PERMANENT GENETIC RESOURCES: Isolation and characterization of microsatellite markers in the white-faced capuchin monkey (Cebus capucinus) and cross-species amplification in other New World monkeys

Seventeen polymorphic microsatellite loci were identified for white-faced capuchin monkeys from an enriched genomic library in addition to one locus found through cross-species comparisons. In a sample of 187 wild individuals, these loci exhibited an average of five alleles and an observed heterozygosity of 0.62. The combined probability of exclusion of a random individual from parentage was 0.99. These loci were screened in 23 other New World monkeys and an average of seven loci was variable per species, suggesting that these loci could be of use in studies of other Neotropical primates.     

Controlled breeding studies to verify the identity of roach and common bream hybrids from a natural population

The occurrence of post-F1 generation hybrids between common bream and roach in natural populations has still to be qualified. To do this, common bream, roach, F1 and F2 hybrid progeny were produced under controlled conditions. All progeny groups exhibited overlaps in the ranges of their meristic characters. Discriminant analysis of meristic data combined with allozymes allowed identification of post-Fl hybrids. Enzyme electrophoresis showed Fl progeny to be heterozygous at diagnostic loci. Back-crossed F2 progeny had a mixture of homozygosity and heterozygosity at diagnostic loci. Meristic and genetic analysis of fish from a natural population indicated that they were all F1 hybrids. Post-Fl hybridization cannot be ruled out from natural populations because Fl hybrids are known to be fertile. It is suggested that post-Fl hybrids were not detected either because of their low incidence of occurrence or due to biological phenomenon Such as inferior fitness.     

Characterization and screening of microsatellite loci in a wild lemur population (Propithecus verreauxi verreauxi).

Sixteen dinucleotide microsatellite loci were isolated from the genome of Propithecus verreauxi verreauxi. All loci were polymorphic when genotyped on a minimum of 16 animals. The number of alleles across these loci ranges from two to 11. Additionally, seven of these loci were genotyped across a minimum of 200 animals in order to estimate heterozygosity and their potential for parentage assignment in this population. Using these seven loci, the mean heterozygosity in this population is 0.705, and the combined probability of these seven loci to exclude a random individual from parentage, when one parent is known, is 0.996. These data suggest that these loci will be useful for estimating a variety of population genetic and genealogical parameters in P. v. verreauxi populations.     

Endocrine disruption in juvenile roach from English rivers: a preliminary study

Juvenile roach Rutilus rutilus from seven rivers of varying water quality were examined for evidence of endocrine disruption. The majority of roach from five of these rivers had female‐like reproductive ducts. The results suggest that juvenile, rather than adult, fish could be used in studies of endocrine disruption in wild fish populations.     

A search for introgressive hybridization in the rudd, Scardinius erythrophthalmus (L.), and the roach, Rutilus rutilus (L.)

Rudd, roach and their hybrids from an interbreeding population at Norwich were examined electrophoretically for seven enzymes; an examination of pharyngeal teeth supplemented the data. The rudd were compared to rudd from Lake Trawsfynydd, Wales, a lake free from roach. No differences were observed between the rudd from the two localities and no evidence was found of introgression within the fish from Norwich.     

Morphological and genetic analysis of the Red Hills roach (Cyprinidae: Lavinia symmetricus)

We performed a morphological and phylogeneticanalysis of a recently discovered population ofCalifornia roach (Red Hills roach; Cyprinidae:Lavinia symmetricus) to determine if thedegree of separation of these populationswarrants subspecies status. Previousmorphological analysis by Brown et al. (1992)suggested that L. symmetricus from theRed Hills roach type locality (Horton Creek)were different for Principal DiscriminantScores (based on 15 morphological characters)from neighboring populations. Similarly,recent work by our lab on the phylogenetics ofthe putative subspecies of L. symmetricushas revealed that the Red Hills roach appearsreciprocally monophyletic for assayedmitochondrial DNA markers. In addition toperforming further morphological and geneticanalysis of the Red Hills roach, we increasedour sampling effort in the Red Hills region todetermine the distribution of this undescribedputative subspecies. Our morphological resultsare generally in agreement with Brown et al.(1992) except in regards to Horton Creek. Asignificant difference between the two studiesexists for all Horton Creek multivariateanalyses as well as frequency of a presumablyderived character (chisel lip). Our geneticresults also support our previous findings thatthe Red Hills roach is a diagnosible,genetically distinct population. Thephylogenetic analysis suggests that populationson the other side of a large reservoir wererecently connected via gene flow to the RedHills populations.     

