Development of Microsatellite Loci Exhibiting Reverse Ascertainment Bias and a Sexing Marker for use in Emperor Geese (Chen Canagica)

2017 ◽  
Vol 10 (4) ◽  
pp. 201-210 ◽  
Author(s):  
Meg C. Gravley ◽  
George K. Sage ◽  
Joel A. Schmutz ◽  
Sandra L. Talbot
Keyword(s):  
Microsatellite Loci ◽  
Statistical Power ◽  
Ascertainment Bias ◽  
Next Generation Sequencing Technology ◽  
Branta Bernicla ◽  
Black Brant ◽  
Expected Heterozygosity ◽  
Cackling Geese ◽  
The 1960S ◽  
Goose Species

The Alaskan population of Emperor Geese ( Chen canagica) nests on the Yukon–Kuskokwim Delta in western Alaska. Numbers of Emperor Geese in Alaska declined from the 1960s to the mid-1980s and since then, their numbers have slowly increased. Low statistical power of microsatellite loci developed in other waterfowl species and used in previous studies of Emperor Geese are unable to confidently assign individual identity. Microsatellite loci for Emperor Goose were therefore developed using shotgun amplification and next-generation sequencing technology. Forty-one microsatellite loci were screened and 14 were found to be polymorphic in Emperor Geese. Only six markers – a combination of four novel loci and two loci developed in other waterfowl species – are needed to identify an individual from among the Alaskan Emperor Goose population. Genetic markers for identifying sex in Emperor Geese were also developed. The 14 novel variable loci and 15 monomorphic loci were screened for polymorphism in four other Arctic-nesting goose species, Black Brant ( Branta bernicla nigricans), Greater White-fronted ( Anser albifrons), Canada ( B. canadensis) and Cackling ( B. hutchinsii) Goose. Emperor Goose exhibited the smallest average number of alleles (3.3) and the lowest expected heterozygosity (0.467). Greater White-fronted Geese exhibited the highest average number of alleles (4.7) and Cackling Geese the highest expected heterozygosity (0.599). Six of the monomorphic loci were variable and able to be characterised in the other goose species assayed, a predicted outcome of reverse ascertainment bias. These findings fail to support the hypothesis of ascertainment bias due to selection of microsatellite markers.

scholarly journals Development and characterization of 29 polymorphic microsatellite loci of Megalobrama pellegrini by next-generation sequencing technology and cross-species amplification in related species

2016 ◽  
Author(s):  
Wen Song ◽  
Dongmei Zhu ◽  
Yefeng Lv ◽  
Weimin Wang
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Related Species ◽  
Polymorphic Information Content ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Expected Heterozygosity ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

Megalobrama pellegrini is one of the economically important freshwater fish in China. Here, we developed 29 polymorphic microsatellite loci of M. pellegrini. The number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (HO), expected heterozygosity (HE) and polymorphic information content (PIC) ranged from 3 to 11 (mean±SD 5.4828±1.9571), 2.8708 to 9.6257 (mean±SD 5.0865±1.6681), 0.4333 to 0.9333 (mean±SD 0.7874±0.1213), 0.6627 to 0.9113 (mean±SD 0.7946±0.0751) and 0.5785 to 0.8868 (mean±SD 0.7439±0.0950), respectively. Cross-species amplification was successful at most loci for related species such as M. amblycephala, M. hoffmanni, M. skolkovii and Parabramis pekinensis. The transferability rate of the 29 polymorphic microsatellite markers in M. amblycephala, M. hoffmanni, M. skolkovii and P. pekinensis were 96.55%, 86.21%, 86.21% and 75.86%, respectively. These polymorphic microsatellites are not only useful in genetic study and conservation of M. pellegrini, but also an effective tool for identifying the related species. We could use 5 microsatellite markers (HHF-63, HHF-104, HHF-113, HHF-148, HHF-163) to distinguish the 5 species.

