Nine polymorphic microsatellite markers in Crepis sancta (Asteraceae)

We describe nine new variable di‐ and trinucleotide microsatellites in the plant Crepis sancta, as well as conditions for multiplexing and simultaneous genotyping sets of loci. Their variability was assessed in four populations. Four to 33 alleles were detected per locus; two to 23 alleles per population. Significant deviations from Hardy–Weinberg equilibrium could be attributed either to a mating system involving partial selfing or to null alleles. Genetic differentiation over all loci was significant among the four populations studied. These markers will constitute an efficient tool for investigating dispersal patterns in fragmented landscapes. Cross‐species amplification provided few loci variability in three other Crepis species (C. pulcra, C. foetida and C. rubra).     

Microsatellite primers for the Atlantic coastal killifish,Fundulus heteroclitus,with applicability to related Fundulus species

The mummichog (Fundulus heteroclitus), a common Atlantic coastal killifish, is a model vertebrate species for the study of molecular genetic variation in natural populations and of environmental toxicology. We report the development of a set of 20 microsatellite loci in this species. Average expected heterozygosity across all loci was 0.84 (range: 0.60–0.97), revealing a high level of variability at most loci. A survey of seven additional Fundulus species yielded one or two robust amplification products in over half (63%) of the species–primer combinations tested. Therefore, many of these loci will also prove useful in studies of other members of the genus Fundulus.     

A single-locus minisatellite discriminates chinook salmon (Oncorhynchus tshawytscha) populations

A knowledge of genetic structure in natural populations is often necessary for conservation and management purposes, especially in declining Pacific salmon populations. To test for genetic differentiation between nine populations of chinook salmon, Oncorhynchus tshawytscha, from south-western British Columbia, Canada, DNA was extracted from 603 fish and hybridized with a single-locus minisatellite probe. Multivariate statistical analyses of the resulting allele size data permitted successful overall population identification of 52% (individual population range: 24–78%; P < 0.005), indicating a high level of genetic differentiation among the nine populations. Two of the nine populations were further analysed using data from a second minisatellite locus. The discrimination success rate improved from 81.1% (one-locus analyses) to 90.0% (two-locus analyses), indicating the potential for greatly increased resolution gained by the addition of more loci. These results indicate that variation at minisatellite loci can be used for assessing population-level genetic structure, even with artificial gene flow.     

Ten microsatellite loci for the strawberry poison frog (Oophaga pumilio)

We describe primers and PCR conditions to amplify nine new tetranucleotide loci and one new dinucleotide locus isolated from the strawberry poison frog (Oophaga pumilio). In 21 individuals from Costa Rica, the number of alleles ranged from 4 to 16, observed heterozygosities from 40 to 100%, and polymorphic information content ranged from 0.60 to 0.90 per locus. Evidence for linkage disequilibrium was found only between two loci, but this pattern was not found in other populations tested. All primer pairs cross-amplified in Oophaga vicentei from Panama.     

Reduced genetic variation and strong genetic population structure in the freshwater killifish Valencia letourneuxi (Valenciidae) based on nuclear and mitochondrial markers

The genetic variation of the critically endangered Corfu killifish (Valencia letourneuxi), an endemic freshwater fish species of the western Balkans, was assessed for nine populations sampled in eight water systems in western continental Greece, the Peloponnese and the Ionian Island of Corfu, using mitochondrial and microsatellite markers. The analyses were based on data from three mtDNA regions (D‐loop, COI and 16S rRNA sequences) and 14 microsatellite loci. Samples from the congeneric species Valencia hispanica and the phylogenetically closely related species Aphanius fasciatus were also used in the study as outgroups. Both the mitochondrial and the microsatellite analyses revealed three distinct population groupings associated with the geographical distribution of the populations: one southern group occupying rivers draining to the Patraikos Gulf, the second one including the populations flowing into the Amvrakikos Gulf and the third, more northern group, including the other populations from rivers in Corfu Island and Epirus flowing into the Ionian Sea. Within these groupings there is limited genetic differentiation between populations; in addition, there is reduced intrapopulation genetic variation, evidenced by low heterozygosity values, number of alleles and haplotype diversity. In terms of taxonomic implications and appropriate management actions for conservation, our data suggest that the major population groups should be regarded at least as three distinct conservation units (CUs), with translocation and restocking actions to take place only within the geographical range of the CU concerned. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 334–349.     

Microsatellite loci for the plains topminnow (Fundulus sciadicus,Fundulidae)

The plains topminnow (Fundulus sciadicus) is a killifish endemic to the Great Plains region. Recent field surveys indicate that populations may be declining in northerly portions of its range and perhaps throughout. Here, we describe the isolation and characterization of 11 microsatellite loci developed for population genetic studies in the species. We also conducted cross‐species amplifications to test primer efficacy in five additional taxa, including four killifishes.     

