucleus scheme, G increased monotonically from 0 to 0.42 kg as the proportion of the population included in the selection programme increased from 0 to 1.0, and Ne decreased correspondingly from 2400 to 1700. 4. In the closed nucleus scheme the lowest value of Ne was 1300. For a given proportion of the population included in the selection programme, the difference in G between a closed nucleus scheme and an open one was up to 0.13 kg. We conclude that for mass selection based on calf weights in herding districts with 2000 animals or more, there are no risks of inbreeding effects caused by selection.

  8. To the Root of the Curl: A Signature of a Recent Selective Sweep Identifies a Mutation That Defines the Cornish Rex Cat Breed.

    Directory of Open Access Journals (Sweden)

    Barbara Gandolfi

    Full Text Available The cat (Felis silvestris catus shows significant variation in pelage, morphological, and behavioral phenotypes amongst its over 40 domesticated breeds. The majority of the breed specific phenotypic presentations originated through artificial selection, especially on desired novel phenotypic characteristics that arose only a few hundred years ago. Variations in coat texture and color of hair often delineate breeds amongst domestic animals. Although the genetic basis of several feline coat colors and hair lengths are characterized, less is known about the genes influencing variation in coat growth and texture, especially rexoid - curly coated types. Cornish Rex is a cat breed defined by a fixed recessive curly coat trait. Genome-wide analyses for selection (di, Tajima's D and nucleotide diversity were performed in the Cornish Rex breed and in 11 phenotypically diverse breeds and two random bred populations. Approximately 63K SNPs were used in the analysis that aimed to localize the locus controlling the rexoid hair texture. A region with a strong signature of recent selective sweep was identified in the Cornish Rex breed on chromosome A1, as well as a consensus block of homozygosity that spans approximately 3 Mb. Inspection of the region for candidate genes led to the identification of the lysophosphatidic acid receptor 6 (LPAR6. A 4 bp deletion in exon 5, c.250_253_delTTTG, which induces a premature stop codon in the receptor, was identified via Sanger sequencing. The mutation is fixed in Cornish Rex, absent in all straight haired cats analyzed, and is also segregating in the German Rex breed. LPAR6 encodes a G protein-coupled receptor essential for maintaining the structural integrity of the hair shaft; and has mutations resulting in a wooly hair phenotype in humans.

  9. Indigenous knowledge of animal breeding and breeds

    OpenAIRE

    I. Kohler-Rollefson

    2004-01-01

    Indigenous knowledge of animal breeding (IK-AB) includes concepts and practices used to influence the genetic composition of herds. Indigenous selection is often based on preferences based on physical characteristics, vigor, social and economic insurance. This issue paper summarizes the value of indigenous knowledge and local breeds to achieve agricultural sustainability. Links to IK-AB information are also provided. Available in SANREM office, ES

  10. Aspen Delineation - Sequoia National Forest [ds378

    Data.gov (United States)

    California Department of Resources — The database represents delineations of aspen stands associated with stand assessment data (SEQUOIA_NF_PTS) collected in aspen stands in the Cannell Meadows Ranger...

  11. Defining Hydrophytes for Wetland Identification and Delineation

    Science.gov (United States)

    2012-01-01

    Engineers); Norman Melvin and Michelle Schuman (U.S. Department of Agriculture Natural Resources Conservation Service); Mary Butterwick and Bill...Corps of Engineers Wetlands Delineation Manual (Environmental Laboratory 1987) “Large plants (macrophytes), such as aquatic mosses , liverworts

  12. Aspen Delineation - Plumas National Forest [ds374

    Data.gov (United States)

    California Department of Resources — The database represents delineations of aspen stands associated with stand assessment data (PLUMAS_NF_PTS) collected in aspen stands in the Plumas National Forest,...

  13. Aspen Delineation - Lassen National Forest [ds372

    Data.gov (United States)

    California Department of Resources — The database represents delineations of aspen stands associated with stand assessment data (LASSEN_NF_EAGLELAKE_PTS) collected in aspen stands in the in the Eagle...

  14. Aspen Delineation - Sierra State Parks [ds380

    Data.gov (United States)

    California Department of Resources — The database represents delineations of aspen stands associated with stand assessment data (SIERRA_SP_PTS) collected in aspen stands on lands administered by the...

  15. Delineating organs at risk in radiation therapy

    CERN Document Server

    Ausili Cèfaro, Giampiero; Perez, Carlos A

    2014-01-01

    This book offers an invaluable guide to the delineation of organs at risk of toxicity in patients undergoing radiotherapy. It details the radiological anatomy of organs at risk as seen on typical radiotherapy planning CT scans.

  16. ADAM: A computer program to simulate selective-breeding schemes for animals

    DEFF Research Database (Denmark)

    Pedersen, L D; Sørensen, A C; Henryon, M

    2009-01-01

    ADAM is a computer program that models selective breeding schemes for animals using stochastic simulation. The program simulates a population of animals and traces the genetic changes in the population under different selective breeding scenarios. It caters to different population structures, gen......, genetic models, selection strategies, and mating designs. ADAM can be used to evaluate breeding schemes and generate genetic data to test statistical tools......ADAM is a computer program that models selective breeding schemes for animals using stochastic simulation. The program simulates a population of animals and traces the genetic changes in the population under different selective breeding scenarios. It caters to different population structures...

  17. Considerations for choosing HOT lane delineation techniques

    Energy Technology Data Exchange (ETDEWEB)

    Hlavacek, I.; Vitek, M. [Texas Univ., Austin, TX (United States); Carrizales, J.; Machemehl, R. [Texas Dept. of Transportation, Austin, TX (Canada)

    2007-07-01

    Transportation agencies are looking for ways to move more vehicles with fewer tax dollars. One innovative technique is managed lanes. These are special purpose lanes on highways with controlled access to allow manipulation of service parameters. An example of a managed facility, high-occupancy toll (HOT) lanes are gaining support as a tool for encouraging higher vehicle occupancy while dealing with many of the shortcomings of high-occupancy vehicle (HOV) lanes. Because managed lanes, including HOT lanes, are controlled access facilities and must be separated from general purpose lanes, one of the principle issues is the type of delineation technique that should be used. Though the specifics of delineating a managed lane are numerous, and allow for a wide variety of possibilities, most delineation techniques used can be categorized into three broad types: concrete barriers, buffer separation, and plastic posts. This paper presented the advantages, disadvantages, required and desirable conditions for implementation of each type. The project involved assembling an expert panel to gather collective knowledge of factors and to share experiences and make recommendations regarding delineation device implementation. Panel recommendations and secondary source information were presented as conceptual guidance regarding managed lane delineation measures. Buffer type delineators were found to be least costly in terms of both initial and maintenance costs, and concrete barriers provide the best means of controlling access so they are the best means of guaranteeing toll collection from all users. 11 refs.

  18. Genomic dairy cattle breeding

    DEFF Research Database (Denmark)

    Mark, Thomas; Sandøe, Peter

    2010-01-01

    The aim of this paper is to discuss the potential consequences of modern dairy cattle breeding for the welfare of dairy cows. The paper focuses on so-called genomic selection, which deploys thousands of genetic markers to estimate breeding values. The discussion should help to structure...... the thoughts of breeders and other stakeholders on how to best make use of genomic breeding in the future. Intensive breeding has played a major role in securing dramatic increases in milk yield since the Second World War. Until recently, the main focus in dairy cattle breeding was on production traits......, unfavourable genetic trends for metabolic, reproductive, claw and leg diseases indicate that these attempts have been insufficient. Today, novel genome-wide sequencing techniques are revolutionising dairy cattle breeding; these enable genetic changes to occur at least twice as rapidly as previously. While...

  19. Genomic dairy cattle breeding

    DEFF Research Database (Denmark)

    Mark, Thomas; Sandøe, Peter

    2010-01-01

    The aim of this paper is to discuss the potential consequences of modern dairy cattle breeding for the welfare of dairy cows. The paper focuses on so-called genomic selection, which deploys thousands of genetic markers to estimate breeding values. The discussion should help to structure...... the thoughts of breeders and other stakeholders on how to best make use of genomic breeding in the future. Intensive breeding has played a major role in securing dramatic increases in milk yield since the Second World War. Until recently, the main focus in dairy cattle breeding was on production traits......, unfavourable genetic trends for metabolic, reproductive, claw and leg diseases indicate that these attempts have been insufficient. Today, novel genome-wide sequencing techniques are revolutionising dairy cattle breeding; these enable genetic changes to occur at least twice as rapidly as previously. While...

  20. Breeding system of Embothrium coccineum (Proteaceae in two populations on different slopes of the Andes Sistema reproductivo de Embothrium coccineum (Proteaceae en dos poblaciones ubicadas en diferentes laderas de los Andes

    Directory of Open Access Journals (Sweden)

    ADRIANA E ROVERE

    2006-06-01

    Full Text Available Plant breeding systems are considered to reflect species' life history characteristics, selection due to biotic or abiotic factors, pollination conditions, or a combination of these. Reproductive systems may vary over ecological gradients. The breeding system of the ornithophilous Embothrium coccineum (Proteaceae from temperate South America was studied by pollination treatments: manual self-pollination, manual cross-pollination, automatic self-pollination, and natural pollination. These treatments were conducted in a coastal western and an Andean eastern population. Embothrium coccineum was found to be self-incompatible and highly dependent on the pollinating agent at both sites. However, pollen limitations were greater in the coastal population, as breeding efficiency was lower. Populations have different floral visitors whose identity differentially affects reproductive efficiency and pollen flow in E. coccineumLos sistemas de compatibilidad reproductiva en las plantas son considerados una manifestación de la historia de vida, de la selección ante factores abióticos ó bióticos, de las condiciones de polinización o una de combinación de esos factores. El sistema reproductivo de una especie puede variar a lo largo de un gradiente ecológico-ambiental. El sistema reproductivo de Embothrium coccineum (Proteaceae, un árbol ornitófilo endémico de los bosques templados de sur de Sudamérica, fue estudiado mediante experimentos de polinización: autopolinización manual, polinización manual cruzada, autopolinización automática y polinización natural en flores descubiertas. Este trabajo se realizó en una población costera al oeste de la cordillera de los Andes y una población andina ubicada al este de la cordillera de los Andes. En ambas poblaciones se encontró que E. coccineum es autoimcompatible y altamente dependiente de los agentes polinizadores en ambos sitios. Sin embargo, la limitación por polen fue mayor en la poblaci

  1. Genetic diversity in Tunisian horse breeds

    Directory of Open Access Journals (Sweden)

    B. Jemmali

    2017-06-01

    Full Text Available This study aimed at screening genetic diversity and differentiation in four horse breeds raised in Tunisia, the Barb, Arab-Barb, Arabian, and English Thoroughbred breeds. A total of 200 blood samples (50 for each breed were collected from the jugular veins of animals, and genomic DNA was extracted. The analysis of the genetic structure was carried out using a panel of 16 microsatellite loci. Results showed that all studied microsatellite markers were highly polymorphic in all breeds. Overall, a total of 147 alleles were detected using the 16 microsatellite loci. The average number of alleles per locus was 7.52 (0.49, 7.35 (0.54, 6.3 (0.44, and 6 (0.38 for the Arab-Barb, Barb, Arabian, and English Thoroughbred breeds, respectively. The observed heterozygosities ranged from 0.63 (0.03 in the English Thoroughbred to 0.72 in the Arab-Barb breeds, whereas the expected heterozygosities were between 0.68 (0.02 in the English Thoroughbred and 0.73 in the Barb breeds. All FST values calculated by pairwise breed combinations were significantly different from zero (p  <  0.05 and an important genetic differentiation among breeds was revealed. Genetic distances, the factorial correspondence, and principal coordinate analyses showed that the important amount of genetic variation was within population. These results may facilitate conservation programs for the studied breeds and enhance preserve their genetic diversity.

  2. Genetic Parameters of Pre-adjusted Body Weight Growth and Ultrasound Measures of Body Tissue Development in Three Seedstock Pig Breed Populations in Korea

    Directory of Open Access Journals (Sweden)

    Yun Ho Choy

    2015-12-01

    Full Text Available The objective of this study was to compare the effects of body weight growth adjustment methods on genetic parameters of body growth and tissue among three pig breeds. Data collected on 101,820 Landrace, 281,411 Yorkshire, and 78,068 Duroc pigs, born in Korean swine breeder farms since 2000, were analyzed. Records included body weights on test day and amplitude (A-mode ultrasound carcass measures of backfat thickness (BF, eye muscle area (EMA, and retail cut percentage (RCP. Days to 90 kg body weight (DAYS90, through an adjustment of the age based on the body weight at the test day, were obtained. Ultrasound measures were also pre-adjusted (ABF, EMA, AEMA, ARCP based on their test day measures. The (covariance components were obtained with 3 multi-trait animal models using the REMLF90 software package. Model I included DAYS90 and ultrasound traits, whereas model II and III accounted DAYS90 and pre-adjusted ultrasound traits. Fixed factors were sex (sex and contemporary groups (herd-year-month of birth for all traits among the models. Additionally, model I and II considered a linear covariate of final weight on the ultrasound measure traits. Heritability (h2 estimates for DAYS90, BF, EMA, and RCP ranged from 0.36 to 0.42, 0.34 to 0.43, 0.20 to 0.22, and 0.39 to 0.45, respectively, among the models. The h2 estimates of DAYS90 from model II and III were also somewhat similar. The h2 for ABF, AEMA, and ARCP were 0.35 to 0.44, 0.20 to 0.25, and 0.41 to 0.46, respectively. Our heritability estimates varied mostly among the breeds. The genetic correlations (rG were moderately negative between DAYS90 and BF (−0.29 to −0.38, and between DAYS90 and EMA (−0.16 to −0.26. BF had strong rG with RCP (−0.87 to −0.93. Moderately positive rG existed between DAYS90 and RCP (0.20 to 0.28 and between EMA and RCP (0.35 to 0.44 among the breeds. For DAYS90, model II and III, its correlations with ABF, AEMA, and ARCP were mostly low or negligible except the

  3. Sistema reprodutivo de populações alógamas e autógamas: modelo básico e equilíbrio. = Breeding system of populations autogamous and allogamous: basic model and equilibrium.

    Directory of Open Access Journals (Sweden)

    Maria Clideana Cabral Maia

    2010-06-01

    Full Text Available A estrutura genética de uma população pode ser bem investigada através de suas freqüências gênicas e alélicas. As populações alógamas transmitem seus alelos às gerações seguintes, enquanto que, as populações autógamas transferem seus genótipos integralmente fi xando-os em gerações avançadas de autofecundações naturais sucessivas. No melhoramento genético dessas populações são aplicados procedimentos distintos. Para fi xar genótipos nas espécies que se reproduzem preferencialmente a partir de cruzamentos estocásticos, normalmente, são obtidos híbridos simples do cruzamento de linhagens puras após consecutivas autofecundações artificiais. = The genetic structure of a population can be better investigated through their gene and allelic frequencies. Allogamous populations transmit their alleles to subsequent generations, whereas autogamous populations transfer their genotypes entirely by setting them in advanced generations of successive natural self pollination. In breeding of these populations different procedures are applied. To establish genotypes in species which reproduce mainly from stochastic crossovers are usually obtained simple hybrids by crossing inbred lines after consecutive artifi cial self pollination.

  4. Emperor penguins breeding on iceshelves.

    Directory of Open Access Journals (Sweden)

    Peter T Fretwell

    Full Text Available We describe a new breeding behaviour discovered in emperor penguins; utilizing satellite and aerial-survey observations four emperor penguin breeding colonies have been recorded as existing on ice-shelves. Emperors have previously been considered as a sea-ice obligate species, with 44 of the 46 colonies located on sea-ice (the other two small colonies are on land. Of the colonies found on ice-shelves, two are newly discovered, and these have been recorded on shelves every season that they have been observed, the other two have been recorded both on ice-shelves and sea-ice in different breeding seasons. We conduct two analyses; the first using synthetic aperture radar data to assess why the largest of the four colonies, for which we have most data, locates sometimes on the shelf and sometimes on the sea-ice, and find that in years where the sea-ice forms late, the colony relocates onto the ice-shelf. The second analysis uses a number of environmental variables to test the habitat marginality of all emperor penguin breeding sites. We find that three of the four colonies reported in this study are in the most northerly, warmest conditions where sea-ice is often sub-optimal. The emperor penguin's reliance on sea-ice as a breeding platform coupled with recent concerns over changed sea-ice patterns consequent on regional warming, has led to their designation as "near threatened" in the IUCN red list. Current climate models predict that future loss of sea-ice around the Antarctic coastline will negatively impact emperor numbers; recent estimates suggest a halving of the population by 2052. The discovery of this new breeding behaviour at marginal sites could mitigate some of the consequences of sea-ice loss; potential benefits and whether these are permanent or temporary need to be considered and understood before further attempts are made to predict the population trajectory of this iconic species.

  5. 红嘴相思鸟的种群繁殖密度与杜鹃巢寄生率的关系%Population Breeding Density and Brood Parasitism Rate in the Red-billed Leiothrix (Leiothrix lutea)

    Institute of Scientific and Technical Information of China (English)

    王娜; 杨灿朝; 梁伟

    2012-01-01

    Population breeding density of hosts is regarded as a valuable index to predict cuckoo parasitism rate in avi- an brood parasitism. To test this hypothesis, population breeding density and brood parasitism rate of Red-billed Leio- thrix (Leiothrix lutea) were investigated from April to August, 2011 in Kuankuoshui National Natural Reserve (KKS), Guizhou, south-western China. Our results showed that the Red-billed Leiothrix is a widespread and dominant species with a population breeding density of 108.37±28.68 individuals per km2 in KKS. The highest density was detected in sec- ondary forest, with 201.41±7.3 individuals per km2, followed by shrub and primary forest. Residential area has the lowest density of 34.15±7.86 individuals per km2. A total of 347 nests of the Red-billed Leiothrix were found from 1999 to 2011 and the cuckoo brood parasitism rate of this host is 0. Breeding time and population density could not explain the ab- sence of cuckoo parasitism in the Red-billed Leiothrix.%在杜鹃与其宿主的协同进化中,宿主种群繁殖密度被认为是预测其是否被杜鹃寄生的重要指标.2011年4-8月,在贵州宽阔水国家级自然保护区对不同类型生境的红嘴相思鸟(Leiothrixlutea)的种群繁殖密度进行调查,以分析其种群繁殖密度与杜鹃(CuculWspp.)寄生之间的关系.红嘴相思鸟在宽阔水自然保护区分布广泛,平均种群繁殖密度为108.37±28.68只/km2,其中在次生林中最高,达201.41±7.36/km2,其次为灌丛和原生林.居民点的密度最低,为34.15±7.86只/km2.1999—2011年的繁殖季,共找到红嘴相思鸟的巢347个,均未发现被杜鹃寄生,巢寄生率为0.分析表明,繁殖时间和种群繁殖密度不是杜鹃未利用红嘴相思鸟的原因.

  6. Ancient mtDNA analysis of early 16(th century Caribbean cattle provides insight into founding populations of New World creole cattle breeds.

    Directory of Open Access Journals (Sweden)

    Camilla F Speller

    Full Text Available The Columbian Exchange resulted in a widespread movement of humans, plants and animals between the Old and New Worlds. The late 15(th to early 16(th century transfer of cattle from the Iberian Peninsula and Canary Islands to the Caribbean laid the foundation for the development of American creole cattle (Bos taurus breeds. Genetic analyses of modern cattle from the Americas reveal a mixed ancestry of European, African and Indian origins. Recent debate in the genetic literature centers on the 'African' haplogroup T1 and its subhaplogroups, alternatively tying their origins to the initial Spanish herds, and/or from subsequent movements of taurine cattle through the African slave trade. We examine this problem through ancient DNA analysis of early 16(th century cattle bone from Sevilla la Nueva, the first Spanish colony in Jamaica. In spite of poor DNA preservation, both T3 and T1 haplogroups were identified in the cattle remains, confirming the presence of T1 in the earliest Spanish herds. The absence, however, of "African-derived American" haplotypes (AA/T1c1a1 in the Sevilla la Nueva sample, leaves open the origins of this sub-haplogroup in contemporary Caribbean cattle.

  7. Native Pig and Chicken Breed Database: NPCDB

    Directory of Open Access Journals (Sweden)

    Hyeon-Soo Jeong

    2014-10-01

    Full Text Available Indigenous (native breeds of livestock have higher disease resistance and adaptation to the environment due to high genetic diversity. Even though their extinction rate is accelerated due to the increase of commercial breeds, natural disaster, and civil war, there is a lack of well-established databases for the native breeds. Thus, we constructed the native pig and chicken breed database (NPCDB which integrates available information on the breeds from around the world. It is a nonprofit public database aimed to provide information on the genetic resources of indigenous pig and chicken breeds for their conservation. The NPCDB (http://npcdb.snu.ac.kr/ provides the phenotypic information and population size of each breed as well as its specific habitat. In addition, it provides information on the distribution of genetic resources across the country. The database will contribute to understanding of the breed’s characteristics such as disease resistance and adaptation to environmental changes as well as the conservation of indigenous genetic resources.

  8. Preliminary report to the Pacific Flyway Committee on the Combined Pacific White-fronted Goose Surveys to Estimate a breeding population index for Alaska, 1985-2002

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Historically the Pacific population of white-fronted geese has been monitored and managed based on wintering inventories conducted in California. In recent years it...

  9. Preliminary report to the Pacific Flyway Study Committee on the combined Pacific White-fronted goose surveys to estimate a breeding population index for Alaska

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Historically the Pacific population of white-fronted geese has been monitored and managed based on wintering inventories conducted in California. In recent years it...

  10. Implementation in breeding programmes

    NARCIS (Netherlands)

    Coffey, M.P.; McParland, S.; Bastin, C.; Wall, E.; Berry, D.P.; Veerkamp, R.F.

    2013-01-01

    Genetic improvement is easy when selecting for one heritable and well-recorded trait at a time. Many industrialised national dairy herds have overall breeding indices that incorporate a range of traits balanced by their known or estimated economic value. Future breeding goals will contain more non-p

  11. Implementation in breeding programmes

    NARCIS (Netherlands)

    Coffey, M.P.; McParland, S.; Bastin, C.; Wall, E.; Berry, D.P.; Veerkamp, R.F.

    2013-01-01

    Genetic improvement is easy when selecting for one heritable and well-recorded trait at a time. Many industrialised national dairy herds have overall breeding indices that incorporate a range of traits balanced by their known or estimated economic value. Future breeding goals will contain more non-p

  12. Methods for Data-based Delineation of Spatial Regions

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, John E.

    2012-10-01

    In data analysis, it is often useful to delineate or segregate areas of interest from the general population of data in order to concentrate further analysis efforts on smaller areas. Three methods are presented here for automatically generating polygons around spatial data of interest. Each method addresses a distinct data type. These methods were developed for and implemented in the sample planning tool called Visual Sample Plan (VSP). Method A is used to delineate areas of elevated values in a rectangular grid of data (raster). The data used for this method are spatially related. Although VSP uses data from a kriging process for this method, it will work for any type of data that is spatially coherent and appears on a regular grid. Method B is used to surround areas of interest characterized by individual data points that are congregated within a certain distance of each other. Areas where data are “clumped” together spatially will be delineated. Method C is used to recreate the original boundary in a raster of data that separated data values from non-values. This is useful when a rectangular raster of data contains non-values (missing data) that indicate they were outside of some original boundary. If the original boundary is not delivered with the raster, this method will approximate the original boundary.

  13. Prospects for Hybrid Breeding in Bioenergy Grasses

    DEFF Research Database (Denmark)

    Aguirre, Andrea Arias; Studer, Bruno; Frei, Ursula

    2012-01-01

    of different hybrid breeding schemes to optimally exploit heterosis for biomass yield in perennial ryegrass (Lolium perenne L.) and switchgrass (Panicum virgatum), two perennial model grass species for bioenergy production. Starting with a careful evaluation of current population and synthetic breeding methods......, we address crucial topics to implement hybrid breeding, such as the availability and development of heterotic groups, as well as biological mechanisms for hybridization control such as self-incompatibility (SI) and male sterility (MS). Finally, we present potential hybrid breeding schemes based on SI...... and MS for the two bioenergy grass species, and discuss how molecular tools and synteny can be used to transfer relevant information for genes controlling these biological mechanisms across grass species...

  14. Forest Delineation Based on Airborne LIDAR Data

    Directory of Open Access Journals (Sweden)

    Norbert Pfeifer

    2012-03-01

    Full Text Available The delineation of forested areas is a critical task, because the resulting maps are a fundamental input for a broad field of applications and users. Different national and international forest definitions are available for manual or automatic delineation, but unfortunately most definitions lack precise geometrical descriptions for the different criteria. A mandatory criterion in forest definitions is the criterion of crown coverage (CC, which defines the proportion of the forest floor covered by the vertical projection of the tree crowns. For loosely stocked areas, this criterion is especially critical, because the size and shape of the reference area for calculating CC is not clearly defined in most definitions. Thus current forest delineations differ and tend to be non-comparable because of different settings for checking the criterion of CC in the delineation process. This paper evaluates a new approach for the automatic delineation of forested areas, based on airborne laser scanning (ALS data with a clearly defined method for calculating CC. The new approach, the ‘tree triples’ method, is based on defining CC as a relation between the sum of the crown areas of three neighboring trees and the area of their convex hull. The approach is applied and analyzed for two study areas in Tyrol, Austria. The selected areas show a loosely stocked forest at the upper timberline and a fragmented forest on the hillside. The fully automatic method presented for delineating forested areas from ALS data shows promising results with an overall accuracy of 96%, and provides a beneficial tool for operational applications.