Trends and Fluctuations in Bird Populations on the Tundra at Cambridge Bay, Nunavut

2012 ◽  
Vol 126 (2) ◽  
pp. 111
Author(s):  
C. Martin Lok ◽  
Jaap A. J. Vink
Keyword(s):  
Relative Abundance ◽  
High Arctic ◽  
Branta Bernicla ◽  
Bird Populations ◽  
Black Brant ◽  
Bay Area ◽  
Branta Bernicla Nigricans ◽  
Low Arctic ◽  
The 1960S ◽  
Victoria Island

Bird observations from the Cambridge Bay area on Victoria Island, Nunavut, in the summer of 2011 are presented and compared with those from the 1960s and 1980s. A total of 38 species was observed, compared with 42 in 1983 and 47 in 1986. Abundance of species of the High Arctic, such as Black Brant, Branta bernicla nigricans, Black-bellied Plover, Pluvialis squatarola, and Baird’s Sandpiper, Calidris bairdii, decreased, whereas numbers of the Red-necked Phalarope, Phalaropus lobatus, usually associated with the Low Arctic, increased markedly. Overall, the number of each species observed is rather stable and, for several species, the relative abundance does not seem to have changed significantly.

scholarly journals Development and characterization of 29 polymorphic microsatellite loci of Megalobrama pellegrini by next-generation sequencing technology and cross-species amplification in related species

2016 ◽  
Author(s):  
Wen Song ◽  
Dongmei Zhu ◽  
Yefeng Lv ◽  
Weimin Wang
Keyword(s):  
Microsatellite Markers ◽  
Microsatellite Loci ◽  
Related Species ◽  
Polymorphic Information Content ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Expected Heterozygosity ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

Megalobrama pellegrini is one of the economically important freshwater fish in China. Here, we developed 29 polymorphic microsatellite loci of M. pellegrini. The number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (HO), expected heterozygosity (HE) and polymorphic information content (PIC) ranged from 3 to 11 (mean±SD 5.4828±1.9571), 2.8708 to 9.6257 (mean±SD 5.0865±1.6681), 0.4333 to 0.9333 (mean±SD 0.7874±0.1213), 0.6627 to 0.9113 (mean±SD 0.7946±0.0751) and 0.5785 to 0.8868 (mean±SD 0.7439±0.0950), respectively. Cross-species amplification was successful at most loci for related species such as M. amblycephala, M. hoffmanni, M. skolkovii and Parabramis pekinensis. The transferability rate of the 29 polymorphic microsatellite markers in M. amblycephala, M. hoffmanni, M. skolkovii and P. pekinensis were 96.55%, 86.21%, 86.21% and 75.86%, respectively. These polymorphic microsatellites are not only useful in genetic study and conservation of M. pellegrini, but also an effective tool for identifying the related species. We could use 5 microsatellite markers (HHF-63, HHF-104, HHF-113, HHF-148, HHF-163) to distinguish the 5 species.

NATAL AND BREEDING PHILOPATRY IN A BLACK BRANT,BRANTA BERNICLA NIGRICANS,METAPOPULATION

Ecology ◽  
1998 ◽  
Vol 79 (6) ◽  
pp. 1893-1904 ◽  
Author(s):  
Mark S. Lindberg ◽  
James S. Sedinger ◽  
Dirk V. Derksen ◽  
Robert F. Rockwell
Keyword(s):  
Branta Bernicla ◽  
Black Brant ◽  
Branta Bernicla Nigricans

scholarly journals Polymorphic Microsatellite Loci in the Independent-founding Wasp Polists versicolor (Hymenoptera: Vespidae)

Sociobiology ◽  
2016 ◽  
Vol 63 (2) ◽  
pp. 845
Author(s):  
Yumi Takahashi ◽  
Ayano Yamada ◽  
Sidnei Mateus ◽  
Ronaldo Zucchi ◽  
Fabio Nascimento ◽  
...  
Keyword(s):  
Social Interactions ◽  
Microsatellite Loci ◽  
Genetic Relatedness ◽  
Conflicts Of Interest ◽  
Microsatellite Primers ◽  
Expected Heterozygosity ◽  
Polistes Wasps ◽  
Polymorphic Microsatellite ◽  
Genetic Conflicts ◽  
Data Banks

