Microsatellite loci for paternity assessment in the black swan (Cygnus atratus: Aves)

Seven polymorphic tetranucleotide microsatellite loci were isolated and characterized from the black swan Cygnus atratus Latham, using nonradioactive PCR‐based techniques to screen an enriched genomic library. These loci were highly variable (mean H _E  = 0.75, mean number of alleles = 9.1), and showed no evidence of linkage disequilibrium or null alleles. This locus set is suitable for detecting extra‐pair copulations (combined exclusion probability = 0.999) and for other population genetic applications.     

Coexistence and population genetic structure of the whooper swan <Emphasis Type="Italic">Cygnus cygnus</Emphasis> and mute swan <Emphasis Type="Italic">Cygnus olor</Emphasis> in Lithuania and Latvia

Two closely related swan species, the mute swan Cygnus olor and the whooper swan Cygnus cygnus, were formerly allopatric throughout their breeding ranges, but during the last decades a sympatric distribution has become characteristic of these species in the Baltic Sea region. The whooper swan has gradually replaced the mute swan in many suitable habitats in Lithuania and Latvia. Marked differences in the genetic population structure of both species may partially explain the dominance of the whooper swan, as genetic population divergence can be a major factor affecting inter-specific competition. A homogenous genetic population structure was defined for mute swans breeding in Lithuania, Latvia, Poland and Belarus. Breeding mute swans in this region are mostly of naturalised origin. A diverse population genetic structure characterizes whooper swans breeding in Lithuania and Latvia.     

Evidence of Alaskan Trumpeter Swan Population Growth Using Bayesian Hierarchical Models

ABSTRACT Alaska (USA) contains a large proportion of the breeding population of trumpeter swans (Cygnus buccinator) in the United States. However, tracking population trends in Alaska trumpeter swans is complicated by variables such as an increase in survey effort over time, periodic surveys (1968 and every 5 yr after 1975), and missing data. We therefore constructed Bayesian hierarchical negative binomial models to account for nuisance variables and to estimate population size of trumpeter swans using aerial survey data from all known breeding habitats in Alaska, 1968–2005. We also performed an augmented analysis, where we entered zeroes for missing data. This approach differed from the standard (nonaugmented) analysis where we generated estimates for missing data through simulation. We estimated that adult swan populations in Alaska increased at an average rate of 5.9% annually (95% credibility interval = 5.2–6.6%) and cygnet production increased at 5.3% annually (95% credibility interval = 2.2–8.0%). We also found evidence that cygnet production exhibited higher rates of increase at higher latitudes in later years, which may be a response to warmer spring temperatures. Augmented analyses always produced higher swan population estimates than the nonaugmented estimates and likely overestimate true population abundance. Our results provide evidence that trumpeter swan populations are increasing in Alaska, especially at northern latitudes. Changes in population size and distribution could negatively affect tundra swans (Cygnus columbianus) breeding in Alaska, and biologists should monitor these interactions. We recommend using nonaugmented Bayesian hierarchical analyses to estimate wildlife populations when missing survey data occur.     

Isolation and characterization of microsatellite loci in Schizolobium parahyba (Leguminosae)

Primer sequences for 16 microsatellite loci were developed from Schizolobium parahyba, a tropical tree species. Twelve loci were found to be polymorphic after screening diversity in individuals from Belize. A total of 39 alleles were found at nine loci. The markers are invaluable tools for studying the population genetics and mating system of the species.     

Development and characterization of 45 novel microsatellite markers for sea cucumber (Apostichopus japonicus)

Simple sequence repeat‐enriched library screening and expressed sequence tag database mining were adopted to develop microsatellite markers for sea cucumber (Apostichopus japonicus). Eighty‐three microsatellite loci were selected for polymorphism assessment using 48 individuals. The results showed that 45 novel loci were polymorphic. The number of alleles ranged from two to 16, and the values of observed and expected heterozygosities varied from 0 to 0.9375 and from 0.1135 to 0.9674, respectively. No significant linkage disequilibrium between pairs of loci was found and 26 loci conformed to the Hardy–Weinberg equilibrium. These markers are therefore a potential tool for studies in the population structure and linkage map construction for A. japonicus.     