  15. Spatial assessment of wolf-dog hybridization in a single breeding period

    Science.gov (United States)

    Pacheco, C.; López-Bao, J. V.; García, E. J.; Lema, F. J.; Llaneza, L.; Palacios, V.; Godinho, R.

    2017-01-01

    Understanding the dynamics of wolf-dog hybridization and delineating evidence-based conservation strategies requires information on the spatial extent of wolf-dog hybridization in real-time, which remains largely unknown. We collected 332 wolf-like scats over ca. 5,000km2 in the NW Iberian Peninsula to evaluate wolf-dog hybridization at population level in a single breeding/pup-rearing season. Mitochondrial DNA (MtDNA) and 18 ancestry informative markers were used for species and individual identification, and to detect wolf-dog hybrids. Genetic relatedness was assessed between hybrids and wolves. We identified 130 genotypes, including 67 wolves and 7 hybrids. Three of the hybrids were backcrosses to dog whereas the others were backcrosses to wolf, the latter accounting for a 5.6% rate of introgression into the wolf population. Our results show a previously undocumented scenario of multiple and widespread wolf-dog hybridization events at the population level. However, there is a clear maintenance of wolf genetic identity, as evidenced by the sharp genetic identification of pure individuals, suggesting the resilience of wolf populations to a small amount of hybridization. We consider that real-time population level assessments of hybridization provide a new perspective into the debate on wolf conservation, with particular focus on current management guidelines applied in wolf-dog hybridization events. PMID:28195213

  16. Reclamation of mosquito breeding sites using Landsat-8 remote sensing data: A case study of Birnin Kebbi, Nigeria

    Science.gov (United States)

    Amusuk, Danboyi Joseph; Hashim, Mazlan; Beiranvand Pour, Amin

    2016-06-01

    It is believed by recent releases of World Health Organization (WHO) that more than half of the world's population (3.2 billion) live in areas that are at risk of malaria transmission. Although increased efforts are dramatically reducing the malaria burden in some places where the rate of new cases indicates a fall by 37% globally and 60% death rate. Unfortunately, the subSaharan Africa still shares 89% of malaria and 91% of malaria deaths. Essentially, attacking the causative vectors and reclamation of the vector breeding sites could be remarkable for the rolling back the malaria epidemic project. Consequently, it is essential to explore the possibility of using recent Landsat-8 data remote sensing data and applications of Geographic Information System (GIS) technique in contributing to the realization of this objective. This investigation used for identifying mosquito breeding habitat (Derelict Ponds) zones the application of supervised classification of the Landsat-8 image in conjunction with GIS layering which allowed identification of high risk prone regions for mosquito breeding habitat. The methodology delineated 10 spatial locations of the Derelict Ponds (DP) spread around the Birnin Kebbi urban environment. Moreover, the results combined with comparative analysis of the link between warm climatic (temperature and rainfall data) conditions and Malaria prevalence that is associated with urban poverty. This study indicates that the application of Landsat-8 data and GIS techniques can be a useful tool for planning and management of environmental health and mapping of hot spot environmental problem areas.

  17. Breeding progress, variation, and correlation of grain and quality traits in winter rye hybrid and population varieties and national on-farm progress in Germany over 26 years.

    Science.gov (United States)

    Laidig, Friedrich; Piepho, Hans-Peter; Rentel, Dirk; Drobek, Thomas; Meyer, Uwe; Huesken, Alexandra

    2017-05-01

    Grain yield of hybrid varieties and population varieties in official German variety trials increased by 23.3 and 18.1%, respectively, over the last 26 years. On-farm gain in grain yield (18.9%) was comparable to that of population varieties in variety trials, yet at a level considerably lower than in variety trials. Rye quality is subject to large year-to-year fluctuation. Increase in grain yield and decline of protein concentration did not negatively influence quality traits. Performance progress of grain and quality traits of 78 winter rye varieties tested in official German trials to assess the value for cultivation and use (VCU) were evaluated during 1989 and 2014. We dissected progress into a genetic and a non-genetic component for hybrid and population varieties by applying mixed models, including regression components to model trends. VCU trial results were compared with grain yield and quality data from a national harvest survey (on-farm data). Yield gain for hybrid varieties was 23.3% (18.9 dt ha(-1)) and for population varieties 18.1% (13.0 dt ha(-1)) relative to 1989. On-farm yield progress of 18.9% (8.7 dt ha(-1)) was considerably lagging behind VCU trials, and mean yield levels were substantially lower than in field trials. Most of the yield progress was generated by genetic improvement. For hybrid varieties, ear density was the determining yield component, whereas for population varieties, it was thousand grain mass. Results for VCU trials showed no statistically significant gains or losses in rye quality traits. For on-farm data, we found a positive but non-significant gain in falling number and amylogram viscosity and temperature. Variation of grain and quality traits was strongly influenced by environments, whereas genotypic variation was less than 19% of total variation. Grain yield was strongly negatively associated with protein concentration, yet was weakly to moderately positively associated with quality traits. In general, our results from VCU

  18. Birds - Breeding [ds60

    Data.gov (United States)

    California Department of Resources — This data set provides access to information gathered on annual breeding bird surveys in California using a map layer developed by the Department. This data layer...

  19. Garlic breeding system innovations

    NARCIS (Netherlands)

    Zheng, S.J.; Kamenetsky, R.; Féréol, L.; Barandiaran, X.; Rabinowitch, H.D.; Chovelon, V.; Kik, C.

    2007-01-01

    This review outlines innovative methods for garlic breeding improvement and discusses the techniques used to increase variation like mutagenesis and in vitro techniques, as well as the current developments in florogenesis, sexual hybridization, genetic transformation and mass propagation. Sexual ste

  20. PRINCIPLES OF ANIMAL BREEDING

    OpenAIRE

    2014-01-01

    University textbook Principles of Animal Breeding is intended for students of agriculture and veterinary medicine. The material is the adapted curricula of undergraduate and graduate level studies in the framework of which the modules Principles of animal breeding as well as Basics of genetics and selection of animals attended are listened. The textbook contains 14 chapters and a glossary of terms. Its concept enables combining fundamental and modern knowledge in the ...

  1. A Multiple QTL-Seq Strategy Delineates Potential Genomic Loci Governing Flowering Time in Chickpea

    Science.gov (United States)

    Srivastava, Rishi; Upadhyaya, Hari D.; Kumar, Rajendra; Daware, Anurag; Basu, Udita; Shimray, Philanim W.; Tripathi, Shailesh; Bharadwaj, Chellapilla; Tyagi, Akhilesh K.; Parida, Swarup K.

    2017-01-01

    Identification of functionally relevant potential genomic loci using an economical, simpler and user-friendly genomics-assisted breeding strategy is vital for rapid genetic dissection of complex flowering time quantitative trait in chickpea. A high-throughput multiple QTL-seq strategy was employed in two inter (Cicer arietinum desi accession ICC 4958 × C reticulatum wild accession ICC 17160)- and intra (ICC 4958 × C. arietinum kabuli accession ICC 8261)-specific RIL mapping populations to identify the major QTL genomic regions governing flowering time in chickpea. The whole genome resequencing discovered 1635117 and 592486 SNPs exhibiting differentiation between early- and late-flowering mapping parents and bulks, constituted by pooling the homozygous individuals of extreme flowering time phenotypic trait from each of two aforesaid RIL populations. The multiple QTL-seq analysis using these mined SNPs in two RIL mapping populations narrowed-down two longer (907.1 kb and 1.99 Mb) major flowering time QTL genomic regions into the high-resolution shorter (757.7 kb and 1.39 Mb) QTL intervals on chickpea chromosome 4. This essentially identified regulatory as well as coding (non-synonymous/synonymous) novel SNP allelic variants from two efl1 (early flowering 1) and GI (GIGANTEA) genes regulating flowering time in chickpea. Interestingly, strong natural allelic diversity reduction (88–91%) of two known flowering genes especially mapped at major QTL intervals as compared to that of background genomic regions (where no flowering time QTLs were mapped; 61.8%) in cultivated vis-à-vis wild Cicer gene pools was evident inferring the significant impact of evolutionary bottlenecks on these loci during chickpea domestication. Higher association potential of coding non-synonymous and regulatory SNP alleles mined from efl1 (36–49%) and GI (33–42%) flowering genes for early and late flowering time differentiation among chickpea accessions was evident. The robustness and

  2. Elephant reproduction: improvement of breeding efficiency and development of a breeding strategy

    NARCIS (Netherlands)

    Thitaram, C.|info:eu-repo/dai/nl/304838608

    2009-01-01

    The efficiency of reproduction of the Asian elephant (Elephas maximus) has become of major concern. Captive breeding programs worldwide have met with limited success and few ex situ elephant populations are self-sustaining. The low birth rate and high mortality cause the captive population to

  3. Elephant reproduction: improvement of breeding efficiency and development of a breeding strategy

    NARCIS (Netherlands)

    Thitaram, C.

    2009-01-01

    The efficiency of reproduction of the Asian elephant (Elephas maximus) has become of major concern. Captive breeding programs worldwide have met with limited success and few ex situ elephant populations are self-sustaining. The low birth rate and high mortality cause the captive population to declin

  4. The effects of selective breeding on the architectural properties of the pelvic limb in broiler chickens: a comparative study across modern and ancestral populations.

    Science.gov (United States)

    Paxton, Heather; Anthony, Nicolas B; Corr, Sandra A; Hutchinson, John R

    2010-08-01

    Intensive artificial selection has led to the production of the modern broiler chicken, which over the last few decades has undergone a dramatic increase in growth rate and noticeable changes in body conformation. Unfortunately, this has been associated with musculoskeletal abnormalities which have altered the walking ability of these birds, raising obvious welfare concerns, as well as causing economic losses. Here we present a comparative study of ancestral and derived muscle anatomy in chickens to begin to tease apart how evolutionary alterations of muscle form in chickens have influenced their locomotor function and perhaps contributed to lameness. We measured the muscle architectural properties of the right pelvic limb in 50 birds, including the Giant Junglefowl, a commercial strain broiler and four pureline commercial broiler breeder lines (from which the broiler populations are derived) to identify which features of the broiler's architectural design have diverged the most from the ancestral condition. We report a decline in pelvic limb muscle mass in the commercial line birds that may compromise their locomotor abilities because they carry a larger body mass. This greater demand on the pelvic limb muscles has mostly led to changes in support at the hip joint, revealing significantly larger abductors and additionally much larger medial rotators in the broiler population. Differences were seen within the commercial line bird populations, which are likely attributed to different selection pressures and may reflect differences in the walking ability of these birds. In addition, Junglefowl seem to have both greater force-generating capabilities and longer, presumably faster contracting muscles, indicative of superior musculoskeletal/locomotor function. We have provided baseline data for generating hypotheses to investigate in greater depth the specific biomechanical constraints that compromise the modern broiler's walking ability and propose that these factors

  5. Breeding for longevity in Italian Chianina cattle

    NARCIS (Netherlands)

    Forabosco, F.

    2005-01-01

    The objective of this thesis was to evaluate genetic aspects of longevity (LPL) in the Chianina beef cattle population in order to define how to include this trait in selection criteria. The Chianina breed has been raised for over twenty-two centuries inItaly

  6. Estimating superpopulation size and annual probability of breeding for pond-breeding salamanders

    Science.gov (United States)

    Kinkead, K.E.; Otis, D.L.

    2007-01-01

    It has long been accepted that amphibians can skip breeding in any given year, and environmental conditions act as a cue for breeding. In this paper, we quantify temporary emigration or nonbreeding probability for mole and spotted salamanders (Ambystoma talpoideum and A. maculatum). We estimated that 70% of mole salamanders may skip breeding during an average rainfall year and 90% may skip during a drought year. Spotted salamanders may be more likely to breed, with only 17% avoiding the breeding pond during an average rainfall year. We illustrate how superpopulations can be estimated using temporary emigration probability estimates. The superpopulation is the total number of salamanders associated with a given breeding pond. Although most salamanders stay within a certain distance of a breeding pond for the majority of their life spans, it is difficult to determine true overall population sizes for a given site if animals are only captured during a brief time frame each year with some animals unavailable for capture at any time during a given year. ?? 2007 by The Herpetologists' League, Inc.

  7. Delineation, characterization, and classification of topographic eminences

    Science.gov (United States)

    Sinha, Gaurav

    Topographic eminences are defined as upwardly rising, convex shaped topographic landforms that are noticeably distinct in their immediate surroundings. As opposed to everyday objects, the properties of a topographic eminence are dependent not only on how it is conceptualized, but is also intrinsically related to its spatial extent and its relative location in the landscape. In this thesis, a system for automated detection, delineation and characterization of topographic eminences based on an analysis of digital elevation models is proposed. Research has shown that conceptualization of eminences (and other landforms) is linked to the cultural and linguistic backgrounds of people. However, the perception of stimuli from our physical environment is not subject to cultural or linguistic bias. Hence, perceptually salient morphological and spatial properties of the natural landscape can form the basis for generically applicable detection and delineation of topographic eminences. Six principles of cognitive eminence modeling are introduced to develop the philosophical foundation of this research regarding eminence delineation and characterization. The first step in delineating eminences is to automatically detect their presence within digital elevation models. This is achieved by the use of quantitative geomorphometric parameters (e.g., elevation, slope and curvature) and qualitative geomorphometric features (e.g., peaks, passes, pits, ridgelines, and valley lines). The process of eminence delineation follows that of eminence detection. It is posited that eminences may be perceived either as monolithic terrain objects, or as composites of morphological parts (e.g., top, bottom, slope). Individual eminences may also simultaneously be conceived as comprising larger, higher order eminence complexes (e.g., mountain ranges). Multiple algorithms are presented for the delineation of simple and complex eminences, and the morphological parts of eminences. The proposed eminence

  8. Broiler breeding : breeding goals, selection schemes and the usefulness of local breeds for China

    NARCIS (Netherlands)

    Jiang, X.

    1999-01-01

    This dissertation considers three aspects of broiler breeding: definition of breeding goals, selection schemes for specialized lines, and the usefulness of local breeds for China. Economic values in broiler breeding were derived based on a deterministic model. A systematic design for the application

  9. Review: Towards the agroecological management of ruminants, pigs and poultry through the development of sustainable breeding programmes. II. Breeding strategies.

    Science.gov (United States)

    Phocas, F; Belloc, C; Bidanel, J; Delaby, L; Dourmad, J Y; Dumont, B; Ezanno, P; Fortun-Lamothe, L; Foucras, G; Frappat, B; González-García, E; Hazard, D; Larzul, C; Lubac, S; Mignon-Grasteau, S; Moreno, C R; Tixier-Boichard, M; Brochard, M

    2016-11-01

    Agroecology uses ecological processes and local resources rather than chemical inputs to develop productive and resilient livestock and crop production systems. In this context, breeding innovations are necessary to obtain animals that are both productive and adapted to a broad range of local contexts and diversity of systems. Breeding strategies to promote agroecological systems are similar for different animal species. However, current practices differ regarding the breeding of ruminants, pigs and poultry. Ruminant breeding is still an open system where farmers continue to choose their own breeds and strategies. Conversely, pig and poultry breeding is more or less the exclusive domain of international breeding companies which supply farmers with hybrid animals. Innovations in breeding strategies must therefore be adapted to the different species. In developed countries, reorienting current breeding programmes seems to be more effective than developing programmes dedicated to agroecological systems that will struggle to be really effective because of the small size of the populations currently concerned by such systems. Particular attention needs to be paid to determining the respective usefulness of cross-breeding v. straight breeding strategies of well-adapted local breeds. While cross-breeding may offer some immediate benefits in terms of improving certain traits that enable the animals to adapt well to local environmental conditions, it may be difficult to sustain these benefits in the longer term and could also induce an important loss of genetic diversity if the initial pure-bred populations are no longer produced. As well as supporting the value of within-breed diversity, we must preserve between-breed diversity in order to maintain numerous options for adaptation to a variety of production environments and contexts. This may involve specific public policies to maintain and characterize local breeds (in terms of both phenotypes and genotypes), which could

  10. THEORY AND METHOD FOR WETLAND BOUNDARY DELINEATION

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Based on the analysis of the subjectivity of wetland boundary criteria and their causes at present, this paper suggested that, under the condition that the mechanism of wetland formation process has not been understood,"black box" method of System Theory can be used to delineate wetland boundaries scientifically. After analyzing the difference of system construction among aquatic habitats, wetlands and uplands, the lower limit of rooted plants was chosen as the lower boundary criterion of wetlands. Because soil diagnostic horizon is the result of the long-term interaction among all environments, and it is less responsive than vegetation to short-term change, soil diagnostic horizon was chosen as the indicator to delineate wetland upper boundary, which lies at the thinning-out point of soil diagnostic horizon. Case study indicated that it was feasible using the lower limit of rooted plants and the thinning-out point of soil diagnostic horizon as criteria to delineate the lower and upper boundaries of wetland. In the study area, the thinning-out line of albic horizon was coincident with the 55.74m contour line, the maximum horizonerror was less than lm, and the maximum vertical error less than 0.04m. The problem on wetland definition always arises on the boundaries. Having delineated wetland boundaries, wetlands can be defined as follows: wetlands are the transitional zones between uplands and deepwater habitats, they are a kind of azonal complex that are inundated or saturated by surface or ground water, with the lower boundary lying at the lower limit of rooted plants, and the upper boundary at the thinning-out line of upland soil diagnostic horizon.

  11. Failed recruitment of southern toads (Bufo terrestris) in a trace element-contaminated breeding habitat: Direct and indirect effects that may lead to a local population sink

    Energy Technology Data Exchange (ETDEWEB)

    Rowe, C.L.; Hopkins, W.A.; Coffman, V.R. [University of Maryland, Solomons, MD (USA). Chesapeake Biology Laboratory, Centre of Environmental Sciences

    2001-07-01

    Embryonic southern toads (Bufo terrestris) were held in a site polluted with coal ash (site AB; containing As, Cd, Cr, Cu, Se, and other elements) and a reference site (site R) through hatching and early larval development. To examine the remainder of the larval period, surviving larvae in AB were then transplanted to R and back-transplanted to AB, whereas surviving larvae from R were back-transplanted to R. Survival through early larval development was lower in AB than in R (34% versus 50%). However, site of hatching did not influence traits later in development (larval metabolic rate, larval morphology, duration of larval period, size at metamorphosis, or average hopping distance by metamorphs). Toads that spent the entire larval period in R had high rates of survival (70-94% of individuals transplanted after the embryonic period) regardless of where they spent the embryonic acid early larval period. However, toads held in AB for the duration of the larval period suffered 100% mortality. The study suggests that the widespread practice of disposing of coal ash in open aquatic basins may result in sink habitats for some amphibian populations.

  12. Recent advances in probabilistic species pool delineations

    Directory of Open Access Journals (Sweden)

    Dirk Nikolaus Karger

    2016-07-01

    Full Text Available A species pool is the set of species that could potentially colonize and establish within a community. It has been a commonly used concept in biogeography since the early days of MacArthur and Wilson’s work on Island Biogeography. Despite their simple and appealing definition, an operational application of species pools is bundled with a multitude of problems, which have often resulted in arbitrary decisions and workarounds when defining species pools. Two recently published papers address the operational problems of species pool delineations, and show ways of delineating them in a probabilistic fashion. In both papers, species pools were delineated using a process-based, mechanistical approach, which opens the door for a multitude of new applications in biogeography. Such applications include detecting the hidden signature of biotic interactions, disentangling the geographical structure of community assembly processes, and incorporating a temporal extent into species pools. Although similar in their conclusions, both ‘probabilistic approaches’ differ in their implementation and definitions. Here I give a brief overview of the differences and similarities of both approaches, and identify the challenges and advantages in their application.

  13. Breeding objectives, selection criteria and breeding system of indigenous goat types in bale zone, oromia, Ethiopia

    Directory of Open Access Journals (Sweden)

    Belete Asefa

    2015-12-01

    Full Text Available The study was undertaken in bale zone to assess farmer’s selective breeding objectives, trait preferences, selection criteria and breeding system October 2012 to November 2013. A purposive and multistage sampling technique was applied for selection of 3 district and 9 kebeles. Then 360 households were selected by using simple random sampling techniques after the list of pastoralist having goats was identified. Statistical analysis system version 9.1 was used for analysis of data. Indices, effective population size and rate of inbreeding were calculated on average each respondent holds about 14 goats. Milk production is the main reason of goat keeping in the study area. Appearance is the first rank as selection criteria for male and female in all studies area. About 47.8% of the respondents have their own buck. The main use of breeding buck in the study area was for mating purpose (76.2%. Mean estimate of effective population size and mean rate of inbreeding was 2.43 and 0.21, respectively when a household flock is herded alone and under random mating. Therefore, any breed improvement strategies that are intended to be implemented in the study area and else- where should consider the traditional breeding practices and breeding objectives of the community.

  14. Assessing effective population size, coancestry and inbreeding effects on litter size using the pedigree and SNP data in closed lines of the Iberian pig breed.

    Science.gov (United States)

    Silió, L; Barragán, C; Fernández, A I; García-Casco, J; Rodríguez, M C

    2016-04-01

    The complete pedigree of two closed Iberian pig lines (Gamito and Torbiscal), with 798 and 4077 reproducers, has been used to measure the evolution of coancestry (f) and inbreeding (F) for autosomal and X-linked genes along 16 and 28 respective equivalent discrete generations. At the last generation, the mean values of each line were f = 0.41 and 0.22, F = 0.35 and 0.18, fX  = 0.46 and 0.22 and FX  = 0.47 and 0.19, respectively. Other calculated parameters were the effective number of founders (final values, 6.8 and 35.2) and non-founders (1.5 and 2.4), founder genome equivalents (1.2 and 2.3) and effective population size (16.0 and 57.7). Measures of Torbiscal effective size based on rates of coancestry (66.1), inbreeding (65.0) and linkage disequilibrium (71.0) were estimated from whole-genome SNP genotyping data. Values of new and old inbreeding and their respective rates by generation were computed to detect purging effects of natural selection. The analysis of 6854 Torbiscal litters showed significant negative impacts of new and fast inbreeding on litter size, as expected from the purging hypothesis: -0.20 born piglets per litter by a 10% of new inbreeding, and -0.03 and -0.02 piglets by 1% of total and new inbreeding rates, respectively. The analysis performed on 1274 litters of the Gamito line failed to show purging effects. The only significant results were reductions in -0.91 and -0.17 piglets by a 10% of old and X-linked genes inbreeding, respectively. These results may be useful for some practical issues in conservation programs of farm or captive wild animals. © 2015 Blackwell Verlag GmbH.

  15. Proximity to mosquito breeding habitat and Ross River virus risk in the Peel region of Western Australia.

    Science.gov (United States)

    Jardine, Andrew; Neville, Peter J; Lindsay, Michael D A

    2015-02-01

    It is intuitive that vector-borne disease exposure risk is related to proximity to sources of vector breeding, but this aspect rarely receives empirical testing. The population of Western Australia (WA) is increasing rapidly, with many new residential developments proposed in close proximity to mosquito breeding habitat. However, potential mosquito-borne disease risks for future residents are given little consideration by planning authorities. The Peel region is one of the fastest growing regions in WA and regularly experiences a large number of cases of the mosquito-borne Ross River virus (RRV) disease with epidemics occuring in the region every few years. A spatial analysis of RRV disease data in the Peel region was undertaken to determine the risk associated with proximity to a mosquito breeding habitat. Geographic Information Systems (GIS) software was used to create buffers between 1 and 6 km from the breeding habitat. The number of cases per 1000 dwellings in each buffer was calculated between 2002/03 to 2011/12 for years with >100 cases across all buffers (n=5) in addition to the cumulative rate over the entire period in each buffer. Residents living within 1 km of a mosquito breeding habitat had a significantly higher rate of RRV disease compared to the background rate across the Peel region in all individual years investigated. The cumulative data over the 10-year study period showed that residents in the 1- and 2-km buffers had a significantly higher rate, whereas those living between 3 and 6 km away did not. This study demonstrates an increased mosquito-borne disease risk associated with living in close proximity to a mosquito breeding habitat in a rapidly expanding region of WA and highlights the importance of considering mosquito-borne disease risks when planning authorities assess new residential development applications. Known mosquito breeding wetlands should be incorporated into land use planning scheme maps to ensure that they are accurately

  16. Welfare in horse breeding

    DEFF Research Database (Denmark)

    Campbell, M.L.H.; Sandøe, Peter

    2015-01-01

    Welfare problems related to the way horses are bred, whether by coitus or by the application of artificial reproduction techniques (ARTs), have been given no discrete consideration within the academic literature. This paper reviews the existing knowledge base about welfare issues in horse breeding...... and identifies areas in which data is lacking. We suggest that all methods of horse breeding are associated with potential welfare problems, but also that the judicious use of ARTs can sometimes help to address those problems. We discuss how negative welfare effects could be identified and limited and how...

  17. Welfare in horse breeding

    DEFF Research Database (Denmark)

    Campbell, M.L.H.; Sandøe, Peter

    2015-01-01

    Welfare problems related to the way horses are bred, whether by coitus or by the application of artificial reproduction techniques (ARTs), have been given no discrete consideration within the academic literature. This paper reviews the existing knowledge base about welfare issues in horse breeding...... and identifies areas in which data is lacking. We suggest that all methods of horse breeding are associated with potential welfare problems, but also that the judicious use of ARTs can sometimes help to address those problems. We discuss how negative welfare effects could be identified and limited and how...

  18. Modelling Growth Curves in a Nondescript Italian Chicken Breed

    National Research Council Canada - National Science Library

    Maria Selvaggi; Vito Laudadio; Cataldo Dario; Vincenzo Tufarelli

    2015-01-01

    ... it. This study was carried out to estimate the parameters of logistic, Gompertz and Richards growth curve models in a nondescript chicken breed population from southern Italy to determine the goodness of fit...

