Characterization of microsatellites for parentage studies of white‐throated magpie‐jays (Calocitta formosa) and brown jays (Cyanocorax morio)

White‐throated magpie‐jays (Calocitta formosa) and brown jays (Cyanocorax morio) are cooperative breeders that live in complex groups composed of helpers and multiple male and female breeders. Behavioral observations and multilocus DNA fingerprinting have indicated that the social and genetic mating systems of these two species are diverse. Extra‐group paternity appears to be common in both species, necessitating the use of single locus genetic methods to efficiently search for fathers. We therefore characterized 19 microsatellite loci for these two species (12 for magpie‐jays and seven for brown jays) to aid in parentage studies.     

Characterization of microsatellite loci in chinook salmon (Oncorhynchus tshawytscha) and cross‐species amplification in other salmonids

Previous studies of population genetic structure of fall‐run chinook salmon (Oncorhynchus tshawytscha) in California’s Central Valley have either not focused on or have been unable to resolve intertributary differences within the San Joaquin River basin. The authors describe the isolation, the polymerase chain reaction conditions, and characterize the cross‐species amplification of 17 microsatellite loci in six species of salmonids. Fourteen of these loci are polymorphic in fall‐run chinook from the San Joaquin River drainage. These results indicate the potential utility of microsatellite markers developed for one species, for both congenerics and species within a closely related genus.     

Characterization of microsatellite loci in village indigobirds Vidua chalybeata and cross‐species amplification in estrildid and ploceid finches

We characterized 11 microsatellite primer pairs for the village indigobird Vidua chalybeata. The loci were highly polymorphic, with 7–13 alleles per locus. Gene diversity, estimated as expected heterozygosity, ranged from 0.52 to 0.86, and was generally matched by levels of observed heterozygosity (0.49–0.91). Many of these primer pairs amplified polymorphic loci in cross‐species amplification trials with a variety of estrildid and ploceid finches and a sparrow, Passer griseus. These primers will be valuable for genetic analyses of the brood parasitic indigobirds and whydahs (genus Vidua) as well as other Old World finches.     

Isolation and characterization of microsatellite loci in Pseudoplatystoma corruscans (Siluriformes: Pimelodidae) and cross‐species amplification

A total of five polymorphic microsatellites loci from Pseudoplatystoma corruscans were isolated and characterized. A population survey involving 43 specimens resolved a large number of alleles (range seven to eight among loci) and high observed heterozygosity (0.500–0.615), indicating its usefulness in population genetics studies. Cross‐species amplification was successful in four other Pimelodidae species.     

Characterization of 20 highly variable tetranucleotide microsatellite loci for bull trout (Salvelinus confluentus) and cross‐amplification in other Salvelinus species

We describe the isolation and development of 20 polymorphic tetranucleotide microsatellite loci for bull trout (Salvelinus confluentus). In a sample of 76 fish, we observed between four and 23 alleles per locus. These loci show greater levels of genetic diversity than other loci previously examined in bull trout. Seventeen of these loci were also polymorphic in at least one of the following species: Salvelinus alpinus, Salvelinus malma, Salvelinus namaycush and Salvelinus fontinalis. These loci will aid in our understanding of the molecular ecology of bull trout and other char.     

Characterization and cross‐species amplification of microsatellite loci in a Cyprinodon species flock

In this study, two new microsatellite loci from a library of Cyprinodon beltrani from Laguna Chichancanab, Mexico, were characterized. Additionally, cross‐species amplification with primer pairs developed for other Cyprinodon species was performed. The 11 markers show moderate to high levels of polymorphism (two to 33 alleles) in six species of the Cyprinodon flock from Laguna Chichancanab and in their sister species Cyprinodon artifrons. These loci were characterized for population genetic study to detect gene flow between the different endemic pupfish species.     

Characterization of microsatellite loci in Sacramento perch (Archoplites interruptus)

We characterized 23 polymorphic tetranucleotide microsatellite loci for Sacramento perch (Archoplites interruptus). This species is extirpated in its native range, the Sacramento–San Joaquin Delta (California, USA), and is therefore targeted for recovery. A concerted effort is currently underway to re‐establish self‐sustaining populations of Sacramento perch in its native range. These microsatellites will be used to analyse the population structure of the species and, in conjunction with life history and physiological data, develop a comprehensive recovery plan.     

