Polymorphic microsatellite markers for the gliding marsupials Petaurus australis and Petaurus breviceps

Habitat destruction is causing population decline of many hollow dependent species such as gliding marsupials of the Family Petauridae. Three petaurid species are now listed in some Australian states as either threatened, rare or vulnerable, precipitating a need for information on their basic biology and population structure. We isolated and characterized three polymorphic microsatellite loci from the yellow‐bellied glider (Petaurus australis) and six polymorphic microsatellite loci from the sugar glider (P. breviceps). Per‐locus heterozygosities range from 42%–92%, and cross‐species amplification studies show that between five and seven loci are polymorphic in the two target species as well as a related species P. norfolcensis.     

Ten polymorphic microsatellite markers developed in the masson pine moth Dendrolimus punctatus Walker (Lepidoptera: Lasiocampidae)

A set of 10 polymorphic di‐ and trinucleotide microsatellite loci were developed for the forestry pest insect, masson pine moth, Dendrolimus punctatus Walker. The expected heterozygosity at these loci ranges from 0.285 to 0.859, and the observed allele numbers from five to 19. Cross species amplification of these loci in four other congeneric pine moth species indicates variable levels of loci conservation and thus cross‐applicability. Therefore, the microsatellite loci reported here should be useful for population genetic and other related studies in the masson pine moth and other closely related species.     

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 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.     

Nine polymorphic microsatellite loci in the Neotropical electric eel Eigenmannia (Teleostei: Gymnotiformes)

Ten microsatellite loci were isolated from a species of the Neotropical electric eel, Eigenmannia, a genus of freshwater fish characterized by small populations and low vagility. Nine microsatellites were polymorphic, the number of alleles ranging from seven to 27, and values of observed heterozygosity ranging from 0.327 to 0.741. These loci were developed for population genetic studies of Eigenmannia sp. 2, however, cross‐amplification carried out with other species of this genus as well as other Gymnotiformes genera indicate that these molecular markers are also potentially useful for population‐level studies in closely related species.     

Development of 28 EST‐SSR markers based on transcriptome sequences of Gobiobotia filifer and cross‐species amplification

Gobiobotia filifer is a small benthic fish distributed in Yangtze River Basin. The abundance of G. filifer increased after impoundment of Xiluodu Dam and Xiangjiaba Dam. The state of population structure and changes of genetic diversity before and after impoundment of Xiluodu Dam and Xiangjiaba Dam were interesting issues. However, efficient molecular markers were rare, which will limit us to solve above problems. Twenty‐eight expressed sequence tag SSRs (EST‐SSRs) were successfully identified and verified as stable amplification and polymorphic loci by polyacrylamide gel electrophoresis (PAGE) and capillary electrophoresis. The number of alleles at these EST‐SSR loci ranged from 3 to 14, the polymorphism information content values were 0.125–0.897, and the observed and expected heterozygosities were 0.0–0.857 and 0.132–0.928, respectively. Cross‐species amplification of the 28 loci developed in this study was examined in seven individuals of each of the 7 taxa. The amplification efficiency of 28 EST‐SSRs primer pairs is related to the distance of genetic relationship between cross‐species with G. filifer, and same subfamily species (Xenophysogobio boulengeri and Xenophysogobio nudicorpa) showed the highest (50%) amplification efficiency. These EST‐SSR markers could be used to analyse genetic diversity and population structure of G. filifer and related species.     

Isolation and characterization of microsatellite loci in wheat stem sawfly Cephus cinctus and cross‐species amplification in related species

The wheat stem sawfly is an important insect pest of wheat that can cause significant damage to yield and grain quality. Five microsatellite loci were isolated and characterized in wheat stem sawfly, Cephus cinctus, to facilitate future population genetic studies and help delineate their geographical origin. These loci were found to be polymorphic with an expected heterozygosity ranging from 0.304 to 0.937 and an observed heterozygosity ranging from 0.05 to 0.65. Successful cross‐species amplification demonstrates the potential for these markers to provide a valuable tool for future population studies among related Cephus species.     

Twelve novel polymorphic microsatellite loci for the Yellow grouper (Epinephelus awoara) and cross-species amplifications

Yellow grouper (Epinephelus awoara) is a commercially important marine fish species. A dinucleotide-enriched genomic library of E. awoara was constructed using the method of FIASCO. Twelve loci were polymorphic in a test population with alleles per locus ranging from two to eight, and observed and expected heterozygosities per locus from 0.13 to 1.00 and from 0.20 to 0.86, respectively. Five loci significantly deviated from Hardy–Weinberg equilibrium 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 diversity of E. awoara and related species. L. Zhao and C. Shao have contributed equally to this work.     

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.     

Additional microsatellites for Sparus aurata and cross‐species amplification within the Sparidae family

Six new microsatellite loci were isolated and characterized in 32 individuals from a farm population of gilthead seabream (Sparus aurata). Expected heterozygosity at all loci was high, ranging from 0.835 to 0.958 with between 10 and 27 alleles per locus. A multiplex polymerase chain reaction protocol was developed using four of the loci. Cross‐species amplification of the loci was tested in six species of the Sparidae family and four loci were successfully amplified in two or more related species.     

Characterization of microsatellite markers in Fagus sylvatica L. and Fagus orientalis Lipsky

Using an enrichment procedure, we cloned microsatellite repeats from European beech (Fagus sylvatica L.) and developed primers for the amplification of microsatellite markers. Six polymorphic loci were characterized which produced 3–21 alleles in 70 individuals from one Italian population, with an observed heterozygosity between 0.58 and 0.85. All six loci amplified fragments which were polymorphic in the closely related species, Fagus orientalis, also. Owing to their very high degree of variation, these markers should be very useful in gene flow studies of these species.     