  19. 1994 waterfowl breeding pair survey Yukon Flats National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The waterfowl breeding population estimate for the refuge (stratum 4) is 581,111. This estimate is down 27% from the ten year mean. Dabbler species estimates...

  20. [Breeding bird survey authorization : Audubon National Wildlife Refuge

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This letter authorizes Larry Igl and Chris Johnson to conduct population estimates of breeding birds on Audubon National Wildlife Refuge. This study is in...

  1. Waterfowl breeding pair survey: Ontario, Quebec, and New York: 1997

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Ontario, Quebec, and New York during 1997. The primary purpose of the survey is to...

  2. Selective breeding for scrapie resistance in sheep

    Directory of Open Access Journals (Sweden)

    Cristina Santos Sotomaior

    2012-11-01

    Full Text Available It is well known that the susceptibility of sheep to scrapie is determined by the host’s prion protein gene (PRNP. PRNP polymorphisms at codons 136 (alanine, A/valine, V, 154 (histidine, H/arginine, R and 171 (glutamine, Q/histidine, H/arginine, R are the main determinants of sheep susceptibility/resistance to classical scrapie. There are four major variants of the wild-type ARQ allele: VRQ, AHQ, ARH and ARR. Breeding programs have been developed in the European Union and the USA to increase the frequency of the resistant ARR allele while decreasing the frequency of the susceptible VRQ allele in sheep populations. In Brazil, little PRNP genotyping data are available for sheep, and thus far, no controlled breeding scheme for scrapie has been implemented. This review will focus on important epidemiological aspects of scrapie and the use of genetic resistance as a tool in breeding programs to control the disease.

  3. 不同群体山女鳟及其杂交F1的生产性能比较%Production Performance of Different Populations of Rainbow Trout Oncorhynchus masou masou and Their Cross-breeding F1

    Institute of Scientific and Technical Information of China (English)

    张玉勇; 张永泉; 贾智英; 贾忠贺; 白庆利

    2013-01-01

    本文系统研究了我国引进的两个山女鳟(Oncorhynchus masou masou)群体及其杂交F1代的生产性能.结果表明,(1)两个杂交组合的早期生产性能,如授精率、发眼率和孵化率等不存在显著优势,自交组合BH 08♀×BH08♂的最终成活率为63.37%,远低于其他三组的成活率(P<0.01);(2)378d的生长对比试验表明,杂交组合与自交组合的体质量、绝对增重率、特定生长率和肥满度等存在一定差异,养殖时间对这些指标的影响达到极显著水平(P<0.01),但组间差异仅为显著水平(P<0.05)或没有差异(P>0.05);(3)378d的生长对比试验结束时,两个杂交组合均表现出一定的杂种优势.方差分析表明,不同生长阶段对杂交组合杂种优势率的影响极显著(P<0.01),不同组合间的杂种优势率也存在极显著差异(P<0.01).%In this paper, the production performance were studied in two populations of rainbow trout Oncorhynchus masou masou and their cross-breeding Fl. The results showed that firstly there were no significant differences in production performance including fertil ization, eyed embryonic rate, and hatching success between the cross-breeding F1 (BH 96 9 ♀×BH 08 6 and BH 08 9 ♂ BH 96 5 ) and the controls (BH 96 ♀× BH 96 6 and BH 08 9 × BH 08 5 (P>0.05), with survival rate of only 63.3% in BH 08 9 ♀× BH 08 ♂ , very significantly lower than in the others (P0.05 ).Thirdly after a 378-day experi ment the cross-breeding Fl appeared some growth heterosis. The analysis of variance showed that the heterosis difference was affected not only by culture-time, but also among different groups (P<0.01).

  4. Breeding kennel management.

    Science.gov (United States)

    Mullen, S

    1992-09-01

    Veterinarians and dog breeders should work together to establish protocols for health care and breeding management that are based on sound scientific principles as well as practical systems. These protocols should involve bitches, stud dogs, and puppies. Tantamount importance must be placed on record keeping so that problems may be identified and solved before they are irreversible.

  5. Plant breeding and genetics

    Science.gov (United States)

    The ultimate goal of plant breeding is to develop improved crops. Improvements can be made in crop productivity, crop processing and marketing, and/or consumer quality. The process of developing an improved cultivar begins with intercrossing lines with high performance for the traits of interest, th...

  6. Travelling to breed

    NARCIS (Netherlands)

    Drent, RJ; Fox, AD; Stahl, J

    2006-01-01

    Traditionally, investigation of the dynamics of avian migration has been heavily biased towards the autumn return trip to the wintering quarters. Since the migratory prelude to breeding has direct fitness consequences, the European Science Foundation recently redressed the balance and sponsored a wo

  7. Penguin breeding in Edinburgh

    NARCIS (Netherlands)

    Gillespie, T.H.; F.R.S.E.,; F.Z.S.,

    1939-01-01

    The Scottish National Zoological Park at Edinburgh has been notably successful in keeping and breeding penguins. It is happy in possessing as a friend and benefactor, Mr Theodore E. Salvesen, head of the firm of Christian Salvesen & Co., Leith, to whose interest and generosity it owes the great numb

  8. The Breeding Bird Survey, 1966

    Science.gov (United States)

    Robbins, C.S.; Van Velzen, W.T.

    1967-01-01

    A Breeding Bird Survey of a large section on North America was conducted during June 1966. Cooperators ran a total of 585 Survey routes in 26 eastern States and 4 Canadian Provinces. Future coverage of established routes will enable changes in the abundance of North American breeding birds to be measured. Routes are selected at random on the basis of one-degree blocks of latitude and longitude. Each 241/2-mile route, with 3-minute stops spaced one-half mile apart, is driven by automobile. All birds heard or seen at the stops are recorded on special forms and the data are then transferred to machine punch cards. The average number of birds per route is tabulated by State, along with the total number of each species and the percent of routes and stops upon which they were recorded. Maps are presented showing the range and abundance of selected species. Also, a year-to-year comparison is made of populations of selected species on Maryland routes in 1965 and 1966.

  9. Reverse breeding: a novel breeding approach based on engineered meiosis

    NARCIS (Netherlands)

    Dirks, R.; Dun, van K.P.M.; Snoo, de B.; Berg, van den M.; Lelivelt, C.L.C.; Voermans, W.; Woudenberg, L.; Wit, de J.P.C.; Reinink, K.; Schut, J.W.; Jong, de J.H.S.G.M.; Wijnker, T.G.

    2009-01-01

    Reverse breeding (RB) is a novel plant breeding technique designed to directly produce parental lines for any heterozygous plant, one of the most sought after goals in plant breeding. RB generates perfectly complementing homozygous parental lines through engineered meiosis. The method is based on re

  10. Owner perceived differences between mixed-breed and purebred dogs

    Science.gov (United States)

    Turcsán, Borbála; Miklósi, Ádám; Kubinyi, Enikő

    2017-01-01

    Studies about the behaviours of mixed-breed dogs are rare, although mixed-breeds represent the majority of the world’s dog population. We have conducted two surveys to investigate the behavioural, demographic, and dog keeping differences between purebred and mixed-breed companion dogs. Questionnaire data were collected on a large sample of dogs living in Germany (N = 7,700 purebred dogs representing more than 200 breeds, and N = 7,691 mixed-breeds). We found that according to their owners, mixed-breeds were (1) less calm, (2) less sociable toward other dogs, and (3) showed more problematic behaviour than purebreds (p 10%) differences: neutering was more frequent among mixed-breeds, and they were acquired at older ages than purebreds (p < 0.001 for both), which could result in the observed behaviour differences. After controlling for the distribution of the demographic and dog keeping factors, we found that mixed-breeds were (1) more trainable than purebreds, (2) less calm, and (3) showed more problematic behaviour than purebreds (p < 0.001 for all). We discuss that these differences at least partly might be due to selective forces. Our results suggest that instead of being the “average” dogs, mixed-breeds represent a special group with characteristic behavioural traits. PMID:28222103

  11. Breeding of high yield, double low and disease resistant rapeseed cultivars by population improvement%应用群体改良法选育高产优质抗病油菜新品种

    Institute of Scientific and Technical Information of China (English)

    陆光远; 张学昆; 李桂英; 程勇; 郑普英; 瞿桢; 付桂萍; 邹崇顺

    2012-01-01

    为了探究轮回选择在油菜品种群体改良中的作用,利用具有高产、双低、抗病等优异性状的种质材料为育种亲本,以显性细胞核雄性不育基因为桥梁,构建了一个随机交配轮回选择群体.针对群体的产量、品质、抗病性等性状进行了多次轮回选择,结果表明经过6轮选择后,群体的主要性状得到改良,产量增加11.3%,每轮遗传增益为1.88%;芥酸和硫苷含量每轮遗传增益达到10.12%和6.37%,改良效果明显;但菌核病的抗性改良效果不明显.经过多轮选择后群体的遗传离散度仍然较高(0.338 3 ~0.377 7),表明遗传多样性并没有明显下降.从不同轮次群体中选择优异单株,经系谱选择后育成了中双5号、中双6号和中双10号等优良品种,在生产上应用广泛,表明轮回选择在油菜品种改良方面具有巨大潜力.%To study the effectiveness of recurrent selection in population improvement of rapeseed variety, a recurrent selection population was constructed by mixing several germplasm populations with high - yield, double -low and disease - resistant characteristics, using dominant genie male sterile line as a bridge for random mating. This recurrent population was then subjected to consecutive selections mainly on yield, quality and Sclerotinia stem rot resistance. Results showed that, after 6 selection cycles on the population, seed yield increased by 11. 3% with a genetic gain of 1. 88% per cycle. Except for stem rot resistance, obvious genetic improvements were found in eru-cic acid and glucosinolates contents, with a respective genetic gain of 10. 12% and 6. 37% . The population genetic dispersion was stable and high (from 0. 338 3 to 0. 377 7) , indicating no obvious penalty on genetic diversity after several cycles of selection. Ideal fertile plants identified in different generations were further developed into breeding lines by pedigree selection method. A number of new cultivars (i

  12. 中南穿梭育种对南斯拉夫玉米群体改良的互补性研究%The Mutual Complement Studies for Yugoslavia Maize Population Improvement Through the Shuttle Breeding

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    1985-1997年对南斯拉夫玉米群体SYN1/9 C0进行半同胞轮回选择。1998年通过把在唐山C1~C6和在贝尔格莱德进行C3~C6共计10个轮回群体与4个标准自交系进行半双列杂交研究,连续2年试验,结果一致。研究结果表明对群体产量和测交组合产量以及产量杂种优势、配合力和田间部分性状一般配合力均存在显著差异,南斯拉夫和唐山两地改良效果极具互补性。实验表明,中南穿梭育种在提高南斯拉夫群体自身产量、测交组合产量的同时,能更为有效地提升群体杂种优势,使产量特殊配合力、一般配合力同时提高。%Yugoslavia maize population improvement was carried out by the method of HSRS and the way of shuttle beeding during 1985 to 1997。The 10 circles including 6 circles achieved in TangShang and 3 circles done in Belgrade were crossed with 4 inbred lined in half dialled-cross。40 hybrids together with 10 circles and 4 inbred lines were planted and studied for 2 years in TangShan。Signifficant difference and Strong complement were discovered,such as population yield and average yield of top-tested crosses。planting traits GCA and heterosis。The studied results also showed that shuttle breeding could improve not only population but also heterosis,especially SCA and GCA of yield were acquired。with the same steps。

  13. Post-breeding migration routes of marine turtles from Bonaire and Klein Bonaire, Caribbean Netherlands

    NARCIS (Netherlands)

    Becking, L. E.; Christianen, M. J. A.; Nava, M. I.; Miller, N.; Willis, S.; van Dam, R. P.

    2016-01-01

    The management of small rookeries is key to conserving the regional genetic diversity of marine turtle populations and requires knowledge on population connectivity between breeding and foraging areas. To elucidate the geographic scope of the populations of marine turtles breeding at Bonaire and Kle

  14. Post-breeding migration routes of marine turtles from Bonaire and Klein Bonaire, Caribbean Netherlands

    NARCIS (Netherlands)

    Becking, L. E.; Christianen, M. J. A.; Nava, M. I.; Miller, N.; Willis, S.; van Dam, R. P.

    2016-01-01

    The management of small rookeries is key to conserving the regional genetic diversity of marine turtle populations and requires knowledge on population connectivity between breeding and foraging areas. To elucidate the geographic scope of the populations of marine turtles breeding at Bonaire and Kle

  15. Monitoring populations of breeding seabirds: Final report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — At Cape Thompson, Alaska, the University of Alaska, mapped locations of census plots during his 1959-61 studies (see Swartz 1966) of the seabird colony there....

  16. Alaska Yukon : Waterfowl Breeding Population Survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Alaska-Yukon was again blessed with a generally widespread, early spring break-up in the interior and on the North Slope with perhaps a more normal spring phenology...

  17. MODELING REGIONAL SYSTEMS OF BREEDING PIGS

    Directory of Open Access Journals (Sweden)

    Svinarev I. Y.

    2015-12-01

    Full Text Available The article contains the experience of the development of the methodology and the computer program for calculation of regional and local systems of pigs hybridization at the example of the Rostov region (Russia. Crossing the GP lines for F1 should be organized in multiplier farm, which may be separate farms and to be part of large commercial farms. For the production of F1 in a multiplier farm, we must breed a purebred specialized paternal and a maternal line, selected on the effect of combining ability. For the successful functioning of the system of hybridization, it is necessary to build a genetic pyramid, including breeding and genetic centers (nucleus farm, multiplier farm, reproducing the baseline. The article gives a detailed calculation of sow population of levels of P, GP, GGP for maternal and paternal breeds of pigs. The program uses user-defined parameters of pigs productivity, of the simulated population, and the parameters characterizing the intensity of selection of young animals. To ensure annual production of 1,822 million pigs in the Rostov region it is necessary to provide the availability of brood stock in the amount of 89 thousand heads, 6 800 heads in the structure of grandparent flocks (GP, 730 heads in the structure of the Grand-Grand-parent stock (GGP, excluding sows second maternal and paternal breeds

  18. Mitochondrial DNA of seven Italian sheep breeds shows faint signatures of domestication and suggests recent breed formation.

    Science.gov (United States)

    Mariotti, Marco; Valentini, Alessio; Marsan, Paolo Ajmone; Pariset, Lorraine

    2013-10-01

    Italy represented a crucial zone for migration and formation of sheep breeds. However, few data on Italian breeds have been published so far. We analysed seven Italian sheep breeds using mitochondrial DNA (mtDNA) sequencing to gain information on their genetic diversity and history. A 721 bp mtDNA control region fragment was amplified and sequenced in a total of 138 samples belonging to seven breeds and to Italian mohuflon (Ovis orientalis musimon) to investigate genetic diversity and phylogenetic evolution. We retrieved 68 variable sites and 79 haplotypes. The sheep breeds in our study are quite diverse, and phylogenetic analyses resulted in 3.6% of the samples belonging to A, 2.2% to D and 94.2% to B mtDNA haplogroups. Principal Component Analysis (PCA) showed a separation of breeds on both dimensions. The results of this study provide data on Italian breeds, presently scarcely investigated, and contribute to the knowledge of Italian sheep breeds and will be useful to the understanding of population genetics and breed evolution.

  19. Does timing of breeding matter less where the grass is greener? Seasonal declines in breeding performance differ between regions in an endangered endemic raptor

    Directory of Open Access Journals (Sweden)

    Marie-Sophie Garcia-Heras

    2016-09-01

    Full Text Available The timing of breeding can strongly influence individual breeding performance and fitness. Seasonal declines in breeding parameters have been often documented in birds, particularly in the Northern Hemisphere. Fewer studies have investigated whether seasonal declines in productivity vary in space, which would have implications for a species’ population dynamics across its distributional range. We report here on variation in the timing of breeding in the Black Harrier (Circus maurus, an endangered and endemic raptor to Southern Africa. We investigated how key breeding parameters (clutch size, nesting success and productivity varied with the timing of breeding, weather conditions (rainfall and temperature and between contrasted regions (coastal vs. interior-mountain. Black Harrier onset of breeding extended over an 8-month period, with a peak of laying between mid-August and end of September. We show a marked seasonal decline in all breeding parameters. Importantly, for clutch size and productivity these seasonal declines differed regionally, being more pronounced in interior-mountain than in coastal regions, where the breeding season was overall shorter. Timing of breeding, clutch size and productivity were also partly explained by weather conditions. In coastal regions, where environmental conditions, in particular rainfall, appear to be less variable, the timing of breeding matters less for breeding output than in interior-mountain regions, and breeding attempts thus occurred over a longer period. The former areas may act as population sources and be key in protecting the long-term population viability of this threatened endemic raptor. This study provides unique evidence for a regionally variable seasonal decline in breeding performance with implications for population biology and conservation.

  20. Evaluation of breeding objectives for purebred and crossbred selection schemes for adoption in indigenous chicken breeding programmes.

    Science.gov (United States)

    Okeno, T O; Kahi, A K; Peters, K J

    2013-01-01

    1. The aim of the study was to evaluate the genetic and economic breeding objectives for an indigenous chicken (IC) breeding programme in Kenya. 2. A closed three-tier nucleus breeding programme with three breeding objectives and two selection schemes was simulated. The breeding objectives included IC dual-purpose (ICD) for both eggs and meat, IC layer (ICL) for eggs and IC broiler (ICB) for meat production. 3. Pure line selection scheme (PLS) for development of IC pure breeds and crossbreeding scheme (CBS) for the production of hybrids were considered. Two-and three-way crossbreeding strategies were evaluated under CBS and the impact of nucleus size on genetic gains and profitability of the breeding programme were investigated. 4. Males were the main contributors to genetic gains. The highest genetic gains for egg number (2·71 eggs) and growth traits (1·74 g average daily gain and 57·96 g live weight at 16 weeks) were realised under PLS in ICL and ICB, respectively. 5. The genetic response for age at first egg was desirable in all the breeding objectives, while that for fertility and hatchability were only favourable under ICL and PLS in ICD. Faecal egg count and immune antibody response had low, but positive gains except under PLS where the later was unfavourable. ICB was the most profitable breeding objective, followed by ICD and ICL under all the selection schemes. 6. Although PLS was superior in genetic gains and profitability and recommended in breeding programmes targeting ICL and ICB, a three line CBS should be considered in development of a dual-purpose breed. 7. Increasing the nucleus size beyond 5% of the IC population was not attractive as it resulted in declining profitability of the breeding programme.

  1. Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information.

    Science.gov (United States)

    Cortés, O; Martinez, A M; Cañon, J; Sevane, N; Gama, L T; Ginja, C; Landi, V; Zaragoza, P; Carolino, N; Vicente, A; Sponenberg, P; Delgado, J V

    2016-07-01

    Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved.

  2. Phylogenetics, phylogeography and population genetics of North American sea ducks (tribe: Mergini)

    Science.gov (United States)

    Talbot, Sandra; Sonsthagen, Sarah A.; Pearce, John M.; Scribner, Kim T.

    2015-01-01

    Many environments occupied by North American sea ducks are remote and difficult to access, and as a result, detailed information about life history characteristics that drive population dynamics within and across species is limited. Nevertheless, progress on this front during the past several decades has benefited by the application of genetic technologies, and for several species, these technologies have allowed for concomitant tracking of population trends and genetic diversity, delineation of populations, assessment of gene flow among metapopulations, and understanding of migratory connectivity between breeding and wintering grounds. This chapter provides an overview of phylogenetic, phylogeographic, and population genetics studies of North American sea duck species, many of which have sought to understand the major and minor genetic divisions within and among sea duck species, and most of which have been conducted with the understanding that the maintenance of genetic variation in wild sea duck populations is fundamental to the group’s long-term persistence.

  3. The role of delineation education programs for improving interobserver variability in target volume delineation in gastric cancer.

    Science.gov (United States)

    Onal, Cem; Cengiz, Mustafa; Guler, Ozan C; Dolek, Yemliha; Ozkok, Serdar

    2017-05-01

    To assess whether delineation courses for radiation oncologists improve interobserver variability in target volume delineation for post-operative gastric cancer radiotherapy planning. 29 radiation oncologists delineated target volumes in a gastric cancer patient. An experienced radiation oncologist lectured about delineation based on contouring atlas and delineation recommendations. After the course, the radiation oncologists, blinded to the previous delineation, provided delineation for the same patient. The difference between delineated volumes and reference volumes for pre- and post-course clinical target volume (CTV) were 19.8% (-42.4 to 70.6%) and 12.3% (-12.0 to 27.3%) (p = 0.26), respectively. The planning target volume (PTV) differences pre- and post-course according to the reference volume were 20.5% (-40.7 to 93.7%) and 13.1% (-10.6 to 29.5%) (p = 0.30), respectively. The concordance volumes between the pre- and post-course CTVs and PTVs were 467.1 ± 89.2 vs 597.7 ± 54.6 cm(3) (p target volume changes on toxicity and local control should be evaluated for further studies. Advances in knowledge: This study demonstrated that a delineation course based on current recommendations helped physicians delineate smaller and more homogeneous target volumes. Better target volume delineation allows proper target volume irradiation and preventing unnecessary normal tissue irradiation.

  4. MARKER ASSISTED SELECTION IN DISEASE RESISTANCE BREEDING

    Directory of Open Access Journals (Sweden)

    Narasimhulu Ragimekula

    2013-08-01

    Full Text Available Feeding ever-increasing population is the main challenge faced by the agricultural scientists and to meet this plant breeders have to put continuous efforts to develop new crop varieties on fast track basis. DNA based polymorphism, commonly known as DNA markers can be used for genetic improvement through selection for favourable traits such as disease resistance. Molecular markers are becoming an essential component in backcross breeding programs for tracking the resistance genes in gene pyramiding. Marker assisted selection (MAS, is expected to increase genetic response by affecting efficiency and accuracy of selection. Even though marker-assisted selection now plays a prominent role in the field of plant breeding, examples of successful, practical outcomes are rare. MAS, with few exceptions, has not yet delivered its expected benefits in commercial breeding. It is clear that DNA markers hold great promise, but realizing that promise remains elusive. The economic and biological constraints such as a low return of investment in small-grain cereal breeding, lack of diagnostic markers, and the prevalence of QTL-background effects hinder the broad implementation of MAS. Until complex traits can be fully dissected, the application of MAS will be limited to genes of moderate-to-large effect and to applications that do not endanger the response to conventional selection. Till then, observable phenotype will remain an important component of genetic improvement programmes, because it takes in to account the collective effect of all genes. In future, chip-based, high-throughput genotyping platforms and the introduction of genomic selection will reduce the current problems of integrating MAS in practical breeding programs and open new avenues for a molecular-based resistance breeding.

  5. Male pseudohermaphroditism: genetics and clinical delineation.

    Science.gov (United States)

    Simpson, J L

    1978-10-19

    The genetics and clinical delineation of male pseudohermaphroditism are reviewed. These disorders are categorized initially by their genetic etiology--cytogenetic, Mendelian, or teratogenic. It is especially important to distinguish cytogenetic forms, usually associated with 45,X/46,XY mosaicism, from Mendelian (genetic) forms because in the former the prevalence of gonadoblastomas or dysgerminomas is about 15--20%. Genetic forms include (1) those associated with a multiple malformation pattern, (2) those due to an error in adrenal or testicular hormonal biosynthesis, (3) complete testicular feminization, (4) incomplete testicular feminization, (5) Reifenstein syndrome, (6) pseudovaginal perineoscrotal hypospadias, and (7) agondia, and possibly other conditions. Incomplete testicular feminization and the Reifenstein syndrome may or may not represent varied expressivity of the same trait. The designation pseudovaginal perineoscrotal hypospadias is appropriate only if constellations of clinical features are present and if no metabolic abnormalities are demonstrable. Etiology and available genetic data are reviewed for each of these disorders.

  6. Trisomy 4 mosaicism: Delineation of the phenotype.

    Science.gov (United States)

    Bouman, Arjan; van der Kevie-Kersemaekers, Anne-Marie; Huijsdens-van Amsterdam, Karin; Dahhan, Nordin; Knegt, Lia; Vansenne, Fleur; Cobben, Jan Maarten

    2016-04-01

    Trisomy 4 mosaicism in liveborns is very rare. We describe a 17-month-old girl with trisomy 4 mosaicism. Clinical findings in this patient are compared to previously reported patients. Based on the few descriptions available in the literature the common phenotype of trisomy 4 mosaicism seems to consist of IUGR, low birth weight/length/OFC, congenital heart defects, characteristic thumb anomalies (aplasia/hypoplasia), skin abnormalities (hypo-/hyperpigmentation), several dysmorphic features, and likely some degree of intellectual disability. When trisomy 4 mosaicism is suspected clinicians should be aware that a normal karyotype in lymphocytes does not exclude mosaicism for trisomy 4. This report contributes to a further delineation of the phenotype associated with trisomy 4 mosaicism.