Microsatellite primers developed for a given species are sometimes useful for another in the same genus, making possible to search for pre-existing suitable primers in the data banks such as GenBank. We examined whether existing primers developed for Polistes wasps could be used for the independent-founding wasp Polistes versicolor. We tested 50 microsatellite primers from three Polistes species and found that five microsatellite loci show polymorphism in size in P. versicolor. These five loci were highly polymorphic, having four to 10 alleles in P. versicolor with an expected heterozygosity of 0.530–0.836. These loci can be used to study parameters concerning genetic relatedness such as social interactions in colonies and genetic conflicts of interest among nestmate individuals.

scholarly journals Large-Scale Variation in Growth of Black Brant Goslings Related to Food Availability

The Auk ◽  
2001 ◽  
Vol 118 (4) ◽  
pp. 1088-1095 ◽  
Author(s):  
James S. Sedinger ◽  
Mark P. Herzog ◽  
Brian T. Person ◽  
Morgan T. Kirk ◽  
Tim Obritchkewitch ◽  
...  
Keyword(s):  
Large Scale ◽  
Grazing Pressure ◽  
The Arctic ◽  
First Year ◽  
Principal Mechanism ◽  
Density Dependent ◽  
Brood Rearing ◽  
Branta Bernicla ◽  
Black Brant ◽  
Arctic Coast

AbstractWe examined variation in growth of Black Brant (Branta bernicla nigricans) goslings among two colonies on the Yukon-Kuskokwim Delta in southwestern Alaska and the Colville River Delta on Alaska's Arctic coast. We simultaneously measured abundance and quality of a key food plant, Carex subspathacea, and grazing pressure on that plant at the three colonies. Our goal was to measure variation in gosling growth in relation to variation in grazing pressure and food abundance because growth of goslings is directly linked to first-year survival, and consequently is the principal mechanism for density-dependent population regulation. Goslings grew substantially faster on the arctic coast and were nearly 30% larger than those on the Yukon-Kuskokwim Delta at four to five weeks old. Faster growth on the arctic coast was associated with 2× greater standing crop of C. subspathacea during brood rearing than on the Yukon-Kuskokwim Delta. Dispersal rates are high enough (Lindberg et al. 1998) to rule out local adaptation and genetic variation as explanations for observed variation in growth. Our results are consistent with lower survival of goslings from the Yukon-Kuskokwim Delta during their first fall migration and stronger density-dependent regulation on the Yukon-Kuskokwim Delta than on the Arctic coast.

scholarly journals Development and characterization of twelve new polymorphic microsatellite loci in the Iberian ribbed newt, Pleurodeles waltl (Caudata: Salamandridae), with data on cross-amplification in P. nebulosus

2014 ◽  
Vol 35 (1) ◽  
pp. 129-134 ◽  
Author(s):  
Jorge Gutiérrez-Rodríguez ◽  
Elena G. Gonzalez ◽  
Íñigo Martínez-Solano
Keyword(s):  
Population Dynamics ◽  
Microsatellite Loci ◽  
Evolutionary History ◽  
The Novel ◽  
Expected Heterozygosity ◽  
History Of ◽  
Southern Iberia ◽  
Polymorphic Microsatellite ◽  
Pleurodeles Waltl

Twelve novel polymorphic microsatellite loci were isolated and characterized for the Iberian ribbed newt, Pleurodeles waltl (Caudata, Salamandridae). The distribution of this newt ranges from central and southern Iberia to northwestern Morocco. Polymorphism of these novel loci was tested in 40 individuals from two Iberian populations and compared with previously published markers. The number of alleles per locus ranged from two to eight. Observed and expected heterozygosity ranged from 0.13 to 0.57 and from 0.21 to 0.64, respectively. Cross-species amplification was tested in Pleurodeles nebulosus, which is listed as Vulnerable by the IUCN. Eight new and seven previously published loci amplified successfully in that species and thus represent a valuable conservation tool. The novel microsatellites will be useful for a better understanding of the population dynamics, demography, genetic structure, and evolutionary history of Pleurodeles waltl and P. nebulosus.