Isolation and characterization of microsatellite loci in Lampsilis abrupta (Bivalvia: Unionidae) and cross‐species amplification within the genus

We have documented the first microsatellites isolated from a unionid and demonstrated that these markers can be useful for surveys of neutral genetic variation in several Lampsilis species. We describe the isolation and characterization of 15 polymorphic microsatellite DNA loci for the endangered unionid Lampsilis abrupta. Among individuals from five collections, allelic diversity ranged from six to 17 alleles and averaged 10.4 alleles per locus. Individual heterozygosity was observed to range from 20.0% to 86.7% and averaged 46.9%. Cross‐species amplification was investigated in nine additional Lampsilis species. A high level of flanking sequence similarity was inferred as 13 of 15 loci amplified in at least seven species.     

Isolation and characterization of microsatellite markers from Fangzheng silver crucian carp,Carassius auratus gibelio (Bloch), and cross‐amplification in the closely related species crucian carp,Carassius auratus auratus (Linnaeus)

We report the development of 20 microsatellite markers for Fangzheng silver crucian carp, Carassius auratus gibelio (Bloch). Nineteen out of 20 showed polymorphism with alleles ranging from two to 14. These loci were screened to amplify the closely related species crucian carp, Carassius auratus auratus (Linnaeus) and all of them can amplify DNA with the size similar to the former. The origin of silver crucian carp is in issue and the population genetic structure is still unclear. Microsatellite markers isolated from the silver crucian carp and their utility in the crucian carp will be useful for these researches.     

Characterization of 35 microsatellite loci in the Pacific lion‐paw scallop (Nodipecten subnodosus) and their cross‐species amplification in four other scallops of the Pectinidae family

Four microsatellite‐enriched DNA libraries yielded 35 microsatellite loci from 100 primer pairs designed for Pacific lion‐paw scallop, Nodipecten subnodosus. The number of alleles ranged from four to 28. Three of the 35 loci were not in Hardy–Weinberg equilibrium and linkage disequilibrium was found for one pair of loci. These microsatellites will be used to analyse the population structure of the species in Mexico's Baja Peninsula to propose management strategies for scallop aquaculture development. Twenty‐six primer pairs cross‐amplified in Nodipecten nodosus, whereas none (Argopecten ventricosus) or few cross‐amplified in the Argopecten species.     

Polymorphic microsatellite loci from the American goldfinch (Carduelis tristis) and their cross‐amplification in a variety of passerine species

Cardueline finches have become important models in studies of sexual selection. Here I describe eight polymorphic microsatellite loci isolated from the American goldfinch (Carduelis tristis) that are useful in parentage and heterozygosity studies. The number of alleles per locus ranged from eight to 38 based on 252 goldfinches. The markers are polymorphic in at least four other Cardueline finch species, and several amplify in nonfinch passerines including red‐winged blackbird (Agelaius phoeniceus), black‐throated blue warbler (Dendroica caerulescens) and tufted titmouse (Baeolophus bicolor), indicating they should be useful in paternity and population studies of a variety of species.     

Positive effects of helpers on reproductive success in the brown treecreeper and the general importance of future benefits

1. Numerous studies of cooperatively breeding species have tested for effects of helpers on reproductive success to evaluate hypotheses for the evolution of cooperation, but relatively few have used experimental or statistical approaches that control for the confounding effects of breeder and territory quality. 2. In the brown treecreeper Climacteris picumnus, most helpers are male offspring of the breeding pair that have delayed dispersal. We analysed 5 years of data (97 territory-years) using hierarchical linear modelling to test for effects of helpers on reproductive success while controlling for confounding factors. 3. The number of helpers was related positively to reproductive success even after controlling for differences between territories and breeders. A threshold effect was observed, with success increasing most with the presence of a second helper (i.e. at group size of four). 4. Feeding at the nest was one mechanism responsible for this effect, as larger groups had higher total feeding rates at all nesting stages. Higher total feeding rates, as well as higher feeding rates by helpers, were correlated in turn with greater reproductive success. 5. An analysis of the effects of helper feeding rate on reproductive success in groups with just one helper produced only weak support for a positive effect of helpers. Controlled comparisons of this kind utilize only a small fraction of the total data available and thus have limited statistical power compared to hierarchical or mixed-modelling. 6. A number of hypotheses to explain the evolution and maintenance of helping behaviour are consistent with our results for brown treecreepers including kin selection and hypotheses based on future direct benefits. 7. A previous synthesis of studies of helper effects that controlled for confounding factors suggested a pattern in which male helpers rarely have positive effects on reproductive success. However, revising that synthesis to include recent hierarchical or mixed-modelling studies suggests that helpers of both sexes usually have positive effects, and that the relative importance of future direct benefits may have been underestimated.     