Loss of genetic variability in reintroduced roach (Rutilus rutilus) populations

Genetic variation at five microsatellite loci and in mtDNA was surveyed in reintroduced and 'control' populations of roach ( Rutilus rutilus ) in Sweden. Microsatellite allelic richness and allele size ranges were significantly reduced in reintroduced populations, and mtDNA diversity was nearly significantly reduced in reintroduced populations. These measures of genetic variability were strongly correlated with lake characteristics that influence population size and food availability.     

Microsatellite markers for woolly monkeys (Lagothrix lagotricha) and their amplification in other New World primates (Primates: Platyrrhini)

Seven polymorphic microsatellite loci were identified for woolly monkeys (Lagothrix lagotricha) from an ‘enriched’ genomic library. For a wild population of 66 animals, these markers averaged over 10 alleles per locus and provided a combined probability for excluding a random individual from parentage of over 98%. These loci were screened in up to 13 other genera of New World monkeys, and many were variable in multiple taxa. Few other platyrrhine‐specific microsatellite markers have been identified; thus, these loci should prove valuable for studying the population genetic structure and mating system not just of Lagothrix but also of other neotropical primates.     

Development and characterization of seven novel di‐, tri‐, and tetranucleotide microsatellite markers in Atka mackerel (Pleurogrammus monopterygius)

We describe the enrichment for and characterization of seven Pleurogrammus monopterygius microsatellite loci. We used (GACA)₄ as an oligonucleotide enrichment probe and screened 484 clones from the enriched library. The seven microsatellite loci include five tetranucleotide, one dinucleotide, and one trinucleotide motif. These markers can potentially be useful tools for use in population genetics studies, parentage analyses, and examining other life history questions.     

Determinants of habitat use in large roach

In this study gillnet catches of large roach Rutilus rutilus and their potential predators, large perch Perca fluviatilis , pikeperch Sander lucioperca and pike Esox lucius , in combination with data on food resources and abiotic variables were used to reveal the variables influencing the habitat use of large roach in Lake Großer Vätersee. The occurrence of large roach was negatively coupled with the occurrence of potential predators. Although almost all roach studied were larger than those actually fed on by the predators, high roach catches never coincided with high predator catches. Since the overall habitat-specific distribution of roach and its predators was nevertheless highly similar, this indicated that large roach obviously avoided the immediate vicinity of the predators without being forced to a full habitat shift. The behavioural response to predators of roach in Lake Großer Vätersee was clearly length dependent, since the patterns of diel habitat use differed between large and small roach. For lake-wide estimates of trophic interactions, size groups of prey should be separated, since size-dependent trait changes may impact habitat-specific resources in a contrasting way.     

Homing precision of roach Rutilus rutilus in Lake Arungen,Norway

Synopsis The present study tests the precision of repeat homing of roach, Rutilus rutilus, to two tributaries of a small Norwegian Lake, Årungen. A sample of 19 959 spawners was tagged or marked in the spawning area. After spawning the roach intermingled with other spawning demes in the lake. The year after marking, 2515 (12.6%) roach were recaptured during spawning in the five tributaries, 340 (13.5) of these were strayers. This straying is considerably larger than found in comparable autumn spawning species, but approximately the same as reported for other spring spawning species. The recapture rate was lower for females than for males, probably due to increased female mortality induced by the tagging manipulation.     