  7. Delineating riparian zones for entire river networks using geomorphological criteria

    Directory of Open Access Journals (Sweden)

    D. Fernández

    2012-03-01

    Full Text Available Riparian zone delineation is a central issue for riparian and river ecosystem management, however, criteria used to delineate them are still under debate. The area inundated by a 50-yr flood has been indicated as an optimal hydrological descriptor for riparian areas. This detailed hydrological information is, however, not usually available for entire river corridors, and is only available for populated areas at risk of flooding. One of the requirements for catchment planning is to establish the most appropriate location of zones to conserve or restore riparian buffer strips for whole river networks. This issue could be solved by using geomorphological criteria extracted from Digital Elevation Models. In this work we have explored the adjustment of surfaces developed under two different geomorphological criteria with respect to the flooded area covered by the 50-yr flood, in an attempt to rapidly delineate hydrologically-meaningful riparian zones for entire river networks. The first geomorphological criterion is based on the surface that intersects valley walls at a given number of bankfull depths above the channel (BFDAC, while the second is based on the surface defined by a~threshold value indicating the relative cost of moving from the stream up to the valley, accounting for slope and elevation change (path distance. As the relationship between local geomorphology and 50-yr flood has been suggested to be river-type dependant, we have performed our analyses distinguishing between three river types corresponding with three valley morphologies: open, shallow vee and deep vee valleys (in increasing degree of valley constrainment. Adjustment between the surfaces derived from geomorphological and hydrological criteria has been evaluated using two different methods: one based on exceeding areas (minimum exceeding score and the other on the similarity among total area values. Both methods have pointed out the same surfaces when looking for those that

  8. Spatial genetic structure of bristle-thighed curlews (Numenius tahitiensis): breeding area differentiation not reflected on the non-breeding grounds

    Science.gov (United States)

    Sonsthagen, Sarah A.; Tibbitts, T. Lee; Gill, Robert E.; Williams, Ian S.; Talbot, Sandra L.

    2015-01-01

    Migratory birds occupy geographically and ecologically disparate areas during their annual cycle with conditions on breeding and non-breeding grounds playing separate and important roles in population dynamics. We used data from nuclear microsatellite and mitochondrial DNA control region loci to assess the breeding and non-breeding spatial genetic structure of a transoceanic migrant shorebird, the bristle-thighed curlew. We found spatial variance in the distribution of allelic and haplotypic frequencies between the curlew's two breeding areas in Alaska but did not observe this spatial structure throughout its non-breeding range on low-lying tropical and subtropical islands in the Central Pacific (Oceania). This suggests that the two breeding populations do not spatially segregate during the non-breeding season. Lack of migratory connectivity is likely attributable to the species' behavior, as bristle-thighed curlews exhibit differential timing of migration and some individuals move among islands during non-breeding months. Given the detrimental impact of many past and current human activities on island ecosystems, admixture of breeding populations in Oceania may render the bristle-thighed curlew less vulnerable to perturbations there, as neither breeding population will be disproportionally affected by local habitat losses or by stochastic events. Furthermore, lack of migratory connectivity may enable bristle-thighed curlews to respond to changing island ecosystems by altering their non-breeding distribution. However, availability of suitable non-breeding habitat for curlews in Oceania is increasingly limited on both low-lying and high islands by habitat loss, sea level rise, and invasive mammalian predators that pose a threat to flightless and flight-compromised curlews during the molting period.

  9. Signatures of diversifying selection in European pig breeds.

    Directory of Open Access Journals (Sweden)

    Samantha Wilkinson

    2013-04-01

    Full Text Available Following domestication, livestock breeds have experienced intense selection pressures for the development of desirable traits. This has resulted in a large diversity of breeds that display variation in many phenotypic traits, such as coat colour, muscle composition, early maturity, growth rate, body size, reproduction, and behaviour. To better understand the relationship between genomic composition and phenotypic diversity arising from breed development, the genomes of 13 traditional and commercial European pig breeds were scanned for signatures of diversifying selection using the Porcine60K SNP chip, applying a between-population (differentiation approach. Signatures of diversifying selection between breeds were found in genomic regions associated with traits related to breed standard criteria, such as coat colour and ear morphology. Amino acid differences in the EDNRB gene appear to be associated with one of these signatures, and variation in the KITLG gene may be associated with another. Other selection signals were found in genomic regions including QTLs and genes associated with production traits such as reproduction, growth, and fat deposition. Some selection signatures were associated with regions showing evidence of introgression from Asian breeds. When the European breeds were compared with wild boar, genomic regions with high levels of differentiation harboured genes related to bone formation, growth, and fat deposition.

  10. Breeding return times and abundance in capture-recapture models.

    Science.gov (United States)

    Pledger, Shirley; Baker, Edward; Scribner, Kim

    2013-12-01

    For many long-lived animal species, individuals do not breed every year, and are often not accessible during non-breeding periods. Individuals exhibit site fidelity if they return to the same breeding colony or spawning ground when they breed. If capture and recapture is only possible at the breeding site, temporary emigration models are used to allow for only a subset of the animals being present in any given year. Most temporary emigration models require the use of the robust sampling design, and their focus is usually on probabilities of annual survival and of transition between breeding and non-breeding states. We use lake sturgeon (Acipenser fulvescens) data from a closed population where only a simple (one sample per year) sampling scheme is possible, and we also wish to estimate abundance as well as sex-specific survival and breeding return time probabilities. By adding return time parameters to the Schwarz-Arnason version of the Jolly-Seber model, we have developed a new likelihood-based model which yields plausible estimates of abundance, survival, transition and return time parameters. An important new finding from investigation of the model is the overestimation of abundance if a Jolly-Seber model is used when Markovian temporary emigration is present.

  11. Applied Genetics and Genomics in Alfalfa Breeding

    Directory of Open Access Journals (Sweden)

    E. Charles Brummer

    2012-03-01

    Full Text Available Alfalfa (Medicago sativa L., a perennial and outcrossing species, is a widely planted forage legume for hay, pasture and silage throughout the world. Currently, alfalfa breeding relies on recurrent phenotypic selection, but alternatives incorporating molecular marker assisted breeding could enhance genetic gain per unit time and per unit cost, and accelerate alfalfa improvement. Many major quantitative trait loci (QTL related to agronomic traits have been identified by family-based QTL mapping, but in relatively large genomic regions. Candidate genes elucidated from model species have helped to identify some potential causal loci in alfalfa mapping and breeding population for specific traits. Recently, high throughput sequencing technologies, coupled with advanced bioinformatics tools, have been used to identify large numbers of single nucleotide polymorphisms (SNP in alfalfa, which are being developed into markers. These markers will facilitate fine mapping of quantitative traits and genome wide association mapping of agronomic traits and further advanced breeding strategies for alfalfa, such as marker-assisted selection and genomic selection. Based on ideas from the literature, we suggest several ways to improve selection in alfalfa including (1 diversity selection and paternity testing, (2 introgression of QTL and (3 genomic selection.

  12. Sampling Rate Independent Filtration Approach for Automatic ECG Delineation

    CERN Document Server

    Chereda, Hryhorii; Tymoshenko, Yury

    2016-01-01

    In this paper different types of ECG automatic delineation approaches were overviewed. A combination of these approaches was used to create sampling rate independent filtration algorithm for automatic ECG delineation that is capable of distinguishing different morphologies of T and P waves and QRS complexes. Created filtration algorithm was compared with algorithme \\`a trous. It was investigated that continuous wavelets transform with proposed automatic adaptation for different sampling rates procedure can be used for delineation problem.

  13. Help for delineation: what kind of tools?; Aide a la delineation: quels outils pratiques?

    Energy Technology Data Exchange (ETDEWEB)

    Pointreau, Y.; Bera, G.; Barillot, I. [Centre Henry-S.-Kaplan, CHU Bretonneau, Clinique d' Oncologie Radiotherapie, 37 - Tours (France); Barillot, I. [Universits Francois-Rabelais, 37 - Tours (France)

    2009-10-15

    The planning of radiotherapy has known major developments during the last years. With the emergence of news techniques such as conformational radiotherapy, intensity modulated radiation therapy or stereotactic radiation therapy, the definition of target volumes was of great importance. The recommendations for the target volumes definition have been defined in the ICRU 50 and 62 reports, without any guidelines for volume delineation. Among the uncertainties that may influence the outcome after irradiation, the intra- and inter observers variations in delineation are the most important. Many teams have offered guidelines or atlases to homogenize these volumes and reduce these variations related to medical intervention. The aim of this paper is to present the main recommendations. (authors)

  14. Aspen Delineation - El Dorado National Forest [ds364

    Data.gov (United States)

    California Department of Resources — The database represents delineations of known aspen stands, where aspen assessments were gathered in the Eldorado National Forest, Eldorado and Amador Counties,...

  15. Aspen Delineation - Klamath National Forest, EUI [ds368

    Data.gov (United States)

    California Department of Resources — The database represents delineations of known aspen stands where aspen assessments were collected in the Klamath National Forest, Siskiyou County, California. The...

  16. Breeding tropical forages

    Directory of Open Access Journals (Sweden)

    L Jank

    2011-01-01

    Full Text Available Brazil has the largest commercial beef cattle herd and is the main beef exporter in the world. Cultivated pastures arethe basis for the Brazilian beef production, and occupy an area of 101.4 million hectares. However, very few forage cultivars arecommercially available, and the majority of these are of apomictic reproduction, thus genetically homogeneous. Tropical foragebreeding is at its infancy, but much investment and efforts have been applied in the last three decades and some new cultivars havebeen released. In this paper, origin of different species, modes of reproduction, breeding programs and targets are discussed andthe resulting new cultivars released are presented.

  17. Spatial scale of local breeding habitat quality and adjustment of breeding decisions.

    Science.gov (United States)

    Doligez, Blandine; Berthouly, Anne; Doligez, Damien; Tanner, Marion; Saladin, Verena; Bonfils, Danielle; Richner, Heinz

    2008-05-01

    Experimental studies provide evidence that, in spatially and temporally heterogeneous environments, individuals track variation in breeding habitat quality to adjust breeding decisions to local conditions. However, most experiments consider environmental variation at one spatial scale only, while the ability to detect the influence of a factor depends on the scale of analysis. We show that different breeding decisions by adults are based on information about habitat quality at different spatial scales. We manipulated (increased or decreased) local breeding habitat quality through food availability and parasite prevalence at a small (territory) and a large (patch) scale simultaneously in a wild population of Great Tits (Parus major). Females laid earlier in high-quality large-scale patches, but laying date did not depend on small-scale territory quality. Conversely, offspring sex ratio was higher (i.e., biased toward males) in high-quality, small-scale territories but did not depend on large-scale patch quality. Clutch size and territory occupancy probability did not depend on our experimental manipulation of habitat quality, but territories located at the edge of patches were more likely to be occupied than central territories. These results suggest that integrating different decisions taken by breeders according to environmental variation at different spatial scales is required to understand patterns of breeding strategy adjustment.

  18. The Effect of Increasing Numbers of Horses of Undefined Breed on Horse Breeding in the Czech Republic

    OpenAIRE

    Iveta Bihuncová; Iva Jiskrová; Martina Kosťuková; Hana Černohorská; Ivana Oravcová; Eva Sobotková

    2015-01-01

    The objective of the present study was to analyse the numbers and division of horses of undefined breed. At the present time this group is the most numerous in the entire population of horses. Horses of undefined breed do not come under any breeder union which would provide reports about these horses; these horses are only registered and breeders are informed only about their numbers. Our study is the first to deal with the problem of increasing numbers of horses of undefined breed. The datab...

  19. Radiation mutation breeding

    Energy Technology Data Exchange (ETDEWEB)

    Song, Hi Sup; Kim, Jae Sung; Kim, Jin Kyu; Shin, In Chul; Lim, Young Taek

    1998-04-01

    In order to develop an advanced technical knowledge for the selection of better mutants, some of the crops were irradiated and the mutation rate, the survival rate and the method for selction of a mutant were studied. Furthermore, this study aimed to obtain basic data applicable to the development of genetic resources by evaluation and analysis the specific character for selection of the superior mutant and its plant breeding. 1. selection of the mutant with a superior resistance against environment in the principal crops 1) New varieties of mutant rices such as Wonpyeongbyeo, Wongwangbyeo, Winmibyeo, and heogseon chalbeyeo (sticky forma) were registered in the national variety list and made an application to crop variety protection right. They are under review now. 2) We also keep on studying on the number of a grain of 8 lines of excellent mutant rice for the purpose of improvement of breeding . 3) We selected 3 lines which have a resistance to pod and stem blight in large soybean, 31 lines with small grain size and higher yield, 112 lines of soybean of cooking, 7 lines of low lipoxygenase content, and 12 lines with decreased phytic acid content by 20 % compared to the previous level. 2. Selection of advanced Mugunwha (Rose of Sharon) mutant 1) Bagseul, a new variety of mutant, was developed and 30 plantlets of it are being proliferated. 2) Fifty-three lines of a mutant having a various morphologies were selected.

  20. Costs Associated with Equine Breeding in Kentucky

    Science.gov (United States)

    Walker, Cassandra L.

    There were approximately 9 million horses in the United States having a 102 billion impact on the U.S. economy (AHC, 2005). Over 1 million of those horses were involved in the breeding sector. In Kentucky, nearly 18% of the horse population have been involved in breeding. Managing an equine enterprise can be difficult, particularly given that many who undertake such endeavors do not have a background or education in business management. Kentucky Cooperative Extension has produced interactive spreadsheets to help horse owners better understand the costs associated with owning horses or managing certain equine businesses, including boarding and training operations. However, there has been little support for breeders. Therefore, the objectives of this study were to provide owners with a list of services offered for breeding and the costs associated with those services. Survey questions were created from a list of topics pertinent to equine breeding and from that list of questions, an electronic survey was created. The survey was sent via Qualtrics Survey Software to collect information on stallion and mare management costs as well as expenses related to owning and breeding. Question topics included veterinary and housing costs, management and advertising expenses, and membership fees. A total of 78 farms were selected from the 2013 breeder's listings for the Kentucky Quarter Horse Association (n = 39) and the Kentucky Thoroughbred Farm Managers' Club (n = 26), and other breed association contacts (n = 13). These farms were selected from the lists by outside individuals who were not related to the project. Participants were asked to answer all questions relevant to the farm. After the initial survey distribution, follow-up e-mails and phone calls were conducted in order to answer any questions participants might have had about the survey. Survey response rate was 32.1% (25 of 78 surveys returned). Farms in Kentucky had an average of two farm-owned and two outside

  1. Genetic diversity revealed by AFLP markers in Albanian goat breeds

    Directory of Open Access Journals (Sweden)

    Hoda Anila

    2012-01-01

    Full Text Available The amplified fragment length polymorphism (AFLP technique with three EcoRI/TaqI primer combinations was used in 185 unrelated individuals, representative of 6 local goat breeds of Albania, and 107 markers were generated. The mean Nei’s expected heterozygosity value for the whole population was 0.199 and the mean Shannon index was 0.249, indicating a high level of within-breed diversity. Wright’s FST index, Nei’s unbiased genetic distance and Reynolds’ genetic distance were calculated. Pairwise Fst values among the populations ranged from 0.019 to 0.047. A highly significant average FST of 0.031 was estimated, showing a low level of breed subdivision. Most of the variation is accounted for by differences among individuals. Cluster analysis based on Reynolds’ genetic distance between breeds and PCA were performed. An individual UPGMA tree based on Jaccard’s similarity index showed clusters with individuals from all goat breeds. Analysis of population structure points to a high level of admixture among breeds.

  2. Delineating groundwater and subsurface structures by

    Science.gov (United States)

    Araffa, Sultan Awad Sultan; Helaly, Ahmed S.; Khozium, Ashraf; Lala, Amir M. S.; Soliman, Shokry A.; Hassan, Noha M.

    2015-06-01

    Geophysical tools such as magnetic, gravity and electric resistivity have been used to delineate subsurface structures, groundwater aquifer around Cairo-Belbies Desert road. A dipole-dipole section was measured at the central part of the study area with 2100 m length and electrode spacing 50 m for greater penetration depth. The results of the inverse resistivity data indicate that the study area includes two groundwater aquifers at different depths. The shallow aquifer water is near the surface and the deep aquifer lies at depth of about 115 m and exhibits low resistivity values ranging from 20 to 100 ohm m. One hundred and fifty-two gravity stations were measured using Autograv gravimeter (CG3), different gravity corrections (drift, elevation and latitude corrections) were applied. The corrected data represented by Bouguer anomaly map were filtered into regional and residual gravity anomaly maps. The residual gravity map indicates that the area is dissected by many faults with NW-SE, N-S, E-W and NE-SW trends. One hundred and fifty-three ground magnetic measurements are collected using two Proton magnetometers (Envimag). The corrected magnetic data are represented by total magnetic intensity map that was reduced to the magnetic pole. 3D magnetic modeling was applied to detect the depth of basaltic sheet and basement complex. The results indicated that the elevation of upper surface of basalt is ranging from 148 to -153 m and the elevation of lower surface of basalt is ranging from 148 to 269 m.

  3. Ultra-low-density genotype panels for breed assignment of Angus and Hereford cattle.

    Science.gov (United States)

    Judge, M M; Kelleher, M M; Kearney, J F; Sleator, R D; Berry, D P

    2017-06-01

    Angus and Hereford beef is marketed internationally for apparent superior meat quality attributes; DNA-based breed authenticity could be a useful instrument to ensure consumer confidence on premium meat products. The objective of this study was to develop an ultra-low-density genotype panel to accurately quantify the Angus and Hereford breed proportion in biological samples. Medium-density genotypes (13 306 single nucleotide polymorphisms (SNPs)) were available on 54 703 commercial and 4042 purebred animals. The breed proportion of the commercial animals was generated from the medium-density genotypes and this estimate was regarded as the gold-standard breed composition. Ten genotype panels (100 to 1000 SNPs) were developed from the medium-density genotypes; five methods were used to identify the most informative SNPs and these included the Delta statistic, the fixation (F st) statistic and an index of both. Breed assignment analyses were undertaken for each breed, panel density and SNP selection method separately with a programme to infer population structure using the entire 13 306 SNP panel (representing the gold-standard measure). Breed assignment was undertaken for all commercial animals (n=54 703), animals deemed to contain some proportion of Angus based on pedigree (n=5740) and animals deemed to contain some proportion of Hereford based on pedigree (n=5187). The predicted breed proportion of all animals from the lower density panels was then compared with the gold-standard breed prediction. Panel density, SNP selection method and breed all had a significant effect on the correlation of predicted and actual breed proportion. Regardless of breed, the Index method of SNP selection numerically (but not significantly) outperformed all other selection methods in accuracy (i.e. correlation and root mean square of prediction) when panel density was ⩾300 SNPs. The correlation between actual and predicted breed proportion increased as panel density increased. Using

  4. Proximate drivers of spatial segregation in non-breeding albatrosses.

    Science.gov (United States)

    Clay, Thomas A; Manica, Andrea; Ryan, Peter G; Silk, Janet R D; Croxall, John P; Ireland, Louise; Phillips, Richard A

    2016-07-21

    Many animals partition resources to avoid competition, and in colonially-breeding species this often leads to divergent space or habitat use. During the non-breeding season, foraging constraints are relaxed, yet the patterns and drivers of segregation both between and within populations are poorly understood. We modelled habitat preference to examine how extrinsic (habitat availability and intra-specific competition) and intrinsic factors (population, sex and breeding outcome) influence the distributions of non-breeding grey-headed albatrosses Thalassarche chrysostoma tracked from two major populations, South Georgia (Atlantic Ocean) and the Prince Edward Islands (Indian Ocean). Spatial segregation was greater than expected, reflecting distinct seasonal differences in habitat selection and accessibility, and avoidance of intra-specific competition with local breeders. Previously failed birds segregated spatially from successful birds during summer, when they used less productive waters, suggesting a link between breeding outcome and subsequent habitat selection. In contrast, we found weak evidence of sexual segregation, which did not reflect a difference in habitat use. Our results indicate that the large-scale spatial structuring of albatross distributions results from interactions between extrinsic and intrinsic factors, with important implications for population dynamics. As habitat preferences differed substantially between colonies, populations should be considered independently when identifying critical areas for protection.

  5. Breeding ecology of the Puaiohi (Myadestes palmeri)

    Science.gov (United States)

    Snetsinger, T.J.; Herrmann, C.M.; Holmes, D.E.; Hayward, C.D.; Fancy, S.G.

    2005-01-01

    We studied the breeding ecology of the critically endangered Puaiohi (Myadestes palmeri), a poorly known Hawaiian thrush endemic to the island of Kauai. From 1996 through 1998, we monitored 96 active nests over the course of three breeding seasons. Mean clutch size was 2.0, and pairs produced an average of 1.5 fledglings/successful nest. Pairs renested after failure and some raised multiple broods. The mean annual reproductive effort was 2.1 nesting attempts/territory, and pairs produced a mean 1.1 fledglings/attempt. Large differences in nesting effort and productivity occurred among years, with mean number of fledglings/territory ranging from 0.4 to 4.9. Predation by owls (probably Short-eared Owls, Asia flammeus) and introduced rats (probably black rats, Rattus rattus) accounted for most nest failures. The presence of non-breeding floaters in the population and their largely unsuccessful attempts to gain territories in the study area suggest that the population is near carrying capacity. The high reproductive potential of the Puaiohi may help explain its persistence despite the species' historical rarity.

  6. Combining Breeding Bird Survey and distance sampling to estimate density of migrant and breeding birds

    Science.gov (United States)

    Somershoe, S.G.; Twedt, D.J.; Reid, B.

    2006-01-01

    We combined Breeding Bird Survey point count protocol and distance sampling to survey spring migrant and breeding birds in Vicksburg National Military Park on 33 days between March and June of 2003 and 2004. For 26 of 106 detected species, we used program DISTANCE to estimate detection probabilities and densities from 660 3-min point counts in which detections were recorded within four distance annuli. For most species, estimates of detection probability, and thereby density estimates, were improved through incorporation of the proportion of forest cover at point count locations as a covariate. Our results suggest Breeding Bird Surveys would benefit from the use of distance sampling and a quantitative characterization of habitat at point count locations. During spring migration, we estimated that the most common migrant species accounted for a population of 5000-9000 birds in Vicksburg National Military Park (636 ha). Species with average populations of 300 individuals during migration were: Blue-gray Gnatcatcher (Polioptila caerulea), Cedar Waxwing (Bombycilla cedrorum), White-eyed Vireo (Vireo griseus), Indigo Bunting (Passerina cyanea), and Ruby-crowned Kinglet (Regulus calendula). Of 56 species that bred in Vicksburg National Military Park, we estimated that the most common 18 species accounted for 8150 individuals. The six most abundant breeding species, Blue-gray Gnatcatcher, White-eyed Vireo, Summer Tanager (Piranga rubra), Northern Cardinal (Cardinalis cardinalis), Carolina Wren (Thryothorus ludovicianus), and Brown-headed Cowbird (Molothrus ater), accounted for 5800 individuals.

  7. Tools to analyse and display variations in anatomical delineation

    NARCIS (Netherlands)

    Ebert, Martin A.; McDermott, L. N.; Haworth, A.; van der Wath, E.; Hooton, B.

    2012-01-01

    Variations in anatomical delineation, principally due to a combination of inter-observer contributions and image-specificity, remain one of the most significant impediments to geometrically-accurate radiotherapy. Quantification of spatial variability of the delineated contours comprising a structure

  8. Genetic distinctiveness of the Herdwick sheep breed and two other locally adapted hill breeds of the UK.

    Directory of Open Access Journals (Sweden)

    Dianna Bowles

    Full Text Available There is considerable interest in locally adapted breeds of livestock as reservoirs of genetic diversity that may provide important fitness traits for future use in agriculture. In marginal areas, these animals contribute to food security and extract value from land unsuitable for other systems of farming. In England, close to 50% of the national sheep flock is farmed on grassland designated as disadvantaged areas for agricultural production. Many of these areas are in the uplands, where some native breeds of sheep continue to be commercially farmed only in highly localised geographical regions to which they are adapted. This study focuses on three of these breeds, selected for their adaptation to near identical environments and their geographical concentration in regions close to one another. Our objective has been to use retrotyping, microsatellites and single nucleotide polymorphisms to explore the origins of the breeds and whether, despite their similar adaptations and proximity, they are genetically distinctive. We find the three breeds each have a surprisingly different pattern of retrovirus insertions into their genomes compared with one another and with other UK breeds. Uniquely, there is a high incidence of the R0 retrotype in the Herdwick population, characteristic of a primitive genome found previously in very few breeds worldwide and none in the UK mainland. The Herdwick and Rough Fells carry two rare retroviral insertion events, common only in Texels, suggesting sheep populations in the northern uplands have a historical association with the original pin-tail sheep of Texel Island. Microsatellite data and analyses of SNPs associated with RXFP2 (horn traits and PRLR (reproductive performance traits also distinguished the three breeds. Significantly, an SNP linked to TMEM154, a locus controlling susceptibility to infection by Maedi-Visna, indicated that all three native hill breeds have a lower than average risk of infection to the

  9. EcoTILLING-based association mapping efficiently delineates functionally relevant natural allelic variants of candidate genes governing agronomic traits in chickpea

    Directory of Open Access Journals (Sweden)

    Deepak eBajaj

    2016-04-01

    Full Text Available The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10-15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea.

  10. Signatures of selection in the genomes of commercial and non-commercial chicken breeds.

    Directory of Open Access Journals (Sweden)

    Martin G Elferink

    Full Text Available Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total using a high-density (58 K SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations.

  11. Signatures of selection in the genomes of commercial and non-commercial chicken breeds.

    Science.gov (United States)

    Elferink, Martin G; Megens, Hendrik-Jan; Vereijken, Addie; Hu, Xiaoxiang; Crooijmans, Richard P M A; Groenen, Martien A M

    2012-01-01

    Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations.

  12. Breeding Management of Captive Asian Elephant (Elephas maximus) in Range Countries and Zoos

    National Research Council Canada - National Science Library

    Chatchote THITARAM

    2012-01-01

    .... The low birth and high mortality rate cause the captive population to decline rapidly. Captive breeding programs in Asian elephants range countries and zoos have met with limited success and few ex situ elephant populations are self-sustaining...

