Characterization of 36 polymorphic microsatellite loci in the Kentish plover (Charadrius alexandrinus) including two sex‐linked loci and their amplification in four other Charadrius species

We isolated 45 new Kentish plover (Charadrius alexandrinus) microsatellite loci. These were tested for polymorphism in 42 Kentish plovers breeding in the Çukurova Delta, Turkey. Thirty‐six of the 45 loci were polymorphic with observed heterozygosity varying between 0.22 and 0.93. Genotypes of individuals of known sex indicated that two loci were sex‐linked (Calex‐26 is located on the Z chromosome and Calex‐31 on the W chromosome). Additionally, we tested all loci for amplification in four other species of Charadridae (Kittlitz's plover, Madagascar plover, three‐banded plover and white‐fronted plover). On average 34 loci amplified per species (range 29–36).     

Isolation and characterization of microsatellite loci from a commercial cultivar of Musa acuminata

A genomic library from the commercial diploid cultivar ‘Ouro’ (Musa acuminata), enriched for CT‐ and GT‐repeats, was used to isolate and characterize 23 microsatellite loci. These loci were tested in 10 Musa genotypes, representing various Musa genomic groups with distinct ploidy level. The number of alleles per locus ranged from one to seven, and 20 loci were highly informative. Four loci appeared to amplify B genome‐specific alleles, while three loci seemed to be absent in the B genome. The polymorphism revealed by these loci will be extremely useful for genetic mapping, marker‐assisted selection, germplasm characterization and evolutionary studies in Musa.     

Conserved genetic regions across angiosperms as tools to develop single‐copy nuclear markers in gymnosperms: an example using cycads

Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single‐copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis‐Populus‐Vitis‐Oryza Shared Single‐Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single‐copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.     

Novel microsatellite loci for the study of the black‐capped vireo (Vireo atricapillus)

We identified 14 novel polymorphic microsatellite loci in the black‐capped vireo (Vireo atricapillus). We also attempted to amplify and genotype these loci in other Vireo species, including the white‐eyed vireo (Vireo griseus), red‐eyed vireo (Vireo olivaceus), and blue‐headed vireo (Vireo solitarius). In 33 genotyped black‐capped vireos from two locations, total alleles ranged from six to 20, with observed heterozygosity ranging from 0.58 to 0.91 and expected heterozygosity from 0.65 to 0.93. Two loci had detectable levels of null alleles. Many of the loci were able to be amplified in the related Vireo species.     

Novel polymorphic microsatellite markers for paternity analysis in the red‐capped robin (Petroica goodenovii: Aves)

Seven microsatellite loci were isolated and characterized from the red‐capped robin Petroica goodenovii, using nonradioactive polymerase chain reaction (PCR)‐based techniques to screen an enriched genomic library. Five loci showed no evidence of null alleles and were variable [mean heterozygosity (H_E) = 0.440, mean number of alleles = 8]. Cross‐amplification using primers for microsatellites in Phylloscopus occipitalis and Emberiza schoeniclus yielded another two polymorphic loci. The combined set of five red‐capped robin and two cross‐amplified loci are suitable for paternity assignment (exclusion probability for seven unlinked loci = 0.9760).     

Characterization of polymorphic microsatellite loci for the polychaete tubeworm Hobsonia florida

Eight dinucleotide microsatellite loci were isolated and characterized from Hobsonia florida, a tube‐dwelling ampharetid polychaete. The identified loci were highly polymorphic, with allelic diversity ranging from six to 11 alleles. Levels of expected heterozygosity were 0.52 or greater in all cases, averaging 0.78 across the complete set of loci. Cross‐species amplification was successful in three of the eight loci for one or both of the other species (Melinna cristata and Ampharete acutifrons) tested. Although these novel loci were designed for immediate utility in H. florida population‐level research, these results indicate they may prove useful in studies of other related taxa.     

Microsatellite loci for the southern pine beetle (Dendroctonus frontalis) and cross‐species amplification in Dendroctonus

We developed microsatellite loci for the southern pine beetle (Dendroctonus frontalis). Twelve microsatellite loci were identified. Eight loci were polymorphic and sufficiently variable in 62 individuals (expected heterozygosity ranged from 0.707 to 0.880) to investigate population structure. All loci conformed to HWE except Dfr‐14, which showed heterozygote excess, and no two loci deviated from linkage equilibrium. The loci were tested for cross‐species amplification in four species of Dendroctonus (D. valens, D. terebrans, D. brevicomis, and D. ponderosae). Seven loci were polymorphic in at least one of the species tested.     