Identification and characterization of microsatellite DNA markers developed in ide Leuciscus idus and Siberian roach Rutilus rutilus

The first five microsatellite markers for the ide, Leuciscus idus, and four microsatellite markers for the Siberian roach, Rutilus rutilus, were designed. Cross‐amplification of ide markers was examined in Siberian roach and vice versa. The number of alleles per locus ranged from three to 13 in ide and from two to eight in roach. The expected heterozygosity ranged from 0.313 to 0.909 in ide and from 0.119 to 0.775 in roach. These markers could be used to evaluate the genetic population structure of these species and other fish from the Cyprinidae family.     

A standardized microsatellite marker panel for parentage and kinship analyses in channel catfish,Ictalurus punctatus

This research was designed to produce a standardized set of microsatellite loci for parentage and kinship analyses in channel catfish, the leading species of US aquaculture. Three panels of five to six markers each were developed that contained a total of two dinucleotide‐, eight trinucleotide‐ and seven tetranucleotide‐microsatellite loci respectively. The loci had a range of nine to 31 alleles per locus in an outbred population. Based on the allele frequencies measured in commercial randomly bred broodstock, the combined probability of non‐exclusion of an unrelated candidate parent pair was 5.36e‐18. The combined probability of non‐exclusion of unrelated identical genotypes was 2.58e‐08. The microsatellite panels were validated by parentage and kinship evaluation in three populations. A total of 697 spawns were collected from matings of outbred broodstock over three spawning seasons, and parents were determined unambiguously for all but three spawns. Genotype analysis also enabled the identification of half‐sibling and full‐sibling families produced by pond spawning. In a second experiment, parentage was unambiguously determined in nine spawns from a population consisting of broodstock derived from only four families. A third experiment demonstrated that all but one of 374 individuals from 10 full‐sibling families could be assigned to a family after coculture in an earthen pond for 1 year. The standardized microsatellite panels enable the development of pedigreed catfish populations and large‐scale performance evaluations in common environments to support the genetic improvement of cultured catfish through selective breeding.     

Temporal changes in genetic diversity of isolated populations of perch and roach

Genetic drift, together with natural selection and gene flow, affects genetic variation and is the major source of changes in allele frequencies in small and isolated populations. Temporal shifts in allele frequencies at five polymorphic loci were used to estimate the amount of genetic drift in an isolated population of perch (Perca fluviatilis L.) and roach (Rutilus rutilus L.). Here, I used the populations from the Biotest basin at Forsmark, Sweden, to investigate genetic diversity between 1977 and 2000, during which time the population can be considered to be totally isolated from other populations. Microsatellite data reveal stable levels of gene diversity over time for both species. Estimates of genetic differentiation (F _ST) showed a significant divergence between 1977 and 2000 for both perch and roach. A positive correlation between genetic distance and time was found (Mantel test, perch: r = 0.724, P = 0.0112; roach: r = 0.59, P = 0.036). Estimates of effective population size (N _e) differed with a factor six between two different estimators (NeEstimator and TempoFS) applying the temporal method. Ratios of N _e/N ranged between 10⁻² and 10⁻³, values normally found in marine species. Despite low N _e the populations have not lost their evolutionary potential due to drift. But two decades of isolation have lead to isolation by time for populations of perch and roach, respectively.     

The use of winter refuges by roach tagged with miniature radio transmitters

Adult roach (Rutilus rutilus) (13–25 cm) from two shallow lakes, one turbid and one with high water transparency, were tagged with surgically implanted miniature radio transmitters and their habitat use was monitored. Repeated tracking series over the course of the year provided information on seasonal changes in behaviour of roach in the two lakes. The results showed that the roach generally used the lakes only as summer habitat, whereas they moved into specific sheltered, restricted areas during winter. This behaviour was most pronounced in the lake with clear water, where roach gathered in large numbers in the stream in- and outlets as well as in other sheltered habitats where they remained rather passively during the 48 h tracking periods. In the turbid lake, many of the tagged roach, were even found in underground channels during the tracking in November. We see this behaviour as a response to low food abundance, decreased food demand and high predation risk, especially from birds. The tracking data from the clear lake showed that some tagged roach undertook swift habitat shifts from one refuge to the other. The traditional perception of the roach as a `lake fish' with an important structuring role in the lake ecosystem is undoubtedly true, but the present results suggest that roach are able to migrate between different habitat types and will do so if they can profit from this behaviour.     