Observations on a hybrid between the whooper swan (<Emphasis Type="Italic">Cygnus cygnus</Emphasis>) and the mute swan (<Emphasis Type="Italic">Cygnus olor</Emphasis>)

The swan obtained by hybridization between Cygnus cygnus and C.olor was delivered to the Moscow Zoo from the Leningrad Zoo in 1989. Between 2002 and 2004, it permanently remained with a female whooper swan in a large pond. The two swans behaved as a breeding pair, although the sex of the hybrid bird remained unknown. We observed no courtship displays addressed by the hybrid swan either to the female whooper swan or to other swans living in the pond. The hybrid swan was exteriorly closer to C. cygnus rather than to C. olor and showed increased aggressiveness. Its threatening behavior was intermediate between parental species in terms of threat displays and motor activity, although behavioral patterns characteristic of C.olor prevailed. The most frequent sounds in the vocal repertoire of the hybrid swan were close to the vibrant throbbing call of C.olor in terms of duration and frequency range. In contrast to these sounds, the call of the hybrid swan was noiselike, with distinct harmonic structure (as in the whooper swan except for extremely narrow interharmonic intervals). These vocal signals of the hybrid swan were shown to be intermediate between those of the parental species. In addition, the acoustic repertoire of the hybrid swan included rarely emitted sounds closely resembling elements of vocalizations of both C. cygnus and C. olor.     

Isolation and characterization of the first microsatellite markers for the endangered swan mussel <Emphasis Type="Italic">Anodonta cygnea</Emphasis> L. (Bivalvia: Unionoidea)

Freshwater molluscs are globally critically threatened, yet little is known about their genetic diversity. We describe the isolation and characterization of the first microsatellite markers for the European swan mussel, Anodonta cygnea. Nine loci were polymorphic in a panel of 110 individuals from seven German and Estonian populations. Number of alleles ranged from 2 to 14 and heterozygosity levels ranged from 0.021 to 0.498 for H _o and from 0.069 to 0.634 for H _e. Deficiency of heterozygous genotypes was observed in six loci. The length of the microsatellite repeat motives was positively correlated with the allele numbers in the respective loci.     

High variability and disomic segregation of microsatellites in the octoploid Fragaria virginiana Mill. (Rosaceae)

The objectives of the present study were to develop microsatellite markers for the wild strawberry, Fragaria virginiana, to evaluate segregation patterns of microsatellite alleles in this octoploid species, and assess genetic variability at microsatellite loci in a wild population. A genomic library was screened for microsatellite repeats and several PCR primers were designed and tested. We also tested the use of heterologous primers and found that F. virginiana primers amplified products in cultivated strawberry, Fragaria × ananassa Duch. and Fragaria chiloensis. Similarly, microsatellite loci developed from cultivated strawberry also successfully amplified F. virginiana loci. We investigated four microsatellite loci in detail, three developed from F. virginiana and one from cultivated strawberry. A survey of 100 individuals from a population of F. virginiana in Pennsylvania demonstrated high heterozygosities (H_e or gene diversity ranged from 0.80 to 0.88 per locus) and allelic diversity (12–17 alleles per locus), but individual plants had no more than two alleles per locus. Segregation patterns in parents and progeny of two controlled crosses at these four loci were consistent with disomic Mendelian inheritance. Together these findings suggest that the genome of F. virginiana is "highly diploidized" and at least a subset of microsatellite loci can be treated as codominant, diploid markers. Significant heterozygote deficiencies were found at three of the four loci for hermaphroditic individuals but for only one locus among females in this gynodioecious species.Communicated by J. Dvorak     