Microsatellite primers for the African mole‐rat genus Cryptomys and cross‐species amplification within the family Bathyergidae

We report 11 microsatellite loci for the African mole‐rat genus Cryptomys (Rodentia: Bathyergidae), isolated from the Damaraland mole‐rat (Cryptomys damarensis) and the Common mole‐rat (C. hottentotus hottentotus). All loci are highly polymorphic in the source species, with between six and 13 alleles and observed heterozygosity ranging from 0.54 to 0.86. Two C. damarensis loci (DMR1 and 6) may be located on the X‐chromosome. Cross‐species amplification was investigated in 10 Bathyergid species, representative of the five genera. The majority of loci amplified polymorphic product in all Cryptomys species tested. Amplification was also widespread in the other genera, except in Heterocephalus.     

Isolation and characterization of 27 polymorphic microsatellite loci for the common snook,Centropomus undecimalis

Here we describe 32 di‐, tri‐ and tetranucleotide microsatellite loci isolated by PIMA, a polymerase chain reaction (PCR)‐based procedure, for the common snook (Centropomus undecimalis). Five loci were monomorphic, and the remaining loci averaged 6.7 alleles per locus in a sample of 45 common snook. For polymorphic loci, expected heterozygosities ranged from 0.02 to 0.91 (mean = 0.538). Significant departures from Hardy–Weinberg equilibrium expectations occurred in two loci. Exact tests for genotype disequilibrium gave evidence for linkage at one pair of loci. Many cross‐species primer assays yielded PCR fragments of the expected size for 11 species of Centropomus and two species of the confamilial genus Lates.     

PCR primers for polymorphic microsatellite loci in the plant‐ant Azteca ulei cordiae (Formicidae: Dolichoderinae)

Twelve microsatellite loci were isolated from the Peruvian tropical plant‐ant, Azteca ulei cordiae (Hymenoptera: Dolichoderinae). High levels of within‐population variation were observed at most loci, with number of alleles ranging from four to 18, and heterozygosity from 0.118 to 1 per population sample. Cross‐species amplification of these loci was also successfully tested in several other species of the same ant genus Azteca.     

Balancing selection maintains sex determining alleles in multiple‐locus complementary sex determination

Hymenopteran species in which sex is determined through a haplo‐diploid mechanism known as complementary sex determination (CSD) are vulnerable to a unique form of inbreeding depression. Diploids heterozygous at one or more CSD loci develop into females but diploids homozygous at all loci develop into diploid males, which are generally sterile or inviable. Species with multiple polymorphic CSD loci (ml‐CSD) may have lower rates of diploid male production than species with a single CSD locus (sl‐CSD), but it is not clear if polymorphism is consistently maintained at all loci. Here, we assess the rate of diploid male production in a population of Cotesia rubecula, a two‐locus CSD parasitoid wasp species, approximately 20 years after the population was introduced for biological control. We show that diploid male production dropped from 8–13% in 2005 and 2006 to 3–4% by 2015. We also show from experimental crosses that the population maintained polymorphism at both CSD loci in 2015. We use theory and simulations to show that balancing selection on all CSD alleles promotes polymorphism at several loci in ml‐CSD populations. Our study supports the hypothesis that ml‐CSD populations have lower diploid male production and are more likely to persist than comparable sl‐CSD populations.     

Characterization of polymorphic microsatellites in the castration parasite plant‐ant Allomerus octoarticulatus cf. demerarae (Formicidae: Myrmicinae)

Fifteen microsatellite loci were isolated from the Peruvian tropical plant‐ant Allomerus octoarticulatus cf. demerarae (Hymenoptera: Myrmicinae) and their polymorphism was characterized. High levels of within‐population variation were observed at most loci, with number of alleles ranging from one to 21, and heterozygosity from 0 to 1 per population sample. Cross‐species amplification of these loci was also tested in one other species of the ant genus Allomerus (Allomerus decemarticulatus), displaying similar life history.     