Isolation and characterization of polymorphic microsatellite loci from bluefin leatherjacket (Navodon septentrionalis Gunther, 1877)

The first set of 18 polymorphic microsatellite markers were developed from bluefin leatherjacket (Navodon septentrionalis Gunther, 1877). From a (GT)_n-enriched genomic library, we got 121 microsatellites, of which 60 were randomly selected for designing microsatellite primers. Eighteen of these loci were polymorphic in a test population of 32 individuals with alleles ranging from 2 to 9, and expected and observed heterozygosities from 0.1463 to 0.8517 and from 0.1562 to 1.0000, respectively. No significant linkage disequilibrium between pairs of loci was found, but three loci significantly deviated from Hardy–Weinberg equilibrium after Bonferroni correction. These polymorphic microsatellite loci should provide sufficient level of genetic diversity to investigate population structure in bluefin leatherjacket.     

Population genetic studies of leafhopper (Empoasca) species

Seven populations of the genus Empoasca Walsh 1864 (Homoptera, Typhlocybinae) collected from six different host-plants were electrophoretically analyzed for thirteen enzyme loci. By using both the allozymes and the morphological characters of the male genitalia we found that these populations consisted of only two Empoasca species; E. decedens and E. decipiens. The use of allozymes proved to be the faster and more efficient method for discrimination; nine out of thirteen enzyme loci were diagnostic. E. decedens was found to be the most abundant species in all populations studied. There are no genetic differences between E. decedens populations associated with different host-plants. The total genetic variability was mainly organized within E. decedens populations, explaining more than 95% of the total variability.     

Isolation and characterization of 145 polymorphic microsatellite loci for the common frog (Rana temporaria)

We describe primers and polymerase chain reaction conditions to amplify 145 di‐, tri‐ and tetranucleotide microsatellite loci from the common frog (Rana temporaria), a species commonly used as a model in ecological and evolutionary research. Primers were tested on 46 individuals from two Fennoscandian populations and yielded an average of six to nine alleles per locus (range = 1–30) depending on the population. Average observed heterozygosities in the two populations were 0.16 (range = 0–0.91) and 0.36 (range = 0–1).     

Population genomics of wild and laboratory zebrafish (Danio rerio)

Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large‐scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST‐based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among‐clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall F_ST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low F_ST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.     

High population differentiation and genetic variation in the endangered Mexican pine Pinus Rzedowskii (Pinaceae)

Pinus rzedowskii is an endangered pine species from Michoaca´n (central Me´xico), which has been previously reported from only three localities. Classified within the subgenus Strobus, it exhibits intermediate morphological characters between subgenera Strobus and Pinus. We analyzed genetic aspects that could shed light on the evolution and conservation of this species. The genetic structure of nine populations was examined using 14 isozyme loci. Pinus rzedowskii has a relatively high level of genetic variation with 46.8% of the loci assayed being polymorphic, a total of 35 alleles, and a mean heterozygosity per population of 0.219. We calculated Wright's F_ST statistic to estimate gene flow indirectly and to evaluate whether or not there was genetic structuring among populations. We found a marked differentiation among populations (F_ST = 0.175) and significant inbreeding (F_IS = 0.247). No pattern of isolation by distance was found. We also constructed a dendrogram based on a genetic distance matrix to obtain an overview of the possible historical relationships among populations. Finally, we found a convex relationship between the genetic distance among populations and the number of ancestral lineages, suggesting that demographically this species has not been at risk recently. Although endangered, with small and fragmented populations, P. rzedowskii shows higher levels of genetic variation than other conifer species with larger populations or similar conservation status.     

Characterization of microsatellite loci isolated in midget faded rattlesnake (Crotalus viridis concolor)

Primers for five polymorphic microsatellite loci were developed for the midget faded rattlesnake (Crotalus viridis concolor), a rare subspecies of western rattlesnake (Crotalus viridus) found only in parts of Wyoming, Colorado, and Utah. Five polymorphic microsatellites were isolated, four of which had relatively high levels of diversity (eight to nine alleles). We found only two departures from Hardy–Weinberg equilibrium and they occurred in different loci, so null alleles are likely not a problem. Moreover, we found that no two loci were linked. These loci will be applicable for population genetic analysis and perhaps analysis of paternity and mating systems.     