  13. A Morphometric Survey among Three Iranian Horse Breeds with Multivariate Analysis

    Directory of Open Access Journals (Sweden)

    M. Hosseini

    2016-12-01

    Full Text Available Three Iranian horse breeds, Turkoman, Caspian, and Kurdish, are the most important Iranian horse breeds which are well known in all around of the world because of their beauty, versatility, great stamina, and  intelligence. Phenotypic characterization was used to identify and document the diversity within and between distinct breeds, based on their observable attributes. Phenotypic characterization and body biometric in 23 traits were measured in 191 purebred horses belonging to three breeds, i.e. Turkoman (70 horses, Kurdish (77 horses, and Caspian (44 horses.  Caspian breed was  sampled from the Provinces of Alborz and Gilan. Kurdish breed was sampled from the Provinces of Kurdistan, Kermanshah, and Hamadan. Turkoman breed was sampled from the Provinces of Golestan, Markazi, and Isfahan. Multivariate analysis of variance (MANOVA was implemented. In addition, Canonical Discriminate Analysis (CDA, Principal Component Analysis (PCA, and Custer analysis were executed for assessing the relationship among the breeds. All statistical analysis was executed by SAS statistical program. The results of our investigation represented the breeds classification into 3 different classes (Caspian, Turkoman, and Kurdish based on different morphometrical traits. Caspian breed with smaller size in most variables was detached clearly from the others with more distance than Kurdish and Turkoman breeds. The result showed that the most variably trait for classification was Hind Hoof Length. Adaptation with different environments causes difference in morphology and difference among breeds. We can identify and classify domestic population using PCA, CDA, and cluster analysis.

  14. Microsatellite based genetic diversity and relationships among ten Creole and commercial cattle breeds raised in Brazil

    Directory of Open Access Journals (Sweden)

    Almeida Leonardo D

    2007-12-01

    Full Text Available Abstract Background Brazil holds the largest commercial cattle populations worldwide. Local cattle breeds can be classified according to their origin, as exotic or Creole. Exotic breeds imported in the last 100 years, both zebuine and taurine, currently make up the bulk of the intensively managed populations. Locally adapted Creole breeds, originated from cattle introduced by the European conquerors derive from natural selection and events of breed admixture. While historical knowledge exists on the Brazilian Creole breeds very little is known on their genetic composition. The objective of this study was to assess the levels of genetic diversity, phylogenetic relationships and patterns of taurine/zebuine admixture among ten cattle breeds raised in Brazil. Results Significant reduction of heterozygosity exists due both to within-population inbreeding and to breed differentiation in both subspecies (taurine and zebuine. For taurine breeds the number of markers that contribute to breed differentiation is larger than for zebuine. A consistently similar number of alleles was seen in both subspecies for all microsatellites. Four Creole breeds were the most genetically diverse followed by the zebuine breeds, the two specialized taurine breeds and the Creole Caracu. Pairwise genetic differentiation were all significant indicating that all breeds can be considered as genetically independent entities. A STRUCTURE based diagram indicated introgression of indicine genes in the local Creole breeds and suggested that occasional Creole introgression can be detected in some Zebuine animals. Conclusion This study reports on a comprehensive study of the genetic structure and diversity of cattle breeds in Brazil. A significant amount of genetic variation is maintained in the local cattle populations. The genetic data show that Brazilian Creole breeds constitute an important and diverse reservoir of genetic diversity for bovine breeding and conservation. The

  15. Next generation breeding.

    Science.gov (United States)

    Barabaschi, Delfina; Tondelli, Alessandro; Desiderio, Francesca; Volante, Andrea; Vaccino, Patrizia; Valè, Giampiero; Cattivelli, Luigi

    2016-01-01

    The genomic revolution of the past decade has greatly improved our understanding of the genetic make-up of living organisms. The sequencing of crop genomes has completely changed our vision and interpretation of genome organization and evolution. Re-sequencing allows the identification of an unlimited number of markers as well as the analysis of germplasm allelic diversity based on allele mining approaches. High throughput marker technologies coupled with advanced phenotyping platforms provide new opportunities for discovering marker-trait associations which can sustain genomic-assisted breeding. The availability of genome sequencing information is enabling genome editing (site-specific mutagenesis), to obtain gene sequences desired by breeders. This review illustrates how next generation sequencing-derived information can be used to tailor genomic tools for different breeders' needs to revolutionize crop improvement. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  16. Biotechnology in maize breeding

    Directory of Open Access Journals (Sweden)

    Mladenović-Drinić Snežana

    2004-01-01

    Full Text Available Maize is one of the most important economic crops and the best studied and most tractable genetic system among monocots. The development of biotechnology has led to a great increase in our knowledge of maize genetics and understanding of the structure and behaviour of maize genomes. Conventional breeding practices can now be complemented by a number of new and powerful techniques. Some of these often referred to as molecular methods, enable scientists to see the layout of the entire genome of any organism and to select plants with preferred characteristics by "reading" at the molecular level, saving precious time and resources. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. Application of molecular markers for genetic studies of maize include: assessment of genetic variability and characterization of germ plasm, identification and fingerprinting of genotypes, estimation of genetic distance, detection of monogamic and quantitative trait loci, marker assisted selection, identification of sequence of useful candidate genes, etc. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible and serve as bases for marker assisted selection. Sequencing of maize genomes would help to elucidate gene function, gene regulation and their expression. Modern biotechnology also includes an array of tools for introducing or deieting a particular gene or genes to produce plants with novel traits. Development of informatics and biotechnology are resulted in bioinformatic as well as in expansion of microarrey technique. Modern biotechnologies could complement and improve the efficiency of traditional selection and breeding techniques to enhance agricultural productivity.

  17. The different breeding strategies of penguins: a review.

    Science.gov (United States)

    Ancel, André; Beaulieu, Michaël; Gilbert, Caroline

    2013-01-01

    The 18 penguin species are exclusively and widely distributed in the Southern hemisphere, from the Equator to the Antarctic continent, and are thus submitted to various ecological constraints in their reproductive strategy. This results in a high variability in all aspects of the breeding biology of the different species. Although penguins appear primarily adapted for a marine existence, they remain dependent on land for breeding, rearing young, and moulting. Here we describe and compare the breeding cycle of all the penguin species, highlighting the characteristics of each species in terms of breeding range, population status, threats induced by environmental changes, duration of the different phases of the breeding cycle, mate fidelity, body mass, body height, egg mass and duration of egg formation. We also focus on the breeding cycle of the genus Aptenodytes, since it largely differs from the breeding cycle of most of the other penguin species. Copyright © 2013 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  18. Brain size-related breeding strategies in a seabird.

    Science.gov (United States)

    Jaatinen, Kim; Öst, Markus

    2016-01-01

    The optimal compromise between decision speed and accuracy may depend on cognitive ability, associated with the degree of encephalization: larger brain size may select for accurate but slow decision-making, beneficial under challenging conditions but costly under benign ones. How this brain size-dependent selection pressure shapes avian breeding phenology and reproductive performance remains largely unexplored. We predicted that (1) large-brained individuals have a delayed breeding schedule due to thorough nest-site selection and/or prolonged resource acquisition, (2) good condition facilitates early breeding independent of relative brain size, and (3) large brain size accrues benefits mainly to individuals challenged by environmental or intrinsic constraints. To test these predictions, we examined how the relative head volume of female eiders (Somateria mollissima) of variable body condition correlated with their breeding schedule, hatching success and offspring quality. The results were consistent with our predictions. First, large head size was associated with a progressively later onset of breeding with increasing breeding dispersal distance. Second, increasing body condition advanced the timing of breeding, but this effect was significantly weaker in large-brained females. Third, larger head volume was associated with increased hatching success mainly among late breeders and those in poor body condition, and duckling body condition was positively related to maternal head volume, but only in poor-condition mothers. Our study is, to our knowledge, the first to demonstrate the presence of brain size-related differences in reproductive strategies within a single natural population.

  19. Mitochondrial D-loop sequence variation among Italian horse breeds

    Directory of Open Access Journals (Sweden)

    Zanotti Marta

    2004-11-01

    Full Text Available Abstract The genetic variability of the mitochondrial D-loop DNA sequence in seven horse breeds bred in Italy (Giara, Haflinger, Italian trotter, Lipizzan, Maremmano, Thoroughbred and Sarcidano was analysed. Five unrelated horses were chosen in each breed and twenty-two haplotypes were identified. The sequences obtained were aligned and compared with a reference sequence and with 27 mtDNA D-loop sequences selected in the GenBank database, representing Spanish, Portuguese, North African, wild horses and an Equus asinus sequence as the outgroup. Kimura two-parameter distances were calculated and a cluster analysis using the Neighbour-joining method was performed to obtain phylogenetic trees among breeds bred in Italy and among Italian and foreign breeds. The cluster analysis indicates that all the breeds but Giara are divided in the two trees, and no clear relationships were revealed between Italian populations and the other breeds. These results could be interpreted as showing the mixed origin of breeds bred in Italy and probably indicate the presence of many ancient maternal lineages with high diversity in mtDNA sequences.

  20. Potato breeding in the Netherlands

    NARCIS (Netherlands)

    Haan, de H.

    1953-01-01

    A remarkable feature of potato breeding in the Netherlands is the great number of private breeders who have concentrated their efforts on the improvement of the potato. The author calls attention to some circumstances and measures that have made potato breeding attractive in the Netherlands

  1. Biological parameters used in setting captive-breeding quotas for Indonesia's breeding facilities.

    Science.gov (United States)

    Janssen, Jordi; Chng, Serene C L

    2017-07-03

    The commercial captive breeding of wildlife is often seen as a potential conservation tool to relieve pressure on wild populations, but laundering of wild-sourced specimens as captive bred can seriously undermine conservation efforts and provide a false sense of sustainability. Indonesia is at the center of such controversy; therefore, we examined Indonesia's captive-breeding production plan (CBPP) for 2016. We compared the biological parameters used in the CBPP with parameters in the literature and with parameters suggested by experts on each species and identified shortcomings of the CBPP. Production quotas for 99 out of 129 species were based on inaccurate or unrealistic biological parameters and production quotas deviated more than 10% from what parameters in the literature allow for. For 38 species, the quota exceeded the number of animals that can be bred based on the biological parameters (range 100-540%) calculated with equations in the CBPP. We calculated a lower reproductive output for 88 species based on published biological parameters compared with the parameters used in the CBPP. The equations used in the production plan did not appear to account for other factors (e.g., different survival rate for juveniles compared to adult animals) involved in breeding the proposed large numbers of specimens. We recommend the CBPP be adjusted so that realistic published biological parameters are applied and captive-breeding quotas are not allocated to species if their captive breeding is unlikely to be successful or no breeding stock is available. The shortcomings in the current CBPP create loopholes that mean mammals, reptiles, and amphibians from Indonesia declared captive bred may have been sourced from the wild. © 2017 Society for Conservation Biology.

  2. Breeding Practices in Sheep Farming

    Directory of Open Access Journals (Sweden)

    M.A. Shejal

    2009-02-01

    Full Text Available The sheep is an important economic livestock species, contributing greatly to the Indian economy, especially in arid, semi arid and mountain areas. The current population in world is 1110.78 millions, around 44.85 millions (1987 sheeps in India (ICAR., 2002. Sheeps are mostly reared for meat and wool. The average annual wool production per sheep is between 3.5 to 5.5 kg of fine quality wool in Australia, New Zealand and U.S.S.R., where as in India except Magra sheep which annually yield more than 2 kg wool having staple length 5.8 cm, the average of rest of the wool produced is less than 1.0 kg per sheep of inferior quality (Banerjee G.C., 1998. Therefore many farmers in southern India adapted sheep rearing for meat production than for wool production. For yielding more production from sheep farming one should have sound knowledge of general information related to the reproduction and different breeding practices. [Vet. World 2009; 2(1.000: 43-44

  3. Candidate genes for idiopathic epilepsy in four dog breeds

    Directory of Open Access Journals (Sweden)

    Mickelson James R

    2011-04-01

    Full Text Available Abstract Background Idiopathic epilepsy (IE is a naturally occurring and significant seizure disorder affecting all dog breeds. Because dog breeds are genetically isolated populations, it is possible that IE is attributable to common founders and is genetically homogenous within breeds. In humans, a number of mutations, the majority of which are genes encoding ion channels, neurotransmitters, or their regulatory subunits, have been discovered to cause rare, specific types of IE. It was hypothesized that there are simple genetic bases for IE in some purebred dog breeds, specifically in Vizslas, English Springer Spaniels (ESS, Greater Swiss Mountain Dogs (GSMD, and Beagles, and that the gene(s responsible may, in some cases, be the same as those already discovered in humans. Results Candidate genes known to be involved in human epilepsy, along with selected additional genes in the same gene families that are involved in murine epilepsy or are expressed in neural tissue, were examined in populations of affected and unaffected dogs. Microsatellite markers in close proximity to each candidate gene were genotyped and subjected to two-point linkage in Vizslas, and association analysis in ESS, GSMD and Beagles. Conclusions Most of these candidate genes were not significantly associated with IE in these four dog breeds, while a few genes remained inconclusive. Other genes not included in this study may still be causing monogenic IE in these breeds or, like many cases of human IE, the disease in dogs may be likewise polygenic.

  4. Opposing selection and environmental variation modify optimal timing of breeding.

    Science.gov (United States)

    Tarwater, Corey E; Beissinger, Steven R

    2013-09-17

    Studies of evolution in wild populations often find that the heritable phenotypic traits of individuals producing the most offspring do not increase proportionally in the population. This paradox may arise when phenotypic traits influence both fecundity and viability and when there is a tradeoff between these fitness components, leading to opposing selection. Such tradeoffs are the foundation of life history theory, but they are rarely investigated in selection studies. Timing of breeding is a classic example of a heritable trait under directional selection that does not result in an evolutionary response. Using a 22-y study of a tropical parrot, we show that opposing viability and fecundity selection on the timing of breeding is common and affects optimal breeding date, defined by maximization of fitness. After accounting for sampling error, the directions of viability (positive) and fecundity (negative) selection were consistent, but the magnitude of selection fluctuated among years. Environmental conditions (rainfall and breeding density) primarily and breeding experience secondarily modified selection, shifting optimal timing among individuals and years. In contrast to other studies, viability selection was as strong as fecundity selection, late-born juveniles had greater survival than early-born juveniles, and breeding later in the year increased fitness under opposing selection. Our findings provide support for life history tradeoffs influencing selection on phenotypic traits, highlight the need to unify selection and life history theory, and illustrate the importance of monitoring survival as well as reproduction for understanding phenological responses to climate change.

  5. Integrating genomic selection into dairy cattle breeding programmes: a review.

    Science.gov (United States)

    Bouquet, A; Juga, J

    2013-05-01

    Extensive genetic progress has been achieved in dairy cattle populations on many traits of economic importance because of efficient breeding programmes. Success of these programmes has relied on progeny testing of the best young males to accurately assess their genetic merit and hence their potential for breeding. Over the last few years, the integration of dense genomic information into statistical tools used to make selection decisions, commonly referred to as genomic selection, has enabled gains in predicting accuracy of breeding values for young animals without own performance. The possibility to select animals at an early stage allows defining new breeding strategies aimed at boosting genetic progress while reducing costs. The first objective of this article was to review methods used to model and optimize breeding schemes integrating genomic selection and to discuss their relative advantages and limitations. The second objective was to summarize the main results and perspectives on the use of genomic selection in practical breeding schemes, on the basis of the example of dairy cattle populations. Two main designs of breeding programmes integrating genomic selection were studied in dairy cattle. Genomic selection can be used either for pre-selecting males to be progeny tested or for selecting males to be used as active sires in the population. The first option produces moderate genetic gains without changing the structure of breeding programmes. The second option leads to large genetic gains, up to double those of conventional schemes because of a major reduction in the mean generation interval, but it requires greater changes in breeding programme structure. The literature suggests that genomic selection becomes more attractive when it is coupled with embryo transfer technologies to further increase selection intensity on the dam-to-sire pathway. The use of genomic information also offers new opportunities to improve preservation of genetic variation. However

  6. 巨桉第二代育种群体遗传变异及早期选择研究%Genetic Variation and Early Selection of the Second Generation Breeding Population of Eucalyptus grandis

    Institute of Scientific and Technical Information of China (English)

    兰俊; 吴永富; 石前; 付淼; 吴兵; 陈东林

    2012-01-01

    A study on genetic variation and early genetic selection was carried out in the second generation breeding population of Eucalyptus grandis at the age of 3.2 years at Guangxi Dongmen state - owned Forest Farm. The study showed that the differences between families in tree height (HT), diameter at breast height (DBH), ratio of HT to DBH (H/D) and individual tree volume (VOL) were highly significant. For the best families, mean HT reached 10.1 m, DBH 9.3 cm, H/D 1.1 and VOL 0. 0446 m3. Growth traits were found to be under low genetic control with individual tree heritability (hi2) for HT being 0.31, for DBH 0.31, for H/D O. 16 and for VOL O. 26. A total of 12 superior families were selected, with the estimated genetic gain reaehing 18.9% for HT, 19.5% for DBH and 42.2% for VOL. Three hundred superior individual trees were selected and the estimated genetie gain with these was 15.4% for HT, 16.7% for DBH and 36.7% for VOL.%对广西东门林场3.2年生巨桉第二代育种群主要生长性状进行遗传变异和早期遗传型选择研究表明:家系平均树高、胸径、高径比和单株材积分别为10.1m、9.3cm、1.1和0.0446m3,且各指标在不同家系水平上存在极显著差异。树高、胸径、高径比和单株材积均受到相对较弱的遗传控制,遗传力分别为0.31、0.31、0.16和0.26,估算的遗传力均在合理范围之内。通过有效的遗传型选择,筛选出优良家系12个,树高、胸径和单株材积的遗传增益分别为18.9%、19.5%和42.2%;筛选出优良单株300个,树高、胸径和单株材积的遗传增益分别为15.4%、16.7%和36.7%,遗传增益显著。

  7. The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data.

    Science.gov (United States)

    Cañon, J; Checa, M L; Carleos, C; Vega-Pla, J L; Vallejo, M; Dunner, S

    2000-02-01

    Partition of the genetic variability, genetic structure and relationships among seven Spanish Celtic horse breeds were studied using PCR amplification of 13 microsatellites on 481 random individuals. In addition, 60 thoroughbred horses were included. The average observed heterozygosity and the mean number of alleles were higher for the Atlantic horse breeds than for the Balearic Islands breeds. Only eight percentage of the total genetic variability could be attributed to differences among breeds (mean FST approximately 0.08; P Jaca Navarra, Caballo Gallego and Pottoka) are not consistently differentiated. Multivariate analysis showed that Asturcon populations, Losina and Balearic Islands breeds are clearly separated from each other and from the rest of the breeds. In addition to this, the use of the microsatellites proved to be useful for breed assignment.

  8. GENETIC CHARACTERIZATION OF ROMANIAN CATTLE BREEDS USING BIOCHEMICAL MARKERS

    Directory of Open Access Journals (Sweden)

    MARIANA REBEDEA

    2013-12-01

    Full Text Available The paper presents a genetic characterization of cattle breeds in Romania based onbiochemical markers in the blood and the milk. The surveyed breeds are: RomanianBlack Spotted Cattle (BNR, Romanian Spotted Cattle (BR, Romanian Brown (Band Romanian Steppe, and the markers identified are represented by some proteins,serum transferrin (Tf, serum albumins (Al, hemoglobin (Hb respectively-from theblood and beta-lactoglobulin (βLg-from the milk. In order to determine thegenotypes in the studied populations electrophoresis was used in three differentvariations, depending on the type of the protein, and the migration substrates usedwere starch and polyacrylamide. The identified genetic structures in the individualsfrom the surveyed breeds allowed their genetic characterization based on gene andgenotype frequencies, as well as using these data in establishing the identity andpaternity of the individuals in the surveyed breeds.

  9. Volcanic calderas delineate biogeographic provinces among Yellowstone thermophiles.

    Science.gov (United States)

    Takacs-Vesbach, Cristina; Mitchell, Kendra; Jackson-Weaver, Olan; Reysenbach, Anna-Louise

    2008-07-01

    It has been suggested that the distribution of microorganisms should be cosmopolitan because of their enormous capacity for dispersal. However, recent studies have revealed that geographically isolated microbial populations do exist. Geographic distance as a barrier to dispersal is most often invoked to explain these distributions. Here we show that unique and diverse sequences of the bacterial genus Sulfurihydrogenibium exist in Yellowstone thermal springs, indicating that these sites are geographically isolated. Although there was no correlation with geographic distance or the associated geochemistry of the springs, there was a strong historical signal. We found that the Yellowstone calderas, remnants of prehistoric volcanic eruptions, delineate biogeographical provinces for the Sulfurihydrogenibium within Yellowstone (chi(2): 9.7, P = 0.002). The pattern of distribution that we have detected suggests that major geological events in the past 2 million years explain more of the variation in sequence diversity in this system than do contemporary factors such as habitat or geographic distance. These findings highlight the importance of historical legacies in determining contemporary microbial distributions and suggest that the same factors that determine the biogeography of macroorganisms are also evident among bacteria.

  10. Genetic Diversity of Old Chicken Breeds Kept in Poland

    Directory of Open Access Journals (Sweden)

    Fabio Maretto

    2013-09-01

    Full Text Available The aim of this study was to compare the genetic variation of five local chicken breeds reared in Poland. Twenty-seven microsatellite markers were investigated in 138 birds belonging to five breeds: Miniature Cochin (MCO, Gold Italian (GI, Green Legged Partridge (GLP, Silver Italian (SI and White Leghorn (WL. One hundred eighty five alleles were detected in the overall population, with a mean number of 6.85 ± 3.32 alleles per locus. For the local breeds, the observed and expected heterozygosity ranged from a minimum of 0.287 to a maximum of 0.458 and from 0.397 to 0.499 for the GI and SI breeds, respectively. The overall population heterozygote deficiency was 0.430, the average Wright’s inbreeding coefficient (FIS was 0.061 and the heterozygote deficiency due to breed subdivision was 0.393. Wright’s fixation index was slightly positive for all breeds excluding MCO (FIS = -0.476 and the estimated molecular inbreeding (fij within breed ranged from 0.296 (GLP and SI to 0.361 (WL evidencing limited coancestry. Mean allelic richness, obtained with rarefaction method based on sixteen observations, was 2.12 being the WL the less variable (1.79. Tomiuk and Loeschcke’s DTL genetic distance values were used to draw a neighbornet network which separated the cluster made of MCO and GLP from the cluster of GI, WL and SI. The results arising from our microsatellites analysis represent a starting point for the valorization of these local Polish chicken breeds for monitoring and preserving their genetic variability.

  11. Research on the Morphological Characteristics Variability of Three Horse Breeds

    Directory of Open Access Journals (Sweden)

    Marian Cătălin Prisacaru

    2012-10-01

    Full Text Available The aim of this study was the characterization of some morphological parameters of some horse population improvedwith stallion of Arab, Hucul and English thoroughbred breeds. The biological material was represented by thestallions belonging to the three breeds and the population improved with them. Measurements have been made inorder to determine the height at withers, oblique length of the trunk, cannon girth and weight. The height at witherspresented smaller dimensions at the Arab and English thoroughbred breeds and at the Hucul breed the stallions had aheight at withers of 140 cm and the improved population 143.80 cm. Oblique length of the trunk presented valuesslightly lower at the improved horses in comparison with the stallions used at mount. The English thoroughbredpresented a value of 21.50 cm of the cannon girth at the improved population in comparison with the value of 19.5cm obtained at the mount stallions. The weight has been lower at the improved populations than the one of thestallions. Most of the morphological characteristics of the improved population are close to the ones if the stallionsused at mount.

  12. A detailed study on Catchment delineation for Urban areas

    Science.gov (United States)

    Sharma, B.; B M, A.; Lohani, B.; Jain, A.

    2015-12-01

    Urban flood modelling is carried out for predicting, analysing and planning of floods in urban areas. Catchment information is an important input for urban flood modelling. Automatic catchment delineation at gully gratings for urban areas using appropriate software packages/methods along with an appropriate set of input data and parameters is still a research challenge. Considering the above, the aim of this study is to (i) identify the best suitable software for automatic catchment delineation by considering gully grating as outlet (ii) understand the effect of resolution of DEM on catchments delineated (iii) understand whether to consider DEM or DSM for catchment delineation (iv) study the effect of grid based and TIN based DEM. In this study catchment delineation has been investigated considering IIT Kanpur as a study site. LiDAR data are used to generate DEM/DSM of the study area. A comparative study of catchment delineation has been carried out between ArcHydro 10.1, BASINS 4.1, ArcSWAT, WMS 7.1, and HEC-GeoHMS approaches. Catchments have been delineated for different drainage threshold areas using gully grating points as outlets and their effects have been compared for the aforementioned software. In order to understand the effect of resolution of data, DEMs of 1m and 5m resolution have been generated and compared against each other. Effects of building ridge lines and their contribution to catchment delineation has been studied by generating a DSM of 1m resolution, and comparing the results with catchments delineated using 1m DEM. In order to assess the effects of the types of DEM over catchment delineation, a grid based DEM and TIN based DEM are compared against each other using WMS 7.1 software. The results for the catchment delineation using various software illustrate that ArcHydro 10.1 performs better than any other aforementioned software. Also, it is noted that varied drainage threshold area parameters, resolutions of DEM, selection of DEM

  13. Effectors as tools in disease resistance breeding against biotrophic, hemibiotrophic, and necrotrophic plant pathogens.

    Science.gov (United States)

    Vleeshouwers, Vivianne G A A; Oliver, Richard P

    2014-03-01

    One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.

  14. Breeding biology of a winter-breeding procellariiform in the North Atlantic, the Macaronesian shearwater Puffinus lherminieri baroli.