PCR primers for polymorphic microsatellite loci in the facultatively polygynous plant‐ant Petalomyrmex phylax (Formicidae)

Fourteen microsatellite loci were isolated and their level of polymorphism characterized in two populations of the facultatively polygynous plant‐ant Petalomyrmex phylax (Formicinae). High levels of within‐population variation were observed at most loci, with number of alleles ranging from two to 15, and heterozygosity from 0.050 to 0.925. Cross‐species amplification of these loci was also tested in four plant‐ant species belonging to three other genera, Aphomomyrmex, Cladomyrma (both Formicinae) and Cataulacus (Myrmicinae).     

Fifteen microsatellite loci characterized in the golden eagle Aquila chrysaetos (Accipitridae,Aves)

Polymorphic microsatellite loci were identified in order to study golden eagle (Aquila chrysaetos) population fragmentation. Twenty‐six published Aquila and eight published Haliaeetus microsatellite loci were tested for polymorphism in A. chrysaetos. Fifteen loci were polymorphic with between two and six alleles detected per locus. Observed heterozygosity ranged from 0.15 to 0.77 among 177 unrelated individuals from Scotland. There was no evidence for null alleles. Two pairs of loci (Hal‐10 & Aa15 and Hal‐10 & Aa26) displayed linkage disequilibrium.     

Cross-species amplification of 44 microsatellite loci developed for Chaetodon trifascialis, C. lunulatus and C. vagabundus in 22 related butterflyfish species

Forty‐four microsatellite primers developed for three species of butterflyfish were cross‐tested against 22 related confamilial species. Amplification success and cross‐species transferability of these markers were moderately high. Between 24 and 37 loci were amplified successfully in each species, with a mean success rate per species of 71.7% (± 1.8 SE). Rates of amplification success were comparable among primers designed for the three source species, ranging from a mean success rate per species of 16.9 loci (± 0.8 SE) for Chaetodon trifascialis source loci to 13.7 loci (± 1.5 SE) for C. vagabundus source loci. Polymorphism rates were high (76.1%± 3.1 SE of all successfully amplified loci), and 10 loci were polymorphic in all successfully amplified species (Tri14, B11, C5, D3, D113, D6, D117, D120, D111, D118). The number of alleles per polymorphic locus ranged from 2 to 8, and the average number of alleles across all polymorphic loci and all species was 3.6 (± 0.07 SE). Polymorphism rates were higher overall in primers designed for C. vagabundus (89.9%± 3.9 SE). Overall cross‐testing success was lowest for Heniochus chrysostomus, the most phylogenetically divergent species. The significant cross‐testing reported here provides a valuable resource that will enable population genetics studies to be undertaken on a range of butterflyfishes without the need for expensive and time‐consuming de novo microsatellite development.     

Isolation and characterization of 15 microsatellite loci in the poplar rust fungus,Melampsora larici‐populina,and cross‐amplification in related species

We developed 15 microsatellite loci in the poplar rust fungus, Melampsora larici‐populina, using two enrichment protocols. Polymorphism of each locus was assessed on a panel of 30 isolates, comprising three subpanels (world, regional and local scales). Thirteen loci were polymorphic with three to eight alleles detected. The 15 loci were also tested on five related Melampsora species, M. allii‐populina, M. medusae f. sp. deltoidae, M. larici‐tremulae, M. rostrupii and M. pinitorqua, and partial or global cross‐amplification events were detected.     

Isolation and characterization of polymorphic microsatellites in the tropical plant‐ant Cataulacus mckeyi (Formicidae: Myrmicinae)

Eleven microsatellite loci were isolated from the plant‐ant Cataulacus mckeyi (Hymenoptera: Myrmicinae) and their polymorphism was characterized. High levels of within‐population variation were observed at most loci, with number of alleles ranging from one to 16, and heterozygosity from 0 to 0.929 per population sample. Cross‐species amplification of these loci was also tested in four other species of the ant genus Cataulacus.     

Microsatellite loci for behavioural studies of rainbow bee‐eaters (Merops ornatus: Aves)

A set of polymorphic microsatellite loci was identified for population and behavioural studies of the rainbow bee‐eater (Merops ornatus). Eight loci were newly isolated from a rainbow bee‐eater genomic library enriched for GA‐containing repeats, and six loci from those previously reported for the European bee‐eater (Merops apiaster). From these two sources, the seven most variable loci that amplified reliably were unlinked and in Hardy–Weinberg equilibrium, had five to 13 alleles (mean 7.7) and an expected heterozygosity of 0.60–0.86 (mean 0.73).