scholarly journals A new set of microsatellite loci for Cattleya walkeriana Gardner, an endangered tropical orchid species and its transferability to Cattleya loddigesii Lindl. and Cattleya nobilior Reichenbach

2017 ◽  
Vol 16 (3) ◽  
pp. 284-287
Author(s):  
Bruno C. Rossini ◽  
Mariá B. Kampa ◽  
Celso L. Marino ◽  
Fernanda Bortolanza Pereira ◽  
Fábio M. Alves ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Null Alleles ◽  
Germplasm Resources ◽  
Significant Linkage Disequilibrium ◽  
Orchid Species ◽  
Expected Heterozygosity ◽  
Tropical Orchid ◽  
Significant Linkage

AbstractIn this study, we isolate and analyse a new set of microsatellite loci for Cattleya walkeriana. Twenty-two primer pairs were screened for C. walkeriana (n = 32) and assessed for their transferability to Cattleya loddigesii (n = 12) and Cattleya nobilior (n = 06). All loci amplified for C. walkeriana; however, for C. loddigesii and C. nobilior, four and five primers, respectively, did not present amplification. The polymorphic loci presented between 2 and 13 alleles per locus for both C. walkeriana and C. loddigesii, with respective averages of 5.1 and 4.2. For C. nobilior, we found between two and five alleles per locus, with an average of 2.6. For C. walkeriana, observed heterozygosity varied from 0.100 to 0.966, whereas expected heterozygosity ranged from 0.097 to 0.900. The observed and expected heterozygosity for C. loddigesii and C. nobilior were also estimated. We found no significant linkage disequilibrium between any pair of loci, and evidence of null alleles at four loci (Cw16, Cw24, Cw30 and Cw31) for C. walkeriana. The combined power to exclude the first parent and combined non-exclusion probability of identity were 0.999 and 2.3 × 10−20, respectively. These new loci can be used in studies of germplasm resources, and assessments of genotypic and genetic diversity and population structure, thus improving the accuracy of such analyses and their applicability in the conservation and protection of these endangered species.

scholarly journals Slave to the Tides: Spatiotemporal Foraging Dynamics of Spring Staging Black Brant

The Condor ◽  
2006 ◽  
Vol 108 (3) ◽  
pp. 661-677 ◽  
Author(s):  
Jeffrey E. Moore ◽  
Jeffrey M. Black
Keyword(s):  
Seasonal Changes ◽  
Negative Binomial ◽  
Bird Species ◽  
Negative Binomial Regression ◽  
Nutrient Content ◽  
Latitudinal Gradients ◽  
Tidal Channels ◽  
Branta Bernicla ◽  
Black Brant ◽  
Site Use

AbstractArctic-nesting geese depend on nutrients acquired during spring migration for reproduction, and thus should attempt to maximize nutrient intake while on staging areas. We investigated site use of Black Brant (Branta bernicla nigricans) at an important staging location—Humboldt Bay, California—to determine whether birds selected the most profitable feeding areas available. Migrating Brant feed almost exclusively on eelgrass (Zostera marina), which is restricted in availability due to daily and seasonal tidal cycles. We mapped foraging Brant locations during low tides and collected eelgrass samples to describe food resources in 31 areas in the bay. We used negative binomial regression to evaluate goose densities during different tidal levels and times of season as a function of food biomass and nutrient content, distance from grit sites, and substrate elevation. Results varied by time of season and tidal depth, but Brant densities were positively correlated with eelgrass protein, calcium, and biomass in most analyses. Brant usually fed in the deepest possible areas permitted by tides, and closer to tidal channels, where biomass and nutrient content of eelgrass were greater and where depletion from grazing was probably less. During higher low tides, Brant fed closer to previously visited grit sites. Tide cycles change over the course of the Brant's staging period on the bay, enabling longer and more frequent access to deeper eelgrass meadows as spring progresses. These seasonal changes in tidal pattern coincide with seasonal changes in Brant use of the bay. Thus, migration patterns for estuarine bird species might be shaped by latitudinal gradients in both food phenology and seasonal tidal patterns.

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