Polymorphic microsatellite loci in peafowl (Pavo cristatus)

Understanding how the genetic characteristics of parents influence reproductive output is central to predicting the dynamics of small, endangered populations. We conducted a breeding experiment to look at the paternal genetic effects on offspring sex, fertility and growth in the peafowl (Pavo cristatus). Microsatellite loci were developed to allow maternity assignment and thus to allow us to separate maternal from paternal effects. We found 19 polymorphic loci in our inbred, captive population, six of which were only slightly polymorphic (H_E range: 0.04–0.70). The remaining 13 loci were polymorphic enough to determine maternity by exclusion in approximately 85% of offspring.     

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.     

Isolation and characterization of 11 polymorphic trinucleotide microsatellite markers in the stonefly Arcynopteryx compacta (Plecoptera: Perlodidae)

We describe the isolation of 11 polymorphic trinucleotide microsatellite loci from the stonefly Arcynopteryx compacta. Loci were highly variable with 3 to 14 alleles (mean = 6.45). Observed heterozygosity ranged from 0 to 0.867. Seven loci showed significant deviation from Hardy–Weinberg equilibrium across both populations. There was no evidence for null alleles, and thus, Hardy–Weinberg departures could have resulted from genetic structure between populations or subpopulations. No linkage between loci was found. The 11 loci should prove highly informative for population genetic studies.     

Development of 10 polymorphic microsatellite loci isolated from the mountain beaver, Aplodontia rufa rufa (Rafinesque)

We developed 10 microsatellite markers for the mountain beaver, Aplodontia rufa rufa. In three populations of A. r. rufa, the number of alleles for these loci ranged from monomorphic to nine. Average observed heterozygosities in these populations ranged from 0.29 to 0.60. We also tested previously published markers from the endangered subspecies A. r. nigra in A. r. rufa populations.     

Development of 11 microsatellite loci for population studies in the swordfish,Xiphias gladius (Teleostei: Scombridae)

Eleven microsatellite loci were developed in the swordfish, Xiphias gladius, to examine population structure. Loci were amplified in samples from two geographically distant populations (Ecuador and Mediterranean Sea). Observed heterozygosity ranged from 0.150 to 0.960. Most loci conformed to Hardy–Weinberg expectations with the exception of locus Xg‐59, which had a heterozygote deficit caused probably by null alleles. Locus Xg‐402 did not show significant divergence between the populations. The remaining nine loci showed statistically significant spatial heterogeneity (genic differentiation) between the two populations, making them useful for future studies of population structure in swordfish.     

PERMANENT GENETIC RESOURCES: Isolation of microsatellite loci from the endangered plant Sibara filifolia (Brassicaceae)

Sibara filifolia (Brassicaceae) is a federally endangered annual herb found on two of the California Channel Islands. Previous studies based on allozymes revealed little genetic variability on San Clemente Island. Nine polymorphic microsatellite loci were isolated from individuals on San Clemente Island. We found low levels of allelic variation (mean N_A = 2.3), with seven loci exhibiting significant deviations from Hardy–Weinberg equilibrium (P < 0.01) and 10 pairs of loci exhibiting significant linkage disequilibrium (P < 0.01). Most of the observed variability (mean H_O = 0.003) occurred among populations or in rare homozygous individuals.     

Isolation of polymorphic microsatellite loci in Hemerocallis fulva and Hemerocallis citrina (Hemerocallidaceae)

Twenty microsatellite loci were isolated from a hybrid of two daylilies, Hemerocallis fulva and Hemerocallis citrina. We characterized individuals from two H. fulva populations and two H. citrina populations in Japan and observed three to 20 alleles per locus in H. fulva and one to 19 alleles per locus in H. citrina. Mean observed heterozygosity within populations ranged from 0.35 to 0.85 in H. fulva and from 0 to 0.95 in H. citrina. In about a half of the loci, the observed heterozygosity did not deviate from Hardy–Weinberg equilibrium. These loci are proved useful in studying gene flow and qualitative trait loci mapping using the two species.     

Isolation and characterization of microsatellite markers for Viola mirabilis (Violaceae) using a next‐generation sequencing platform

We isolated and characterized microsatellite loci in Viola mirabilis (Violaceae), an endangered species from South Korea. Twenty‐three polymorphic microsatellite loci were developed and tested in Korean, Chinese and Japanese populations. The number of alleles per locus varied from two to eight. The observed and expected heterozygosities within the three populations were 0.000–0.625 and 0.469–0.695, respectively. A total of six loci in the Korean population, one locus in the Chinese population and seven loci in the Japanese population deviated from Hardy–Weinberg equilibrium. We expect that these newly developed microsatellite markers will contribute to understanding the phylogeography and population genetics of V. mirabilis, which will aid in developing conservation strategies for this species.