    Science.gov (United States)

    Fagundes, Ana Isabel; Ramos, Jaime A; Ramos, Urtelinda; Medeiros, Renata; Paiva, Vitor H

    2016-10-01

    The breeding success of burrow-nesting seabirds may be influenced by both nest site characteristics and oceanographic conditions influencing food availability at sea. In this study we describe the breeding biology of the winter-breeding Macaronesian shearwater (Puffinus lherminieri baroli), including nest site characteristics and interspecific competition. We also evaluate the possible effects of changing oceanographic conditions on breeding phenology and breeding success. The study was carried out over two breeding seasons on two islands in the North Atlantic Ocean, Cima Islet and Selvagem Grande. Oceanographic characteristics differed between years. On a regional scale, the North Atlantic Oscillation (NAO) index was low and negative in 2011, and on a local scale, birds used areas with significantly lower values of chlorophyll a concentration and significantly higher values of sea surface temperature anomalies. Hatching success was higher in 2012 than in 2011. At both colonies, egg cracking was the main cause of hatching failure, but in 2011 several eggs on Selvagem Grande were deserted. In 2012 birds laid earlier and chicks had longer wings and were heavier. At both colonies, nests that were deeper, were sheltered from prevailing winds and had small chambers and a soil substrate had a higher probability of being used successfully by the birds. Nests occupied solely by Macaronesian shearwaters were much deeper and had less volume than nests shared with other species. Our study suggests that the breeding success of Macaronesian shearwaters is strongly related to nest site characteristics and that at-sea environmental conditions exert a strong influence on reproductive parameters, with birds breeding in a poor year (evaluated in terms of lower marine productivity) laying much later and their chicks growing at a slower rate than in a good year. The influence of nest site characteristics and environmental conditions may be very important for understanding the breeding

  15. RosBREED: Enabling Marker-Assisted Breeding in Rosaceae

    Science.gov (United States)

    Genomics research has not yet been translated into routine practical application in breeding Rosaceae fruit crops (peach, apple, strawberry, cherry, apricot, pear, raspberry, etc.). Through dedicated efforts of many researchers worldwide, a wealth of genomics resources has accumulated, including ES...

  16. RosBREED: Enabling marker-assisted breeding in Rosaceae

    NARCIS (Netherlands)

    Iezzoni, A.F.; Weebadde, C.; Luby, J.; Yue, C.; Weg, van de W.E.; Fazio, G.; Main, D.; Peace, C.P.; Bassil, N.V.; McFerson, J.

    2010-01-01

    Genomics research has not yet been translated into routine practical application in breeding Rosaceae fruit crops (peach, apple, strawberry, cherry, apricot, pear, raspberry, etc.). Through dedicated efforts of many researchers worldwide, a wealth of genomics resources has accumulated, including EST

  17. Impact of Molecular Technologies on Faba Bean (Vicia faba L.) Breeding Strategies

    OpenAIRE

    Tao Yang; Xuxiao Zong; Haobing Li; Tony Leonforte; Sukhjiwan Kaur; Ana Torres; Jeff Paull; Annathurai Gnanasambandam; Michael Materne

    2012-01-01

    Faba bean (Vicia faba L.) is a major food and feed legume because of the high nutritional value of its seeds. The main objectives of faba bean breeding are to improve yield, disease resistance, abiotic stress tolerance, seed quality and other agronomic traits. The partial cross-pollinated nature of faba bean introduces both challenges and opportunities for population development and breeding. Breeding methods that are applicable to self-pollinated crops or open-pollinated crops are not highly...

  18. Breeding bird survey data

    Data.gov (United States)

    U.S. Environmental Protection Agency — The data are maintained by the USGS (https://www.pwrc.usgs.gov/bbs/RawData/) and provides information on the trends and status of North American bird populations...

  19. Aspen Delineation - Plumas National Forest, FRRD [ds376

    Data.gov (United States)

    California Department of Resources — The database represents delineations of aspen stands associated with stand assessment data (PLUMAS_NF_FEATHERRIVER_PTS) collected in aspen stands in the Plumas...

  20. Deviations in delineated GTV caused by artefacts in 4DCT

    DEFF Research Database (Denmark)

    Persson, Gitte Fredberg; Nygaard, Ditte Eklund; Brink, Carsten;

    2010-01-01

    BACKGROUND AND PURPOSE: Four-dimensional computed tomography (4DCT) is used for breathing-adapted radiotherapy planning. Irregular breathing, large tumour motion or interpolation of images can cause artefacts in the 4DCT. This study evaluates the impact of artefacts on gross tumour volume (GTV......) size. MATERIAL AND METHODS: In 19 4DCT scans of patients with peripheral lung tumours, GTV was delineated in all bins. Variations in GTV size between bins in each 4DCT scan were analysed and correlated to tumour motion and variations in breathing signal amplitude and breathing signal period. End......-expiration GTV size (GTVexp) was considered as reference for GTV size. Intra-session delineation error was estimated by re-delineation of GTV in eight of the 4DCT scans. RESULTS: In 16 of the 4DCT scans the maximum deviations from GTVexp were larger than could be explained by delineation error. The deviations...

  1. Remote sensing application for delineating coastal vegetation - A case study

    Digital Repository Service at National Institute of Oceanography (India)

    Kunte, P.D.; Wagle, B.G.

    Remote sensing data has been used for mapping coastal vegetation along the Goa Coast, India. The study envisages the use of digital image processing techniques for delineating geomorphic features and associated vegetation, including mangrove, along...

  2. Illinois’ 2000 breeding season report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the 2000 breeding season for grassland birds in Illinois. The report begins by summarizing weather conditions throughout the season and...

  3. Atlantic Flyway Breeding Waterfowl Survey

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The Atlantic Flyway Technical Section initiated this breeding waterfowl survey in 11 northeast states ranging from New Hampshire to Virginia.

  4. Tricolored Blackbird - Breeding [ds20

    Data.gov (United States)

    California Department of Resources — These data come from observations of breeding tricolored blackbirds throughout their range in California. NAD27 coordinates are given in the data for each record....

  5. Transit Traffic Analysis Zone Delineating Method Based on Thiessen Polygon

    Directory of Open Access Journals (Sweden)

    Shuwei Wang

    2014-04-01

    Full Text Available A green transportation system composed of transit, busses and bicycles could be a significant in alleviating traffic congestion. However, the inaccuracy of current transit ridership forecasting methods is imposing a negative impact on the development of urban transit systems. Traffic Analysis Zone (TAZ delineating is a fundamental and essential step in ridership forecasting, existing delineating method in four-step models have some problems in reflecting the travel characteristics of urban transit. This paper aims to come up with a Transit Traffic Analysis Zone delineation method as supplement of traditional TAZs in transit service analysis. The deficiencies of current TAZ delineating methods were analyzed, and the requirements of Transit Traffic Analysis Zone (TTAZ were summarized. Considering these requirements, Thiessen Polygon was introduced into TTAZ delineating. In order to validate its feasibility, Beijing was then taken as an example to delineate TTAZs, followed by a spatial analysis of office buildings within a TTAZ and transit station departure passengers. Analysis result shows that the TTAZs based on Thiessen polygon could reflect the transit travel characteristic and is of in-depth research value.

  6. Adaptive breeding habitat selection: Is it for the birds?

    Science.gov (United States)

    Chalfoun, Anna D.; Schmidt, Kenneth A.

    2012-01-01

    The question of why animals choose particular habitats has important implications for understanding behavioral evolution and distribution of organisms in the wild and for delineating between habitats of different quality for conservation and management. Habitats chosen by animals can influence fitness outcomes via the costs (e.g., predation risk) and benefits (e.g., food availability) of habitat use. Habitat preferences should therefore be under selection to favor those that confer fitness advantages (Clark and Shutler 1999). Indeed, prevailing theory suggests that the habitat preferences of animals should be adaptive, such that fitness is higher in preferred habitats (Hildén 1965, Southwood 1977, Martin 1998). However, studies have often identified apparent mismatches between observed habitat preferences and fitness outcomes across a wide variety of taxa (Valladares and Lawton 1991, Mayhew 1997, Kolbe and Janzen 2002, Arlt and Pärt 2007, Mägi et al. 2009). Certainly, one limitation of studies may be that assessment of “fitness” is typically constrained to fitness surrogates such as nest success rather than lifetime reproductive success or classic Fisherian fitness (Endler 1986). Nevertheless, important habitat choices such as nest sites influence the probability that temporarily sedentary, dependent young are discovered by enemies such as predators and parasites. We therefore expect, on average, to see congruence between evolved habitat preferences and relevant components of fitness (e.g., nest success). Here, we (1) review the prevalence of apparent mismatches between avian breeding-habitat preferences and fitness outcomes using nest-site selection as a focus; (2) describe several potential mechanisms for such mismatches, including anthropogenic, methodological, and ecological–evolutionary; and (3) suggest a framework for understanding the contexts in which habitat preferences represent adaptive decisions, with a primary focus on ecological information

  7. Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds.

    Directory of Open Access Journals (Sweden)

    Hasan Alhaddad

    Full Text Available Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r(2 was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r(2 was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r(2 ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r(2 ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds' population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits.

  8. Mutations induced in plant breeding

    Energy Technology Data Exchange (ETDEWEB)

    Barriga B, P. (Universidad Austral de Chile, Valdivia. Inst. de Produccion y Sanidad Vegetal)

    1984-10-01

    The most significant aspects of the use of ionizing radiations in plant breeding are reviewed. Aspects such as basic principles of mutation, expression and selection in obtention of mutants, methods for using induced mutations and sucess achieved with this methodology in plant breeding are reviewed. Results obtained in a program of induced mutation on wheat for high content of protein and lysine at the Universidad Austral de Chile are presented.

  9. Captive breeding, reintroduction, and the conservation of amphibians.

    Science.gov (United States)

    Griffiths, Richard A; Pavajeau, Lissette

    2008-08-01

    The global amphibian crisis has resulted in renewed interest in captive breeding as a conservation tool for amphibians. Although captive breeding and reintroduction are controversial management actions, amphibians possess a number of attributes that make them potentially good models for such programs. We reviewed the extent and effectiveness of captive breeding and reintroduction programs for amphibians through an analysis of data from the Global Amphibian Assessment and other sources. Most captive breeding and reintroduction programs for amphibians have focused on threatened species from industrialized countries with relatively low amphibian diversity. Out of 110 species in such programs, 52 were in programs with no plans for reintroduction that had conservation research or conservation education as their main purpose. A further 39 species were in programs that entailed captive breeding and reintroduction or combined captive breeding with relocations of wild animals. Nineteen species were in programs with relocations of wild animals only. Eighteen out of 58 reintroduced species have subsequently bred successfully in the wild, and 13 of these species have established self-sustaining populations. As with threatened amphibians generally, amphibians in captive breeding or reintroduction programs face multiple threats, with habitat loss being the most important. Nevertheless, only 18 out of 58 reintroduced species faced threats that are all potentially reversible. When selecting species for captive programs, dilemmas may emerge between choosing species that have a good chance of surviving after reintroduction because their threats are reversible and those that are doomed to extinction in the wild as a result of irreversible threats. Captive breeding and reintroduction programs for amphibians require long-term commitments to ensure success, and different management strategies may be needed for species earmarked for reintroduction and species used for conservation

  10. Delineating genetic relationships among the Maya.

    Science.gov (United States)

    Ibarra-Rivera, Lisa; Mirabal, Sheyla; Regueiro, Manuela M; Herrera, Rene J

    2008-03-01

    By 250 AD, the Classic Maya had become the most advanced civilization within the New World, possessing the only well-developed hieroglyphic writing system of the time and an advanced knowledge of mathematics, astronomy and architecture. Though only ruins of the empire remain, 7.5 million Mayan descendants still occupy areas of Mexico, Guatemala, Belize, El Salvador, and Honduras. Although they inhabit distant and distinct territories, speak more than 28 languages, and have been historically divided by warfare and a city-state-like political system, and they share characteristics such as rituals, artistic, architectural motifs that distinguish them as unequivocally Maya. This study was undertaken to determine whether these similarities among Mayan communities mirror genetic affinities or are merely a reflection of their common culture. Four Mayan populations were investigated (i.e., the K'iche and Kakchikel from Guatemala and the Campeche and Yucatan from Mexico) and compared with previously published populations across 15 autosomal STR loci. As a whole, the Maya emerge as a distinct group within Mesoamerica, indicating that they are more similar to each other than to other Mesoamerican groups. The data suggest that although geographic and political boundaries existed among Mayan communities, genetic exchanges between the different Mayan groups have occurred, supporting theories of extensive trading throughout the empire.

  11. Post-breeding migration of Dutch-breeding black-tailed godwits: timing, routes, use of stopovers, and nonbreeding destinations

    Science.gov (United States)

    Hooijmeijer, Jos C. E. W.; Senner, Nathan R.; Tibbitts, T. Lee; Gill, Robert E.; Douglas, David C.; Bruinzeel, Leo W.; Wymenga, Eddy; Piersma, Theunis

    2014-01-01

    Conservation of long-distance migratory shorebirds is complex because these species use habitats spread across continents and hemispheres, making identification of critical habitats and potential bottlenecks in the annual cycle especially difficult. The population of Black-tailed Godwits that breeds in Western Europe, Limosa limosa limosa, has declined precipitously over the past few decades. Despite significant efforts to identify the root causes of this decline, much remains unclear. To better understand the migratory timing, use of stopover and nonbreeding sites, and the potential impact of breeding success on these parameters, we attached 15 Argos satellite transmitters and 10 geolocation tracking devices to adult godwits nearing completion of incubation at breeding sites in southwest Friesland, The Netherlands during the spring of 2009. We successfully tracked 16 adult godwits for their entire southward migration and two others for part of it. Three migration patterns and four regions of use were apparent. Most godwits left their breeding sites and proceeded south directly to stopover sites in the Mediterranean — e.g. Spain, Portugal, and Morocco — before flying on to non-breeding sites in West Africa. Other individuals spent the entire nonbreeding season in the Mediterranean. A third pattern included a few individuals that flew nonstop from their Dutch breeding sites to nonbreeding sites in West Africa. Tracking data from this study will be immediately useful for conservation efforts focused on preserving the dispersed network of sites used by godwits during their southward migration.

  12. Breeding numbers of Great Cormorants Phalacrocorax carbo in the Western Palearctic, 20122013

    DEFF Research Database (Denmark)

    Bregnballe, Thomas; Lynch, Jennifer Rose; Parz-Gollner, Rosemarie;

    This report presents the status of the breeding population of Great Cormorants Phalacrocorax carbo in Europe and neighbouring countries in 2012. It gives an overview of numbers and distribution and describes changes since 2006. It compiles 38 detailed national and sub-national reports on breeding...

  13. Merino and Merino-derived sheep breeds: a genome-wide intercontinental study

    NARCIS (Netherlands)

    Ciani, Elena; Lasagna, Emiliano; D'Andrea, Mariasilvia; Alloggio, Ingrid; Marroni, Fabio; Ceccobelli, Simone; Delgado Bermejo, Juan V; Sarti, Francesca M; Kijas, James; Lenstra, Johannes A; Pilla, Fabio

    2015-01-01

    BACKGROUND: Merino and Merino-derived sheep breeds have been widely distributed across the world, both as purebred and admixed populations. They represent an economically and historically important genetic resource which over time has been used as the basis for the development of new breeds. In orde

  14. Parental care strategies in Eurasian penduline tit are not related to breeding densities and mating opportunities

    NARCIS (Netherlands)

    van Dijk, Rene E.; Brinkhuizen, Dusan M.; Szekely, Tamas; Komdeur, Jan

    2010-01-01

    Population size and density may influence various aspects of breeding systems. For example, the number of potential mates may influence the mating system and parental care strategies. The breeding system of Eurasian penduline fits, Remiz pendulinus, involves sequential polygamy by both sexes and uni

  15. AlphaSim: Software for Breeding Program Simulation.

    Science.gov (United States)

    Faux, Anne-Michelle; Gorjanc, Gregor; Gaynor, R Chris; Battagin, Mara; Edwards, Stefan M; Wilson, David L; Hearne, Sarah J; Gonen, Serap; Hickey, John M

    2016-11-01

    This paper describes AlphaSim, a software package for simulating plant and animal breeding programs. AlphaSim enables the simulation of multiple aspects of breeding programs with a high degree of flexibility. AlphaSim simulates breeding programs in a series of steps: (i) simulate haplotype sequences and pedigree; (ii) drop haplotypes into the base generation of the pedigree and select single-nucleotide polymorphism (SNP) and quantitative trait nucleotide (QTN); (iii) assign QTN effects, calculate genetic values, and simulate phenotypes; (iv) drop haplotypes into the burn-in generations; and (v) perform selection and simulate new generations. The program is flexible in terms of historical population structure and diversity, recent pedigree structure, trait architecture, and selection strategy. It integrates biotechnologies such as doubled-haploids (DHs) and gene editing and allows the user to simulate multiple traits and multiple environments, specify recombination hot spots and cold spots, specify gene jungles and deserts, perform genomic predictions, and apply optimal contribution selection. AlphaSim also includes restart functionalities, which increase its flexibility by allowing the simulation process to be paused so that the parameters can be changed or to import an externally created pedigree, trial design, or results of an analysis of previously simulated data. By combining the options, a user can simulate simple or complex breeding programs with several generations, variable population structures and variable breeding decisions over time. In conclusion, AlphaSim is a flexible and computationally efficient software package to simulate biotechnology enhanced breeding programs with the aim of performing rapid, low-cost, and objective in silico comparison of breeding technologies. Copyright © 2016 Crop Science Society of America.

  16. Glacial Delineation and Ice Retreat on Pico de Orizaba, Mexico

    Science.gov (United States)

    Colby, A. E.; Weissling, B.; Xie, H.

    2011-12-01

    Pico de Orizaba, a dormant stratovolcano at the eastern end of the Trans-Mexican Volcanic Belt at approximately 19 degrees of latitude and the third largest peak in North America (5636 m), hosts what is likely the last significant tropical zone glacier (Jamapa Glacier) in the Northern Hemisphere. Not since the International Geophysical Year of 1957-58 has Pico's glacial environment been studied with any focused effort, perhaps due to the general innaccessibility, high altitude, and steep slopes. As are most glaciers around the world, the Jamapa Glacier is retreating, with a remarkable loss of ice in the past 2 decades. The rate and pattern of retreat is important to understanding climate change forcing as well as understanding environmental and water supply impacts to a substantial human population who live along the base of the volcano. Through the use of satellite imagery (LandSat, ASTER, IKONOS), legacy hand-drawn maps, aerial photographs, and first-hand accounts from climber's expeditions, a reasonably accurate map of almost 60 years of glacial retreat has been produced. Legacy hand-drawn maps of the ice edge, that pre-date the satellite era, did not fit perfectly with modern images when layered in ArcGIS. Oblique perspectives in Google Earth and various aerial and surface-based photographs of the mountain were used to help fit the ice edge to the actual topography. The disparity of satellite image pixel resolution (from 1 m IKONOS to 60 m LandSat) was addressed using various imagery analysis tools (eg. edge detection convolution filters and pixel unmixing) in order to delineate an approximate ice edge for the respective image date. The final map shows the nature of ice edge retreat on Pico de Orizaba from 1945 up until the present (Feb 2011).

  17. Estimation of genetic diversity in Gute sheep: pedigree and microsatellite analyses of an ancient Swedish breed.

    Science.gov (United States)

    Rochus, Christina M; Johansson, Anna M

    2017-01-01

    Breeds with small population size are in danger of an increased inbreeding rate and loss of genetic diversity, which puts them at risk for extinction. In Sweden there are a number of local breeds, native breeds which have adapted to specific areas in Sweden, for which efforts are being made to keep them pure and healthy over time. One example of such a breed is the Swedish Gute sheep. The objective of this study was to estimate inbreeding and genetic diversity of Swedish Gute sheep. Three datasets were analysed: pedigree information of the whole population, pedigree information for 100 animals of the population, and microsatellite genotypes for 94 of the 100 animals. The average inbreeding coefficient for lambs born during a six year time period (2007-2012) did not increase during that time period. The inbreeding calculated from the entire pedigree (0.038) and for a sample of the population (0.018) was very low. Sheep were more heterozygous at the microsatellite markers than expected (average multilocus heterozygosity and Ritland inbreeding estimates 1.01845 and -0.03931) and five of seven microsatellite markers were not in Hardy Weinberg equilibrium due to heterozygosity excess. The total effective population size estimated from the pedigree information was 155.4 and the average harmonic mean effective population size estimated from microsatellites was 88.3. Pedigree and microsatellite genotype estimations of inbreeding were consistent with a breeding program with the purpose of reducing inbreeding. Our results showed that current breeding programs of the Swedish Gute sheep are consistent with efforts of keeping this breed viable and these breeding programs are an example for other small local breeds in conserving breeds for the future.

  18. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

    Directory of Open Access Journals (Sweden)

    Jordana Jordi

    2001-07-01

    Full Text Available Abstract Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P A distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans.

  19. Eradication of scrapie with selective breeding: are we nearly there?

    Directory of Open Access Journals (Sweden)

    Davidse Aart

    2010-05-01

    Full Text Available Abstract Background Following EU decision 2003/100/EC Member States have recently implemented sheep breeding programmes to reduce the prevalence of sheep with TSE susceptible prion genotypes. The present paper investigates the progress of the breeding programme in the Netherlands. The PrP genotype frequencies were monitored through time using two sets of random samples: one set covers the years 2005 to 2008 and is taken from national surveillance programme; the other is taken from 168 random sheep farms in 2007. The data reveal that although the level of compliance to the breeding programme has been high, the frequency of susceptible genotypes varies substantially between farms. The 168 sheep farms are a subset of 689 farms participating in a postal survey inquiring about management and breeding strategies. This survey aimed to identify how much these strategies varied between farms, in order to inform assessment of the expected future progress towards eradication of classical scrapie. Results On the one hand, we found that compliance to the national breeding program has been high, and the frequency of resistant genotypes is expected to increase further in the next few years. On the other hand, we observed a large variation in prevalence of the scrapie resistant PrP genotype ARR between farms, implicating a large variation of genetic resistance between farms. Substantial between-flock differences in management and breeding strategies were found in the postal survey, suggesting considerable variation in risk of scrapie transmission between farms. Conclusions Our results show that although there has been a good progress in the breeding for scrapie resistance and the average farm-level scrapie susceptibility in the Netherlands has been significantly reduced, still a considerable proportion of farms contain high frequencies of susceptible genotypes in their sheep population. Since 2007 the breeding for genetic resistance is voluntarily again, and

  20. The Effect of Increasing Numbers of Horses of Undefined Breed on Horse Breeding in the Czech Republic

    Directory of Open Access Journals (Sweden)

    Iveta Bihuncová

    2015-01-01

    Full Text Available The objective of the present study was to analyse the numbers and division of horses of undefined breed. At the present time this group is the most numerous in the entire population of horses. Horses of undefined breed do not come under any breeder union which would provide reports about these horses; these horses are only registered and breeders are informed only about their numbers. Our study is the first to deal with the problem of increasing numbers of horses of undefined breed. The database contained 22 211 horses not entered registered in any of the stud books. In the database we filed approved horses born between 1972 and 1 September 2012 and horses registered from 1987. The data were processed in the Excel programme and results were evaluated in graphs. The most frequent horse in this group was the warm-blood type (n = 9 303, pony type (n = 6 285, cold-blooded type (n = 2 663 and unlisted horses (n = 2 278. Since 2001 the number of registered horses of undefined breed has increased. The most numerous dams of horses of undefined breed is the Czech warm-blood with 1 912 offspring; dams of the English Thoroughbred with 552 offspring and mares of the utility Huzule horse with 492 offspring. In the group of registered horses of undefined breed the Czech warm-blood appears in the pedigree of 507 colts and the American Paint Horse in the pedigree of sires of 506 colts. Why the numbers of horses of undefined breed are increasing is the boom of leisure horsemanship and unqualified horse breeding.

  1. Diversifying Selection Between Pure-Breed and Free-Breeding Dogs Inferred from Genome-Wide SNP Analysis

    Directory of Open Access Journals (Sweden)

    Małgorzata Pilot

    2016-08-01

    Full Text Available Domesticated species are often composed of distinct populations differing in the character and strength of artificial and natural selection pressures, providing a valuable model to study adaptation. In contrast to pure-breed dogs that constitute artificially maintained inbred lines, free-ranging dogs are typically free-breeding, i.e., unrestrained in mate choice. Many traits in free-breeding dogs (FBDs may be under similar natural and sexual selection conditions to wild canids, while relaxation of sexual selection is expected in pure-breed dogs. We used a Bayesian approach with strict false-positive control criteria to identify FST-outlier SNPs between FBDs and either European or East Asian breeds, based on 167,989 autosomal SNPs. By identifying outlier SNPs located within coding genes, we found four candidate genes under diversifying selection shared by these two comparisons. Three of them are associated with the Hedgehog (HH signaling pathway regulating vertebrate morphogenesis. A comparison between FBDs and East Asian breeds also revealed diversifying selection on the BBS6 gene, which was earlier shown to cause snout shortening and dental crowding via disrupted HH signaling. Our results suggest that relaxation of natural and sexual selection in pure-breed dogs as opposed to FBDs could have led to mild changes in regulation of the HH signaling pathway. HH inhibits adhesion and the migration of neural crest cells from the neural tube, and minor deficits of these cells during embryonic development have been proposed as the underlying cause of “domestication syndrome.” This suggests that the process of breed formation involved the same genetic and developmental pathways as the process of domestication.