Microsatellite loci for the North American tortoises (genus Gopherus) and their applicability to other turtle species

We describe the development of nine microsatellite loci from the gopher tortoise (Gopherus polyphemus). Screening 270 individuals, we found these loci to be highly variable (from two to 15 alleles per locus) and thus likely to be applicable in parentage and population‐level analyses for G. polyphemus. All nine loci amplified readily in the other three species of Gopherus as well. This observation, together with successful cross amplification of several loci in two additional families (Cheloniidae, Kinosternidae), underscores their potential utility among turtles in general.     

Microsatellite markers characterized in the barn owl (Tyto alba) and of high utility in other owls (Strigiformes: AVES)

We have identified 15 polymorphic microsatellite loci for the barn owl (Tyto alba), five from testing published owl loci and 10 from testing non‐owl loci, including loci known to be of high utility in passerines and shorebirds. All 15 loci were sequenced in barn owl, and new primer sets were designed for eight loci. The 15 polymorphic loci displayed two to 26 alleles in 56–58 barn owls. When tested in 10 other owl species (n = 1–6 individuals), between four and nine loci were polymorphic per species. These loci are suitable for studies of population structure and parentage in owls.     

Development and characterization of novel tetra‐, tri‐, and dinucleotide microsatellite markers in rainbow trout (Oncorhynchus mykiss)

We discuss the development and characterization of 40 polymorphic rainbow trout (Oncorhynchus mykiss) microsatellite loci. We used enriched libraries to isolate 14 dinucleotide, seven trinucleodide, eight compound di/tetranucleotide, and 11 tetranucleotide loci. These markers will be useful for selective breeding via marker‐assisted selection, population genetics studies, parentage analysis, and have already been used for genome mapping.     

Behavioral differences of various ecological groups of roach Rutilus rutilus and perch Perca fluviatilis

The intrapopulation morphological and behavioral polymorphism of roach (Rutilus rutilus) and perch Perca fluviatilis) was studied. It was shown that marker indices for distinguishing intrapopulation groups are the size of the mouth opening and the index of the body shape in roach and the coefficient of pigmentation in perch. Based on analysis of the data of indices, it was found that there are two ecological groups—coastal and pelagic in populations of roach and perch. Several behavioral differences in individuals of various ecological groups were revealed. Comparison of the defense reaction of perch individuals belonging to various ecological groups was performed. The assessment of the effects of hydrodynamic activity on the survival of perch individuals belonging to various ecological groups was made. Differences in the swimming capacity of juvenile roach developing under conditions of biotopes of various types were established. Suggestions were made on the mechanisms of formation of intrapopulation groups of roach and river perch.     

Assessing probability of ancestry using simple sequence repeat profiles: applications to maize inbred lines and soybean varieties

Determining parentage is a fundamental problem in biology and in applications such as identifying pedigrees. Difficulties inferring parentage derive from extensive inbreeding within the population, whether natural or planned; using an insufficient number of hypervariable loci; and from allele mismatches caused by mutation or by laboratory errors that generate false exclusions. Many studies of parentage have been limited to comparisons of small numbers of specific parent-progeny triplets. There have been few large-scale surveys of candidates in which there is no prior knowledge of parentage. We present an algorithm that determines the probability of parentage in circumstances where there is no prior knowledge of pedigree and that is robust in the face of missing data and mistyped data. The focus is parentage of an inbred line having uncertain ancestry. The algorithm is a variation of a previously published hybrid-focused algorithm. We describe the algorithm and demonstrate its performance in determining parentage of 43 inbred varieties of soybean that have been profiled using 236 SSR loci and from seven inbred varieties of maize that were profiled using 70 SSR loci. We include simulations of additional levels of missing and mistyped data to show the algorithm's utility and flexibility.