Isolation and characterisation of polymorphic microsatellite loci in the vulnerable spectacled flying fox, Pteropus conspicillatus

The spectacled flying fox, Pteropus conspicillatus, is listed as vulnerable in Australia and is under threat from numerous impacts. Primers to amplify eight co-dominant microsatellite loci were designed for Pteropus conspicillatus, based on an enriched genomic library. Four loci were monomorphic in this species while the remaining four loci were highly polymorphic with 16–23 alleles. Two of the four monomorphic loci were found to be polymorphic in Pteropus alecto, a closely related congener. All but one of the six polymorphic loci were in Hardy Weinberg equilibrium. Additionally, six microsatellite loci isolated for Pteropus rodricensis were tested against individuals of P. conspicillatus with all loci amplifying reliably. These loci will be used to investigate population genetic structure in the vulnerable spectacled flying fox.     

Identification of microsatellite loci in Collinsia verna (Veronicaceae)

We developed eight polymorphic microsatellite loci for Collinsia verna (Veronicaceae). In a sample of 18–35 individuals from a single population, we found two to 15 alleles per locus (mean 8.3). We also tested these loci for cross‐amplification in all 22 species in the tribe Collinseae. Overall, more than half the species in the tribe amplified one microsatellite while three species most closely related to C. verna (Collinsia violacea, Collinsia parviflora and Collinsia grandiflora) amplified multiple microsatellite loci. These microsatellite loci will be used in future studies of mating system in this tribe and other quantitative genetic and population genetic studies.     

Isolation and characterization of microsatellites in yellow perch (Perca flavescens)

A total of 45 microsatellite loci from yellow perch, Perca flavescens, were isolated and characterized. Among the 45 microsatellite loci, 32 had more than two alleles. A wild population of P. flavescens (n = 48) was used to examine the allele range of the microsatellite loci. Mendelian inheritance of alleles was confirmed by examining the amplified products in pair‐mated families. The number of alleles for the 32 polymorphic loci varied from two to 16, and observed heterozygosity ranged between 0.024 (YP79) and 0.979 (YP60). Cross‐species polymorphic amplification in four other Percidae species was successful for 22 loci.     

Isolation and characterization of polymorphic microsatellite loci from a dinucleotide-enriched genomic library of seven-band grouper (Epinephelus septemfasciatus) and cross-species amplification

Seven-band grouper (Epinephelus septemfasciatus) is a commercially important fishery species. Sixty-six microsatellite loci were isolated from a dinucleotide-enriched genomic library of E. septemfasciatus. Twelve of these loci were polymorphic in a test population with alleles per locus ranging from two to five, and observed and expected heterozygosities per locus from 0.04 to 1.00 and from 0.28 to 0.76, respectively. Three loci significantly deviated from Hardy–Weinberg equilibrium and no significant linkage disequilibrium was found between pairs of loci after Bonferroni correction. Cross-species amplification of these polymorphic microsatellite loci was performed in additional two related species. These polymorphic microsatellite loci would be useful for investigating genetic resource of E. septemfasciatus and other related species. Lili Zhao and Changwei Shao have contributed equally.     

Isolation and characterization of polymorphic microsatellites in European chestnut (Castanea sativa Mill.)

Thirteen polymorphic microsatellite loci were isolated from Castanea sativa (Mill.). Six contained dinucleotide repeats, six contained trinucleotide repeats, and one contained a compound microsatellite of a trinucleotide and a tetranucleotide repeat. The loci were characterized using C. sativa trees from three populations in the UK and the parents and six seedlings from a Turkish mapping population. The number of alleles revealed varied from two to 14 (mean = 5.15) per loci. Eight loci were found to be useful in the mapping family.     