  2. Kin-bias, breeding site selection and female fitness in a cannibalistic Neotropical frog.

    Science.gov (United States)

    Muralidhar, P; de Sá, F P; Haddad, C F B; Zamudio, K R

    2014-02-01

    Resource availability influences sexual selection within populations and determines whether behaviours such as territoriality or resource sharing are adaptive. In Thoropa taophora, a frog endemic to the Atlantic Coastal Rainforest of Brazil, males compete for and defend limited breeding sites while females often share breeding sites with other females; however, sharing breeding sites may involve costs due to cannibalism by conspecific tadpoles. We studied a breeding population of T. taophora to determine (i) whether this species exhibits polygynous mating involving female choice for territorial males and limited breeding resources; (ii) whether limited breeding resources create the potential for male-male cooperation in defence of neighbouring territories; and (iii) whether females sharing breeding sites exhibit kin-biased breeding site choice, possibly driven by fitness losses due to cannibalism among offspring of females sharing sites. We used microsatellites to reconstruct parentage and quantify relatedness at eight breeding sites in our focal population, where these sites are scarce, and in a second population, where sites are abundant. We found that at localities where the appropriate sites for reproduction are spatially limited, the mating system for this species is polygynous, with typically two females sharing a breeding site with a male. We also found that females exhibit negative kin-bias in their choice of breeding sites, potentially to maximize their inclusive fitness by avoiding tadpole cannibalism of highly related kin. Our results indicate that male territorial defence and female site sharing are likely important components of this mating system, and we propose that kinship-dependent avoidance in mating strategies may be more general than previously realized. © 2013 John Wiley & Sons Ltd.

  3. Multiple Breed Validation of Five QTL Affecting Mastitis Resistance

    DEFF Research Database (Denmark)

    Vilkki, Johanna; Dolezal, Marlies A; Sahana, Goutam;

    (on BTA3, BTA6, BTA8, BTA19, and BTA27) agreed across the breeds, but no identical associated SNPs were detected. Higher power (imputation to bigger population samples) will be needed to confirm results. On BTA6 the results indicate several QTL within a 5 Mb region. The results provide a basis...

  4. The relevance of milk protein polymorphisms for dairy cattle breeding.

    NARCIS (Netherlands)

    Bovenhuis, H.

    1992-01-01

    An isoelectric focusing method is described that is suitable for phenotyping a large number of milk samples due to its short separation time and its high capacity. To estimate milk protein gene frequencies for breeds represented in the crossbred population and to estimate the fraction of animals mis

  5. Adult sex ratio variation : Implications for breeding system evolution

    NARCIS (Netherlands)

    Szekely, T.; Weissing, F. J.; Komdeur, J.

    2014-01-01

    Adult sex ratio (ASR) exhibits immense variation in nature, although neither the causes nor the implications of this variation are fully understood. According to theory, the ASR is expected to influence sex roles and breeding systems, as the rarer sex in the population has more potential partners to

  6. Residual feed intake and breeding approaches for enteric methane mitigation

    NARCIS (Netherlands)

    Berry, D.P.; Lassen, J.; Haas, de Y.

    2015-01-01

    The expanding world human population will require greater food production within the constraints of increasing societal pressure to minimize the resulting impact on the environment. Breeding goals in the past have achieved substantial gains in environmental load per unit product produced, despite no

  7. Impact of Molecular Technologies on Faba Bean (Vicia faba L. Breeding Strategies

    Directory of Open Access Journals (Sweden)

    Tao Yang

    2012-07-01

    Full Text Available Faba bean (Vicia faba L. is a major food and feed legume because of the high nutritional value of its seeds. The main objectives of faba bean breeding are to improve yield, disease resistance, abiotic stress tolerance, seed quality and other agronomic traits. The partial cross-pollinated nature of faba bean introduces both challenges and opportunities for population development and breeding. Breeding methods that are applicable to self-pollinated crops or open-pollinated crops are not highly suitable for faba bean. However, traditional breeding methods such as recurrent mass selection have been established in faba bean and used successfully in breeding for resistance to diseases. Molecular breeding strategies that integrate the latest innovations in genetics and genomics with traditional breeding strategies have many potential applications for future faba bean cultivar development. Hence, considerable efforts have been undertaken in identifying molecular markers, enriching genetic and genomic resources using high-throughput sequencing technologies and improving genetic transformation techniques in faba bean. However, the impact of research on practical faba bean breeding and cultivar release to farmers has been limited due to disconnects between research and breeding objectives and the high costs of research and implementation. The situation with faba bean is similar to other small crops and highlights the need for coordinated, collaborative research programs that interact closely with commercially focused breeding programs to ensure that technologies are implemented effectively.

  8. CASSAVA BREEDING I: THE VALUE OF BREEDING VALUE

    Directory of Open Access Journals (Sweden)

    Hernán Ceballos

    2016-08-01

    Full Text Available Breeding cassava relies on several selection stages (single row trial-SRT; preliminary; advanced; and uniform yield trials - UYT. This study uses data from 14 years of evaluations. From more than 20,000 genotypes initially evaluated only 114 reached the last stage. The objective was to assess how the data at SRT could be used to predict the probabilities of genotypes reaching the UYT. Phenotypic data from each genotype at SRT was integrated into the selection index (SIN used by the cassava breeding program. Average SIN from all the progenies derived from each progenitor was then obtained. Average SIN is an approximation of the breeding value of each progenitor. Data clearly suggested that some genotypes were better progenitors than others (e.g. high number of their progenies reaching the UYT, suggesting important variation in breeding values of progenitors. However, regression of average SIN of each parental genotype on the number of their respective progenies reaching UYT resulted in a negligible coefficient of determination (r2 = 0.05. Breeding value (e.g. average SIN at SRT was not efficient predicting which genotypes were more likely to reach the UYT stage. Number of families and progenies derived from a given progenitor were more efficient predicting the probabilities of the progeny from a given parent reaching the UYT stage. Large within-family genetic variation tends to mask the true breeding value of each progenitor. The use of partially inbred progenitors (e.g. S1 or S2 genotypes would reduce the within-family genetic variation thus making the assessment of breeding value more accurate. Moreover, partial inbreeding of progenitors can improve the breeding value of the original (S0 parental material and sharply accelerate genetic gains. For instance, homozygous S1 genotypes for the dominant resistance to cassava mosaic disease could be generated and selected. All gametes from these selected S1 genotypes would carry the desirable allele

  9. Cassava Breeding I: The Value of Breeding Value

    Science.gov (United States)

    Ceballos, Hernán; Pérez, Juan C.; Joaqui Barandica, Orlando; Lenis, Jorge I.; Morante, Nelson; Calle, Fernando; Pino, Lizbeth; Hershey, Clair H.

    2016-01-01

    Breeding cassava relies on several selection stages (single row trial-SRT; preliminary; advanced; and uniform yield trials—UYT). This study uses data from 14 years of evaluations. From more than 20,000 genotypes initially evaluated only 114 reached the last stage. The objective was to assess how the data at SRT could be used to predict the probabilities of genotypes reaching the UYT. Phenotypic data from each genotype at SRT was integrated into the selection index (SIN) used by the cassava breeding program. Average SIN from all the progenies derived from each progenitor was then obtained. Average SIN is an approximation of the breeding value of each progenitor. Data clearly suggested that some genotypes were better progenitors than others (e.g., high number of their progenies reaching the UYT), suggesting important variation in breeding values of progenitors. However, regression of average SIN of each parental genotype on the number of their respective progenies reaching UYT resulted in a negligible coefficient of determination (r2 = 0.05). Breeding value (e.g., average SIN) at SRT was not efficient predicting which genotypes were more likely to reach the UYT stage. Number of families and progenies derived from a given progenitor were more efficient predicting the probabilities of the progeny from a given parent reaching the UYT stage. Large within-family genetic variation tends to mask the true breeding value of each progenitor. The use of partially inbred progenitors (e.g., S1 or S2 genotypes) would reduce the within-family genetic variation thus making the assessment of breeding value more accurate. Moreover, partial inbreeding of progenitors can improve the breeding value of the original (S0) parental material and sharply accelerate genetic gains. For instance, homozygous S1 genotypes for the dominant resistance to cassava mosaic disease (CMD) could be generated and selected. All gametes from these selected S1 genotypes would carry the desirable allele and

  10. Post-breeding migration of Dutch-breeding black-tailed godwits : Timing, routes, use of stopovers, and nonbreeding destinations

    NARCIS (Netherlands)

    Hooijmeijer, Jos; Senner, Nathan R.; Tibbitts, T. Lee; Gill Jr, Robert E.; Douglas, David C.; Bruinzeel, Leo W.; Wymenga, Eddy; Piersma, Theunis

    2014-01-01

    Conservation of long-distance migratory shorebirds is complex because these species use habitats spread across continents and hemispheres, making identification of critical habitats and potential bottlenecks in the annual cycle especially difficult. The population of Black-tailed Godwits that breeds

  11. Genetic diversity and bottleneck studies in the Marwari horse breed

    Indian Academy of Sciences (India)

    A. K. Gupta; M. Chauhan; S. N. Tandon; Sonia

    2005-12-01

    Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 (± 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (± s.e.) effective number of alleles (3.3 ± 1.27), observed heterozygosity (0.5306 ± 0.22), expected Levene’s heterozygosity (0.6612 ± 0.15), expected Nei’s heterozygosity (0.6535 ± 0.14), and polymorphism information content (0.6120 ± 0.03). Low values of Wright’s fixation index, $F_{\\text{IS}}$ (0.2433 ± 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal ‘L’ shaped distribution of mode–shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significant ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers.

  12. Structure and genetic relationships between Brazilian naturalized and exotic purebred goat domestic goat (Capra hircus breeds based on microsatellites

    Directory of Open Access Journals (Sweden)

    Joelliton Domingos de Oliveira

    2007-03-01

    Full Text Available The genetic relationships and structure of fourteen goat (Capra hircus populations were estimated based on genotyping data from 14 goat populations (n = 410 goats at 13 microsatellite loci. We used analysis of molecular variance (AMOVA, principal component analysis (PCA and F statistics (F IS, F IT and F ST to evaluate the genetic diversity (Ho, He and ad of the goats. Genetic distances between the 14 goat populations were calculated from allelic frequency data for the 13 microsatellite markers. Moderate differentiation was observed for the populations of the undefined breeds (including the Anglo-Nubian-M breed, the naturalized Brazilian breeds (Moxotó, Canindé, the exotic purebred breeds (Alpine, Saanen, Toggenbourg and Anglo-Nubian and the naturalized Brazilian Graúna group. Our AMOVA showed that a major portion (88.51% of the total genetic variation resulted from differences between individual goats within populations, while between-populations variation accounted for the remaining 11.49% of genetic variation. We used a Reynolds genetic distance matrix and PCA to produce a phenogram based on the 14 goat populations and found three clusters, or groups, consisting of the goats belonging to the undefined breed, the naturalized breeds and the exotic purebred breeds. The closer proximity of the Canindé breed from the Brazilian state of Paraíba to the Graúna breed from the same state than to the genetically conserved Canindé breed from the Brazilian state of Ceará, as well as the heterozygosity values and significant deviations from Hardy-Weinberg equilibrium suggests that there was a high number of homozygotes in the populations studied, and indicates the importance of the State for the conservation of the local breeds. Cataloguing the genetic profile of Brazilian goat populations provides essential information for conservation and genetic improvements programs.

  13. Ten inherited disorders in purebred dogs by functional breed groupings

    OpenAIRE

    Oberbauer, A. M.; Belanger, J. M.; Bellumori, T.; Bannasch, D.L.; Famula, T. R.

    2015-01-01

    Background Analysis of 88,635 dogs seen at the University of California, Davis Veterinary Medical Teaching Hospital from 1995 to 2010 identified ten inherited conditions having greater prevalence within the purebred dog population as compared to the mixed-breed dog population: aortic stenosis, atopy/allergic dermatitis, gastric dilatation volvulus (GDV), early onset cataracts, dilated cardiomyopathy, elbow dysplasia, epilepsy, hypothyroidism, intervertebral disk disease (IVDD), and hepatic po...

  14. Diet of canvasbacks during breeding

    Science.gov (United States)

    Austin, J.E.; Serie, J.R.; Noyes, J.H.

    1990-01-01

    We examined diets of canvasbacks (Aythya valisineria) breeding in southwestern Manitoba during 1977-81. Percent volume of animal foods consumed did not differ between males and females nor among prenesting, rapid follicle growth, laying, incubation, and renesting periods in females (mean = 50.1%). Tubers and shoots of fennelleaf pondweed (Potamogeton pectinatus) and midge larvae (Chironomidae) were the predominant foods, comprising on average 45% and 23% of the diet volume, respectively. Continued importance of plant foods to canvasbacks throughout reproduction contrasts with the mostly invertebrate diets of other prairie-breeding ducks, and does not fit current theories of nutritional ecology of breeding anatids (i.e., females meet the protein requirements of reproduction by consuming a high proportion of animal foods).

  15. Delineation of Crystalline Extended Defects on Multicrystalline Silicon Wafers

    Directory of Open Access Journals (Sweden)

    Mohamed Fathi

    2007-01-01

    Full Text Available We have selected Secco and Yang etch solutions for the crystalline defect delineation on multicrystalline silicon (mc-Si wafers. Following experimentations and optimization of Yang and Secco etching process parameters, we have successfully revealed crystalline extended defects on mc-Si surfaces. A specific delineation process with successive application of Yang and Secco agent on the same sample has proved the increased sensitivity of Secco etch to crystalline extended defects in mc-Si materials. The exploration of delineated mc-Si surfaces indicated that strong dislocation densities are localized mainly close to the grain boundaries and on the level of small grains in size (below 1 mm. Locally, we have observed the formation of several parallel dislocation lines, perpendicular to the grain boundaries. The overlapping of several dislocations lines has revealed particular forms for etched pits of dislocations.

  16. Phylogenetic Relationships of the Mangalitsa Swine Breed Inferred from Mitochondrial DNA Variation

    Directory of Open Access Journals (Sweden)

    Sergiu Emil Georgescu

    2012-07-01

    Full Text Available The Mangalitsa pig, a swine breed belonging to the protected gene fund of original and primitive animal breeds of the FAO (Food and Agriculture Organization, has been known to inhabit Romanian territories since the 19th century. The aim of this study was to compare the Mangalitsa breed with several European and Asiatic swine breeds in order to emphasize its uniqueness and to elucidate its origin. For this purpose, we analyzed a 613 bp mitochondrial DNA D-loop fragment and 1140 bp of the cytochrome b gene in a population of Mangalitsa pigs and the polymorphic sites were compared with sequences from GenBank originating from other swine breeds. Taking into account the total of 24 breeds and 5 different Wild Boar populations analyzed, 86 polymorphic sites representing 32 haplotypes were observed, with an average percentage of polymorphic sites of 4.9%. Three Neighbor-Joining phylogenetic trees were constructed based on Kimura 2-parameter distances, using D-loop, cytochrome b and mitochondrial reunited sequences. For the analyzed Mangalitsa population, four distinct haplotypes were identified, including one that was common to other breeds. Our study suggests that the Mangalitsa swine originate from primitive breeds which might be directly derived from the Wild Boar.

  17. Analysis of the Genetic Diversity and Origin of Some Chinese Domestic Duck Breeds

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yang; CHEN Guo-hong; CHEN Yang; ZHEN Ting; HUANG Zheng-yang; CHEN Chang-yi; LI Xin-yu; DUAN Xiu-jun; DONG Biao; XU Qi

    2014-01-01

    Twelve lfuorescence-labeled microsatellite markers were used to analyze the genetic diversity of 12 domestic duck breeds and 2 wild duck breeds to determine the relationship and origin of Chinese domestic duck breeds. Gene frequency, effective number of alleles (Ne), expected heterozygosity (He), polymorphism information contents (PIC), inbreeding coefficient in population (Fis), standard genetic distance (DS), and genetic distance (DA) were calculated by FSTAT and distance and phylogenetic analysis after the dates which were output from the Microsatellite-Toolkit software. Genetic distances between 12 domestic duck breeds and 2 wild duck breeds were analyzed by variance analysis. Unweighted pair group method with arithmetic mean (UPGMA) and phylogenetic trees used for cluster analysis were structured. The results indicated that 11 loci had medium-or high-level genetic diversity among the 12 loci, which could be efifciently used in the detection of the genetic parameters of each population. The values of He were 0.5414 to 0.7343, those of PIC proved similar, and those of Fis were 0.1101 to 0.3381 among all populations. All breeds were clustered into three groups by UPGMA phylogenetic trees. Banzui duck was clustered into a separate group. Differences of the DA were analysed by t-test. The results showed that difference in DA between the 12 domestic duck breeds and Lvtou duck and the Banzui duck were very signiifcant (P<0.01), indicating that these 12 domestic duck breeds originated from Lvtou wild duck, but not Banzui duck.

  18. Analysis of beta-casein gene (CSN2 polymorphism in different breeds of cattle

    Directory of Open Access Journals (Sweden)

    Martina Miluchová

    2014-11-01

    Full Text Available Normal 0 21 false false false SK X-NONE X-NONE MicrosoftInternetExplorer4 The goal of work was identification of b - casein gene polymorphism in different breeds of cow. The beta - casein constitutes up to 45 % of the casein of bovine milk. The most common forms of beta-casein in dairy cattle breeds are A1 and A2, while B is less common. The b-casein A1 variant was associated with the incidence of diabetes mellitus 1st type, coronary heart disease and autism. The A2 variant reduces serum cholesterol. The material involved 287 cows (Simmental breed – 111 cows, Pinzgau breed – 89 cows, Holstein breed – 87 cows. Bovine genomic DNA was extracted from whole blood by using commercial kit and used in order to estimate b - casein genotypes by means of PCR-RFLP method. In the populations included in the study were detected all three genotypes – homozygote genotype A1A1, heterozygote genotype A1A2 and homozygote genotype A2A2 with frequencies 0.1261, 0.3333 and 0.5405 in Simmental breed; 0.1379, 0.4598 and 0.4023 in Holstein breed, 0.3034, 0.5168 and 0.1798 in Pinzgau breed. In population of Simmental breed and Holstein breed was higher frequency of allele A2 (0.7072 and 0.6322. In opposite, in population of Pinzgau breed was present higher frequency of the allele A1 (0.5618.

  19. Breeding monkeys for biomedical research

    Science.gov (United States)

    Bourne, G. H.; Golarzdebourne, M. N.; Keeling, M. E.

    1973-01-01

    Captive bred rhesus monkeys show much less pathology than wild born animals. The monkeys may be bred in cages or in an outdoor compound. Cage bred animals are not psychologically normal which makes then unsuited for some types of space related research. Compound breeding provides contact between mother and infant and an opportunity for the infants to play with their peers which are important requirements to help maintain their behavioral integrity. Offspring harvested after a year in the compound appear behaviorally normal and show little histopathology. Compound breeding is also an economical method for the rapid production of young animals. The colony can double its size about every two and a half years.

  20. Energetic and fitness costs of mismatching resource supply and demand in seasonally breeding birds.

    Science.gov (United States)

    Thomas, D W; Blondel, J; Perret, P; Lambrechts, M M; Speakman, J R

    2001-03-30

    By advancing spring leaf flush and ensuing food availability, climatic warming results in a mismatch between the timing of peak food supply and nestling demand, shifting the optimal time for reproduction in birds. Two populations of blue tits (Parus caeruleus) that breed at different dates in similar, but spatially distinct, habitat types in Corsica and southern France provide a unique opportunity to quantify the energetic and fitness consequences when breeding is mismatched with local productivity. As food supply and demand become progressively mismatched, the increased cost of rearing young pushes the metabolic effort of adults beyond their apparent sustainable limit, drastically reducing the persistence of adults in the breeding population. We provide evidence that the economics of parental foraging and limits to sustainable metabolic effort are key selective forces underlying synchronized seasonal breeding and long-term shifts in breeding date in response to climatic change.

  1. Development of breeding objectives for beef cattle breeding ...

    African Journals Online (AJOL)

    Mnr J F Kluyts

    The purpose of this article is to review the development of breeding objectives in beef cattle ... selection criteria, and estimation of phenotypic and genetic parameters. ... Unfortunately, the evolution from a performance .... The beef cattle industry has a history of chasing and promoting maximum values (e.g. maximum weight).

  2. Breed base representation in dairy animals of 5 breeds

    Science.gov (United States)

    Inheritance of DNA from different dairy breeds can be determined by genotyping, just as individual ancestors such as parents, grandparents, or even great grandparents can be identified correctly in a high percentage of the cases by genotyping even if not reported or reported incorrectly in pedigrees...

  3. Interobserver delineation variation in lung tumour stereotacticbody radiotherapy

    DEFF Research Database (Denmark)

    Persson, G. F.; Nygaard, D. E.; Hollensen, Christian;

    2012-01-01

    Objectives In radiotherapy, delineation uncertainties are important as they contribute to systematic errors and can lead to geographical miss of the target. For margin computation, standard deviations (SDs) of all uncertainties must be included as SDs. The aim of this study was to quantify...... the interobserver delineation variation for stereotactic body radiotherapy (SBRT) of peripheral lung tumours using a cross-sectional study design. Methods 22 consecutive patients with 26 tumours were included. Positron emission tomography/CT scans were acquired for planning of SBRT. Three oncologists and three...

  4. The scurs inheritance: new insights from the French Charolais breed

    Directory of Open Access Journals (Sweden)

    Gautier Mathieu

    2009-07-01

    Full Text Available Abstract Background Polled animals are valued in cattle industry because the absence of horns has a significant economic impact. However, some cattle are neither polled nor horned but have so-called scurs on their heads, which are corneous growths loosely attached to the skull. A better understanding of the genetic determinism of the scurs phenotype would help to fine map the polled locus. To date, only one study has attempted to map the scurs locus in cattle. Here, we have investigated the inheritance of the scurs phenotype in the French Charolais breed and examined whether the previously proposed localisation of the scurs locus on bovine chromosome 19 could be confirmed or not. Results Our results indicate that the inheritance pattern of the scurs phenotype in the French Charolais breed is autosomal recessive with complete penetrance in both sexes, which is different from what is reported for other breeds. The frequency of the scurs allele (Sc reaches 69.9% in the French Charolais population. Eleven microsatellite markers on bovine chromosome 19 were genotyped in 267 offspring (33 half-sib and full-sib families. Both non-parametric and parametric linkage analyses suggest that in the French Charolais population the scurs locus may not map to the previously identified region. A new analysis of an Angus-Hereford and Hereford-Hereford pedigree published in 1978 enabled us to calculate the frequency of the Sc allele in the Hereford breed (89.4% and to study the penetrance of this allele in males heterozygous for both polled and scurs loci (40%. This led us to revise the inheritance pattern of the scurs phenotype proposed for the Hereford breed and to suggest that allele Sc is not fully but partially dominant in double heterozygous males while it is always recessive in females. Crossbreeding involving the Charolais breed and other breeds gave results similar to those reported in the Hereford breed. Conclusion Our results suggest the existence of

  5. The Breeding Ecology of White-faced Ibis in the Carson River Basin, Nevada

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — To ensure long-term breeding population viability of White-faced Ibis, it may be necessary to develop local water management strategies with consideration of habitat...

  6. Alaska-Yukon waterfowl breeding pair survey, May 17 to June 7, 1969

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Alaska during 1969. The primary purpose of the survey is to provide information on...

  7. Aerial Breeding Pair Surveys of the Arctic Coastal Plain of Alaska : Distribution and Abundance 1995

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — An aerial breeding pair survey was conducted on the Arctic Coastal Plain of Alaska for the 10th consecutive year in 1995. The population estimate for the northern...

  8. Progress report: Waterfowl breeding ground aerial surveys in southern Saskatchewan: 1960

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey and Waterfowl Production and Habitat Survey for southern Saskatchewan during 1960. The...

  9. Waterfowl breeding pair survey for northern Alberta, northeastern British Columbia, and the Northwest Territories: 1978

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for northern Alberta, northeastern British Columbia, and the Northwest Territories during...

  10. Waterfowl breeding pair survey: Southern Saskatchewan: May 6 - May 20, 1969

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for southern Saskatchewan during 1969. The primary purpose of the survey is to provide...

  11. Malheur NWR: Initial Survey Instructions for Sandhill Crane Breeding Pair Count [PRIMR

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is a refuge survey effort that documents actual size of the Refuge breeding population and captures long-term trend data to inform the Pacific Flyway.The survey...

  12. Alaska-Yukon: Waterfowl breeding pair survey: May 20 to June 14, 1977

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for Alaska-Yukon during 1977. The primary purpose of the survey is to provide information...

  13. Waterfowl breeding pair survey for western Ontario: May 27 through June 1, 1973

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report summarizes the Waterfowl Breeding Population and Habitat Survey for western Ontario during 1973. The primary purpose of the survey is to provide...

  14. Tracing cattle breeds with principal components analysis ancestry informative SNPs.

    Directory of Open Access Journals (Sweden)

    Jamey Lewis

    Full Text Available The recent release of the Bovine HapMap dataset represents the most detailed survey of bovine genetic diversity to date, providing an important resource for the design and development of livestock production. We studied this dataset, comprising more than 30,000 Single Nucleotide Polymorphisms (SNPs for 19 breeds (13 taurine, three zebu, and three hybrid breeds, seeking to identify small panels of genetic markers that can be used to trace the breed of unknown cattle samples. Taking advantage of the power of Principal Components Analysis and algorithms that we have recently described for the selection of Ancestry Informative Markers from genomewide datasets, we present a decision-tree which can be used to accurately infer the origin of individual cattle. In doing so, we present a thorough examination of population genetic structure in modern bovine breeds. Performing extensive cross-validation experiments, we demonstrate that 250-500 carefully selected SNPs suffice in order to achieve close to 100% prediction accuracy of individual ancestry, when this particular set of 19 breeds is considered. Our methods, coupled with the dense genotypic data that is becoming increasingly available, have the potential to become a valuable tool and have considerable impact in worldwide livestock production. They can be used to inform the design of studies of the genetic basis of economically important traits in cattle, as well as breeding programs and efforts to conserve biodiversity. Furthermore, the SNPs that we have identified can provide a reliable solution for the traceability of breed-specific branded products.