Isolation and characterization of novel microsatellite loci for the short‐beaked common dolphin (Delphinus delphis) and cross‐amplification in other cetacean species

Seven tetranucleotide and three dinucleotide microsatellite loci were isolated from the short‐beaked common dolphin (Delphinus delphis). Number of alleles and observed heterozygosity ranged from three to twelve (mean 8.4) and from 0.087 to 0.978 (mean 0.741), respectively. All loci were tested in four other odontocete species and showed polymorphisms in most locus–species combinations. This panel of nuclear markers will be useful for the investigation of population ecology and social interactions in common dolphins and other cetacean species.     

Polymorphic microsatellite loci for the mustached tamarin (Saguinus mystax) and their cross‐species amplification in other New World monkeys

We isolated and characterized 10 polymorphic microsatellite loci for the mustached and cotton‐top tamarin (Saguinus mystax and S. oedipus) and also tested their applicability in other New World monkey genera. Six loci proved to be variable in Cebus apella and Saimiri sciureus/S. boliviensis, respectively. We also show that faeces‐derived DNA is suitable for polymerase chain reaction (PCR) analyses of a primate taxon that gives birth to twins with individuals exhibiting a haematopoetic chimaerism. The microsatellite fingerprint patterns do not display a complex mixture of the PCR‐products derived from the alleles of both dizygotic twins, but exhibit the constitutive alleles of one sibling only.     

Isolation and characterization of microsatellites in Leuciscus cephalus (Cypriniformes,Cyprinidae) and cross‐species amplification within the family Cyprinidae

Thirteen polymorphic microsatellites were isolated from Leuciscus cephalus, a widespread cyprinid species with great ecological tolerance. Together with the cross‐species amplification of six additional loci originally published for three cyprinid fish species, we optimized a multiplex panel for L. cephalus allowing the genotyping of 19 polymorphic loci. Number of alleles and heterozygosity per locus in a sample of 20 fish individuals ranged from two to 16 and from 0.05 to 0.90, respectively. These primers will be useful in determining the population structure of L. cephalus. In addition, successful cross‐amplification was obtained for several species of Cyprinidae.     

Isolation and characterization of microsatellite loci from yellowtail Seriola quinqueradiata and cross‐species amplification within the genus Seriola

We developed five microsatellite primer pairs for the yellowtail Seriola quinqueradiata. The loci were highly polymorphic, with eight to 14 alleles per locus, and can be used to study kinship and/or population structure. Many of these primer pairs amplified polymorphic loci in cross‐species amplification tests for two other Seriola species (S. lalandi and S. dumerili).     

Isolation,characterization and cross‐species amplification of microsatellite DNA loci in the tropical American yam Dioscorea trifida

We developed microsatellite markers in American yam (Dioscorea trifida). A microsatellite sequence‐enriched genomic library was screened, and after sequencing, primers were designed for 20 microsatellites. Among these, eight primer pairs yielded amplification products that were both interpretable and polymorphic in 24 yam cultivars. The number of alleles per locus ranged from two to 13 and the overall expected heterozygosity was around 0.5. Six of the eight Dioscorea trifida microsatellite loci gave amplification products in other Dioscorea species.     

Characterization of microsatellite loci in Humboldt penguin (Spheniscus humboldti) and cross‐amplification in other penguin species

The Humboldt penguin (Spheniscus humboldti) was once very common throughout its range along the coast of Peru and Chile. Today, listed as endangered, it is crucial to gain an understanding of gene flow and levels of genetic variation between breeding colonies to protect this species effectively. We developed seven microsatellite primers to investigate gene flow and population structure among four colonies. Locus‐specific allelic diversity ranges from five to 11 alleles and observed heterozygosity ranges from 0.50 to 0.88. These markers cross‐amplify in eight penguin species over five genera.     

Characterization of microsatellite loci in Kearney's bluestar (Amsonia kearneyana) and cross‐amplification in other Amsonia species

Kearney's bluestar (Amsonia kearneyana) is a highly endangered herbaceous perennial in the family Apocynaceae. The species is found only in the Baboquivari Mountains of southern Arizona. We report the isolation and development of 12 microsatellite loci for Kearney's bluestar. Numbers of alleles ranged from two to four and observed heterozygosities ranged from 0.20 to 0.80 in the nine loci found to be polymorphic in the test population. All loci were also tested for cross‐amplification in five other Amsonia species representing two subgenera from the southwestern United States. Some loci that were not polymorphic in the Kearney's bluestar were polymorphic in other species.