Characterization of polymorphic microsatellite loci for the Tawny Pipit Anthus campestris and their utility in other steppe birds

New microsatellite loci for Tawny Pipit Anthus campestris were isolated from a genomic library. We were able to unambiguously score six loci: two were dinucleotide, one trinucleotide, two tetranucleotide and one pentanucleotide that turned out to be sex-linked. Four out of six loci were polymorphic with 7–23 alleles in our population and an observed heterozygosity ranging between 0.286 and 0.936. Cross-utility of these markers was tested in other 17 steppe-bird species of six families. In addition, 16 microsatellite loci developed for other species were tested for cross-species amplification in A. campestris. Eight microsatellite markers were successfully amplified; seven of them were polymorphic with 2–43 alleles and an observed heterozygosity of 0.040–0.863. Overall, 14 functional locus markers have been characterized for A. campestris that could be useful for future studies of paternity, genetic variability and population structure.     

Isolation and characterization of polymorphic microsatellite loci from black sea bass (Centropristis striata) and cross-species amplification

Black sea bass (Centropristis striata) is an economically important serranid species. A number of 39 microsatellite loci were isolated from two enriched genomic library of C. striata. Eleven of these loci were polymorphic in a test population with alleles per locus ranging from 3 to 8, and observed and expected heterozygosities per locus from 0.26 to 1.00 and from 0.61 to 0.84, respectively. Four loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium was found between pairs of loci. Cross-species amplification of these polymorphic microsatellite loci was performed in additional two related species. These polymorphic microsatellite loci would be useful for investigating genetic resource of C. striata and other related species.     

Isolation and characterization of polymorphic microsatellite loci from fat greenling (Hexagrammos otakii)

Fat greenling (Hexagrammos otakii) is an economocally important marine fish species. Thirtyfive microsatellite loci were isolated from two enriched genomic library of Hexagrammos otakii. Ten of these loci were polymorphic in a test population with alleles per locus ranging from two to six, and observed and expected heterozygosities per locus from 0.2581 to 1.0000 and from 0.2892 to 0.7726, respectively. Four loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium was found between pairs of loci. These polymorphic microsatellite loci would be useful for investigating genetic diversity of Hexagrammos otakii.     

Isolation and characterization of 10 polymorphic microsatellite loci from small yellow croaker (Pseudosciaena polyactis)

Small yellow croaker (Pseudosciaena polyactis) is an economically important marine fish species. About 43 microsatellite loci were isolated from two enriched genomic library of Pseudosciaena polyactis. Ten of these loci were polymorphic in a test population with alleles per locus ranging from two to six, and observed and expected heterozygosities per locus from 0.3750 to 0.8750 and from 0.3112 to 0.8121, respectively. No loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium was found between pairs of loci. These polymorphic microsatellite loci would be useful for investigating genetic diversity of Pseudosciaena polyactis.     

Isolation and characterization of polymorphic microsatellite loci in the Hawaiian flycatcher,the elepaio (Chasiempis sandwichensis)

Thirteen polymorphic microsatellite loci were isolated and characterized from two clades of an endemic Hawaiian flycatcher, the elepaio (Chasiempis sandwichensis). Seven dinucleotide repeats and one trinucleotide repeat were cloned from Kauai elepaio; five dinucleotide repeats were cloned from Oahu elepaio. Polymorphism was assessed in a sample of Oahu elepaio (n = 22) revealing two to 16 alleles per locus. Observed heterozygosity ranged from 0.14 to 0.91. However, linkage analysis exposed highly significant linkage disequilibrium between two of the most polymorphic loci. Twelve loci are therefore expected to be useful for investigations of population structure.     

Identification of 13 polymorphic microsatellite loci in the zebra finch,Taeniopygia guttata (Passeridae,Aves)

Polymorphic microsatellite loci were identified in order to determine paternity in a captive population of the zebra finch, Taeniopygia guttata. Primer sets from 93 published passerine microsatellite sequences were tested for cross‐species amplification. Thirteen loci were found to be polymorphic, of which, eight displayed null alleles and one locus (Ase50) was found to be Z‐chromosome linked.