  15. Replication of an empirical approach to delineate the heterogeneity of chronic unexplained fatigue

    Directory of Open Access Journals (Sweden)

    White Peter D

    2009-10-01

    Full Text Available Abstract Background Chronic fatigue syndrome (CFS is defined by self-reported symptoms. There are no diagnostic signs or laboratory markers, and the pathophysiology remains inchoate. In part, difficulties identifying and replicating biomarkers and elucidating the pathophysiology reflect the heterogeneous nature of the syndromic illness CFS. We conducted this analysis of people from defined metropolitan, urban, and rural populations to replicate our earlier empirical delineation of medically unexplained chronic fatigue and CFS into discrete endophenotypes. Both the earlier and current analyses utilized quantitative measures of functional impairment and symptoms as well as laboratory data. This study and the earlier one enrolled participants from defined populations and measured the internal milieu, which differentiates them from studies of clinic referrals that examine only clinical phenotypes. Methods This analysis evaluated 386 women identified in a population-based survey of chronic fatigue and unwellness in metropolitan, urban, and rural populations of the state of Georgia, USA. We used variables previously demonstrated to effectively delineate endophenotypes in an attempt to replicate identification of these endophenotypes. Latent class analyses were used to derive the classes, and these were compared and contrasted to those described in the previous study based in Wichita, Kansas. Results We identified five classes in the best fit analysis. Participants in Class 1 (25% were polysymptomatic, with sleep problems and depressed mood. Class 2 (24% was also polysymptomatic, with insomnia and depression, but participants were also obese with associated metabolic strain. Class 3 (20% had more selective symptoms but was equally obese with metabolic strain. Class 4 (20% and Class 5 (11% consisted of nonfatigued, less symptomatic individuals, Class 4 being older and Class 5 younger. The classes were generally validated by independent variables. People

  16. Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection

    National Research Council Canada - National Science Library

    Kijas, James W; Lenstra, Johannes A; Hayes, Ben; Boitard, Simon; Porto Neto, Laercio R; San Cristobal, Magali; Servin, Bertrand; McCulloch, Russell; Whan, Vicki; Gietzen, Kimberly; Paiva, Samuel; Barendse, William; Ciani, Elena; Raadsma, Herman; McEwan, John; Dalrymple, Brian

    2012-01-01

    .... We find the majority of sheep populations contain high SNP diversity and have retained an effective population size much higher than most cattle or dog breeds, suggesting domestication occurred...

  17. Population structure and genetic diversity of Sudanese native chickens

    African Journals Online (AJOL)

    User

    2013-11-06

    Nov 6, 2013 ... origin of breeding populations, molecular marker informa-. *Corresponding .... on the phenotypic characteristics of each local breed (Desai, 1962). ..... Development of a genetic map of the chicken with markers of ... variation and population structure of Italian native sheep breeds ... evolutionary studies. Mol.

  18. Evidence for frequent incest in a cooperatively breeding mammal.

    Science.gov (United States)

    Nichols, H J; Cant, M A; Hoffman, J I; Sanderson, J L

    2014-12-01

    As breeding between relatives often results in inbreeding depression, inbreeding avoidance is widespread in the animal kingdom. However, inbreeding avoidance may entail fitness costs. For example, dispersal away from relatives may reduce survival. How these conflicting selection pressures are resolved is challenging to investigate, but theoretical models predict that inbreeding should occur frequently in some systems. Despite this, few studies have found evidence of regular incest in mammals, even in social species where relatives are spatio-temporally clustered and opportunities for inbreeding frequently arise. We used genetic parentage assignments together with relatedness data to quantify inbreeding rates in a wild population of banded mongooses, a cooperatively breeding carnivore. We show that females regularly conceive to close relatives, including fathers and brothers. We suggest that the costs of inbreeding avoidance may sometimes outweigh the benefits, even in cooperatively breeding species where strong within-group incest avoidance is considered to be the norm.

  19. Reliabilities of genomic estimated breeding values in Danish Jersey

    DEFF Research Database (Denmark)

    Thomasen, Jørn Rind; Guldbrandtsen, Bernt; Su, Guosheng;

    2012-01-01

    In order to optimize the use of genomic selection in breeding plans, it is essential to have reliable estimates of the genomic breeding values. This study investigated reliabilities of direct genomic values (DGVs) in the Jersey population estimated by three different methods. The validation methods...... of DGV. The data set consisted of 1003 Danish Jersey bulls with conventional estimated breeding values (EBVs) for 14 different traits included in the Nordic selection index. The bulls were genotyped for Single-nucleotide polymorphism (SNP) markers using the Illumina 54 K chip. A Bayesian method was used...... index pre-selection only. Averaged across traits, the estimates of reliability of DGVs ranged from 0.20 for validation on the most recent 3 years of bulls and up to 0.42 for expected reliabilities. Reliabilities from the cross-validation were on average 0.24. For the individual traits, the reliability...

  20. Genetic diversity within and among four South European native horse breeds based on microsatellite DNA analysis: implications for conservation.

    Science.gov (United States)

    Solis, A; Jugo, B M; Mériaux, J C; Iriondo, M; Mazón, L I; Aguirre, A I; Vicario, A; Estomba, A

    2005-01-01

    In the present study, genetic analyses of diversity and differentiation were performed on four Basque-Navarrese semiferal native horse breeds. In total, 417 animals were genotyped for 12 microsatellite markers. Mean heterozygosity was higher than in other horse breeds, surely as a consequence of management. Although the population size of some of these breeds has declined appreciably in the past century, no genetic bottleneck was detected in any of the breeds, possibly because it was not narrow enough to be detectable. In the phylogenetic tree, the Jaca Navarra breed was very similar to the Pottoka, but appeared to stand in an intermediate position between this and the meat breeds. Assuming that Pottoka is the breed less affected by admixture, the others gradually distanced themselves from it through varying influences from outside breeds, among other factors. In a comparative study with other breeds, the French breeds Ardanais, Comtois, and Breton were the closest to the four native breeds. Three different approaches for evaluating the distribution of genetic diversity were applied. The high intrabreed variability of Euskal Herriko Mendiko Zaldia (EHMZ) was pointed out in these analyses. In our opinion, cultural, economic, and scientific factors should also be considered in the management of these horse breeds.

  1. Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands.

    Science.gov (United States)

    Gama, Luis T; Martínez, Amparo M; Carolino, Inês; Landi, Vincenzo; Delgado, Juan V; Vicente, Antonio A; Vega-Pla, José L; Cortés, Oscar; Sousa, Conceição O

    2013-06-14

    Native pig breeds in the Iberian Peninsula are broadly classified as belonging to either the Celtic or the Mediterranean breed groups, but there are other local populations that do not fit into any of these groups. Most of the native pig breeds in Iberia are in danger of extinction, and the assessment of their genetic diversity and population structure, relationships and possible admixture between breeds, and the appraisal of conservation alternatives are crucial to adopt appropriate management strategies. A panel of 24 microsatellite markers was used to genotype 844 animals representing the 17 most important native swine breeds and wild populations existing in Portugal and Spain and various statistical tools were applied to analyze the results. Genetic diversity was high in the breeds studied, with an overall mean of 13.6 alleles per locus and an average expected heterozygosity of 0.80. Signs of genetic bottlenecks were observed in breeds with a small census size, and population substructure was present in some of the breeds with larger census sizes. Variability among breeds accounted for about 20% of the total genetic diversity, and was explained mostly by differences among the Celtic, Mediterranean and Basque breed groups, rather than by differences between domestic and wild pigs. Breeds clustered closely according to group, and proximity was detected between wild pigs and the Mediterranean cluster of breeds. Most breeds had their own structure and identity, with very little evidence of admixture, except for the Retinto and Entrepelado varieties of the Mediterranean group, which are very similar. Genetic influence of the identified breed clusters extends beyond the specific geographical areas across borders throughout the Iberian Peninsula, with a very sharp transition from one breed group to another. Analysis of conservation priorities confirms that the ranking of a breed for conservation depends on the emphasis placed on its contribution to the between- and

  2. Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds.

    Science.gov (United States)

    Choi, Jung-Woo; Chung, Won-Hyong; Lee, Kyung-Tai; Cho, Eun-Seok; Lee, Si-Woo; Choi, Bong-Hwan; Lee, Sang-Heon; Lim, Wonjun; Lim, Dajeong; Lee, Yun-Gyeong; Hong, Joon-Ki; Kim, Doo-Wan; Jeon, Hyeon-Jeong; Kim, Jiwoong; Kim, Namshin; Kim, Tae-Hun

    2015-08-01

    Pigs have been one of the most important sources of meat for humans, and their productivity has been substantially improved by recent strong selection. Here, we present whole-genome resequencing analyses of 55 pigs of five breeds representing Korean native pigs, wild boar and three European origin breeds. 1,673.1 Gb of sequence reads were mapped to the Swine reference assembly, covering ∼99.2% of the reference genome, at an average of ∼11.7-fold coverage. We detected 20,123,573 single-nucleotide polymorphisms (SNPs), of which 25.5% were novel. We extracted 35,458 of non-synonymous SNPs in 9,904 genes, which may contribute to traits of interest. The whole SNP sets were further used to access the population structures of the breeds, using multiple methodologies, including phylogenetic, similarity matrix, and population structure analysis. They showed clear population clusters with respect to each breed. Furthermore, we scanned the whole genomes to identify signatures of selection throughout the genome. The result revealed several promising loci that might underlie economically important traits in pigs, such as the CLDN1 and TWIST1 genes. These discoveries provide useful genomic information for further study of the discrete genetic mechanisms associated with economically important traits in pigs.

  3. The use of digital spaceborne SAR data for the delineation of surface features indicative of malaria vector breeding habitats

    Science.gov (United States)

    Imhoff, M. L.; Vermillion, C. H.; Khan, F. A.

    1984-01-01

    An investigation to examine the utility of spaceborne radar image data to malaria vector control programs is described. Specific tasks involve an analysis of radar illumination geometry vs information content, the synergy of radar and multispectral data mergers, and automated information extraction techniques.

  4. North European short-tailed breeds of sheep: a review.

    Science.gov (United States)

    Dýrmundsson, O R; Niżnikowski, R

    2010-08-01

    The short-tailed sheep, native of an area stretching from Russia to Iceland, are generally considered a primitive type. These robust northern sheep seem to have been spread by Norse vikings to several countries in this area from the late eighth century to the middle of the eleventh century ad. They have several common characteristics in addition to the fluke-shaped and tapered short tail, such as a wide range of colour patterns, dual-coated wool and the ability to thrive under harsh environmental conditions, often in isolated marginal areas. While 34 short-tailed breeds of North European origin can still be identified, it is clear that their population sizes have declined in most cases and several of them are now rare and endangered. Although these breeds have mainly been confined to certain localities, some of them have gained considerable distribution due to their genetic merits, such as prolificacy. Of these, the Finnsheep and the Romanov are best known being exported to several countries in the world where their genetic material has been utilized through crossbreeding with local sheep. This has resulted in the production of some new synthetic breeds. Meat is now generally the main product of the North European short-tailed breeds and their crossbreds, whereas wool, skins and milk are normally regarded as byproducts, yet of considerable economic importance in some cases. Such breeds have clearly a role to play in sustainable grassland-based production systems in the future.

  5. Dynamic distributions and population declines of Golden-winged Warblers

    Science.gov (United States)

    Rosenberg, Kenneth V.; Will, Tom; Buehler, David A.; Barker Swarthout, Sara; Thogmartin, Wayne E.; Chandler, Richard

    2016-01-01

    With an estimated breeding population in 2010 of 383,000 pairs, the Golden-winged Warbler (Vermivora chrysoptera) is among the most vulnerable and steeply declining of North American passerines. This species also has exhibited among the most dynamic breeding distributions, with populations expanding and then contracting over the past 150 years in response to regional habitat changes, interactions with closely related Blue-winged Warblers (V. cyanoptera), and possibly climate change. Since 1966, the rangewide population has declined by >70% (-2.3% per year; latest North American Breeding Bird Survey data), with much steeper declines in the Appalachian Mountains bird conservation region (-8.3% per year, 98% overall decline). Despite apparently stable or increasing populations in the northwestern part of the range (Minnesota, Manitoba), population estimates for Golden-winged Warbler have continued to decline by 18% from the decade of the 1990s to the 2000s. Population modeling predicts a further decline to roughly 37,000 individuals by 2100, with the species likely to persist only in Manitoba, Minnesota, and possibly Ontario. To delineate the present-day distribution and to identify population concentrations that could serve as conservation focus areas, we compiled rangewide survey data collected in 2000-2006 in 21 states and 3 Canadian provinces, as part of the Golden-winged Warbler Atlas Project (GOWAP), supplemented by state and provincial Breeding Bird Atlas data and more recent observations in eBird. Based on >8,000 GOWAP surveys for Golden-winged and Blue-winged warblers and their hybrids, we mapped occurrence of phenotypically pure and mixed populations in a roughly 0.5-degree grid across the species’ ranges. Hybrids and mixed Golden-winged-Blue-winged populations occurred in a relatively narrow zone across Minnesota, Wisconsin, Michigan, southern Ontario, and northern New York. Phenotypically pure Golden-winged Warbler populations occurred north of this

  6. The evolution of potato breeding

    Science.gov (United States)

    Potato cultivars in most regions of the world are tetraploid and clonally propagated. For over a century, the breeding strategy has been phenotypic recurrent selection. However, the polyploid nature of the crop prevents breeders from eliminating deleterious alleles and assembling positive alleles fo...

  7. Rose breeding: past, present, prospects

    NARCIS (Netherlands)

    Vries, de D.P.; Dubois, L.A.M.

    1996-01-01

    In this review the PAST, PRESENT and PROSPECT will be considered as three separate periods in the history of the breeding and development of rose cultivars. The recurring theme is the genetic variation. This theme was chosen because there is justified doubt as to sufficient genetic variation

  8. Rose breeding: past, present, prospects

    NARCIS (Netherlands)

    Vries, de D.P.; Dubois, L.A.M.

    1996-01-01

    In this review the PAST, PRESENT and PROSPECT will be considered as three separate periods in the history of the breeding and development of rose cultivars. The recurring theme is the genetic variation. This theme was chosen because there is justified doubt as to sufficient genetic variation availab

  9. A recursive method for computing expected kinship and inbreeding in complex and dynamic breeding programmes.

    Science.gov (United States)

    Sitzenstock, F; Ytournel, F; Simianer, H

    2013-02-01

    In many livestock breeding programmes, the development of inbreeding is of critical importance. Thus, the assessment of the expected development of inbreeding should be an essential element in the design of breeding programmes. We propose a new method to deterministically predict the rate of inbreeding based on the gene-flow method in well-defined complex and dynamic breeding programmes. In the suggested approach, a breeding programme has to be structured in homogeneous age-sex-groups, so called cohorts, with a defined origin of genes. Starting from an initial setup (usually an unrelated and non-inbred base population), transition rules to calculate the kinship within and between cohorts originating from reproduction or ageing, respectively, are defined. Using this approach recursively provides the expected development of kinship within and between all cohorts over time, which can be combined into average kinships for the whole population or defined subsets. From these quantities, relevant parameters like the inbreeding rate or the effective population size are easily derived. We illustrate the method with a simple static example breeding programme in sheep. Based on this reference breeding programme, we demonstrate the use of our approach for dynamic breeding programmes, in which cohort sizes or vectors of gene origin change over time: here, we model the situation of exponential population growth and a bottleneck situation, respectively. The suggested approach does not account for the effect of selection on the development of inbreeding, but ideas to overcome this limitation are discussed.

  10. Breeding ecology of ground tits in northeastern Tibetan plateau, with special reference to cooperative breeding system

    Institute of Scientific and Technical Information of China (English)

    Xin LU; Ran HUO; Yang LI; Wenbo LIAO; Chen WANG

    2011-01-01

    Data on breeding ecology of a color-band marked population of the ground tit Parus humilis were collected in north Qinghai on the Tibetan plateau,during 2008 and 2009.In spring the birds excavated 0.8-3.2 m long nesting burrows under the ground.First-egg laying occurred between late April and late June during which a pair produced one brood.Incubation was done by female alone for 15-16 days and nestling-feeding by both sexes and helpers in any for 23-25 days.Average brood size at fledging was 5.8 (± 1.4 SD,3-8) and all the 27 observed nesting attempts fledged at least one young.At the population level,brood sex ratio did not differ from 1∶1.The birds are a territory-living resident,with annual resight rates being 48% (22 of 46) in adult breeders and 10% (7 of 67) in yearlings.Pairs were socially monogamous,of which 23% (9 of 40) contained one and sometimes two male helpers,most likely being philopatric sons of the breeders.The formation of cooperative groups is similar to the population in central Tibet but differs from that in south Guansu where breeding ground tits exhibit a high level of annual turnover [Current Zoology 57 (6):751-757,2011].

  11. Breeding ecology of ground tits in northeastern Tibetan plateau, with special reference to cooperative breeding system

    Directory of Open Access Journals (Sweden)

    Xin LU, Ran HUO, Yang LI, Wenbo LIAO, Chen WANG

    2011-12-01

    Full Text Available Data on breeding ecology of a color-band marked population of the ground tit Parus humilis were collected in north Qinghai on the Tibetan plateau, during 2008 and 2009. In spring the birds excavated 0.8-3.2 m long nesting burrows under the ground. First-egg laying occurred between late April and late June during which a pair produced one brood. Incubation was done by female alone for 15-16 days and nestling-feeding by both sexes and helpers in any for 23-25 days. Average brood size at fledging was 5.8 (± 1.4 SD, 3-8 and all the 27 observed nesting attempts fledged at least one young. At the population level, brood sex ratio did not differ from 1:1. The birds are a territory-living resident, with annual resight rates being 48% (22 of 46 in adult breeders and 10% (7 of 67 in yearlings. Pairs were socially monogamous, of which 23% (9 of 40 contained one and sometimes two male helpers, most likely being philopatric sons of the breeders. The formation of cooperative groups is similar to the population in central Tibet but differs from that in south Guansu where breeding ground tits exhibit a high level of annual turnover [Current Zoology 57 (6: 751–757, 2011].

  12. The Breeding Bird Survey, 1967 and 1968

    Science.gov (United States)

    Robbins, C.S.; Van Velzen, W.T.

    1969-01-01

    In the Breeding Bird Survey of North America, cooperators ran 982 survey routes in 1967 and 1,174 in 1968. All States except Hawaii and all Canadian Provinces except Newfoundland were included. Roadside routes are selected at random within 1-degree blocks of latitude and longitude. Each 24 1/2-mile route, with 3-minute stops spaced half a mile apart, is driven by automobile. All birds heard or seen at the stops are recorded on special forms, and the data are transferred to magnetic tape for analysis. The average number of birds of each species per route is tabulated by State and Province, presenting for the first time a record of the comparative abundance of each species across the continent. The sample size is given for each species recorded. A sophisticated analysis program, here employed for the first time, is used to compute weighted mean values of the survey results for selected species at the State, stratum, regional, and continental level. The statistical significance of year-to-year changes at the 80, 90, 95, and 99 percent levels of probability are part of the computer output. An index for comparing populations of each species from year to year is established, with 1968 as the base year. Maps show the breeding range and comparative abundance of selected species.

  13. Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers.

    Directory of Open Access Journals (Sweden)

    Abiye Shenkut Abebe

    Full Text Available This study aimed at investigating the genetic diversity, relationship and population structure of 110 local Swedish chickens derived from five breeds (Gotlandshöna, Hedemorahöna, Öländsk dvärghöna, Skånsk blommehöna, and Bohuslän- Dals svarthöna, in the rest of the paper the shorter name Svarthöna is used using 24 microsatellite markers. In total, one hundred thirteen alleles were detected in all populations, with a mean of 4.7 alleles per locus. For the five chicken breeds, the observed and expected heterozygosity ranged from 0.225 to 0.408 and from 0.231 to 0.515, with the lowest scores for the Svarthöna and the highest scores for the Skånsk blommehöna breeds, respectively. Similarly, the average within breed molecular kinship varied from 0.496 to 0.745, showing high coancestry, with Skånsk blommehöna having the lowest and Svarthöna the highest coancestry. Furthermore, all breeds showed significant deviations from Hardy-Weinberg expectations. Across the five breeds, the global heterozygosity deficit (FIT was 0.545, population differentiation index (FST was 0.440, and the global inbreeding of individuals within breed (FIS was 0.187. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed two main clusters, with Hedemorahöna and Öländsk dvärghöna breeds in one cluster, and Gotlandshöna and Svarthöna breeds in the second cluster leaving the Skånsk blommehöna in the middle. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the five breeds was at K = 4, with Hedemorahöna, Gotlandshöna and Svarthöna breeds forming their own distinct clusters, while Öländsk dvärghöna and Skånsk blommehöna breeds clustered together. Losses in the overall genetic diversity of local Swedish chickens due to breeds extinction varied from -1.46% to -6

  14. Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers.

    Science.gov (United States)

    Abebe, Abiye Shenkut; Mikko, Sofia; Johansson, Anna M

    2015-01-01

    This study aimed at investigating the genetic diversity, relationship and population structure of 110 local Swedish chickens derived from five breeds (Gotlandshöna, Hedemorahöna, Öländsk dvärghöna, Skånsk blommehöna, and Bohuslän- Dals svarthöna, in the rest of the paper the shorter name Svarthöna is used) using 24 microsatellite markers. In total, one hundred thirteen alleles were detected in all populations, with a mean of 4.7 alleles per locus. For the five chicken breeds, the observed and expected heterozygosity ranged from 0.225 to 0.408 and from 0.231 to 0.515, with the lowest scores for the Svarthöna and the highest scores for the Skånsk blommehöna breeds, respectively. Similarly, the average within breed molecular kinship varied from 0.496 to 0.745, showing high coancestry, with Skånsk blommehöna having the lowest and Svarthöna the highest coancestry. Furthermore, all breeds showed significant deviations from Hardy-Weinberg expectations. Across the five breeds, the global heterozygosity deficit (FIT) was 0.545, population differentiation index (FST) was 0.440, and the global inbreeding of individuals within breed (FIS) was 0.187. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed two main clusters, with Hedemorahöna and Öländsk dvärghöna breeds in one cluster, and Gotlandshöna and Svarthöna breeds in the second cluster leaving the Skånsk blommehöna in the middle. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the five breeds was at K = 4, with Hedemorahöna, Gotlandshöna and Svarthöna breeds forming their own distinct clusters, while Öländsk dvärghöna and Skånsk blommehöna breeds clustered together. Losses in the overall genetic diversity of local Swedish chickens due to breeds extinction varied from -1.46% to -6.723%. The results

  15. 12 CFR 228.41 - Assessment area delineation.

    Science.gov (United States)

    2010-01-01

    ....41 Banks and Banking FEDERAL RESERVE SYSTEM (CONTINUED) BOARD OF GOVERNORS OF THE FEDERAL RESERVE SYSTEM COMMUNITY REINVESTMENT (REGULATION BB) Records, Reporting, and Disclosure Requirements § 228.41..., but the Board reviews the delineation for compliance with the requirements of this section. (b...

  16. The Regionalization of Africa: Delineating Africa's Subregions Using Airline Data

    Science.gov (United States)

    Good, Pieter R.; Derudder, Ben; Witlox, Frank J.

    2011-01-01

    Current regionalizations of Africa have limitations in that they are attribute-based and regions are delineated according to national boundaries. Taking the world city network approach as starting point, it is possible to use relational data (i.e., information about the relationships between cities) rather than attribute data, and moreover, it…

  17. Crowdsourcing for error detection in cortical surface delineations

    DEFF Research Database (Denmark)

    Ganz, Melanie; Kondermann, Daniel; Andrulis, Jonas

    2017-01-01

    crowdsourcing platform were asked to annotate errors in automatic cortical surface delineations on 100 central, coronal slices of MR images. RESULTS: On average, annotations for 100 images were obtained in less than an hour. When using expert annotations as reference, the crowd on average achieves a sensitivity...

  18. Delineating psychomotor slowing from reduced processing speed in schizophrenia

    NARCIS (Netherlands)

    Morrens, M.; Hulstijn, W.; Matton, C.; Madani, Y.; Bouwel, L. van; Peuskens, J.; Sabbe, B.G.C.

    2008-01-01

    Introduction. Psychomotor slowing is an intrinsic feature of schizophrenia that is poorly delineated from generally reduced processing speed. Although the Symbol Digit Substitution Test (SDST) is widely used to assess psychomotor speed, the task also taps several higher-order cognitive processes. Re

  19. Contested delineations: planning, law, and the governance of protected areas

    NARCIS (Netherlands)

    Beunen, R.; Assche, van K.

    2013-01-01

    In this paper we reflect on the relationship between planning and law. We analyse the Dutch interpretation and implementation of the European Union Habitats and Birds Directives by investigating the practices of delineation of protected areas. These directives provide a legislative framework for the

  20. Dynamic Stereochemistry: A Simple Approach to Delineating Relative Configuration

    Science.gov (United States)

    Mandal, Dipak K.

    2007-01-01

    A simple approach for delineating the stereochemistry of the products relative to that of the reactants in reactions involving stereogenic centers is addressed. The reaction at the tetrahedral center involves the cleavage of a bond to one of the ligands in the reactant and the resulting new ligand in the product is labeled by affixing prime to the…