Isolation and characterization of microsatellites in Drosophila virilis and their cross species amplification in members of the D. virilis group

We report the isolation and cross species amplification of 42 Drosophila virilis microsatellite loci. Nine loci were isolated from mapped P1 bacteriophage clones and 33 were obtained from genomic DNA or GenBank searches. Cross species amplification was tested for all members of the D. virilis group. The amplification success was high (varying from 45% to 100%) and most of the loci were polymorphic. This set of loci can be applied for several genetic studies such as mapping behavioural quantitative trait loci (QTL) and for studying population structure in a phylogeographical framework in D. virilis group species.     

Isolation and characterization of microsatellite loci in Greater Sage‐Grouse (Centrocercus urophasianus)

Primers for five polymorphic microsatellite loci were developed for Greater Sage‐Grouse (Centrocercus urophasianus) using an enrichment/detection protocol. The high level of polymorphism (nine to 33 alleles) suggests that these loci will be applicable for investigating mating systems and paternity analysis as well as population genetics. Cross‐species amplification was successful for each locus in at least two other galliform species.     

Microsatellite primers for the Western Pebble‐mound Mouse (Pseudomys chapmani) that show cross amplification for other species of Australian rodent

We describe 12 dinucleotide and one tetranucleotide microsatellite loci for the Western Pebble‐mound Mouse (Pseudomys chapmani) that can be amplified with the polymerase chain reaction. All primers produced clear and highly polymorphic amplification patterns containing between seven and 14 alleles and with high expected heterozygosities. The amplification of these primers across seven related conspecifics makes them useful for population genetic studies and conservation work in several of these species.     

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.     

New polymorphic microsatellite loci,cross‐species amplification and PCR multiplexing in the black aphid,Aphis fabae Scopoli

Aphis fabae includes four morphological cryptic subspecies, which are mostly identified by their partially distinct secondary host range. To determine the extent of gene flow and isolation between these four taxa, we isolated and characterized 12 microsatellite loci from Aphis fabae fabae and tested cross‐species amplification of eight loci from the closely related species Aphis gossypii. Using eight previously described microsatellite loci, we have developed the polymerase chain reaction (PCR) multiplexing of 24 loci, which were separated in tree sets and five PCRs. These sets of microsatellite loci provide high throughput capacity for large‐scale population genetic studies at a minimum cost.     

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.     

A panel of polymorphic microsatellite markers in Himalayan monal Lophophorus impejanus developed by cross-species amplification and their applicability in other Galliformes

Isolation and development of new microsatellite markers for any species is still labour-intensive and requires substantial inputs of time, money and expertise. Therefore, cross-species microsatellite amplification can be an effective way in obtaining microsatellite loci for closely related taxa in bird species. We have reported microsatellite loci for Himalayan monal for the first time. Fifteen microsatellite markers developed for chicken were cross-amplified in Himalayan monal. All the tested 15 microsatellite markers were polymorphic, with mean (± s.e.) allelic number of 4 ± 1.51, ranging 2–7 per locus. The observed heterozygosity in the population ranged between 0.285 and 0.714, with mean (± s.e.) of 0.499 ± 0.125, indicating considerable genetic variation in this population. While 12 loci conformed to Hardy–Weinberg equilibrium (P > 0.05), 3 loci, i.e. MCW0295, MCW0081, MCW0330 deviated from it (P < 0.05). No evidence for linkage disequilibrium was observed among pair of loci. Our study show that these 15 microsatellites loci could be employed in population genetic studies for Himalayan monal and their applicability in Jungle Bush Quail, Grey francolin and Kalij pheasant.

     

Widespread hybridization in the introduced hog deer population of Victoria,Australia, and its implications for conservation

In Australia, many species have been introduced that have since undergone drastic declines in their native range. One species of note is the hog deer (Axis porcinus) which was introduced in the 1860s to Victoria, Australia, and has since become endangered in its native range throughout South‐East Asia. There is increased interest in using non‐native populations as a source for genetic rescue; however, considerations need to be made of the genetic suitability of the non‐native population. Three mitochondrial markers and two nuclear markers were sequenced to assess the genetic variation of the Victorian population of hog deer, which identified that the Victorian population has hybrid origins with the closely related chital (Axis axis), a species that is no longer present in the wild in Victoria. In addition, the mitochondrial D‐loop region within the Victorian hog deer is monomorphic, demonstrating that mitochondrial genetic diversity is very low within this population. This study is the first to report of long‐term persistence of hog deer and chital hybrids in a wild setting, and the continual survival of this population suggests that hybrids of these two species are fertile. Despite the newly discovered hybrid status in Victorian hog deer, this population may still be beneficial for future translocations within the native range. However, more in‐depth analysis of genetic diversity within the Victorian hog deer population and investigation of hybridization rates within the native range are necessary before translocations are attempted.     

Highly polymorphic microsatellite loci for the Parsley frog (Pelodytes punctatus): characterization and testing for cross-species amplification

A microsatellite library was developed using genomic DNA of the Parsley frog, Pelodytes punctatus, an amphibian species which inhabits Mediterranean temporary pond systems. Number of alleles and heterozygosity ranged from 10 to 25 and from 0.66 to 0.90, respectively. Cross-species amplification was successful for 13 of the 15 developed loci for the related species, Pelodytes ibericus. The high levels of polymorphism revealed by these loci will be extremely useful for characterizing the population genetic diversity and structure and to estimate levels of dispersal and gene flow in the species P. punctatus and P. ibericus.